United States Court of Appeals 

for the Federal Circuit ______________________ 

BIOGEN MA, INC.,

Plaintiff-Appellant

v.

JAPANESE FOUNDATION FOR CANCER 

RESEARCH, BAYER PHARMA AG,

Defendants-Appellees

______________________ 

2014-1525

______________________ 

Appeal from the United States District Court for the 

District of Massachusetts in No. 1:13-cv-13061-FDS, 

Judge F. Dennis Saylor IV.

______________________ 

Decided: May 7, 2015 

______________________ 

 EDWARD ANTHONY FIGG, Rothwell, Figg, Ernst & 

Manbeck, P.C., Washington, DC, argued for plaintiffappellant. Also represented by DANIEL MCCALLUM,

ROBERT DANNY HUNTINGTON, SETH EDWARD COCKRUM; 

CLAIRE LAPORTE, DONALD ROSS WARE, Foley Hoag LLP, 

Boston, MA.

S. CALVIN WALDEN, Wilmer Cutler Pickering Hale and 

Dorr LLP, New York, NY, argued for defendant-appellee
2 BIOGEN IDEC MA, INC. v. JAPANESE FOUNDATION FOR CANCER

Japanese Foundation for Cancer Research. Also represented by BRITTANY BLUEITT AMADI, Washington, DC;

NELS LIPPERT, Tarter Krinsky & Drogin LLP, New York, 

NY; PAULA JOANNE ESTRADA DE MARTIN, Baker, Donelson, 

Bearman, Caldwell & Berkowitz, PC, New Orleans, LA. 

DAVID I. BERL, Williams & Connolly LLP, Washington, DC, argued for defendant-appellee Bayer Pharma 

AG. Also represented by THOMAS S. FLETCHER, DAVID M.

KRINSKY, BRUCE GENDERSON. 

______________________ 

Before DYK, SCHALL, and CHEN, Circuit Judges.

DYK, Circuit Judge. 

Biogen MA, Inc. (“Biogen”) brought suit in district 

court, pursuant to 35 U.S.C. § 146, to challenge an interference decision by the Patent Trial and Appeal Board 

(“PTAB” or the “Board”). The Board concluded that patent 

applicant Walter Fiers was estopped from establishing 

priority in Interference No. 105,939 (the “’939 interference” or the “third interference”) because he had lost two 

prior interferences covering the same subject matter. The 

district court held that it lacked subject matter jurisdiction because the Leahy-Smith America Invents Act, Pub. 

L. No. 112–29, 125 Stat. 284 (2011) (“AIA”), eliminated 

district court jurisdiction under 35 U.S.C. § 146 with 

respect to interferences commenced after September 15, 

2012. The district court transferred this case to this court 

pursuant to 28 U.S.C. § 1631.

We conclude that we have jurisdiction to consider the 

district court’s jurisdiction; that the district court correctly decided that it lacked jurisdiction under 35 U.S.C. 

§ 146; and that the Board’s priority decision was not 

erroneous. We affirm the Board’s decision. 
BIOGEN IDEC MA, INC. v. JAPANESE FOUNDATION FOR CANCER 3

BACKGROUND

Beginning in 1983, a series of interferences were 

declared between Fiers and Haruo Sugano, Masami 

Muramatsu, and Tadatsugu Taniguchi (collectively, 

“Sugano”) generally relating to claims to DNA sequences 

that encode the precursor and/or mature forms of human 

fibroblast interferon (“hFIF”) proteins, which promote 

viral resistance in human tissue, see Fiers v. Revel, 984 

F.2d 1164, 1165 (Fed. Cir. 1993), and in the case of the 

most recent interference, to claims for the proteins themselves. All of Fiers’ applications claimed priority to United 

Kingdom Patent Application No. GB 8011306, filed on 

April 3, 1980, while Sugano’s applications and patents 

claimed priority to Japanese Patent Application No. 

33931/80, filed on March 19, 1980 (the “Japanese Application”).

 The first, Interference No. 101,096 (the “’096 interference” or the “first interference”), declared August 30, 

1983, was between Sugano’s U.S. Patent Application No. 

06/201,359 and Fiers’ U.S. Patent Application No.

06/250,609. The count was directed to the DNA sequences 

coding for hFIF proteins. Fiers moved to add counts 

directed to hFIF proteins, but this motion was denied. On 

June 5, 1991, the Board of Patent Appeals and Interferences (“BPAI” or the “Board”) awarded priority to Sugano. 

We affirmed. See Fiers, 984 F.2d at 1172. 

The second, Interference No. 105,661 (the “’661 interference” or the “second interference”), declared March 4, 

2009, was between Sugano’s U.S. Patent Nos. 5,236,859 

and 5,514,567 and Fiers’ Application No. 08/471,646. The 

count was directed to the DNA sequence encoding the 

mature hFIF proteins, and the Board ordered Fiers to 

show cause why the interference should continue given 

that its subject matter was the same as in the first interference. On August 4, 2009, the Board found that Fiers 
4 BIOGEN IDEC MA, INC. v. JAPANESE FOUNDATION FOR CANCER

failed to discharge his burden, entering judgment in favor 

of Sugano. Fiers did not appeal that decision.

Finally, on July 16, 2013, the Board declared the ’939 

interference between Fiers’ U.S. Patent Application No. 

08/253,843 (the “Fiers ’843 application”), filed on June 3, 

1994, and Sugano’s U.S. Patent Application No. 

08/463,757 (the “Sugano ’757 application”), filed on June 

5, 1995. The counts were directed to precursor and mature hFIF proteins. Biogen owns the Fiers ’843 application. The Japanese Foundation for Cancer Research 

(“JFC”) owns the Sugano ’757 application.1 The specifications of the patent applications in the ’939 interference 

are largely the same as the specifications of the applications or patents in the prior two interferences. 

On July 16, 2013, the Board again ordered Fiers to 

show cause as to why Fiers should not be estopped from 

proceeding, given that Fiers lost the prior interferences 

and the subject matter was again the same as in the prior 

interferences. 

In its response to the order, Fiers argued against

applying to the interference two forms of interference 

estoppel: estoppel by judgment and estoppel for failure to 

file a motion. Fiers argued that estoppel by judgment did 

not apply because his claims to hFIF proteins are patentably distinct from the DNA sequences encoding those 

proteins (the subject matter of the earlier interferences). 

Fiers submitted several pieces of purported evidence to 

support his argument. Fiers also argued that estoppel for 

failure to file a motion did not apply because Fiers had 

moved in prior interferences to add counts reciting hFIF 

1 Bayer Pharma AG is a party to this case because 

it is a successor to an exclusive license agreement with 

the JFC. 

 
BIOGEN IDEC MA, INC. v. JAPANESE FOUNDATION FOR CANCER 5

proteins, and had been barred from doing so by the Board.

Sugano responded that Fiers was properly estopped 

from pursuing the hFIF protein claims because he had 

failed to submit sufficient evidence to show that the 

protein claims were patentably distinct from the lost 

counts, and that Fiers’ failure in its prior motions to 

follow the Board’s procedural rules, as well as its failure 

to petition for review, also resulted in estoppel.

The Board agreed with Sugano and held that estoppel 

applied. The Board concluded that Fiers failed to discharge his burden to show patentable distinctness and

that Fiers was estopped from continuing the interference 

by reason of the two earlier interference proceedings. The 

Board entered judgment in favor of Sugano on October 3, 

2013.

On December 2, 2013, Biogen filed a civil action in 

district court under pre-AIA 35 U.S.C. § 146 to set aside 

the Board’s determination. JFC moved to dismiss the case 

for lack of subject matter jurisdiction. On May 22, 2014, 

the district court granted the motion to dismiss, holding 

that the AIA had eliminated § 146 jurisdiction to review 

interferences, such as the one here, that were filed after 

September 15, 2012. The district court transferred the 

case to this court pursuant to 28 U.S.C. § 1631 so that we 

could review the Board’s decision under pre-AIA 35 U.S.C. 

§ 141. 

DISCUSSION

I 

A threshold issue is whether we have jurisdiction to 

determine the correctness of the district court’s determination that it lacked subject matter jurisdiction under 

pre-AIA 35 U.S.C. § 146. JFC contends that the district 

court’s determination that it lacked jurisdiction under 

§ 146 is not reviewable.
6 BIOGEN IDEC MA, INC. v. JAPANESE FOUNDATION FOR CANCER

In In re Teles AG Informationstechnologien, 747 F.3d 

1357 (Fed. Cir. 2014), we concluded that we had jurisdiction in a case virtually indistinguishable in principle from 

this case. In Teles, the district court dismissed a patentee’s action brought under 35 U.S.C. § 145 to review a 

Board ex parte reexamination decision for lack of subject 

matter jurisdiction. The district court then transferred

the case to this court pursuant to § 1631. We held that the 

dismissal was improper and that the district court should 

have only transferred the case. Teles, 747 F.3d at 1359–

61. Treating the case as though it had been properly 

transferred, we then proceeded to address the question of 

the district court’s jurisdiction under 35 U.S.C. § 145 and 

the question of statutory interpretation underlying that 

issue under a de novo standard. See id. at 1361. We held 

that amendments to the patent statute had eliminated 

district court review of actions under 35 U.S.C. § 145 for 

patent owners (as opposed to applicants) and “affirm[ed] 

that the district court lacked jurisdiction over the § 145 

action.” Id. at 1366.

Since we did not explicitly discuss the basis for adjudicating the district court’s jurisdiction in Teles, we find it 

appropriate to do so here. It is well-established that 

transfer orders are generally not appealable. See Subsalve 

USA Corp. v. Watson Mfg., Inc., 462 F.3d 41, 47 (1st Cir. 

2006) (“[E]very court of appeals to have confronted [the 

issue] has concluded that section 1631 transfer orders are 

not immediately appealable.”).2 We have not been asked, 

however, to sit in appellate review of the district court’s 

transfer order. We are instead the transferee court, and 

Biogen, despite its having styled its request as a “remand,” is effectively asking us to retransfer this case to 

2 There is a limited exception for transfers to the 

Court of Federal Claims. See 28 U.S.C. § 1292(d)(4).

 
BIOGEN IDEC MA, INC. v. JAPANESE FOUNDATION FOR CANCER 7

the district court because the district court had jurisdiction under pre-AIA § 146 and we do not have jurisdiction

under pre-AIA § 141. See 28 U.S.C. § 1631.

 It is undisputed that we have “inherent jurisdiction to 

determine [our] own jurisdiction.” C.R. Bard, Inc. v. 

Schwartz, 716 F.2d 874, 877 (Fed. Cir. 1983) (citing 

United States v. United Mine Workers of Am., 330 U.S. 

258 (1947)). In this context, Congress has provided two 

mutually exclusive avenues of review under § 146 and 

§ 141, so the question of our jurisdiction and the district 

court’s jurisdiction are different sides of the same coin. If 

the district court lacked jurisdiction under § 146, we have 

jurisdiction under § 141 (as a result of the transfer), and if 

the district court court had jurisdiction under § 146, we 

lack jurisdiction under § 141. This latter proposition 

requires some explanation.

 Courts have repeatedly held in the context of § 1413

3 Section 141 provided in relevant part:

A party to an interference dissatisfied with 

the decision of the Board of Patent Appeals and 

Interferences on the interference may appeal the 

decision to the United States Court of Appeals for 

the Federal Circuit, but such appeal shall be dismissed if any adverse party to such interference, 

within twenty days after the appellant has filed 

notice of appeal in accordance with section 142 of 

this title, files notice with the Director that the 

party elects to have all further proceedings conducted as provided in section 146 of this title. If 

the appellant does not, within thirty days after filing of such notice by the adverse party, file a civil 

action under section 146, the decision appealed 

 
8 BIOGEN IDEC MA, INC. v. JAPANESE FOUNDATION FOR CANCER

and § 146,4 and their predecessor statutes, that Congress 

provided “alternative paths for judicial review of an 

interference decision of the Board.” AbbVie Deutschland 

GmbH v. Janssen Biotech, Inc., 759 F.3d 1285, 1296 (Fed. 

Cir. 2014). As the Supreme Court explained in Hoover Co. 

v. Coe, 325 U.S. 79 (1945), “[i]t is evident that alternative 

rights of review are accorded an applicant—one by appeal 

to the United States Court of Customs and Patent Appeals, the other by bill in equity filed in one of the federal 

district courts.” 325 U.S. at 83. The Court thoroughly 

reviewed the legislative history of the patent acts since 

1836, which revealed continued maintenance of alternative paths of review. See id. at 84–87. The Court held that 

in 1927, “Congress decided . . . to allow an applicant ‘to 

have the decision of the Patent Office reviewed either by 

the court of appeals or by filing a bill in equity, but not 

both.’” Id. at 87 (emphasis added) (quoting S. Rep. No. 

1313, at 4 (1927)); see also P.J. Federico, Commentary on 

from shall govern the further proceedings in the 

case.

35 U.S.C. § 141 (2006). Unless otherwise specified, we 

refer to the pre-AIA versions of both § 141 and § 146.

4 Section 146 provided in relevant part:

Any party to an interference dissatisfied with 

the decision of the Board of Patent Appeals and 

Interferences on the interference, may have remedy by civil action, if commenced within such time 

after such decision, not less than sixty days, as 

the Director appoints or as provided in section 141

of this title, unless he has appealed to the United 

States Court of Appeals for the Federal Circuit, 

and such appeal is pending or has been decided.

35 U.S.C. § 146 (2006).

 
BIOGEN IDEC MA, INC. v. JAPANESE FOUNDATION FOR CANCER 9

the New Patent Act, reprinted in 75 J. Pat. & Trademark 

Off. Soc’y 161, 199 (1993) (explaining that “[d]ecisions of 

the Patent Office in refusing to grant patents, and in 

interferences, are reviewable by the courts in either of two 

ways” and that “since 1927 they have been mutually 

exclusive”).

Our predecessor court and other circuits have been 

uniform in treating § 141 and § 146 or their predecessors 

as mutually exclusive alternative paths of review that 

parties irrevocably elect. In general, if a party elects one 

path of review (§ 141 or § 146), the other is waived.5 See 

Hofstein v. Silver, 201 U.S.P.Q. 77, 79 (CCPA 1979) 

(explaining that the “clear import of the statute is to allow 

a dissatisfied party the option of either seeking review in 

this court or filing a civil action, but not both” and that 

choosing one path would be an “irrevocable election”); In 

re Isler, 152 F.2d 1002, 1004 (CCPA 1946) (noting that the 

predecessor statutes to §§ 141 and 146 are “alternative 

5 The statute was explicit about the waiver in several respects. Section 146 stated that a party has a remedy in district court “unless” he has appealed in the 

Federal Circuit, 35 U.S.C. § 146 (2006), and § 141 stated

that an applicant may appeal a BPAI decision under 

§ 134, but “[b]y filing such an appeal the applicant waives 

his or her right to proceed under section 145 of this title,” 

35 U.S.C. § 141 (2006).

However, § 141 provided for one limited exception to 

the rule that the patentee’s informed election governs: an 

“appeal shall be dismissed if any adverse party to such 

interference, within twenty days after the appellant has 

filed notice of appeal . . . , files notice with the Director 

that the party elects to have all further proceedings 

conducted as provided in section 146 of this title.” 35 

U.S.C. § 141 (2006).

 
10 BIOGEN IDEC MA, INC. v. JAPANESE FOUNDATION FOR CANCER

and mutually exclusive” (quoting Hemphill Co. v. Coe, 121 

F.2d 897, 898 (D.C. Cir. 1941))); Cleveland Trust Co. v. 

Berry, 99 F.2d 517, 521 (6th Cir. 1938) (noting that an 

appellant “could not be deprived of its right to file a bill in 

equity except by its own election to appeal to the [appellate court]”); Jensen v. Lorenz, 92 F.2d 992, 994–95 (D.C. 

Cir. 1937) (“It is evident that Congress intended to require an election by the party as between the two remedies offered to him . . . and that when such election is 

made by the litigant it is to be final.”); Bakelite Corp. v. 

Nat’l Aniline & Chem. Co., 83 F.2d 176, 177 (2d Cir. 1936) 

(noting it “cannot be doubted” the statutes provide alternative remedies); Walther v. Vanderveer, 64 F.2d 540, 541

(CCPA 1933) (holding that because parties “elected” to 

bring the case to the appellate court in the first instance, 

the appeal could not then be dismissed just to confer 

jurisdiction upon the district court to determine the 

issues). 

Thus, an election of § 146 review would foreclose § 141 

review in this court and deprive us of jurisdiction.6 But of 

course, this is true only if § 146 review were available, 

since, in general, “an election will be found only if a party 

has chosen to pursue one position that is inconsistent 

with another possible position . . . .” 18B Charles A. 

Wright, Arthur R. Miller & Edward H. Cooper, Federal 

Practice & Procedure § 4476 (2d ed. 2002). 

In short, we have jurisdiction under § 141 as a result 

6 Section 145, the section we interpreted in Teles, is 

similar. See Hyatt v. Kappos, 625 F.3d 1320, 1321 n.2 

(Fed. Cir. 2010) (en banc) (noting that sections 145 and 

146 are “parallel provisions”). The predecessor statute to 

§ 146, Revised Statute 4915, is the same one as the predecessor to § 145. See Kappos v. Hyatt, 132 S. Ct. 1690, 

1698–99 (2012).

 
BIOGEN IDEC MA, INC. v. JAPANESE FOUNDATION FOR CANCER 11

of the transfer if § 146 review was unavailable, but we 

lack jurisdiction if this case was properly brought to the 

district court under § 146. We thus must determine if the 

district court indeed lacked jurisdiction under § 146 in 

order to determine whether we lack jurisdiction and 

should retransfer the case.

Contrary to what JFC argues, the Supreme Court’s 

decision in Christianson v. Colt Industries Operating 

Corp., 486 U.S. 800 (1988), is not to the contrary. In 

Christianson, the Court held that, in order to avoid a 

“perpetual game of jurisdictional ping pong” of transfers 

and retransfers, a court of appeals should defer to another 

court of appeal’s transfer order under § 1631 unless the 

transferee court considers the transfer “clearly erroneous.” Id. at 818–19. “[I]f the transferee court can find the 

transfer decision plausible, its jurisdictional inquiry is at 

an end.” Id. at 819. Christianson thus recognized that the 

transferee court has the authority to determine its own 

jurisdiction, and only stands for the proposition that 

courts ought to “apply law-of-the-case principles to transfer decisions of coordinate courts.” Id. at 816 (emphasis 

added). Christianson does not suggest that a court of 

appeals should defer to a non-coordinate district court on 

a jurisdictional issue. Such deference would be particularly odd here since we would have appellate jurisdiction if 

the district court had determined that it did have jurisdiction. See Trayco, Inc. v. United States, 994 F.2d 832, 835 

(Fed. Cir. 1993). If we can determine that a district court 

erred in accepting jurisdiction, it follows that we can 

equally review the district court’s determination that it 

lacked jurisdiction.

II

We turn now to the question of whether pre-AIA § 146 

conferred jurisdiction on the district court in this case. 

That depends on whether the AIA, enacted on September 
12 BIOGEN IDEC MA, INC. v. JAPANESE FOUNDATION FOR CANCER

16, 2011, eliminated the district court’s § 146 jurisdiction 

to review decisions from interference proceedings declared 

after September 15, 2012. Ultimately, we conclude that 

specific statutory provisions in the AIA as amended7

govern the availability of § 146 review for interferences 

declared after September 15, 2012, and that for interferences declared after that date, § 146 review is not available. 

The AIA changed the patent system, among other 

things, from a first-to-invent to a first-inventor-to-file 

regime for determining patent priority. See AIA § 3; 

Madstad Eng’g, Inc. v. U.S. Patent & Trademark Office, 

756 F.3d 1366, 1368 (Fed. Cir. 2014). In doing so, it 

amended the patent statute’s central provisions on patentability, including 35 U.S.C. §§ 102–103, AIA § 3(a)–

(c); established derivation proceedings and eliminated

interference proceedings, AIA § 3(i)–(j); and changed the 

BPAI to the PTAB, AIA §§ 3(j), 7(a). This case concerns

the effective date of these provisions as to interferences. 

In interpreting a statute, we start with the statute’s 

language. Hughes Aircraft Co. v. Jacobson, 525 U.S. 432, 

438 (1999). Unfortunately, the effective date provisions in 

the AIA are far from a model of clarity. In general, the 

statute contains a hodgepodge of express reservations of 

pre-AIA provisions, see AIA § 6(c)(2)(C) (pre-AIA provisions regarding inter partes reexamination “shall continue to apply to requests for [certain] inter partes 

reexamination[s]”); implicit reservations, see AIA 

§ 18(a)(1)(C) (mentioning a petitioner who challenges a 

patent in a covered business method proceeding on a 

ground raised under pre-AIA §§ 102, 103); TCA § 1(k)(3) 

7 The AIA was amended by the Leahy-Smith America Invents Technical Corrections Act, Pub. L. No. 112–

274, 126 Stat. 2456 (2013) (“TCA”).

 
BIOGEN IDEC MA, INC. v. JAPANESE FOUNDATION FOR CANCER 13

(mentioning interferences declared under pre-AIA § 135); 

and sometimes simply silence, see AIA § 3 (amending but 

saying nothing about preserving pre-AIA §§ 102, 103).

 Here, Biogen argues that AIA § 3(n)(1) makes the new 

AIA provisions applicable only to new applications and 

implicitly preserves interference proceedings and judicial 

review provisions concerning interference proceedings for 

patent applications filed before March 16, 2013, including 

§ 146 review for Board decisions in interferences. JFC, on 

the other hand, apparently argues that § 3(n)(1) provides 

that the new AIA provisions shall apply not only to new 

applications but also to old applications pending on March 

16, 2013. We think JFC’s interpretation in this respect is 

untenable since it is clear from the structure of the statute that new provisions cannot be applied in their entirety to old applications. See Tobinick v. Olmarker, 753 F.3d 

1220, 1223 n.1 (Fed. Cir. 2014) (explaining that pre-AIA 

law applies generally to old interferences). Indeed, JFC 

agrees that pre-AIA law generally applies to interferences 

before the PTO. While we thus construe § 3(n)(1) as 

applying the new AIA provisions only to new applications, 

it does not follow that § 3(n)(1) requires application of preAIA judicial review provisions to old applications.

Section § 3(n)(1) provides: 

(1) IN GENERAL.—Except as otherwise provided in 

this section, the amendments made by this section 

shall take effect upon the expiration of the 18-

month period beginning on the date of the enactment of this Act [i.e., March 16, 2013], and shall 

apply to any application for patent, and to any patent issuing thereon, that contains or contained at 

any time— 

 (A) a claim to a claimed invention that has 

an effective filing date as defined in section 100(i) 

of title 35, United States Code, that is on or after 
14 BIOGEN IDEC MA, INC. v. JAPANESE FOUNDATION FOR CANCER

the effective date described in this paragraph; or

 (B) a specific reference under section 120, 

121, or 365(c) of title 35, United States Code, to 

any patent or application that contains or contained at any time such a claim.

This provision on its face is silent as to whether interference proceedings and judicial review of these proceedings

continues with respect to patent applications filed prior to 

March 16, 2013. That silence, says Biogen, means that the 

old interference provisions, including § 146 review, continue to apply to previously-filed patent applications. 

It is certainly true, as we have noted above and as the 

parties agree, that under AIA § 3(n)(1) interference proceedings are to continue with respect to previously-filed 

patent applications, that is, applications filed before 

March 16, 2013.8 But we think Congress specifically 

addressed the manner of judicial review of Board deci8 One exception is § 6(f)(3)(A), which provides that 

the Director may dismiss a pending interference in favor 

of a post-grant review. See AIA § 6(f)(3)(A).

Continuance of interference proceedings is also apparent from § 3(n)(2), which provides that pre-AIA interference provisions § 102(g), § 135, and § 291 continue to 

apply to patent applications with claims with “mixed” 

filing dates, i.e., applications with claims with filing dates 

before March 16, 2013, and claims with filing dates after 

March 15, 2013. See AIA § 3(n)(2). Section 3(n)(2) does 

not, however, provide for judicial review of such interferences. Nor, as Biogen points out, was the district court 

correct in concluding that § 3(n)(2), which in fact only 

deals with patent applications with mixed filing dates, 

“provides the basis for the PTAB to continue to declare 

interferences.” Appellant’s Br. at 22 n.9. 

 
BIOGEN IDEC MA, INC. v. JAPANESE FOUNDATION FOR CANCER 15

sions in continuing interference proceedings and that the 

specific provisions with respect to judicial review trump 

any general rule of survivorship that could be inferred 

from § 3(n)(1).

In the AIA, Congress included § 6(f)(3)(C), which 

provides: 

(C) APPEALS.—The authorization to appeal or 

have remedy from derivation proceedings in sections 141(d) and 146 of title 35, United States 

Code, as amended by this Act, and the jurisdiction 

to entertain appeals from derivation proceedings 

in section 1295(a)(4)(A) of title 28, United States 

Code, as amended by this Act, shall be deemed to 

extend to any final decision in an interference 

that is commenced before the effective date set 

forth in paragraph (2)(A) of this subsection [i.e., 

September 16, 2012] and that is not dismissed 

pursuant to this paragraph.

This section provides that amended § 146 (which now 

authorizes review only of derivation proceedings) shall be 

“deemed” to provide review of interferences declared 

before September 16, 2012.9 The section does not, however, explicitly provide for judicial review for interferences 

declared after September 15, 2012.

Congress corrected this omission in TCA § 1(k)(3). It 

provides: 

(3) REVIEW OF INTERFERENCE DECISIONS.—The 

provisions of sections 6 and 141 of title 35, United 

9 Section 6(f)(3)(B) also provides that the PTAB 

shall be “deem[ed]” the BPAI for purposes of conducting 

“any further proceedings in [such] interference[s].” AIA 

§ 6(f)(3)(B).

 
16 BIOGEN IDEC MA, INC. v. JAPANESE FOUNDATION FOR CANCER

States Code, and section 1295(a)(4)(A) of title 28, 

United States Code, as in effect on September 15, 

2012, shall apply to interference proceedings that 

are declared after September 15, 2012, under section 135 of title 35, United States Code, as in effect before the effective date under section 3(n) of 

the Leahy-Smith America Invents Act. The Patent 

Trial and Appeal Board may be deemed to be the 

Board of Patent Appeals and Interferences for 

purposes of such interference proceedings.

For interferences declared after September 15, 2012, this 

provision explicitly authorizes pre-AIA § 141 review, but 

unlike AIA § 6(f)(c)(3), does not authorize pre-AIA § 146 

review. Therefore, AIA § 6(f)(3)(C) and TCA § 1(k)(3) 

together make clear that pre-AIA § 146 review was eliminated for interference proceedings declared after September 15, 2012. 

The specific provisions in § 6(f)(3)(C) and § 1(k)(3) 

require us to apply the basic tenet of statutory interpretation that the specific governs the general. As the Supreme 

Court said in RadLAX Gateway Hotel, LLC v. Amalgamated Bank, 132 S. Ct. 2065 (2012), it is “a commonplace 

of statutory construction that the specific governs the 

general,” especially where Congress “has enacted a comprehensive scheme and has deliberately targeted specific 

problems with specific solutions.” Id. at 2071 (internal 

quotation marks and citations omitted). This principle 

equally applies when it comes to interpreting effective 

date provisions. For instance, in Gozlon-Peretz v. United 

States, 498 U.S. 395 (1991), the Supreme Court interpreted a specific provision in the Anti-Drug Abuse Act of 1986 

governing supervised release. The petitioner had argued 

that the effective date of that specific provision should be 

delayed pursuant to a more general effective date provision in a different section of the statute. Id. at 406. Rejecting that argument, the Court noted that a “specific 
BIOGEN IDEC MA, INC. v. JAPANESE FOUNDATION FOR CANCER 17

provision controls over one of more general application.” 

Id. at 407 (citing Crawford Fitting Co. v. J.T. Gibbons, 

Inc., 482 U.S. 437, 445 (1987)). 

Here, even if the general effective date provision in 

§ 3(n)(1) suggests that in general Congress preserved preAIA provisions for pre-March 16, 2013, patent applications, it does not follow that we should myopically apply

§ 3(n)(1) independently of the specific provisions in AIA 

§ 6(f)(3)(C) and § 1(k)(3). Here, Congress “deliberately 

targeted specific problems with specific solutions,” 

RadLAX, 132 S. Ct. at 2071, so we cannot ignore them.

Nor does the legislative history of the AIA suggest otherwise. While Senator Kyl recognized “the continuing need 

to allow appeals of pending interferences,” 157 Cong. Rec. 

1377 (2011) (emphasis added), the legislative history is 

silent about the specific question of what pre-AIA review 

was available for interference proceedings declared after

September 15, 2012. The regulations and commentary of 

the Patent and Trademark Office (“PTO”) that Biogen 

cites are equally unhelpful. They do not say that § 146 

review is available for interferences commenced after 

September 15, 2012. See 77 Fed. Reg. 48,612, 48,625 (Aug. 

14, 2012) (“[C]ertain interferences may be deemed to be 

eligible for judicial review as though they were derivation 

proceedings.” (emphasis added));10 37 C.F.R. § 90.1 

(“[W]here available, judicial review of decisions arising out 

10 The commentary also states that AIA § 3 “makes 

review of interference decisions by a District Court under 

35 U.S.C. [§] 146 available only if the provisions of 

§ 3(n)(1) . . . are not satisfied.” 77 Fed. Reg. 6,879, 6,891 

(Feb. 9, 2012). It is difficult to parse this particular comment, but it certainly does not clearly state § 146 review 

remains available for interferences commenced after 

September 15, 2012.

 
18 BIOGEN IDEC MA, INC. v. JAPANESE FOUNDATION FOR CANCER

of interferences declared pursuant to 35 U.S.C. [§] 135 

continue to be governed by the pertinent regulations . . . .” 

(emphasis added)). In any case, the PTO’s regulations 

interpreting the scope of the district court’s subject matter 

jurisdiction would not be entitled to Chevron deference. 

See Love v. Thomas, 858 F.2d 1347, 1352 n.9 (9th Cir. 

1988) (Chevron “deference does not extend to the question 

of judicial review, a matter within the particular expertise 

of the courts”). 

We must accordingly follow the express provisions in 

the statute. Biogen’s other convoluted efforts to argue 

that Congress’ specific approach should not govern require no further discussion.

In short, because the AIA and its technical corrections 

provided that only pre-AIA § 141 review in this court 

would be available for interferences declared after September 15, 2012, and the ’939 interference here was 

declared July 16, 2013, the district court properly found 

that it lacked subject matter jurisdiction. It follows that 

we have jurisdiction to hear Biogen’s appeal pursuant to 

§ 141. 

III 

We now turn to the merits of Biogen’s appeal of the 

Board’s judgment against Fiers in the ’939 interference. 

The Board’s judgment was based on Fiers’ failure to meet 

his burden in responding to the July 16, 2013, order to 

show cause why Fiers should not be estopped from continuing with the interference, given that he had lost two 

prior interferences. 

Interference estoppel “by judgment” applies where “a 

losing party in a previous interference between the same 

parties” tries to patent a claim “not patentably distinct 

from the counts in issue in that [prior] interference.” 

Woods v. Tsuchiya, 754 F.2d 1571, 1579 (Fed. Cir. 1985); 
BIOGEN IDEC MA, INC. v. JAPANESE FOUNDATION FOR CANCER 19

see also In re Deckler, 977 F.2d 1449, 1452 (Fed. Cir. 

1992) (holding that a losing priority judgment in an 

interference proceeding bars the loser from obtaining a 

patent containing claims that are patentably indistinguishable from the claims corresponding to the lost 

count); MPEP § 2308.03 (9th ed. March 2014) (interference estoppel applies where a “losing party is barred on 

the merits from seeking a claim that would have been 

anticipated or rendered obvious by the subject matter of 

the lost count”).

The parties do not dispute that estoppel by judgment, 

if applicable, is itself sufficient to estop Fiers from continuing the interference even if Fiers’ motion to add protein 

counts to the earlier interferences failed.11 Estoppel by 

11 That unsuccessful efforts to add a count do not 

prevent estoppel by judgment is clear from Stoudt v. 

Guggenheim, 651 F.2d 760 (CCPA 1981), a case on which 

Biogen relies. As the court in Stoudt explained: “Where 

the prior judgment between the same parties is not strictly res judicata because it resolves a different and distinct 

issue [e.g., a patentably distinct count], that judgment 

may nonetheless create an estoppel as to matters actually 

in issue or points controverted.” Id. at 764 (bracketed 

content in original). The court treated estoppel by judgment and estoppel for failure to file a motion separately, 

holding that neither applied in that case:

We agree with the board’s adoption of the examiner’s ex parte determination that the present 

count is patentably distinct from [the count in] the 

previous interference. No identity of issues is 

therefore present in the two interferences and the 

doctrine of res judicata is inapplicable.

 
20 BIOGEN IDEC MA, INC. v. JAPANESE FOUNDATION FOR CANCER

judgment rests on the principle that a “judgment in an 

action precludes relitigation of claims or issues that were 

. . . raised in [the earlier] proceeding.” In re Deckler, 977 

F.2d at 1452. This is “an application of settled principles 

of res judicata,” id., under which “a final judgment on the 

merits of an action precludes . . . relitigating issues.” San 

Remo Hotel, L.P. v. City & Cnty. of S.F., Cal., 545 U.S. 

323, 336 n.16 (2005). Claims that are not patentably 

distinct from lost counts were already adjudicated in the 

prior interference and are thus conclusive. Even if Fiers’ 

filing of the motion to add the protein count would suffice 

to avoid other forms of estoppel, it is irrelevant to estoppel 

by judgment. See Restatement (Second) of Judgments, 

§ 26 cmt. b (1980) (noting that the “mere refusal of the 

court . . . to allow an amendment . . . , even where the 

refusal of the amendment was urged by the defendant, is 

not a reservation by the court [of the right to maintain a 

second action]”).

We agree with the Board that Fiers failed to meet his 

burden to show patentable distinctness to avoid interference estoppel by judgment.

This issue of patentable distinctness arose in the most 

recent interference proceeding when the Board issued a 

show cause order requiring Fiers to “show why it will be 

able to prove an earlier date of conception in the current 

Stoudt moved to add the proposed count. The 

interference examiner’s denial of that motion was 

not appealable to the board, and Stoudt could do 

nothing further to bring the matter before the 

board in the earlier interference. The estoppel 

doctrine [based on failure to file a motion] therefore finds no application to the facts of this case.

Id. at 765.

 
BIOGEN IDEC MA, INC. v. JAPANESE FOUNDATION FOR CANCER 21

interference when it could not do so in the prior interference [the ’096 interference].” J.A. 2807. Noting that a 

losing party to an interference is barred from obtaining a 

patent on claims that are patentably indistinguishable 

from the subject matter of the earlier count, the Board 

stated that “[i]n light of [the fact] that DNA and the

known genetic code indicating which DNA sequences 

encode each amino acid, those of skill in the art would 

have considered the polypeptide Fiers now claims to have 

been obvious.” J.A. 2808.

Biogen argues on appeal that the hFIF proteins are 

patentably distinct because they are “functional,” complaining that Fiers “should be entitled to introduce evidence in the ’939 interference to demonstrate that in 1980 

mere possession of the DNA sequence fell far short of 

possession of the functional protein required by the 

claims.” Appellant’s Br. at 43. But in fact, Biogen did have 

that opportunity in its response to the show cause order.

It failed to properly submit evidence showing patentable 

distinctness, and cannot now argue that the proteins are 

patentably distinct from the DNA. 

Biogen does not contend that the show cause order 

was issued erroneously, and does not dispute that Fiers 

had the burden to provide evidence to show patentable 

distinctness. Instead, Biogen argues that there is no 

estoppel by judgment here because Fiers showed in his 

response to the show cause order that the hFIF proteins 

claimed in the ’939 interference are not obvious over the 

DNA sequences encoding those proteins that were at issue 

in the prior interferences. In his response, Fiers pointed 

to four pieces of alleged evidence. 

First, Fiers pointed to the fact that, on April 15, 1982,

the PTO imposed a restriction requirement during prosecution of Fiers’ U.S. Application No. 06/250,609 (the “’609 

application,” of which the ’843 application is a divisional), 
22 BIOGEN IDEC MA, INC. v. JAPANESE FOUNDATION FOR CANCER

filed April 3, 1981, between claims directed to the DNA 

sequences and claims directed to the proteins. However, a 

restriction requirement is not substantive evidence that 

Fiers’ claims are patentably distinct over the DNA sequences. At most, it is evidence that the examiner 

thought that there were “two or more independent and 

distinct inventions” claimed in a single application. 35 

U.S.C. § 121; 37 C.F.R. § 1.142; MPEP § 802.01 (9th ed. 

March 2014). Restriction requirements are discretionary 

decisions, primarily for administrative convenience, and 

do not represent a final determination that the relevant 

claims are patentably distinct. See Applied Materials, Inc. 

v. Advanced Semiconductor Materials Am., Inc., 98 F.3d 

1563, 1568 (Fed. Cir. 1996) (noting restriction requirement is for “administrative convenience”); Transco Prods. 

Inc. v. Performance Contracting, Inc., 38 F.3d 551, 558–59 

(Fed. Cir. 1994) (same); In re Watkinson, 900 F.2d 230, 

233 (Fed. Cir. 1990) (restriction is “a matter within the 

discretion of the examiner and not tantamount to a rejection of claims”); In re Hengehold, 440 F.2d 1395, 1403 

(CCPA 1971) (restriction is a “discretionary, procedural or 

nonsubstantive” matter).12

12 Biogen argues that the equitable principles underlying the safe harbor provision in 35 U.S.C. § 121 should 

apply here to protect Fiers from estoppel. See 35 U.S.C. 

§ 121 (“A patent issuing on an application with respect to 

which a requirement for restriction under this section has 

been made, or on an application filed as a result of such a 

requirement, shall not be used as a reference either in the 

Patent and Trademark Office or in the courts against a 

divisional application or against the original application 

or any patent issued on either of them, if the divisional 

application is filed before the issuance of the patent on 

the other application.”). Section 121 provides a safe har-

 
BIOGEN IDEC MA, INC. v. JAPANESE FOUNDATION FOR CANCER 23

Second, Fiers argued that separate interferences, Interferences No. 105,334 and No. 105,337, were declared 

between Sugano and a different party, Goeddel. Those 

interferences separately involved counts corresponding to 

hFIF proteins and the DNA encoding them. See Goeddel 

v. Sugano, 617 F.3d 1350, 1352 (Fed. Cir. 2010). But once 

again, this fact is not substantive evidence of patentable 

distinctness. The discretionary decision to declare separate interferences in another proceeding is not necessarily 

a determination, let alone a final one, of patentable distinctness.

Third, Fiers pointed to a Board decision in the initial 

ex parte proceeding concerning Fiers’ ’843 application 

reversing an examiner’s determination that protein 

claims in the Fiers application were unpatentable as 

anticipated over Sugano’s ’859 and ’567 patents. But in 

that decision, the Board reversed because the examiner 

had not established an evidentiary basis, and expressly 

said that it was making “no ruling as to whether the 

subject matter of the rejected claims is patentably distinct 

from” the DNA count in the first interference. J.A. 5212.

Finally, in a section of his response dedicated to arguing, not that the protein claims were patentably distinct, 

but that Fiers can prevail on priority, Fiers cited a declabor from double patenting rejections against a patentee 

on claims that were a result of an earlier restriction 

requirement because it would be inequitable to reject 

divided claims on the ground of double patenting when 

the division was required on the theory that the original 

application contained claims for more than one invention. 

See Pfizer, Inc. v. Teva Pharm. USA, Inc., 518 F.3d 1353, 

1361 (Fed. Cir. 2008). Section 121 is on its face inapplicable here, and in any case, the restriction requirement did 

not result in Fiers’ losing in the prior interferences.

 
24 BIOGEN IDEC MA, INC. v. JAPANESE FOUNDATION FOR CANCER

ration by Dr. David A. Jackson. However, in that declaration, Dr. Jackson addressed only whether the Japanese 

application contains a written description of an embodiment within the scope of the counts in the ’939 interference, and whether the Japanese application provides 

sufficient information for one skilled in the art to practice 

such an embodiment without undue experimentation. J.A. 

5198. There was nothing in the declaration about how 

Fiers’ hFIF protein claims were not obvious over the lost 

counts directed to the DNA sequences. 

We thus see no error in the Board’s conclusion that 

Fiers submitted no relevant evidence on patentable 

distinctness and was thus estopped from continuing with 

the interference.

CONCLUSION

We conclude that as a result of the transfer we have 

jurisdiction under pre-AIA 35 U.S.C. § 141 to hear Biogen’s appeal. This is so because the AIA eliminated district courts’ subject matter jurisdiction under pre-AIA 35 

U.S.C. § 146 to review decisions in interference proceedings declared after September 15, 2012. We therefore 

decline to transfer this case back to the district court.

On the merits, we conclude that the Board did not err 

in entering judgment against Fiers on the basis of interference estoppel because Fiers did not discharge its burden in response to the Board’s show cause order to 

provide evidence of the patentable distinctness of its hFIF 

protein claims over the DNA sequences encoding for such 

proteins. 

Biogen’s request for retransfer is:

DENIED

The Board’s decision is: 

AFFIRMED
BIOGEN IDEC MA, INC. v. JAPANESE FOUNDATION FOR CANCER 25

COSTS

Costs to appellees.