3

Critical Gaps in the Scope of the Draft BDCP

The panel concludes that the draft BDCP is missing critical elements, including an effects analysis, a description of how and where scientific information was used in the draft BDCP, and a description of the BDCP’s relationship to other ongoing efforts. In addition, the draft has several structural or systematic problems, including lack of clarity as to the purpose of the BDCP; an unclear linkage of various parts of the BDCP to the effects analysis4 and among its other components; and lack of detail about analyses of various future scenarios, including a lack of analyses of tradeoffs among the BDCP’s goals in various scenarios. The panel offers some guidance on how these systematic problems might be addressed and how the draft BDCP might be completed more usefully.

At the outset of its review the panel identified a problem with the geographical and hydrologic scope of the draft BDCP. The BDCP aims to address management and restoration of the San Francisco Bay Delta Estuary, an estuary that extends from the Central Valley to the mouth of San Francisco Bay. Thus, given that the BDCP purports to describe a Bay Delta Conservation Plan, the omission of analyses of the effects of the BDCP efforts on San Francisco Bay (aside from Suisun Bay) is notable. This omission should be of concern to all BDCP parties because the Bay-Delta system is an estuary, and there are significant physical, biogeochemical, and ecological connections between the various sub-embayments as well as between the Bay-Delta and the Pacific Ocean (e.g., Cloern et al., 2010). In particular, changes in outflows and in the tidal prism associated with changing water-project operations and restoration actions would be expected to cause changes in San Francisco Bay, and not only in the Delta. A plan intended to be comprehensive should incorporate these fundamental features of the system. Although the statutory basis of the BDCP may argue against consideration of the effects outside the statutory Delta, the BDCP’s failure to address issues related to San Francisco Bay is a significant flaw that should be corrected in subsequent versions of the plan.

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4 Even though the effects analysis is not yet complete, the BDCP’s authors should at least be able to describe how the completed parts of the BDCP will be linked to the effects analysis.



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3  Critical Gaps in the Scope of the Draft  BDCP  The panel concludes that the draft BDCP is missing critical elements, in- cluding an effects analysis, a description of how and where scientific informa- tion was used in the draft BDCP, and a description of the BDCP’s relationship to other ongoing efforts. In addition, the draft has several structural or systemat- ic problems, including lack of clarity as to the purpose of the BDCP; an unclear linkage of various parts of the BDCP to the effects analysis4 and among its other components; and lack of detail about analyses of various future scenarios, in- cluding a lack of analyses of tradeoffs among the BDCP’s goals in various sce- narios. The panel offers some guidance on how these systematic problems might be addressed and how the draft BDCP might be completed more usefully. At the outset of its review the panel identified a problem with the geograph- ical and hydrologic scope of the draft BDCP. The BDCP aims to address man- agement and restoration of the San Francisco Bay Delta Estuary, an estuary that extends from the Central Valley to the mouth of San Francisco Bay. Thus, given that the BDCP purports to describe a Bay Delta Conservation Plan, the omission of analyses of the effects of the BDCP efforts on San Francisco Bay (aside from Suisun Bay) is notable. This omission should be of concern to all BDCP parties because the Bay-Delta system is an estuary, and there are significant physical, biogeochemical, and ecological connections between the various sub- embayments as well as between the Bay-Delta and the Pacific Ocean (e.g., Cloern et al., 2010). In particular, changes in outflows and in the tidal prism associated with changing water-project operations and restoration actions would be expected to cause changes in San Francisco Bay, and not only in the Delta. A plan intended to be comprehensive should incorporate these fundamental fea- tures of the system. Although the statutory basis of the BDCP may argue against consideration of the effects outside the statutory Delta, the BDCP’s failure to address issues related to San Francisco Bay is a significant flaw that should be corrected in subsequent versions of the plan. 4  Even though the effects analysis is not yet complete, the BDCP’s authors should at least be able to  describe how the completed parts of the BDCP will be linked to the effects analysis.   20 

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Critical Gaps in the Scope of the Draft BDCP  21  THE LACK OF AN EFFECTS ANALYSIS The draft BDCP describes an effects analysis as: “the  principal  component  of  a  habitat  conservation  plan  [HCP].  .  .  .  The  analysis includes the effects of the proposed project on covered species, in‐ cluding federally and state listed species, and other sensitive species poten‐ tially affected by the proposed project.  The effects analysis is a systematic,  scientific  look  at  the  potential  impacts  of  a  proposed  project  on  these  spe‐ cies  and  how  these  species  would  benefit  from  conservation  actions”   (draft BDCP p. 5‐2).    Clearly, such an effects analysis, which is in preparation, is intended to be the basis for the choice and details of those conservation actions. Its absence in the BDCP, therefore, is critical gap in the scope of the science and the conservation actions. Nevertheless, the panel presents its vision of the structure and content of a useful effects analysis. The above description of the effects analysis to be included in the BDCP is rather narrowly cast, because it focuses on the BDCP as a habitat conservation plan (HCP), that is, as an application for an incidental take permit. It thus pre- supposes the choice of the project to be permitted. By contrast, a broadly fo- cused conservation strategy, which the draft BDCP also says it is5, requires a similarly broadly focused, comprehensive effects analysis. Such an effects analysis would include a systematic analysis of the factors affecting species and ecosystems of concern and the likely contribution of human-caused changes in the system. Such an analysis would then lead to the informed choice of options for reversing the decline of the ecosystem and its components, rather than only analyzing a pre-chosen option. What would such an effects analysis look like? Effects analyses are used in a range of disciplines to understand complex systems. As noted in the quote above, their main attribute is that they are sys- tematic scientific analysis. Their precise form is not critical. For example, failure mode and effects analysis (FMEA) is commonly applied in the automotive, aer- ospace, and software industries to understand whether and how the failure of individual components impact the reliability of the overall system (Gilchrest, 1993; McDermott et al., 2009). In the environmental field, effects analyses are used to understand and compare likely responses to alternative management schemes (e.g., Marcot et al., 2001). The National Research Council has re- viewed the application of effects analysis within the environmental arena (NRC, 2009). In addition, several NRC reports have discussed or applied the tech- niques of effects analysis even though they were not necessarily called “effect 5  The following statement appears on p. 1‐1 of the draft BDCP:  “The [BDCP] sets out a comprehen‐ sive conservation strategy for the Delta designed to advance the co‐equal planning goals of restor‐ ing ecological functions of the Delta and improving water supply reliability to large portions of the  state of California.”  

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22    A Review of California’s Draft Bay Delta Conservation Plan  analysis” (e.g., NRC, 1995, 2002, 2004a, 2004b, 2005; Appendix E of this re- port provides an example of an effects analysis from NRC 2004b). Effects ana- lyses are commonly used because they integrate empirical data and expert opi- nion to guide management decisions (e.g., NRC, 2004b). The analytical ap- proaches used in the different types of effects analyses vary from classical risk priority numbers, to simulation modeling (e.g., Legault, 2005), to complex Bayesian network models (Ellison, 1996; Uusitalo, 2007). However, certain important elements are common to all of these analyses, including the need to describe how individual components in the system are connected. It is an effects analysis of this scope that the panel envisions for the BDCP. Here, the panel provides guidance regarding the structure and essential elements that it would expect to see in the completed effects analysis for the draft BDCP. The panel draws on a recent paper by Murphy and Weiland (2011) for a description of a useful effects analysis, itself based to some degree on NRC (2009), because it sets forth specifics for an effects analysis that would be appropriate for the Del- ta. The panel agrees with Murphy’s and Weiland’s general approach. An effects analysis is an essential element of the final BDCP, because it will help meet the legal requirement for a habitat conservation plan to evaluate whether the preferred action aids in the recovery of the species (state require- ment) and does not appreciably reduce the likelihood or the survival and recov- ery of the listed species in the wild (federal requirement). These requirements are initially triggered because as an HCP/NCCP (natural communities conserva- tion plan), the BDCP deals with listed species. However, even if this were not the case, an effects analysis provides the framework within which the impacts of alternative management options can be compared and thus could be justified from a purely logical point of view. An effects analysis is further justified be- cause it also may inform the adaptive management process by identifying which components or processes are the most sensitive indicators of the status and struc- ture of the ecosystem (McCann et al., 2006). Once the goal of the effects analysis has been defined, the first element of any effects analysis must be an integrated description of the components of the system and how they relate to one another. This description should include a clear statement of the alternative management actions proposed, including that of no action. The activities in this first section naturally lead to a clear definition of the management goal and the temporal and spatial domain of the impacted area. At this introductory level, it is not necessary to quantify the relationships. One needs to mainly indicate the connections. Such a description is essential for several reasons. Most important, it formalizes the understanding of the connec- tions among processes and components in the system. It defines which processes and components are expected to respond to any perturbation and which ones will not. Secondarily, in formulating the problem, a conceptual dia- gram can serve to identify and rank in importance data on different processes and components within the system. Finally, the system description provides a broader context into which information on the status and trends of species cov- ered by state and federal statues can be placed―such that the dependencies of

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Critical Gaps in the Scope of the Draft BDCP  23  these listed species on processes and components of the system are identified. The second stage of the effects analysis should be the collection, review and critical assessment of the best relevant scientific information available. The determination of which data need to be assembled is guided largely by the con- ceptual framework identified in the first stage. It is neither necessary nor helpful for the assembled data to be encyclopedic in coverage. However, it is essential that data on those processes and components identified in the first stage are compiled, assessed and summarized. This information may be in the form of empirical data or in instances where data are unavailable, in the form of expert opinion. Expert and stakeholder opinion has been successfully used in several management questions involving water use or fish stocks (Borsuk et al., 2001; Miller et al., 2010). The objectives of the data assembly phase are to clearly describe the baseline or reference condition6 and to quantify the expected rela- tionships among system processes and components. An important feature of this stage is the need to include information on the uncertainties around estimates of processes or component levels. Additionally, the spatial and temporal scale of processes and components under consideration are a vital concern. Different processes and components likely respond at characteristic spatial and temporal scales. For example, the response of many chemical or physical variables might scale with the residence time of water in the system, whereas the response of biological variables might scale with the generation time of the organisms in- volved. Similarly, salinity gradients affect much of the central and western Del- ta, while some organisms like salmon, which spend a portion of their life cycles in sea water, occupy much of the North Pacific as well as the Delta and its tribu- taries. Within the biological realm, rates of primary production, nutrient and oxygen cycling, as well as microbial growth may respond rapidly to ecosystem conditions whereas the abundance of long-lived animals such as sturgeon is ex- pected to integrate ecosystem dynamics over extended periods. The Compre- hensive Everglades Restoration Plan (CERP) provides a good example of the use of measurable outcomes for these purposes (NRC, 2008, 2010c). The next stage of the effects analysis is the most challenging–that of representing the dynamic response of the system. For simple systems, this may be in the form of a simple model. For example, decisions regarding quota levels in fisheries management are often made with guidance from a single assessment model, albeit one with hundreds of parameters (Miller et al., 2010). However, even in simple systems, the level of uncertainty present in individual processes and components of the system may be of such magnitude that state-variable models are unreliable. In these cases probabilistic models have been developed (Legault, 2005). More recently, Bayesian approaches have been used to guide management in the face of uncertainty for complex environmental questions 6   Large  restoration  programs  usually  include  methods  for  assessing  their  effects  so  that  adaptive  management  can  occur.    The  basic  prerequisite  for  such  assessments  is  the  establishment  and  characterization of a reference condition against which future conditions and proposed alternatives  can be compared. 

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24 A Review of California’s Draft Bay Delta Conservation Plan (Borsuk et al., 2004; McCann et al., 2006; Rieman et al., 2001). For an example of incorporating uncertainty into management options, see Box 1. In the case of the BDCP, it is unlikely that a single analytical framework, even one as flexible as Bayesian network analysis, will be adequate. Thus, it is likely that multiple models will be used to assess the response of different sys- tem components to each management alternative. Ultimately a range of inte- grated scenarios should be developed that link the models’ outputs to an inte- grated response. It is particularly important that each set of the models and ana- lyses be clearly related back to the original conceptual framework generated in the first stage of the effects analysis. Analysts should be explicit about the mod- el inputs and assumptions for each stage of the process. One of the risks of this approach is error propagation, that is, that uncertainty inherent in the forecasts made for one component are not fully carried forward to models of other com- ponents. It would be highly advantageous if outcomes in the effects analysis were quantifiable empirically and could thus become components of the BDCP’s Monitoring and Evaluation Program (e.g., NRC, 2000, 2008; Orians and Poli- cansky 2009). As noted above, the CERP has considered and described these issues in considerable detail (NRC, 2008 and references therein). This informa- tion, when gathered in the BDCP’s Monitoring and Evaluation Program, could then be used to conduct statistical analyses and calibrate models and the model- ing framework to inform the adaptive management phase over the decades fol- lowing implementation of the BDCP actions. BOX 1 The 2008 Federal Columbia River Power System Biological Opinion A suitable example of an attempt to incorporate uncertainty is evidenced in the 2008 Federal Columbia River Power System (FCRPS) Biological Opinion (NOAA, 2008) and in the 2010 Supplemental FCRPS Biological Opinion (NOAA, 2010) prepared after the 2008 opinion was voluntarily remanded. The com prehensive analysis in this biological opinion focused on determining the ef fects of different dam operation alternatives, on key ESA listed anadromous salmonid populations in the Columbia River Basin. In that analysis, water delivery and dam operation models create conditions that route juvenile sal mon through different routes at eight dams in the FCRPS, resulting in net smolt survival downstream of the last dam (Bonneville). Changes in smolt system survival associated with different operation alternatives are then linked to a broader life cycle analysis to assess the potential for population level responses to selected management actions.

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Critical Gaps in the Scope of the Draft BDCP  25  During the meeting on December 8, 2010, in San Francisco, presenters in- dicated that the effects analysis that will be included in the BDCP will be only a first step, that is, that it would be iteratively updated as empirical data from the operation of the approved alternatives become available. This approach is cer- tainly compatible with the use of the effects analysis framework as the founda- tion of the adaptive management framework. If this is indeed how the BDCP developers intend to use the effects analysis, the panel recommends that the final version of the plan articulate a clear vision of how the effects analysis will be updated and how these results will be used to generate the ranges that will be the foundation for subsequent adaptive management. As an example, much of the recent discussion of changes in the Delta eco- system has focused on declining planktonic primary production in the Delta and Northern San Francisco Bay (Jassby et al., 2002) as driving food-web changes, notably declines in planktonic grazers (secondary producers), that may underlie to some extent the decline of pelagic fish species like delta and longfin smelt (Baxter et al., 2008). Accordingly, significant elements of the BDCP involve efforts to enhance primary and secondary production through creation of addi- tional tidal wetlands mostly around the edges of the Delta, a plan that strongly echoes CALFED’s earlier focus on the creation of shallow water habitat (c.f. Brown, 2003). The bases for this strategy are twofold: (1) in the face of light limitations, shallow water habitats for which the photic zone is a greater fraction of the water column should have higher rates of primary production than deeper waters, e.g., channels (Cloern, 2007); and (2) empirically it is observed that the periodically flooded shallow waters of the Yolo Bypass can support high rates of export of phytoplankton biomass (Schemel et al., 2004). However, if an effects analysis is indeed “the principal component of a ha- bitat conservation plan” (draft BDCP p. 5-2), then it is difficult to see how these and other conservation strategies described in the BDCP can be scientifically justified before the effects analysis is completed. THE LACK OF CLARITY AS TO THE BDCP’S PURPOSE The legal framework underlying the BDCP is extraordinarily complex. In attempting to comply with all relevant laws and regulations, the BDCP’s authors have undertaken to develop a habitat conservation plan of great importance, scope, and difficulty. The panel recognizes that the authors face significant chal- lenges and that the BDCP is a work in progress. With these caveats in mind, the panel observes that it would be helpful for the draft BDCP to clarify and place into context a number of legal issues, because their nature and interpretation are closely tied to the BDCP’s scientific elements. Any lack of legal clarity makes it difficult for the panel and the public to properly understand, interpret, and re- view the science of the BDCP.

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26    A Review of California’s Draft Bay Delta Conservation Plan  Ambiguous Role of Co-Equal Goals and Their Relationship to the BDCP According to the draft BDCP (p. 1-8), it: “has  been  prepared  as  a  joint  [habitat  conservation  plan]  HCP/  [Natural  Communities  Conservation  Plan]  NCCP,  which  will  support  the  issuance  of  incidental  take  authorizations  from  the  US  [Fish  and  Wildlife  Service]  FWS  and [National Marine Fisheries Service] NMFS pursuant to Section 10 of the  [federal Endangered Species Act] ESA and take authorizations from the Cali‐ fornia Department of Fish and Game (DFG) under Section 2835 of the [Nat‐ ural  Communities  Conservation  Planning  Act]  NCCPA  to  the  non‐federal  applicants.  The BDCP has also been designed to meet the standards of Sec‐ tion  2081  of  the  California  Endangered  Species  Act  (CESA).   The  BDCP  will  further  provide  the  basis  for  biological  assessments  (BA)  to  support  the  is‐ suance of incidental take authorizations from USFWS and NMFS to [the Bu‐ reau  of]  Reclamation  pursuant  to  Section  7  of  the  ESA,  for  its actions  in  the  Delta.”    Thus, the BDCP is clearly and specifically an application for the incidental take of listed species as set forth in federal and state statutes. To apply for an exemption from the § 9 “take”7 prohibition of the federal Endangered Species Act (ESA), the water users must submit a habitat conserva- tion plan (here, the BDCP) that will minimize and mitigate the harmful impacts of their water usage. HCPs prepared as part of an application for an incidental take permit under federal law are not required to help listed species recover, but they must demonstrate that “the taking will not appreciably reduce the likelih- ood of the survival and recovery of the species in the wild” (ESA § 10).8 Under state law, the water users must submit a Natural Community Conservation Plan (NCCP) that, among other things, “aids in the recovery of the species.” (Natural Communities Conservation Planning Act [NCCPA], Cal. Fish and Game Code §§ 2800-2835). Neither the ESA nor the NCCPA specifically requires applicants to advance the “co-equal goals.” Despite this, the first paragraph of the draft BDCP (p. 1-1) states that it “sets out a comprehensive conservation strategy for the Delta designed to ad- 7   Take  means  “to  harass,  harm,  pursue,  hunt,  shoot,  wound,  kill,  trap,  capture,  or  collect,  or  to  attempt to engage in any such conduct.” ESA, Section 3, 16 U.S.C. 1532.  Harm,  within  the  statutory  definition  of  “take”  has  been  further  defined  by  regulation:  “Harm  in  the  definition  of  take  in  the  Act  means  an  act  which  actually  kills  or  injures  wildlife.   Such  act  may  include  significant  habitat  modification  or  degradation  where  it  actually  kills  or  injures  wildlife  by  significantly  impairing  essential  behavioral  patterns,  including  breeding,  feeding,  or  sheltering.”  50  C.F.R. 17.3.  8    ESA § 10 also requires successful applicants to demonstrate that (1) “ the taking will be incidental  [to  an  otherwise  lawful  activity],”  (2)  “the  applicant  will,  to  the  maximum  extent  practicable,  mi‐ nimize  and  mitigate  the  impacts  of  such  taking,”  (3)  “the  applicant  will  ensure  that  adequate  fund‐ ing  for  the  plan  will  be  provided,”  and  (4)  “[such  other  measures  that  the  Secretary  may  require  as  being necessary or appropriate for purposes of the plan] will be met.” 16 USC § 1539(a)(2)(B). 

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Critical Gaps in the Scope of the Draft BDCP  27  vance the co-equal planning goals of restoring ecological functions of the Delta and improving water supply reliability to large portions of the state of Califor- nia.” This and similar statements throughout the plan make it difficult to under- stand and evaluate the purposes of HCPs and NCCPs, and the methods of im- plementing them. Moreover, the methods of implementation are considerably different from the purposes and methods for achieving the two co-equal goals specified in California statutes. Indeed, California has begun to develop a broader “Delta Plan” in accordance with a recent state statute (Cal. Water Code §§ 85300-85309). Thus, the question arises as to the degree of importance to the BDCP of its purpose as an HCP/NCCP and of its purpose as a broader conserva- tion plan designed to achieve California’s two co-equal goals. The BDCP and the Delta Plan address the same ecosystem and are somewhat overlapping, but their goals and legal requirements are not identical. Unless the BDCP’s relation- ship to the Delta Plan is clearly described, and its purposes clearly delineated, it will be difficult to assess the BDCP’s underlying scientific basis, because the purposes of a broad conservation plan like the Delta Plan are not necessarily the same as those of a habitat conservation plan. The body of the BDCP contains some elements of both purposes, but not in a coherent and consistent way. For example, despite the statement that achiev- ing the two co-equal goals is one of its purposes, the BDCP focuses on one of the goals at the expense of the other. Additional sources of the confusion are multiple, but two stand out. First, the BDCP document lists some eight planning goals of which providing a “basis for permits necessary to lawfully take covered species” is only one of these eight goals (draft BDCP, p. 1-6). Yet, the remaind- er of the BDCP appears to focus disproportionately on this goal. As such, much of the BDCP appears to be a post-hoc rationalization of the water supply ele- ments contained in the BDCP. A consequence of the lack of clarity is related to this post-hoc rationaliza- tion. To the extent that the BDCP is simply a request for an incidental take per- mit then the water users would first identify their desired action (such as con- struction of a specifically configured “alternative conveyance”), and then ana- lyze its impacts and to develop measures to minimize and mitigate adverse ef- fects. However, to the extent that the BDCP seeks incorporation into the broad- er Delta Plan, then an effects analysis would precede the choice of all conserva- tion and alternative-operation options, and only then would an effects analysis of those options be performed. That is, if the proposed conveyance system and other measures such as wetlands restoration have been developed as measures to further the restoration of the Delta ecosystem, then one would expect that the effects analysis would be completed before coming to a conclusion as to the preferred type of water delivery system. The absence of an effects analysis and of consideration of water supply alternatives (other than the 45 mile tunnel or possibly an open canal; see section below on alternatives) suggests that the BDCP’s major purpose is to provide the basis for an application for an inciden- tal take permit. Yet, this is contrary to what is stated throughout the plan with respect to the attainment of co-equal goals.

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28    A Review of California’s Draft Bay Delta Conservation Plan  Despite these ambiguities, the draft BDCP has concluded that an “isolated conveyance facility” should be constructed consisting of a 45-mile tunnel or pipeline, capable of conveying 15,000 cubic feet per second (cfs) of Sacramento River water around the Delta to the south Delta’s existing water export pumping plants, to allow for “dual operation” with the existing south Delta diversion fa- cilities (draft BDCP, Chapter 4.2.2.1.1 and Table 4-1). (Again, the “note to re- viewers” on p. 4-14 of the draft BDCP suggests that the conveyance system might be a canal, but there is no analysis of a canal in the draft BDCP or even a statement as to whether the findings from the analysis of a canal would differ from the analysis of a tunnel system.) Alternative Actions To support the issuance of an ESA § 10 take permit, the BDCP must specify “what alternative actions to such taking the applicants considered and the rea- sons why such alternatives are not being utilized” (ESA § 10, 16 U.S.C. § 1539(a)(2)(A)). Even if the proposed action has been decided on, an analysis of alternatives is still required. This analysis does not appear prominently in the draft BDCP. Not only is the analysis a legal requirement, but it also is important scientifically, because to the degree that the reasons for not utilizing the alterna- tives are scientific reasons, the absence of the analysis hinders the ability to eva- luate the BDCP’s use of science. If the BDCP also seeks incorporation into the Delta Plan (and thereby qualifying for state funding of public benefits), then it should also include an analysis of “conveyance” alternatives. As a prerequisite to incorporation, the BDCP must undertake “a comprehensive review and anal- ysis of . . . [a] reasonable range of Delta conveyance alternatives, including through-Delta, dual conveyance, and isolated conveyance alternatives and in- cluding further capacity and design options of a lined canal, an unlined canal, and pipelines” (Cal. Water Code, § 85320). Finally, the federal approval process also will require an environmental impact statement that considers alter- natives to the “proposed action,” which includes construction of the alternative conveyance (National Environmental Policy Act, 42 U.S.C. § 4332(2)(C)(iii)). Once again, this legally required analysis of alternatives is scientifically impor- tant. Therefore, to permit a complete scientific evaluation of the BDCP, it should include an analysis of such alternatives to “take” and to the construction and design of the contemplated isolated conveyance.