The opinion of the court was delivered by: Ellen Segal Huvelle United States District Judge
Plaintiffs The Humane Society of the United States, Will Anderson and Sharon Young have sued Carlos M. Gutierrez, Secretary of the United States Department of Commerce; Conrad C. Lautenbacher, Administrator of the National Oceanic and Atmospheric Administration; William T. Hogarth, Assistant Administrator of the National Marine Fisheries Service; and the National Marine Fisheries Service, claiming violations of the National Environmental Policy Act ("NEPA"), 42 U.S.C. § 4321 et seq.; the Endangered Species Act ("ESA"), 16 U.S.C. § 1531 et seq.; the Marine Mammal Protection Act ("MMPA"), 16 U.S.C. § 1374 et seq.; and the Administrative Procedures Act ("APA"), 5 U.S.C. § 701 et seq. They challenge the issuance and amendment of various permits that authorize research on threatened and endangered populations of Steller sea lions. Pending before the Court are plaintiffs' Motion for Summary Judgment and defendants' Cross-Motion for Summary Judgment. For the reasons discussed below, the Court grants plaintiffs' motion with respect to their NEPA claims.
Following a dramatic decline in the Alaskan population of Steller sea lions over thirty years, they were first classified as threatened in 1990. See Listing of Steller Sea Lions as Threatened Under the Endangered Species Act, 55 Fed. Reg. 49,204, 49,208 (Nov. 26, 1990) (final rule) (noting that the number of Steller sea lions living from Kenai Peninsula to Kiska Island, Alaska declined by 82 percent between 1960 and 1989). (See also AR 259 at 338 ("Th[e] species has experienced a marked decline from an estimated 240,000-300,000 individuals in the 1960s . . . to an estimated 116,000 individuals in 1989. Population numbers in the United States have declined by about 75% over the past 20 years . . . with most of the decline occurring in the western stock.").) In the wake of this classification, two distinct populations of Steller sea lions were identified in their range along the North Pacific Rim: an eastern stock, including all animals distributed from central California northward to Cape Suckling, Alaska, and a western stock, including all animals distributed from Cape Suckling to Hokkaido, Japan. See Change in Listing Status of Steller Sea Lions Under the Endangered Species Act, 62 Fed. Reg. 24,345, 24,346 (May 5, 1997); Listing of Steller Sea Lions as Threatened Under the Endangered Species Act, 55 Fed. Reg. 29,793, 29,795 (Jul. 20, 1990) (proposed rule). In 1997, after determining that the subsequent two decades would be crucial to the western population's survival, the Department of Commerce's National Marine Fisheries Service ("NMFS") reclassified the western stock as endangered, maintaining the eastern stock's threatened classification. 62 Fed. Reg. at 24,346-347 (noting that one model "predicted a 100 percent probability of extinction [for the western population segment] within 100 years from the 1985-94 trend data, and a 65 percent probability of extinction within 100 years if the 1989-94 trend continue[d]").
While researchers began investigating the decline of the Steller sea lion with its identification in the 1980s, funding for such research remained modest for more than a decade. See 62 Fed. Reg. at 24,346 (discussing research); 55 Fed. Reg. at 29,795 (same). (Answer ¶ 59 ("NOAA . . . research funding during the 1990s was less than $1 million.").) This changed with the passage of the Consolidated Appropriations Act of 2001, which declared that "the western population of Steller sea lions ha[d] substantially declined over the last 25 years" and thus "scientists should closely research and analyze all possible factors relating to such decline . . . ." Pub. L. No. 106-554, § 209(a)(1)-(2), 114 Stat. 2763, 2763A-176 (2000). In furtherance of this research, Congress appropriated more than $40 million for studies regarding "available prey species . . . [,] predation by other marine mammals . . . [,] interactions between fisheries and Steller sea lions . . . [,] regime shift, climate change, and other impacts associated with changing environmental conditions in the North Pacific and Bering Sea . . . [,] juvenile and pup survival rates . . . [,] nutritional stress" and other potential factors contributing to the sea lions' decline. Id. §§ 206, 209, 114 Stat. at 2763A-176; see also Steller Sea Lion Research Initiative (SSLRI), 66 Fed. Reg. 15,842 (Mar. 21, 2001) (notice of availability of funds). This amount was augmented by an almost identical sum the following year. (See AR 406 at 7-8, 53 (summarizing the various federal appropriations for Steller sea lion research).) The resulting research fund was the largest ever dedicated to a single species. (Compl. ¶ 59; Answer ¶ 59.)
After receiving numerous applications for permits and permit amendments authorizing research relating to the threatened and endangered Steller sea lion populations,*fn1 NMFS opened an investigation into the potential effects of the proposed studies on the environment in 2002. (See AR 406 at 11.) In a June 2002 Environmental Assessment ("EA") and Finding of No Significant Impact ("FONSI"), the agency concluded that authorization of the requested studies through 2004,*fn2 with certain mitigating measures, would not significantly affect the human environment. (Id. at 12-13.) A November 2002 Biological Opinion ("BO") determined that the permits were "not likely to jeopardize the continued existence of the endangered western population of Steller sea lions or the threatened eastern population of Steller sea lions." (AR 389 at 73 (Nov. 12, 2002 BO).) Based on these findings, NMFS issued research permits and permit amendments allowing the "harassment" of sea lion populations through aerial and boat-based surveys; ground counts; scat, blood and biopsy collection; capture and restraint; tagging and branding; tooth extraction; attachment of scientific instruments; and other research activities. (See AR 406 at 79-83; AR 389 at 10-31.) The permits also authorized stated amounts of "incidental mortality." (Id.)*fn3
On April 4, 2005, NMFS published notice that eight individuals or institutions had submitted applications for five-year permits or three-year permit extensions authorizing further research of a similar character. (See AR 395 at 1 (Marine Mammals, 70 Fed. Reg. 17,072 (Apr. 4, 2005)).) In the same notice, the agency indicated that a related draft EA, which concluded that an Environmental Impact Statement ("EIS") need not be prepared as the proposed research would not have a significant effect on the human environment, was also available for review and comment. (See AR 395 at 3; AR 406.) The "scope" of the draft assessment included six environmental impact issues:
(1) Is NMFS able to coordinate research under the various permits and ensure that activities are not unnecessarily duplicative and do not result in significant adverse impacts on threatened and endangered Steller sea lions? (2) Is NMFS able to adequately monitor the effects of the overall research program on Steller sea lions? (3) Can NMFS coordinate and synthesize the data generated by this research program in a way that is useful or meaningful for conservation of Steller sea lions? (4) Are all of the research proposals consistent with permit issuance criteria under the MMPA and ESA, such as whether all of the projects are likely to contribute to conservation of Steller sea lions? (5) Does the amount of incidental mortality to be authorized represent a significant adverse impact on Steller sea lions? (6) What are the potential effects of various research activities, either individually or cumulatively, on Steller sea lions as a species?
Pursuant to federal regulations, NMFS was required to submit the permit applications for review by an independent federal agency, the Marine Mammal Commission ("MMC"), which had been established to provide oversight of the government's marine mammal conservation policies and programs. See 16 U.S.C. § 1401; 50 C.F.R. § 216.33(d)(2) (providing that permit applications must be forwarded to the MMC "for comment" and "[i]f no comments are received within 45 days . . . the Office Director will consider the Commission to have no objection to issuing a permit"). On May 19, 2005, the MMC submitted a five-page set of "preliminary comments" in response to the agency's request that it "expedite . . . review of the permit applications because of a pressing need to issue the permits." (Barrett Decl. Ex. 1 at 1.) While noting its "expect[ation]" that the agency would "defer final action on the applications" until it had had an opportunity to "complete [a] full review of the applications . . . in consultation with the Committee of Scientific Advisors as required under the Marine Mammal Protection Act," the MMC recommended that NMFS reconsider its finding and either offer additional explanation for its conclusion that the research would not have a significant impact on the environment, reduce the scope of the approved research projects, or prepare an EIS. (Id. at 5.) This recommendation, the MMC indicated, was essentially identical to that it had made following a review of the agency's 2002 EA and related permit applications. (Id.)
On May 24, 2005, prior to the MMC's completion of its final comments on the action,*fn4 NMFS issued its Final EA, a FONSI declaring that "preparation of an Environmental Impact Statement . . . [was] not required by . . . the National Environmental Policy Act[,]" and a BO (the "2005 BO") concluding that "the research program, as proposed, [was] not likely to jeopardize the continued existence of the endangered western population of Steller sea lions or the threatened eastern population of Steller sea lions." (AR 404 at 1 (FONSI); AR 406 (EA); AR 407 at 69 (BO).) Soon thereafter, the agency issued the requested permits and amendments, authorizing the repeated taking of more than 200,000 sea lions in the course of annual vessel and aerial surveys; the taking of more than 140,000 sea lions during ground-based research; an annual incidental mortality of up to 60 sea lions, including up to 20 from the endangered western stock; the annual capture or restraint of more than 3,000 sea lions; the branding of more than 2,900 sea lions; the annual attachment of scientific instruments to more than 700 sea lions; and various other research activities. (See Answer ¶ 69 (indicating that the agency issued the first of the permits on May 27, 2005); AR 113 at 1 (June 16, 2005 Federal Register notice of permit and permit amendment issuance); AR 406 App. E (activity tables for proposed action); Defs.' Opp'n at 7-8 ("In 2005, NMFS increased the maximum number of animals that could be studied during this research to 527,690 western and eastern sea lions, an increase of approximately 59 percent.").) The action increased the number of issued permits, extended the duration of the permitted research, authorized new research methods,*fn5 and raised both the number of annual takes and their frequency. (AR 406 at 27-30, 43.) The permits did not, however, authorize the intentional killing of any Steller sea lions as part of any scientific study. (See id. 53, 103-119.)
Following the conclusion of the agency's inquiry into the ecological impacts of the various permit applications, Assistant Administrator for Fisheries William T. Hogarth met with representatives of The Humane Society in order to discuss the Society's objections to the agency's issuance of the permits. (See Barrett Decl. Ex. 3 (Hogarth letter); AR 402 (Society's May 17, 2005 letter to Hogarth).) In a June 27, 2005 letter to the Society's counsel, Hogarth stated that NMFS "share[d] [the Society's] concerns over the scope of the research on Steller sea lions" and indicated that the agency had accordingly "decided to prepare an environmental impact statement . . . on the effects of scientific research on this species." (Barrett Decl. Ex. 3.) This decision was announced publicly on December 28, 2005, when NMFS published notice of its "intent to prepare an Environmental Impact Statement . . . to analyze the environmental impacts of administering grants and issuing permits associated with research on endangered and threatened Steller sea lions (Eumetopias jubatus) and depleted northern fur seals (Callorhinus ursinus)." Notice of Intent to Prepare an Environmental Impact Statement on Impacts of Research on Steller Sea Lions and Northern Fur Seals Throughout Their Range in the United States, 70 Fed. Reg. 76,780 (Dec. 28, 2005). "Based on comments received on Environmental Assessments prepared in 2002 and 2005 for permitting research on Steller sea lions," the agency identified the following six issues for public comment and later consideration in its EIS: the "[t]ypes of research methods and protocols permitted[;]" the "[l]evel of research effort" required for management and conservation, and potential means of limiting takes; the "[c]oordination of research" among various individuals and institutions; the "[e]ffects of research" on animal populations; the "[q]ualification of researchers" operating under permits; and possible "[c]riteria for allowing modifications or amendments to existing grants and permits[,] for denying permit amendments[,] and for suspending or revoking permits." Id. at 76,781-82.
On July 12, 2005, and prior to the agency's Federal Register notice announcing its intent to prepare an EIS, plaintiffs filed suit alleging that defendants had violated NEPA by declining to prepare an EIS and by relying on an EA that failed to satisfy the statute's requirements; that their 2005 BO contravened the ESA by failing to properly evaluate the direct, indirect and cumulative impacts on Steller sea lions from the research activities authorized by the permits; and that they had violated the MMPA by failing to follow regulations requiring that they not issue permits until the MMC had completed its comments and by authorizing incidental mortalities that would exceed the Steller sea lion's Potential Biological Removal level ("PBR level"). Defendants respond by arguing that the agency's EA, FONSI and 2005 BO constitute a thorough analysis of the environmental factors; that the permits, which do not authorize a level of mortality sufficient to significantly impair the recovery of the western stock, were issued only after NMFS had the benefit of the MMC's comments; and, in any event, that the plaintiffs' challenge to the 2005 BO is now moot since a revised BO (the "2006 BO") was issued on March 3, 2006.*fn6
Under the judicial review provisions of the APA, an administrative action may be set aside only where it is "arbitrary, capricious, an abuse of discretion, or otherwise not in accordance with law." See 5 U.S.C. § 706(2)(A)-(D); Marsh v. Oregon Natural Res. Council, 490 U.S. 360, 375 (1989). The question is therefore one of reasonableness -- "this court will not second guess an agency decision or question whether the decision made was the best one." C & W Fish Co., Inc. v. Fox, Jr., 931 F.2d 1556, 1565 (D.C. Cir. 1991). While agency actions are presumed valid and granted substantial deference, especially in cases involving a scientific determination within an agency's area of expertise, see Baltimore Gas & Elec. Co. v. NRDC, 462 U.S. 87, 103 (1983), they are not spared a "thorough, probing, in-depth review." Citizens to Preserve Overton Park v. Volpe, 401 U.S. 402, 415 (1971); see also Marsh, 490 U.S. at 378 (A court's review of administrative action "must be searching and careful," though "the ultimate standard of review is a narrow one.") (internal quotations omitted). Agencies must consider the relevant information and provide a satisfactory explanation for their actions, including a "rational connection between the facts found and the choice made." Burlington Truck Lines v. United States, 371 U.S. 156, 168 (1962). When reviewing an agency's explanation, courts must "'consider whether the decision was based on a consideration of the relevant factors and whether there has been a clear error of judgment.'" Motor Vehicle Mfrs. Ass'n v. State Farm Mut. Auto. Ins. Co., 463 U.S. 29, 43 (1983) (quoting Bowman Transp., Inc. v. Arkansas-Best Freight Sys., Inc., 419 U.S. 281, 285 (1974)).
Normally, an agency [action] would be arbitrary and capricious if the agency has relied on factors which Congress has not intended it to consider, entirely failed to consider an important aspect of the problem, offered an explanation for its decision that runs counter to the evidence before the agency, or is so implausible that it could not be ascribed to a difference in view or the product of agency expertise.
Id. When an agency has proceeded in such a manner, the resulting action must be abandoned, for courts "may not supply a reasoned basis for the agency's action that the agency itself has not ...