Here's the technical background on viral vaccine invention.

Some vaccines against a virus (the “target virus”) incorporate harmless fragments of the target virus’s genetic material into a second virus, called a “viral vector.” When a person is vaccinated, the viral vector produces harmless fragments of the target virus, ultimately conferring immunity against it. To prevent the viral vector from itself causing a harmful infection in the inoculee, it must be attenuated. Attenuation is achieved by deleting or inactivating one or more genes responsible for the vector’s growth and infectiousness. However, because the vaccine is produced by essentially “growing” the vector virus (accompanied by its inserted target virus gene), attenuation makes it difficult to manufacture the vaccine. The traditional solution to this problem has been to inactivate genes known as “inessential” genes. With inessential genes inactivated, the viral vector is substantially less pathogenic. At the same time, because the vector virus can still fully reproduce itself, albeit more slowly, the vaccine can be produced in commercial quantities. However, the traditional approach carried a disadvantage, namely the risk that the vector virus, though attenuated, could still cause a harmful infection in the inoculee.

The inventors discovered a way of making vaccines safer by deleting or inactivating an essential, rather than an inessential, gene from the viral vector’s genome, while at the same time solving the production problem by growing the vaccines in cells that were complementarily modified to produce the absent essential viral gene product “on behalf of” the vector virus. Thus, the modified vector virus could be readily grown in these complementarily-modified cells, but not in other cells, such as those of an inoculee.

This approach is applicable to many different kinds of vector viruses, e.g., adenoviruses, herpesviruses, poxviruses and retroviruses. The subject matter of this interference, however, is directed specifically to vaccines in which the vector virus is a poxvirus. For many vector viruses, there is a risk that vectors that have been attenuated in essential genes can “swap” genes with the host cell genome, thereby reacquiring their deleted genes and reverting to wild-type virus. This risk can be minimized through the use of viruses that are “cytoplasmic”, meaning that they are unlikely to enter the cell nucleus. Because a cell’s genes are located in the nucleus, cytoplasmic viruses such as poxvirus cannot swap genes with the cell genome and possibly revert to a virulent wild-type virus.

Both the priority dates of Falkner & Inlgis were backdated through related applications, which is how the Administrative Patent Judge (APJ) awarded Inglis the senior, which the BPAI affirmed.

Both parties sought the benefit of earlier-filed applications to establish dates of constructive reduction to practice. The APJ accorded the Inglis ’040 application (filed June 2, 1995) the benefit of several earlier-filed applications, dating back to September 25, 1990. Likewise, the APJ accorded the Falkner ’212 patent (issued June 23, 1998 from an application filed February 21, 1997) the benefit of earlier-filed applications, but these dated back only to April 29, 1994. Consequently, the APJ designated Inglis as the senior party.

Inglis had focued on herpesvirus, but covered poxvirus in "several passages". Falkner was focused solely on poxvirus. Falkner brought the challenge that the claims were indefinite in light of the specification (35 U.S.C. § 112), and the disclosure did not enable the claims.

Here is the basis for Appeals Court (CAFC) review of BPAI rulings: written description is a fact determination, thus a BPAI ruling can only be overturned if "unsupported by substantial evidence." Enablement is a question of law based upon underlying facts.

Written description is a question of fact, judged from the perspective of one of ordinary skill in the art as of the relevant filing date. See Vas-Cath, Inc. v. Mahurkar, 935 F.2d 1555, 1563-64 (Fed. Cir. 1991). Enablement is a question of law involving underlying factual inquiries. See Genentech, Inc. v. Novo Nordisk A/S, 108 F.3d 1361, 1365 (Fed. Cir. 1997); see also In re Wands, 858 F.2d 731, 737 (Fed. Cir. 1988) (holding that whether undue experimentation is required is a “conclusion reached by weighing many factual considerations. . . . includ[ing] (1) the quantity of experimentation necessary, (2) the amount of direction or guidance presented, (3) the presence or absence of working examples, (4) the nature of the invention, (5) the state of the prior art, (6) the relative skill of those in the art, (7) the predictability or unpredictability of the art, and (8) the breadth of the claims.”).

This court applies the standards of the Administrative Procedure Act (“APA”) in reviewing decisions of the Board. See Dickinson v. Zurko, 527 U.S. 150, 152 (1999) (holding that 5 U.S.C. § 706 governs our review of PTO appeals). Accordingly, we will set aside actions of the Board if they are arbitrary, capricious, an abuse of discretion, or otherwise not in accordance with law, and we set aside factual findings that are unsupported by substantial evidence. See In re McDaniel, 293 F.3d 1379, 1382 (Fed. Cir. 2002) (citing 5 U.S.C. § 706); see also In re Sullivan, 362 F.3d 1324, 1326 (Fed. Cir. 2004) (substantial evidence review of factual findings). We review questions of law de novo. See Rapoport v. Dement, 254 F.3d 1053, 1058 (Fed. Cir. 2001).

Substantial evidence is defined as that which a reasonable person might accept as adequate to support a conclusion. See In re Zurko, 258 F.3d 1379, 1384 (Fed. Cir. 2001). It requires an examination of the record as a whole, taking into account both the evidence that justifies and detracts from an agency’s opinion. See In re Gartside, 203 F.3d 1305, 1312 (Fed. Cir. 2000). An agency decision can be supported by substantial evidence, even where the record will support several reasonable but contradictory conclusions. See id.; see also In re Jolley, 308 F.3d 1317, 1320 (Fed. Cir. 2002).

The CAFC agreed with the BPAI that, given the high level of skill required to work in this technology area, enablement has a somewhat stronger presumption, as "difficult and time consuming" experimentation, owing to the nature of the technology, does not necessarily equate to "undue experimentation." Someone working in this field carries enough knowledge to know how to proceed given scant direction, as so much is known in the prior art, and inventions incremental.

Because the adequacy of the disclosure is judged from the perspective of one of ordinary skill in the art, we start our review of the Board’s decision by noting that the parties stipulated to a high level of skill in the art.

Indeed, “[a] patent need not teach, and preferably omits, what is well known in the art.” Spectra-Physics, Inc. v. Coherent, Inc., 827 F.2d 1524, 1534 (Fed. Cir. 1987).

The Board observed that “the mere fact that the experimentation may have been difficult and time consuming does not mandate a conclusion that such experimentation would have been considered to be ‘undue’ in this art. Indeed, great expenditures of time and effort were ordinary in the field of vaccine preparation.” Thus, the Board found the Inglis applications to be enabling.

The CAFC addressed the issue of meeting the written description requirement.

Specifically, we hold, in accordance with our prior case law, that (1) examples are not necessary to support the adequacy of a written description (2) the written description standard may be met (as it is here) even where actual reduction to practice of an invention is absent; and (3) there is no per se rule that an adequate written description of an invention that involves a biological macromolecule must contain a recitation of known structure.

The CAFC affirmed the BPAI ruling, that Falkner's '212 patent was dead because of Inglis.