Trinity Industries, Inc. v. United States , 757 F.3d 400 ( 2014 )


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  •      Case: 12-11012    Document: 00512685765     Page: 1   Date Filed: 07/02/2014
    IN THE UNITED STATES COURT OF APPEALS
    FOR THE FIFTH CIRCUIT   United States Court of Appeals
    Fifth Circuit
    FILED
    July 2, 2014
    No. 12-11012
    Lyle W. Cayce
    Clerk
    TRINITY INDUSTRIES, INC., for Itself and on Behalf of Certain Subsidiaries,
    Plaintiff–Appellant,
    v.
    UNITED STATES OF AMERICA,
    Defendant–Appellee.
    Appeal from the United States District Court
    for the Northern District of Texas
    Before OWEN, SOUTHWICK, and GRAVES, Circuit Judges.
    PRISCILLA R. OWEN, Circuit Judge:
    Trinity Industries, Inc. (Trinity) designed and built vessels during the
    taxable years ending March 1994 and March 1995 (the claim years). On its
    amended tax returns, Trinity claimed research tax credits under Internal
    Revenue Code (I.R.C.) § 41 based on several of these vessel projects. The I.R.S.
    denied these claims. Trinity then filed this tax refund action in federal court,
    seeking research tax credits based on the projects. After a two-phase bench
    trial, the district court held that the tax credit due Trinity was $135,787.60 for
    1994 and $0 for 1995. Trinity now appeals, asserting that it is entitled to a tax
    credit of $1,808,832.53 for 1994 and $2,712,977.00 for 1995. We affirm in part
    and vacate and remand in part.
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    I
    Trinity’s amended tax returns for 1994 and 1995 claimed that it was
    entitled to a research tax credit because its claim year expenses in developing
    certain vessels constituted qualified research expenses (QREs). As discussed
    more fully below, I.R.C. § 41 generally provides a 20% credit for claim year
    QREs that exceed what the taxpayer spent on research in an earlier
    comparison period (the base amount). 1 The base amount, in turn, is a “fixed
    base percentage” multiplied by the company’s average annual gross receipts
    for the four years preceding the claim year. 2 In calculating its research tax
    credit, Trinity’s amended tax returns reported a fixed base percentage (the
    ratio of base period QREs over base period gross receipts 3) of 1.3152% for the
    taxable year ending March 1994 and 1.3125% for the year ending March 1995.
    The tax returns themselves do not report the base period QREs or the base
    period gross receipts used to calculate the fixed base percentage. The I.R.S.
    denied these claims in a 2001 claim disallowance letter.
    Trinity subsequently filed this tax refund action in federal court. Before
    trial began, Trinity retained James Bennett as an expert. Bennett submitted
    a report finding that the “consistency rule” under I.R.C. § 41(c)(6)—which
    requires that claim year QREs and base period QREs be computed on a
    consistent basis 4—was satisfied on Trinity’s amended tax returns. Bennett
    noted only one caveat to this conclusion: the records available for the claim
    years were more complete than those available for the base period years, so he
    1   I.R.C. § 41(a)(1) (codified at 
    26 U.S.C. § 41
    (a)(1)).
    2   
    Id.
     § 41(c)(1).
    3   Id. § 41(c)(3)(A).
    4  Id. § 41(c)(6)(A) (“[T]he [QREs] taken into account in computing [the fixed base]
    percentage shall be determined on a basis consistent with the determination of [QREs] for
    the credit year.”).
    2
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    estimated certain costs for the base period. Based on documentation provided
    by Trinity, Bennett also provided specific calculations of the base period QREs,
    the base period gross receipts, and the fixed base percentage.                           Bennett
    calculated the overall base period QREs as $49,483,136. Dividing this base
    period QRE figure by the base period gross receipts ($3,851,683,536) yielded a
    fixed base percentage of 1.2847%, which was slightly lower than the fixed base
    percentages reported in the amended tax returns. Although Bennett based his
    calculations on the same records used to complete the amended tax returns, it
    is not clear why his fixed base percentage figure was slightly lower.
    The district court conducted a two-phase bench trial. In Phase I, the
    court considered claimed tax credits for six vessel development projects. In its
    order following Phase I, the court decided that Trinity was wrongly denied
    credits for only two of the six projects it considered because these two projects
    (the Mark V and the Dirty Oil Barge) met all four requirements for constituting
    QREs. 5 According to the court, the other four vessels (the XFPB, the T-AGS
    60, the Crew Rescue Boat, and the Hurley Dredge) did not meet the fourth
    QRE requirement: that substantially all of the research activities in developing
    the project (i.e., 80% or more) were part of a process of experimentation. 6
    In reaching these conclusions, the court explained that the “shrinking-
    back rule” in the Treasury regulations ordinarily allows taxpayers to show that
    smaller      subcomponents          of   a    given     project     satisfy    the    process-of-
    experimentation test even if the entire project does not. 7 For instance, if a
    5   See id. § 41(d)(1) (providing that to constitute QREs, (1) the expenses must be
    deductible under I.R.C. § 174; (2) the research must be for the purpose of discovering
    technological information; (3) the application of that information must be intended to be
    useful in the development of a new or improved business component; and (4) substantially
    all of the research must constitute elements of a process of experimentation).
    6   Id. § 41(d)(1)(C); 
    Treas. Reg. § 1.41-4
    (a)(6) (codified at 
    26 C.F.R. § 1.41-4
    (a)(6)).
    7   See 
    Treas. Reg. § 1.41-4
    (b)(2).
    3
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    whole vessel project does not satisfy the test, perhaps the development of the
    vessel’s engine is sufficiently experimental. In this case, however, the court
    noted that “Trinity took an all or nothing approach” because it did not offer
    proof of its claim year expenses at the subcomponent level. Trinity was unable
    to offer evidence of its expenses at a more specific level partly because
    Hurricane Katrina destroyed many of its records. The court thus made its
    determination on the fourth QRE requirement based on whether, considering
    each of the six claim year projects as a whole, 80% of the costs incurred in the
    development of each project were part of a process of experimentation. It did
    not apply the shrinking-back rule in analyzing the claim year QREs.
    In Phase II of the trial, two other vessel projects (the Queen of New
    Orleans and the Penn Tugs), as well as the method of calculating Trinity’s base
    period QREs were at issue. With regard to its base period QRE calculation,
    Trinity called as a witness Phil Nuss, Trinity’s former Vice President of
    Engineering. Nuss first confirmed that the ten vessels identified by Bennett
    in his report were the vessels used in computing the base period QREs on the
    amended tax returns. Trinity’s counsel then asked Nuss whether he believed
    expenses related to those ten vessels should still be counted as QREs given the
    district court’s Phase I order holding that certain claim year vessel expenses
    were not QREs. Nuss answered that expenses relating to four of the ten base
    period vessels should no longer be counted. According to Nuss, two of the base
    period vessels—the LSV and the North Carolina Auto Ferry—were similar to
    the Hurley Dredge, one of the claim year vessels held not to be qualified
    research in Phase I, since they all involved Trinity constructing a vessel based
    on a design provided to Trinity by a third party. In addition, Nuss believed
    that another base period vessel—the Cajun Queen—was like the Crew Rescue
    Boat, a claim year vessel held not to be qualified research in Phase I, since the
    Cajun Queen was also not a complicated technological boat to build. Finally,
    4
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    Nuss testified that a fourth base period vessel—the Ecuador—was like the
    XFPB, which the district court held was not qualified research in Phase I, since
    the Ecuador similarly had some experimental features but not enough to
    satisfy the QRE test. Nuss thus concluded that these four base period vessels
    should no longer be included in the base period QRE figure, though the other
    six base period vessels still should be. There was also similar testimony from
    Sam Charters, Trinity’s former Chief Project Engineer, that the LSV was
    similar, in terms of the amount of experimentation involved, to the Hurley
    Dredge held not to constitute qualified research.
    After Phase II of the trial concluded, the parties submitted briefing
    addressing whether the two vessel projects at issue constituted QREs, as well
    as the proper base period QRE figure under the consistency rule. Trinity made
    two distinct arguments about the consistency rule. Its first was that it had
    followed the consistency rule on its amended tax returns by calculating both
    its claim year QREs and its base period QREs using an all-or-nothing
    approach. In making this argument, Trinity acknowledged that it did not use
    the shrinking-back rule in computing its base period QREs on its returns:
    On the Amended Returns, Trinity sought a tax credit for only
    certain vessels that could be considered prototypes. In presenting
    its claim, Trinity took an “all or nothing” approach—i.e., it did not
    seek shrink-back credit for any subcomponents of any vessels
    constructed in the Claim Years. To be consistent with this
    determination of Claim Year expenditures, Trinity included in the
    Base Period only expenditures for those vessels that it believed were
    sufficiently experimental such that the entire vessel constituted
    qualified research. Consistent with the manner in which it
    determined QREs for the Claim Years, Trinity did not shrink-back
    to subcomponents of any vessels in the Base Period.
    5
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    In taking this position, Trinity was not asking the court to allow it to
    recalculate its base year QREs; it was simply defending how it originally
    calculated its base period QREs on its amended tax returns.
    Trinity then made a second, distinct argument regarding the consistency
    rule. Relying primarily on the testimony of Nuss but also citing Charters’s
    testimony, Trinity asserted it should be able to remove four vessels from its
    base period QREs as calculated on its amended tax returns, since those vessels
    were similar, in terms of how much experimentation was involved, to the four
    vessels held not to be claim year QREs in Phase I:
    In Trinity I the Court articulated a different standard for
    “prototype” than Trinity applied on the Amended Return. The
    Court’s holding defined the universe of QREs allowable in the
    Claim Years. . . . With respect to four of the projects claimed by
    Trinity, the Court found that the integration of subsystems did not
    rise to the level required for the cost of developing and constructing
    the entire vessel to qualify.
    Given this standard, pursuant to [the consistency rule]
    Trinity’s Base Period QREs must be reevaluated in light of the
    uncontroverted evidence to ensure they are determined consistent
    with the QREs in the Claim Years. Mr. Nuss . . . considered
    whether any of the vessels originally included in the Base Period
    would no longer be considered prototypes under the standard
    articulated in Trinity I. . . . Mr. Nuss testified that expenditures
    on four vessel projects in the Base Period should not be treated as
    QRE[s] . . . . For each of these vessels, Mr. Nuss testified that the
    identification, configuration and integration of the components of
    the vessels were not sufficiently complex for the vessels to
    constitute prototypes under the Court’s standard.
    Trinity contended that, after removing the four base period vessels from the
    base period QRE figure of $49,483,136 provided by Bennett’s report, the base
    period QRE figure would total $26,706,987. Trinity’s second consistency rule
    argument thus asked the district court to allow it to reduce its base period QRE
    6
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    figure by over $20 million, which in turn would reduce its fixed base percentage
    and increase its overall research tax credit.
    In its Phase II order, the district court concluded that Trinity was
    wrongly denied tax credit for the Queen of New Orleans but was correctly
    denied credit for the Penn Tugs. According to the court, the Penn Tugs did not
    meet the fourth QRE requirement. With respect to the consistency rule, the
    court only addressed the merits of Trinity’s first consistency rule argument—
    Trinity’s defense of its use of an all-or-nothing, “entire project” approach in
    both the base period years and the claim years:
    Trinity now argues that, in view of the consistency rule, its base
    period QREs should include only projects that were overall 80% or
    more research. The Court disagrees. . . . Here the Court applied
    the 80% rule only to entire projects due to a lack of evidence to
    permit application of the “shrinkback rule.” This . . . simply
    reflects the absence of evidence of costs incurred on a subset of an
    entire vessel . . . . Accordingly, the Court will not exclude from the
    base period QREs any QREs incurred that were less than 80% of
    an entire project.
    The court accordingly rejected the merits of Trinity’s first argument but failed
    to address the merits of Trinity’s second argument based on Nuss’s testimony.
    The court also failed to acknowledge that Trinity did not use the shrinking-
    back rule in calculating the base period QREs in its amended tax returns, and
    therefore the base period QREs already excluded any QREs incurred that were
    less than 80% of an entire project. The same order provided that “[o]ther than
    Trinity’s consistency argument, the Court credits the testimony of Trinity’s
    witnesses and finds Trinity’s calculation to be a reasonable estimate of the base
    amount.”
    After additional briefing, the district court issued its final judgment
    holding that Trinity was entitled to $135,787.60 in tax credit for 1994 and $0
    for 1995. Trinity now appeals.
    7
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    II
    “The standard of review for a bench trial is well established: findings of
    fact are reviewed for clear error and legal issues are reviewed de novo.” 8 A fact
    finding “is clearly erroneous if it is without substantial evidence to support it,
    the court misinterpreted the effect of the evidence, or this court is convinced
    that the findings are against the preponderance of credible testimony.” 9 Mixed
    questions of law and fact are also reviewed de novo. 10
    III
    Trinity first contends that the district court erred in applying the
    consistency rule in calculating its base period QREs.                    We begin with an
    overview of the research tax credit calculation and the consistency rule, and
    then consider Trinity’s position regarding the consistency rule.
    A
    Under I.R.C. § 41, companies can claim a 20% credit for QREs that
    exceed what they spent in an earlier comparison period. 11                          Using the
    terminology of the I.R.C., the research tax credit is calculated as follows:
    • Research credit = the lesser of: 20% x (claim year QREs – base amount),
    and 20% x (50% x claim year QREs); 12
    • Base amount = fixed base percentage x average annual gross receipts for
    the four years preceding claim year; 13
    8 Coe v. Chesapeake Exploration, L.L.C., 
    695 F.3d 311
    , 316 (5th Cir. 2012) (quoting
    Preston Exploration Co. v. GSF, L.L.C., 
    669 F.3d 518
    , 522 (5th Cir. 2012)).
    9 Petrohawk Props., L.P. v. Chesapeake La., L.P., 
    689 F.3d 380
    , 388 (5th Cir. 2012)
    (quoting French v. Allstate Indem. Co., 
    637 F.3d 571
    , 577 (5th Cir. 2011)).
    10   
    Id.
     (citing Dickerson v. Lexington Ins. Co., 
    556 F.3d 290
    , 294 (5th Cir. 2009)).
    11   I.R.C. § 41(a)(1).
    12   Id. § 41(a)(1), (c)(2).
    13   Id. § 41(c)(1).
    8
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    • Fixed base percentage = aggregate base period QREs / aggregate base
    period gross receipts, where base period here = taxable year ending
    3/31/1985 through taxable year ending 3/31/1989. 14
    The research tax credit can be summarized in the following formula:
    To constitute QREs, four requirements must be met:
    (1) the expenses must be of the type deductible under I.R.C.
    § 174; (2) the research must be undertaken “for the purpose of
    discovering information . . . which is technological in nature;”
    (3) the application of that information must be “intended to be
    useful in the development of a new or improved business
    component of the taxpayer;” and (4) substantially all of the
    research activities must “constitute elements of a process of
    experimentation.” 15
    Under Treasury regulations, the fourth requirement is met if 80% or more of
    the research activities constitute elements of a process of experimentation. 16
    This four-part QRE test is to be applied separately to each business
    component of the taxpayer, which is defined to include any product held for
    sale, lease, or license, or used by the taxpayer in its trade or business. 17 If,
    14   See id. § 41(c)(3)(A).
    15United States v. McFerrin, 
    570 F.3d 672
    , 676 (5th Cir. 2009) (alteration in original)
    (quoting I.R.C. § 41(d)(1)).
    16   
    Treas. Reg. § 1.41-4
    (a)(6).
    17   I.R.C. § 41(d)(2).
    9
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    however, each of the four requirements is not met with respect to an entire
    business component, the shrinking-back rule under Treasury Regulation
    § 1.41-4(b)(2) is implicated.             Under the shrinking-back rule, these four
    requirements “are to be applied first at the level of the discrete business
    component,” but “[i]f these requirements are not met at that level, then they
    apply at the most significant subset of elements of the product.” 18                 “This
    shrinking back of the product is to continue until either a subset of elements
    of the product that satisfies the requirements is reached, or the most basic
    element of the product is reached and such element fails to satisfy the test.” 19
    Accordingly, the rule “is applied only if a taxpayer does not satisfy the [four
    requirements] with respect to the overall business component.” 20
    The consistency rule also plays a role in computing QREs. The rule
    ensures that the research tax credit due is not overstated or understated
    because the taxpayer inconsistently compares QREs in the base period years
    and the claim year. The rule provides that “the [QREs] taken into account in
    computing [the fixed base] percentage shall be determined on a basis
    consistent with the determination of [QREs] for the credit year.” 21                   The
    corresponding Treasury regulation uses similar language. 22
    18   
    Treas. Reg. § 1.41-4
    (b)(2).
    19   
    Id.
    20   
    Id.
    21   I.R.C. § 41(c)(6)(A).
    22 
    Treas. Reg. § 1.41-3
    (d)(1) (“[QREs] and gross receipts taken into account in
    computing a taxpayer’s fixed-base percentage and a taxpayer’s base amount must be
    determined on a basis consistent with the definition of [QREs] and gross receipts for the
    credit year, without regard to the law in effect for the taxable years taken into account in
    computing the fixed-base percentage or the base amount.”).
    10
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    B
    On appeal, Trinity challenges the district court’s application of the
    consistency rule in calculating its base period QREs, and it presents two
    distinct arguments as to why the rule was violated. The first argument is that
    the district court violated the consistency rule by applying the shrinking-back
    rule in the base period years but not applying it in the claim years. This
    argument hinges on the assumption that the district court used a shrink-back
    analysis for the base period QREs, so that if expenses related to the entire
    vessel did not constitute qualified research, expenses related to subcomponents
    of the vessel were still counted as qualified research. The Government has not
    contested Trinity’s understanding of the facts, so the parties argue over
    whether, as a legal matter, when the shrinking-back rule could not be applied
    in calculating the claim year QREs because of a lack of evidence, the base
    period QREs also had to be calculated on an all-or-nothing, “whole ship” basis.
    There is a significant issue, however, regarding the facts assumed in
    much of the briefing in our court: the briefs assumed that the shrinking-back
    rule was applied by the district court, while the record reflects that it was not
    applied in the district court’s calculation of the base period QREs. In fact,
    neither Trinity’s amended tax returns, nor Bennett’s report, nor the district
    court judgment based on Bennett’s report used the shrinking-back rule in
    computing Trinity’s base period QREs. Trinity’s briefing before the district
    court acknowledged that it did not use the shrinking-back rule in its amended
    tax returns.    Moreover, Bennett’s report confirms that neither Trinity’s
    amended tax returns nor his report could have used the shrinking-back rule in
    computing Trinity’s base period QREs. For one, Bennett’s report stated that
    he calculated the base period QREs “based on 100% of the wages, supplies and
    contract labor costs, less overhead costs” for the ten vessel projects in the base
    period. Including all of the projects’ expenses shows that entire projects were
    11
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    considered qualified research, not just “subcomponents” of the projects like the
    vessels’ engines. Second, Bennett noted that Trinity’s records for the base
    period years were even less detailed than the records for the claim years, in
    which Trinity was unable to avail itself of the shrinking-back rule because
    records were lacking. This further establishes that neither Bennett’s report
    nor Trinity’s amended returns applied the shrinking-back rule in the base
    period.
    The district court’s order also did not employ the shrinking-back rule in
    computing the base period QREs. In its final judgment, the district court held
    Trinity was entitled to $135,787.60 for 1994 and $0 for 1995. These figures are
    the same as those in Trinity’s post-trial briefing, which asked the court to adopt
    the base amount figures from Bennett’s report. This means that the base
    amounts used in the final judgment were calculated using the fixed base
    percentage, including the base period QREs, used in Bennett’s report, and
    Bennett’s report did not employ the shrinking-back rule in calculating the base
    period QREs. As a result, the district court’s judgment incorporated a base
    period QRE figure calculated using an all-or-nothing approach, thereby
    excluding any QREs incurred that were less than 80% of an entire project, even
    though it held that it would “not exclude from the base period QREs any QREs
    incurred that were less than 80% of an entire project.” Trinity’s attorney at
    oral argument acknowledged that the district court did not apply a shrink-back
    analysis in calculating the base period QREs.
    In short, the district court did not use the shrinking-back rule in
    calculating Trinity’s base period QREs. Trinity argues that the district court
    should have applied a “whole ship” methodology in calculating its base period
    QREs, but this is exactly what the district court did by calculating the base
    amount based on Bennett’s report. Moreover, any argument—from either
    party—about whether the shrinking-back rule should have been applied in the
    12
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    base period years need not be addressed as the lack of records from the base
    period years apparently would have precluded the shrinking-back rule from
    being applied in the base period. Trinity’s first consistency rule argument
    therefore entitles it to nothing more than what the district court awarded it.
    C
    Trinity presents a second argument as to why the consistency rule was
    violated and why it is therefore entitled to a lower base period QRE figure of
    $26,706,987. The $26,706,987 amount is the base period QRE used in the
    Bennett report less the QREs attributable to the four base period vessels Nuss
    testified would not constitute qualified research under the standard
    articulated by the district court in Phase I of trial.
    Nuss testified that he did not believe that four base period vessels—the
    LSV, the North Carolina Auto Ferry, the Cajun Queen, and the Ecuador—
    involved the level of experimentation necessary to constitute QREs since they
    were similar, in terms of how much experimentation was involved, to the claim
    year vessels the district court held not to be QREs after Phase I. In other
    words, if the district court found that certain claim year vessels—including the
    XFPB, the T-AGS 60, the Crew Rescue Boat, and the Hurley Dredge—did not
    satisfy the QRE test, then four of the base period vessels should not have
    satisfied the QRE test, either. As discussed above, Nuss testified that two of
    the base period vessels—the LSV and the North Carolina Auto Ferry—were
    similar to the Hurley Dredge, since they all involved Trinity constructing a
    vessel based on a design provided to Trinity by a third party. There was also
    testimony from Charters that the LSV was comparable to the Hurley Dredge
    since both were based in part on an existing design. Nuss believed that another
    base period vessel—the Cajun Queen—was like the Crew Rescue Boat, another
    claim year vessel held not to be qualified research, since the Cajun Queen was
    also not a complicated technological boat to build. Finally, Nuss testified that
    13
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    a fourth base period vessel—the Ecuador—was like the XFPB, which the
    district court held was not qualified research, since the Ecuador similarly had
    some experimental features but not enough to satisfy the QRE test. Nuss
    testified that to calculate the QREs on a consistent basis, the four base period
    vessels should be removed from the base period QRE calculation.
    Though much of Trinity’s briefing on appeal focused on its first
    consistency rule argument concerning the shrinking-back rule, Trinity has
    adequately raised its second argument based on Nuss’s testimony. In its
    opening brief, Trinity argued that, under a proper application of the
    consistency rule, this court should calculate its base period QREs as
    $26,706,987: the base period QRE amount used in the Bennett report less the
    QREs attributable to the four vessels Nuss said would not satisfy the district
    court’s Phase I QRE standard. Trinity’s reply brief again referenced Nuss’s
    testimony, noting that “[b]ased on the District Court’s ruling in Phase I, [Nuss
    and Charters] identified four comparable vessels, out of the [ten] submitted by
    Trinity in the base years, that similarly would not qualify for research credit
    as whole ships under the Court’s analysis.” Trinity also contended that the
    panel could reverse and render judgment in its favor based on “Nuss’s
    testimony of why four ships from the base years . . . should be removed under
    the consistency rule” and referred to “Nuss’s and Charters’s testimony on
    removing four partial ships from the base years.” At oral argument, Trinity’s
    counsel again urged that if the district court disqualified certain claim year
    vessels, it should have also disqualified the four base period vessels, which
    involved a similar level of experimentation, as not satisfying the process-of-
    experimentation test. Trinity therefore sufficiently raised this argument on
    appeal.
    Assuming the district court would credit Nuss’s and Charters’s
    testimony, we agree with Trinity that if certain base period vessels are just as
    14
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    experimental as claim-year vessels held not to be qualified research, those base
    period vessels should not be counted as qualified research for purposes of the
    base period QRE calculation. I.R.C. § 41 allows a taxpayer to claim a tax credit
    for claim year research expenses that exceed the research expenses spent in
    an earlier comparison period, the base period years. 23 To equitably measure
    the increase in qualified research spending between the two periods, the same
    standard should be applied in determining whether certain projects pursued
    in the two periods are sufficiently experimental to be qualified research.
    The consistency rule addresses this very issue: it aims to ensure that the
    research tax credit due is not overstated or understated because the taxpayer
    inconsistently compares QREs in the base period years and the claim year.
    The rule provides that the QREs “taken into account in computing [the fixed-
    base] percentage shall be determined on a basis consistent with the
    determination of [QREs] for the credit year.” 24 The corresponding Treasury
    regulation uses language very similar to the consistency rule itself but adds
    the word “definition”:
    [QREs] . . . taken into account in computing a taxpayer’s fixed-base
    percentage and a taxpayer’s base amount must be determined on
    a basis consistent with the definition of [QREs] . . . for the credit
    year, without regard to the law in effect for the taxable years taken
    into account in computing the fixed-base percentage or the base
    amount. 25
    The regulation then provides two illustrations. In the first, for a hypothetical
    taxpayer, the statutory definition of QRE for its first two base period years
    (1984 and 1985) is different than a revised QRE definition applicable in its last
    23   I.R.C. § 41(a)(1).
    24   Id. § 41(c)(6)(A).
    25   
    Treas. Reg. § 1.41-3
    (d)(1).
    15
    Case: 12-11012           Document: 00512685765           Page: 16   Date Filed: 07/02/2014
    No. 12-11012
    three base period years (1986, 1987, and 1988) and in its claim year (2001). 26
    To compute the credit for 2001, the taxpayer must apply the new QRE
    definition to its 1984 and 1985 base period years “to reflect the change in the
    definition of qualified research” beginning in 1986. 27 The second illustration
    following the regulation shows another slightly different application of the
    consistency rule.         It states that if the taxpayer counts “a certain type of
    expenditure”—such as the wages of its research assistants—as QREs in the
    claim year, it must also count “similar expenditures” as QREs in its base period
    years. 28 In sum, the consistency rule calls for consistent application of the QRE
    definition across the base period years and the claim year, including the types
    of expenditures the taxpayer treats as QREs.
    The consistency rule is equally applicable to a case like this one. Here,
    the district court decided that certain claim year projects were not sufficiently
    experimental to pass the fourth QRE requirement—that 80% or more of the
    research activities involved in the project constitute elements of a process of
    experimentation 29—and Trinity simply asked the court to consider whether
    four of its base period projects were also not sufficiently experimental to pass
    that same test. If, for instance, the Ecuador and the XFPB projects involved
    exactly the same level of experimentation, then it would violate the consistency
    rule (and understate Trinity’s tax credit) not to count the XFPB as qualified
    research in the claim year but to count the Ecuador as qualified research in
    26   
    Id.
     § 1.41-3(d)(2) (Example 1).
    27   Id.
    28Id. (Example 2); see also Union Carbide Corp. v. Comm’r, 
    97 T.C.M. (CCH) 1207
    ,
    
    T.C. Memo 2009-50
    , at *75 (2009) (“[T]he taxpayer must include the same types of activities
    from the credit year and the base period when identifying qualified research activities and
    include the same types of costs as QREs for the credit year and the base period.”), aff’d, 
    697 F.3d 104
     (2d Cir. 2012).
    29   See I.R.C. § 41(d)(1); 
    Treas. Reg. § 1.41-4
    (a)(6).
    16
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    No. 12-11012
    the base period years. Trinity is entitled to have a consistent QRE test applied
    to projects in the base period years and the claim years.
    The only matter still unsettled is whether the district court would credit
    Nuss’s and Charters’s testimony that the four base period vessels were similar
    to the four claim year vessels held not be qualified research, in terms of how
    much experimentation was involved. In its order after Phase II of the trial,
    the district court stated that, “[o]ther than Trinity’s consistency argument, the
    Court credits the testimony of Trinity’s witnesses and finds Trinity’s
    calculation to be a reasonable estimate of the base amount.” But again, though
    Trinity raised in the district court the second consistency rule argument based
    on Nuss’s and Charters’s testimony, the district court did not address this
    issue, so it is unclear whether the district court credited those witnesses’
    testimony on the four base period vessels.
    We therefore remand to the district court for a limited purpose: making
    a factual finding as to whether to credit the testimony of Nuss and Charters
    that the four base period vessels were as experimental as (or less experimental
    than) the four claim year vessels held not to satisfy the fourth QRE
    requirement. If the district court credits this testimony against any possible
    conflicting testimony or evidence, then those four base period vessels should
    be removed from the base period QRE calculation, and the resulting base
    period QRE figure would be $26,706,987. If the district court finds that the
    four base period vessels (or some of them) were more experimental than the
    four claim year vessels and were sufficiently experimental to qualify as QREs,
    then the base period QRE figure should include the expenses associated with
    those vessel projects. We thus vacate the district court’s holding as to the
    consistency rule and remand for findings as to whether, in light of the district
    court’s Phase I order, the four base period vessels at issue are sufficiently
    experimental to constitute qualified research.
    17
    Case: 12-11012          Document: 00512685765       Page: 18     Date Filed: 07/02/2014
    No. 12-11012
    IV
    Trinity also challenges the district court’s conclusion that its research
    expenses in developing the Penn Tugs did not satisfy the fourth QRE
    requirement and therefore did not constitute claim year QREs. Trinity first
    argues that because the I.R.S. already determined that the Penn Tugs met the
    fourth QRE requirement, the Government was either conclusively or
    presumptively bound by that decision in this litigation. When the I.R.S. issued
    its claim disallowance letter, it incorporated a revenue agent report stating
    that, with respect to the Penn Tugs, the fourth requirement—the process-of-
    experimentation test—was satisfied, even though two other QRE requirements
    were not. Even if the Government is not conclusively bound by the conclusion
    in Trinity’s favor on the fourth QRE requirement, Trinity argues it is entitled
    to a presumption of correctness, so the Government bore the burden of
    rebutting it by affirmative evidence.
    We disagree.          The district court correctly held that the report’s
    conclusion, though admissible evidence, 30 was neither binding nor entitled to
    a presumption of correctness. In tax refund actions, the district court reviews
    de novo the Commissioner’s decision regarding a taxpayer’s tax liability. 31 The
    taxpayer has the burden of proving by a preponderance of the evidence that
    the Commissioner’s assessment—its final determination of the taxpayer’s
    liability—was erroneous, since the assessment is presumed to be correct. 32
    30   See FED. R. EVID. 801(d)(2)(D).
    31 See Clapp v. Comm’r, 
    875 F.2d 1396
    , 1403 (9th Cir. 1989) (“In tax cases . . . [the]
    United States District Court review[s] the Commissioner’s decision on the merits de novo.”);
    Int’l Paper Co. v. United States, 
    36 Fed. Cl. 313
    , 320 (1996) (recognizing the “de novo nature
    of tax refund proceedings in the Court of Federal Claims (as well as in the district courts)”).
    32Carson v. United States, 
    560 F.2d 693
    , 695-96 (5th Cir. 1977) (“The burden and the
    presumption, which are for the most part but the opposite sides of a single coin, combine to
    require the taxpayer always to prove by a preponderance of the evidence that the
    Commissioner’s determination was erroneous.”) (citing United States v. Janis, 
    428 U.S. 433
    ,
    18
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    No. 12-11012
    While the assessment itself is entitled to a presumption of correctness, the
    “reasons for the Commissioner’s determination are not relevant for the Court
    does not review those reasons.” 33 Accordingly, here, while the I.R.S.’s ultimate
    determination of Trinity’s tax liability is presumptively correct, the revenue
    agent report’s subsidiary conclusion that the Penn Tugs met the process-of-
    experimentation test is neither binding on the Government nor presumptively
    correct.
    Trinity’s second contention is that, even if the conclusions in the revenue
    agent report are not binding or presumptively correct in this litigation, the
    district court erred in deciding that the Penn Tugs did not satisfy the process-
    of-experimentation test under the fourth QRE requirement.                           Under this
    requirement, substantially all (i.e., 80%) of the taxpayer’s research activities,
    “measured on a cost or other consistently applied reasonable basis,” must
    constitute elements of a process of experimentation. 34                       As the Treasury
    regulations elaborate, a “process of experimentation”
    involves three steps: (1) “the identification of uncertainty
    concerning the development or improvement of a business
    component,” (2) “the identification of one or more alternatives
    intended to eliminate that uncertainty,” and (3) “the identification
    and the conduct of a process of evaluating the alternatives
    440 (1976)); see also Cook v. United States, 
    46 Fed. Cl. 110
    , 113-14 (2000) (discussing the
    presumption of correctness and the taxpayer’s burden in tax refund suits).
    33Int’l Paper Co., 36 Fed. Cl. at 320 (quoting Pierson v. United States, 
    428 F. Supp. 384
    , 390 (D. Del. 1977)); see also MICHAEL I. SALTZMAN & LESLIE BOOK, IRS PRACTICE AND
    PROCEDURE ¶ 1.05[2][a] (explaining that in a tax refund suit in federal court, “any ‘record’
    made in the Service, including the reasons for its assessment, is irrelevant” and that the
    “action involves a de novo determination of the correct tax and is not a review of the
    administrative processing of the case”).
    34   I.R.C. § 41(d)(1)(C); 
    Treas. Reg. § 1.41-4
    (a)(6).
    19
    Case: 12-11012           Document: 00512685765          Page: 20   Date Filed: 07/02/2014
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    (through, for example, modeling, simulation, or a systematic trial
    and error methodology).” 35
    Case law applying the Treasury regulations explains that the process-of-
    experimentation test is not satisfied when the taxpayer uses “a method of
    simple trial and error to validate that a process or product change meets the
    taxpayer’s needs.” 36         Instead, at a minimum, the research activities must
    involve a “systematic trial and error methodology” 37—“a methodical plan
    involving a series of trials to test a hypothesis, analyze the data, refine the
    hypothesis, and retest the hypothesis so that it constitutes experimentation in
    the scientific sense.” 38
    The Penn Tugs were each designed to connect to a barge by an
    articulating arm (the “Intercon coupler”) so that the tugboat and the barge
    could function as a single ship with high horsepower. In this tug-coupler-barge
    combination, or articulated tug barge (ATB), “the tug functioned as the
    propeller for the barge, rather than as a traditional tug that pulls another
    vessel.”       Trinity designed the Penn Tugs to avoid the Coast Guard’s
    requirement that large cargo ships have a 20-person crew with advanced
    licenses. Instead of treating the ATB as a cargo ship, the Coast Guard would
    certify the vessel as a tug and a barge, so it could be manned by a smaller crew
    with simpler licenses, resulting in cost savings for the operator.
    35 United States v. McFerrin, 
    570 F.3d 672
    , 677 (5th Cir. 2009) (quoting 
    Treas. Reg. § 1.41-4
    (a)(5)(i)).
    36 Union Carbide Corp. v. Comm’r, 
    97 T.C.M. (CCH) 1207
    , 
    T.C. Memo 2009-50
    , at *81
    (2009), aff’d, 
    697 F.3d 104
     (2d Cir. 2012); see United States v. Davenport, 
    897 F. Supp. 2d 496
    ,
    506 (N.D. Tex. 2012) (same).
    37   
    Treas. Reg. § 1.41-4
    (a)(5)(i).
    Union Carbide Corp., 
    T.C. Memo 2009-50
    , at *81; see Davenport, 897 F. Supp. 2d at
    38
    506 (same).
    20
    Case: 12-11012       Document: 00512685765          Page: 21     Date Filed: 07/02/2014
    No. 12-11012
    In addressing the Penn Tugs, the district court first noted that the
    Intercon coupler part of the ATB was invented, developed, and built by other
    companies. The court then considered the first Penn Tug and noted that, in
    designing it, Trinity modified an existing hull design. The court acknowledged
    this modification involved assessing “the structural integrity of the tug-coupler
    combination” since “portions of the tug can be ‘hanging’ from the Intercon
    coupler, depending on wave action on the barge.”                   The court nonetheless
    concluded that less than 80% of the costs were incurred in a process of
    experimentation “because third parties designed and manufactured the
    coupler system itself and the first Penn Tug was only a modification of an
    existing design.”
    The district court then separately addressed the second Penn Tug.
    Trinity made the elevated pilot house on the first Penn Tug out of aluminum
    to save weight, but due to changes in Coast Guard fire regulations, Trinity was
    required to make the pilot house on the second Penn Tug out of steel. Although
    the heavier steel pilot house required other design changes, the district decided
    that “the only process of experimentation between the first and second Penn
    Tugs was the change to the composition of the pilot house.” The district court
    concluded that the second Penn Tug also failed the process-of-experimentation
    test.
    This determination on the Penn Tugs is best characterized as a mixed
    question of law and fact, since the underlying facts and applicable legal
    standard are basically undisputed, and the question is whether those facts
    satisfy the legal standard. 39 We therefore review any underlying fact findings
    39See Ornelas v. United States, 
    517 U.S. 690
    , 696-97 (1996) (explaining that for mixed
    questions of law and fact, “historical facts are admitted or established, the rule of law is
    undisputed, and the issue is whether the facts satisfy the [relevant statutory standard]”)
    (internal quotation marks and citation omitted).
    21
    Case: 12-11012          Document: 00512685765          Page: 22     Date Filed: 07/02/2014
    No. 12-11012
    for clear error, but we review the legal conclusion that the Penn Tugs failed
    the process-of-experimentation test de novo. 40 In addition, Trinity had the
    burden of proof, including the burden of going forward with evidence and the
    burden of persuasion, that 80% of its Penn Tugs research activities constituted
    a process of experimentation. 41
    Trinity has not established that 80% of the research activities for the
    Penn Tugs constituted elements of a process of experimentation.                          Trinity
    argues that modifying the existing hull design involved some systematic trial
    and error—“[f]inding a working hull design required testing and retesting,
    including computer modeling and at least four design revisions”—and has cited
    testimony to support this assertion. However, Trinity has failed to establish
    which other aspects of its research involved the sort of systematic trial and
    error required under the process-of-experimentation test. For instance, in
    arguing that changing the composition of the pilot house involved a process of
    experimentation, Trinity says it “experimented” with an aluminum tower and
    pilothouse but does not allege that designing the tower involved the sort of
    systematic trial and error that the hull design involved. While designing the
    hull involved some systematic experimentation, Trinity has not shown that
    substantially all of its Penn Tugs research activities involved the type of
    systematic experimentation courts have required. 42
    40 See Dunn v. Comm’r, 
    301 F.3d 339
    , 348 (5th Cir. 2002) (holding that the
    “determination of fair market value” of common stock under Treasury regulations is a mixed
    question of fact and law, and that the factual premises of mixed questions are reviewed for
    clear error and the legal conclusions are reviewed de novo).
    41   Int’l Paper Co. v. United States, 
    36 Fed. Cl. 313
    , 322 (1996).
    42 See Union Carbide Corp., 
    T.C. Memo 2009-50
    , at *7, *85-86 (holding that
    substantially all of the research activities in connection with an “anticoking project” (a project
    aimed at reducing the build-up of carbon in the taxpayer’s furnaces) constituted elements of
    a process of experimentation because the project involved collecting and analyzing data to
    compare existing technologies with alternatives and ultimately refining the process to
    improve it overall); see also Davenport, 897 F. Supp. 2d at 514-15 (holding that the taxpayer’s
    22
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    No. 12-11012
    Moreover, since the coupler was not designed by Trinity, the district
    court correctly focused on research activities with respect to the tugs only.
    Trinity does not dispute that it did not invent, design, or build the coupler; it
    only claims it “had to work alongside the company manufacturing the coupler
    to design the support structure required for it to work within this prototype.”
    While Trinity had to consider how the tugs would support the coupler, it did
    not design the coupler itself.
    The district court also did not err in finding that, even if aspects of
    designing the hull involved a process of experimentation, the hull’s design was
    still based on an existing hull design to some extent. Although there was
    testimony that Trinity had “to start over from scratch with a different hull,”
    the testimony also established that designing the new hull involved
    “modifications” of old hulls, and that the ultimate hull design had similarities
    to existing hulls. Additionally, it was not error to consider the two Penn Tugs
    “separately and sequentially,” as Trinity argues. Trinity cites no authority
    requiring the court to treat the tugs together, and even if Trinity had, Trinity
    has not shown how the 80% threshold would be surpassed by doing so.
    Accordingly, the district court did not err in its analysis of the Penn Tugs.
    *        *         *
    For the foregoing reasons, the judgment of the district court is
    AFFIRMED in part, and VACATED and REMANDED in part for proceedings
    consistent with this opinion.
    project “did not involve a process of experimentation or the type of systematic plan involving
    a series of trials to test a hypothesis, analyze the data, refine the hypothesis, and retest the
    hypothesis; nor did it involve a series of experiments with one or more alternatives to develop
    the [project]”) (internal quotation marks and citation omitted).
    23