dissenting:
The 1990 conformity amendments to the Clean Air Act (“CAA”) were intended to harmonize the transportation planning process for polluted metropolitan areas with air quality plans (technically, “state implementation plans” or “SIPs”) established by state authorities. In particular, the conformity amendments prohibit certain transportation activities from going forward unless relevant entities have determined that the activities are “in conformity” — that is, that they meet certain criteria relating to air quality. The Act’s conformity requirements are astonishingly confusing, and could if interpreted as stringently as possible seriously disrupt state and local transportation planning. That would “frustrate the process of state and federal cooperation and the integrated plan*652ning that section 176(c)(1) was created to foster.” EDF v. EPA, 82 F.3d 461, 468 (D.C.Cir.1996). The EPA attempted in this rule to reduce disruption and make the conformity determination process “more logical and feasible;” 62 Fed.Reg. 43,780, 43,781 (1997), by allowing greater flexibility than it had permitted in its 1993 conformity regulations. See 62 Fed.Reg. at 43,780. In accepting all the petitioners’ challenges to the rule, the majority undoes much of what EPA intended to accomplish. Although I believe there are three respects in which the EPA has not adequately explained itself, I cannot find it guilty of the thoroughgoing misunderstanding of the statute that leads the majority to find for EDF on every issue. Accordingly, I dissent.
Of course when a congressional effort to micromanage local transportation planning in as much detail as this statute is followed by a judicial decision that the agency must put states and localities in an even tighter straightjacket, one may feel that Congress asked for it. But one cannot say the same for the hapless citizens who must live with the results.
I. Local approval of nonfederal projects not from currently conforming plan and program
The first regulation the majority strikes down is 40 C.F.R. § 93.121(a)(1). It allows certain nonfederal entities to adopt or approve projects contained in the first three years of a transportation plan and program (i.e., designated for implementation within those years) that was once in conformity, even if conformity has since lapsed. I disagree with the majority here because I think the regulation reflects a reasonable interpretation of 42 U.S.C. § 7506(c)(2)(C). That provision prohibits metropolitan planning organizations (known as “MPOs”) and other recipients of federal funds from approving certain transportation projects, including those covered by the challenged regulation, unless the projects “eome[ ] from a conforming plan and program.” The majority holds that this phrase requires the projects in question to come from a plan and program that conforms at the time of approval.
EPA argues that the phrase allows approval of any project that comes from a plan and program that conformed at one time, even if the approval is given after conformity has lapsed. The statutory text permits EPA’s view, and the agency’s interpretation is reasonable in light of its goal of protecting localities from disruption caused by conformity lapses, which appear frequently to be beyond local control. The Department of Transportation must redetermine the conformity of plans and programs every three years, and must also make a new conformity determination within 18 months of EPA approval of a SIP revision that establishes or changes emissions budgets, among other circumstances. If the DOT fails to make the required determinations within the prescribed time frames, conformity will lapse. See 40 C.F.R. §§ 93.104(b)(3), 93.104(e).
The majority argues that since the phrase “comes from a conforming plan and program” is in the present tense, its “ordinary meaning” is “comes from a currently conforming plan and program.” Maj. Op. at 646. But that is too simple; the phrase is ambiguous. “Comes from X” can mean “has its origin in X,” and when the phrase is used that way, the time for determining X’s qualities can be the time of origination. A Bel-faster who 10 years from now says he “comes from a bleeding land” will be understood — no matter how effective the recent peace accord. A layabout who says he “comes from a hardworking family” can be telling the truth even if all his relatives are dead.1
*653The majority advances three arguments against EPA’s interpretation here — one based on the use of the word “conforming” elsewhere in the statute, another on the requirements of another statutory provision dealing with conformity, and the third on the legislative history. None is persuasive.
First, the majority appeals to the use of the word “conforming” as an adjective in § 7506(c)(2)(D). This argument starts with the decision that the “conforming” is used in that provision to mean “currently conforming.” Next, the majority argues that since (e)(2)(D) and (c)(2)(C) provide alternate ways of determining project conformity, the term should be read to mean the same thing in each paragraph. Together, these propositions lead the majority to the conclusion that (c)(2)(C) also requires a “currently conforming” plan.
The determination that (c)(2)(D) requires a “currently conforming” plan is surely contestable.2 But even if it is correct, it was reasonable for EPA to decide that this stricture did not carry over to (c)(2)(C). First, the provisions differ in language: the former provision lacks the phrase “comes from,” and has no other linguistic hook suggesting that one should look back to an earlier time of origin. Second, I find nothing “odd,” Maj. Op. at 646-47, from a substantive point of view about the difference EPA’s interpretation creates between the two ways of determining project conformity. Section 7506(c)(2)(C) governs projects that were included in plans and programs that have gone through a conformity determination, while (c)(2)(D) governs projects that were never before considered in such a determination. In light of the intent of the Clean Air Act amendments to foster state-federal partnership, it is not unreasonable for EPA to protect states’ reliance interest where a project has already been considered in a conformity determination; no such reliance interest exists for projects that fall under (c)(2)(D).
The majority next finds EPA’s regulation flawed because it allows approval of projects that violate § 7506(c)(1), which defines conformity in general terms and applies to all federal activities, not just transportation-related ones. In its essence § 7506(c)(1) forbids federal activities that will cause, worsen, or prolong violations of air quality standards. It also forbids MPO approval of projects with such effects.
The majority holds that because EPA’s rule allows MPO approval of transportation projects from transportation plans that are not in conformity at the time of approval, it allows MPOs to approve projects that do not meet § 7506(c)(l)’s requirements and thus violates that section.
In doing so, the majority embraces an argument that EDF’s opening brief raised only in a novel and somewhat deceptive way. It mentioned the claim in two sentences of its “Summary of Argument,” but not at all thereafter. See EDF Br. at 13. In its main argument, instead, EDF claimed that § 93.121 violated § 7506(c)(2). Its only argument from § 7506(c)(1) was a general one— that EPA should issue further regulations implementing that provision; and on that subject it didn’t mention § 93.121, although it gave examples of other regulations that in its view showed that the new conformity rule allowed violations of § 7506(c)(1). Unsurprisingly, EPA did not respond to the (c)(1) argument.
The majority argues that EDF did come through with an elaboration of its (c)(1) claim at pages 23-25 of its brief. But the referenced argument is quite distinct. It is based on a perceived tension between EPA’s interpretation of (c)(2)(C) and another statutory provision, § 7506(c)(4). There is no explicit mention of (c)(1) in the passage, nor is there an implicit claim that EPA’s interpretation violates (c)(1). Instead, the discussion elaborates on the supposed problems for EPA’s *654interpretation created by § 7506(c)(4), which calls for periodic redetermination of the conformity of transportation plans and programs. EDF’s heading says that the EPA’s regulation “Eviscerates Congress’ Decision to Set Time Limits on Plan, TIP and Project Conformity,” EDF Br. at 23, and the text goes on immediately to cite § 7506(c)(4), which indeed sets such time limits. Raising one argument is not an implicit raising of the other.
The closest EDF comes to making the (c)(1) argument is its claim that EPA’s interpretation allows regions to “continue implementing transportation systems designed to meet older emissions targets no longer adequate to - attain the NAAQS.” EDF Br. at 24. This sentence appears in the midst of the (c)(4) argument and is best read as an illustration of the alleged tension between that provision and EPA’s regulation, not as raising a claim based on (c)(1). Though the sentence does contain the word “attainment,” which also appears in (c)(1), there is no other textual reference to the statutory provision, and no implicit reference is obvious. A project does not violate the relevant provisions of (c)(1) unless it actually causes, worsens, or prolongs a violation of the NAAQS, or is not in “conformity to [the relevant SIP’s] purpose of ... achieving expeditious attainment” of the NAAQS. It is by no means clear that progress toward targets that are “no longer adequate” fits into any of those categories. The vaguely drafted last category (requiring “conformity to [a plan’s] purpose of ... achieving expeditious attainment”) is the most likely candidate, but EDF never even hints at an explanation of how a purpose is thwarted by inadequate contribution to its realization. That judges are able to find a dim connection between EDF’s argument and (c)(1) — after the fact — is hardly a showing that EDF raised a (c)(1) argument.
In the interests of fairness to parties and avoidance of improvident decisions, we normally refuse to consider arguments that are raised only in the reply brief. See, e.g., Doolin Sec. Sav. Bank v. OTS, 156 F.3d 190, 191 (D.C.Cir.1998). This rule also extends to arguments raised in only a conclusory fashion in the opening brief and not addressed by appellee. See Texas Rural Legal Aid, Inc. v. Legal Servs. Corp., 940 F.2d 685, 697-98 (D.C.Cir.1991). The rule is especially compelling when the statutory and regulatory scheme presents as many opportunities for error as this one.
In any event, even if the argument had been properly raised it should have been rejected. To understand why, we have to look at the overall structure of § 7506(c). Section 7506(c)(1) is a general requirement covering federal activities. It forbids federal entities to engage in activities that do not conform to an applicable SIP and, in subpar-agraphs (A) and (B), gives a definition of conformity. Sections 7506(c)(2) and (3) both address transportation and provide rules for conformity determinations in that context. Section 7506(c)(3) establishes interim rules, and § 7506(c)(2) is the main transportation conformity provision.
The majority’s opinion assumes that situations governed by (c)(2) are also governed by (c)(1). But the statute can reasonably be read to say that (c)(2) and (c)(3) govern exclusively in their own domains. On this reading, § 93.121(a)(1), which governs a situation covered by (c)(2)(C), would not be subject to invalidation under (c)(1).
The most obvious support for this reading comes from the fact that the specific transportation conformity requirements are not entirely consistent with the general conformity requirements, so that applying (c)(1) to all situations governed by (e)(2) and (c)(3) produces contradiction. Section 7506(c)(3), for instance, provides that “conformity” of a plan “will be demonstrated” if the plan contributes to annual emissions reductions of ozone and carbon monoxide and meets certain other requirements not relevant here. See § 7506(e)(3)(A)(iii). Thus, a plan allowing activities that cause a violation of (for example) particulate matter standards is in conformity under (c)(3) as long as the other requirements are met. Not so under the general rules of (c)(1), since that provision forbids activities that cause violations of “any standard.” See § 7506(c)(l)(B)(i). The transportation-specific (c)(3) rule triumphs in this conflict. Each statutory provision is normally presumed to serve a function; thus a *655specific provision governing a set of circumstances entirely within a more general one must, within its own scope, prevail over the more general. Otherwise it would be deprived of its function. Cf. Hemenway v. Peabody Coal Co., 159 F.3d 255, 264 (7th Cir.1998) (noting that where the scope of one provision is not completely contained within the scope of the other it is impossible to call either “more specific”). That is the case here. Subsection (c)(1) nominally covers all federal activities, and (c)(3) covers only transportation activities, and those only for a limited time.
Section 7506(c)(2)(A) also supports the view that the specific requirements replace the general ones. It requires a finding that a transportation plan or program “will conform to the requirements of [§ 7506(c)(1)(B)]” before the plan or program can be found in conformity. The majority dubs my observation to this effect a “concession.” Maj. Op. at 647. But since the issue here is what (c)(2)(C) requires, (c)(2)(A)’s specific imposition of the requirement makes clear that the draftsmen, contrary to the majority, understood that the generality of (e)(2) situations did not require compliance with (e)(1).
Thus, it appears that it would be reasonable for EPA to find that (c)(l)’s requirements do not apply to situations governed by (c)(2) and (c)(3) except where specifically incorporated. There is no such specific incorporating language in (c)(2)(C), the transportation project conformity provision that governs here. I cannot find any assertion of this analysis in the record of the rulemaking, but as EDF did not properly raise the issue, EPA has had no real opportunity to explain its view of how (c)’s subsections relate to each other.
Finally, the majority points to statements in the legislative history. In general these say that one purpose of the CAA amendments was to promote integration of the air quality and transportation planning processes, a proposition with which neither EPA nor anyone else has any quarrel. And the majority ends as it began, with an appeal to (e)(2)(D)’s purported requirement of a “currently conforming” plan. As I explained above, this stricture, if it exists, does not bind EPA in interpreting (c)(2)(C).
Thus, Congress has not “directly addressed the precise question at issue” in this case, Chevron U.S.A. Inc. v. NRDC, 467 U.S. 837, 843, 104 S.Ct. 2778, 81 L.Ed.2d 694 (1984), so we must uphold the EPA’s resolution of the statutory ambiguities if it is reasonable. And it is, given the Act’s overall purpose to promote a cooperative regime of integrated planning.
Although the EPA’s treatment of non-federally funded projects seems to me reasonable as a matter of statutory interpretation, I have found nothing in the record adequately explaining its different treatment of federally and non-federally funded projects. Under § 93.121(a)(1), a project that is not federally funded may be approved by an MPO as long as it comes from the first three years of a transportation plan that once was in conformity. But a federally funded project may not be approved unless there is a “currently conforming transportation plan and currently conforming TIP at the time of project approval.” See 40 C.F.R. § 93.114. Nothing in the statute appears to justify such a distinction, and EPA’s only explanation for the disparate treatment appears to be that “the existence of a conforming plan and TIP is not necessary to facilitate the implementation of [nonfederal] projects.” 62 Fed.Reg. 43,780, 43,790 (1997). It is undisputed that nonfed-eral projects can be funded without a currently conforming plan and TIP in place, while federal projects cannot. 42 U.S.C. § 7506(c)(2) provides that “[n]o Federal agency may ... fund any ... project unless such ... project has been found to conform to any applicable implementation plan.... ”, while no such restriction covers nonfederal projects. But EPA has not explained why that difference is relevant to the project approval, as to which the statutory requirements draw no evident distinction between federal and nonfederal contexts. Because the EPA may be able to explain the difference, and if not might adopt for federal projects the rule it has chosen for non-federal ones, and in order to avoid the disruption that would be caused by an interim change that might itself be changed, I would simply *656remand for further explanation. See A.L. Pharma, Inc. v. Shalala, 62 F.3d 1484, 1492 (D.C.Cir.1995).
II. Grandfathering of federally funded projects unless three years elapse between major steps
40 CFR § 93.102(c)(1) provides that transportation projects that have been once determined to be in conformity may proceed toward completion without further conformity determinations unless more than three years elapse between “major steps” of the project. The majority invalidates this so called “grandfathering” provision on the basis of the same construction of the statute that leads it to invalidate § 93.121(a)(1) — its reading of the words “comes from a conforming plan and program” in § 7506(e)(2)(C)(i). For the reasons given in the preceding section, I disagree.
III. Use of emissions budgets from unapproved/disapproved SIP revisions and reallocation of safety margins
The majority next addresses three regulations that allow conformity to be determined on the basis of emissions budgets contained in SIP revisions that EPA has not approved, remanding two and vacating one. The first of these, 40 C.F.R. § 93.118(e)(1), allows an MPO or DOT to show consistency with emissions budgets in zmapproved SIP revisions in conformity determinations starting 45 days after submission of the revision. In short, anticipating that sometimes it will be unable to pass on proposed SIP revisions promptly, the agency provides for use of a second-best substitute after 45 days.
The majority’s sole basis for remanding this provision is the proposition that the regulation is insufficient to ensure compliance with 42 U.S.C. § 7506(c)(1)(B), the government-wide conformity requirements. The theory is faulty. Even if we assume that (c)(1) applies generally to transportation projects covered by §§ 7506(c)(2) and (3) (contrary to my analysis in part I), § 93.118(e)(1) does not allow violations of (c)(1).3
Section 7506(c)(1) makes it the “affirmative responsibility” of an agency engaging in or supporting a federal activity to assure that the activity does not cause, exacerbate, or prolong any violation of air quality standards. For various reasons § 93.118(e)(1) is adequate to ensure that the DOT (and MPOs) carry out this mandate when emissions budgets have been submitted but not yet approved. First, because EPA will approve SIP revisions only if the revised SIP, including the budgets, includes enforceable control measures to reach and maintain air quality standards by specified dates, see 42 U.S.C. §§ 7410(a)(1), (a)(2)(A), (k)(3), states have an incentive not to submit the “inflated emissions budget[s]” about which EDF is concerned. EDF Br. at 33. Furthermore, EPA’s regulations require a public hearing and consultation between state, federal, and local agencies before the SIP revision can be submitted. See 62 Fed.Reg. 43,780, 43,781 (1997).
Just as the substantive rules and procedural controls on SIP revisions create some probability that states will file emissions budgets conforming to law, § 93.118(e)(6) makes the MPOs and DOT a further screen. It provides that when conformity determinations are made under § 93.118(e)(1), “the MPO and DOT’s conformity determinations will be deemed to be a statement that the MPO and DOT are not aware of any information that would indicate that emissions consistent with the motor vehicle emissions budget” would violate (c)(1). If an MPO or DOT official is legally deemed to be making such a statement, presumably he or she will be reasonably careful that its factual underpinnings are valid — on pain, surely, of at least a bureaucratic black eye if later experience should falsify the implicit representations.
Taken together, §§ 93.118(e)(1) and (e)(6) establish a high probability that submitted emissions budgets meet the requirements of *657(c)(1). And a decent probability is all that any system can assure: even the EPA might err in giving an approval. In light of the purpose of the Clean Air Act to “foster” a “process of state and federal cooperation,” EDF v. EPA, 82 F.3d 451, 468 (D.C.Cir.1996), and the procedures nurturing sound state decisionmaking, it is hardly unreasonable for EPA to allow the implied representation of an MPO or DOT as to fulfill its “affirmative responsibility” to assure conformity.
The majority emphasizes the fact that the MPO or DOT bears an “affirmative responsibility” to assure conformity. But “affirmative” can be used essentially as an intensifier that emphasizes the existence of a responsibility, rather than as a prescription of some means for its accomplishment. See, e.g., Dayton Bd. of Educ. v. Brinkman, 443 U.S. 526, 538-39, 99 S.Ct. 2971, 61 L.Ed.2d 720 (1979); CBS v. DNC, 412 U.S. 94, 110-11, 93 S.Ct. 2080, 36 L.Ed.2d 772 (1973).
EDF’s principal argument against § 93.118(e)(1) — not addressed by the majority — is that that the regulation illegally allows conformity determinations to be made on the basis of something other than the “applicable implementation plan,” as required by § 7506(c)(2) or (c)(3), or an implementation plan that has been “approved,” as required by § 7506(c)(1), because it allows a submitted SIP revision to be treated as approved before approval. This somewhat overstates the case. The regulation provides only that the emissions budgets are to be used to determine conformity; neither the regulation nor EPA’s comments state that the revision may be treated as approved. The potential problem with tbe regulation is that it does not provide a reasonable way of determining conformity with the “applicable,” that is, existing, SIP — not that it illegally allows revisions to be treated as approved before they actually are. And the regulation does provide a reasonable basis for determining conformity with the applicable SIP, at least in some cases.
Section 93.118(e)(1) applies only when the most recent approved SIP contains no motor vehicle emissions budgets. In the absence of emissions budgets, the only possible relevant statutory provisions for finding conformity with the “applicable implementation plan” are §§ 7506(c)(3), which governs an interim period that began with the passage of the CAA amendment, and (c)(1), which as I argued at 656 n.3 above, may govern any gap between the end of the (c)(3) interim period and the approval of SIPs with emissions budgets. My conclusion above that §§ 93.118(e)(1) and (e)(6) together provide a reasonable means of determining conformity addresses any application of (c)(1).
That leaves the possible application of (c)(3). EPA has included no requirement that the entity making the conformity finding consider the activity’s consistency with (c)(3). So there may be a deficiency here. But it is not clear whether § 93.118(e)(1) and § 7506(c)(3) are ever in effect at the same time; some statements of EPA in the rule-making suggest that the interim period (c)(3) covers is over before the emissions budget submission that triggers § 93.118(e)(1) takes place. See 58 Fed.Reg. 62,188, 62,191/1 (1993) (stating that although the interim period lasts only until the “conformity SIP revisions are approved, EPA is extending the interim requirements until the control strategy SIPs [i.e., the SIPs with emissions budgets] are submitted”). Since no party has briefed the issue and the present record is insufficient to answer the question, I would remand the issue for further explanation.
The next regulation that the majority remands, 40 C.F.R. § 93.120(a)(2), allows use of emissions budgets in SIP revisions that EPA has disapproved for 120 days after the disapproval. The majority rejects it on the same ground as § 93.118(e)(1) — failure to ensure compliance with (c)(1). I agree with the majority that if (e)(1) is applicable, § 93.120(a)(2) cannot be said to satisfy it. Unlike § 93.118(e)(1), this section cannot be defended as governing cases where there are reasonable guarantees that the permitted transportation activities will not violate § 7506(c)(1); the budgets at issue have actually been rejected as inadequate. If (c)(3) is applicable to situations covered by § 93.120(a)(2), that section is likely violated as well; (c)(3)(A)(iii) requires plans and programs to “contribute to annual reductions” in ozone and carbon monoxide nonattainment *658areas, and there is no reason to believe that emissions budgets specifically disapproved without a protective finding meet that criterion. It is possible, however, that none of (c)(1), (2), or (3) apply. Perhaps (c)(2) and (3) entirely preempt (c)(1) with respect to transportation and § 93.120(a)(2) applies only during a gap that may, as I explained above, exist between those two provisions. Although EPA argues that § 93.120(a)(2) exists in a statutory gap, its brief and rulemaking statements fail to explain just why such a gap exists. Thus, I would require further explanation of the statutory basis for this regulation as well.
The last of the challenged regulations, 40 C.F.R. § 93.124(b), applies to states with SIPs that indicate that emissions from all sources are less than the total emissions that would be consistent with attainment of air quality standards and that quantify that “safety margin.” The regulation allows such states to submit a SIP revision that assigns some of the safety margin to transportation sources and to use the revision for conformity purposes before it is approved by EPA. The majority invalidates this provision for the same reason EDF argues the last two provisions should be invalidated — the regulation violates the requirement that conformity determinations be “based on a SIP ‘approved or promulgated under section 7410 of this title.’ ” Maj. Op. at 651. Here, it seems clear that activities found in conformity on the basis of the “safety margin” will not cause, worsen, or prolong violations of air quality standards, and thus that they conform to the applicable implementation plan under § 7506(c)(1). EDF has given no reason to doubt this conclusion, or to believe that activities producing emissions within the “safety margin” violate § 7506(c)(3). Thus, as above, the regulation can reasonably be read to authorize the “use” of the revision as a reasonable alternate means of finding conformity with the existing SIP, rather than an illegitimate means of prematurely amending one.
I dissent.
. It might be said that transportation projects do not "originate” in transportation plans or programs; projects in a plan may be more like stories in an anthology than chapters in a novel. But the hypothesis is not strong enough to give the phrase "comes from a conforming plan” the clear meaning that the majority finds. . The statute establishing the federal transportation planning process prescribes the designation of MPOs to carry out a "continuing, cooperative, and comprehensive” planning process, 23 U.S.C. § 134(a), by developing plans and programs that contain the projects to be implemented, id. § 134(h)(2)(A). This language, if anything, suggests the novel metaphor more than the anthology; in any event, it cannot be said to establish the anthology metaphor with the clarity necessary for the majority’s interpretation.
. The majority cites two pieces of evidence for its idea that the plan must be currently conforming, the Clean Air Conference Report and a statement by EPA. Assertions contained in the former document, despite what the majority says, are not interpretations by "Congress,” Maj. Op. at 647-48, but by committee drafts persons. With respect to the EPA’s statement, even if the majority were correct that the agency has contradicted itself in its interpretations of (c)(2)(D) and (c)(2)(C), the existence of that contradiction tells us at most that one of the interpretations must be wrong — not that the EPA's reading of (c)(2)(D) must be right.
. The EPA argues that § 93.118(e)(1) covers a gap between (c)(2) and (c)(3). If so, then even if (c)(2) and (c)(3) preempt (c)(1) where they apply, (c)(1) might spring to life for areas left blank by them. On the other hand, (c)(2) and (c)(3) might preempt (c)(l)’s independent effect over the entire field of transportation, including any gaps. Because I find that § 93.118(e)(1) is sufficient to guard against violations of (c)(1), I need not reach that argument here.