No. 08-964
================================================================
In The
Supreme Court of the United States
----------------- ♦ -----------------
BERNARD L. BILSKI and RAND A. WARSAW,
Petitioners,
v.
JOHN J. DOLL, ACTING UNDER SECRETARY
OF COMMERCE FOR INTELLECTUAL
PROPERTY AND ACTING DIRECTOR,
PATENT AND TRADEMARK OFFICE,
Respondent.
----------------- ♦ -----------------
On Writ Of Certiorari To The
United States Court Of Appeals
For The Federal Circuit
----------------- ♦ -----------------
BRIEF OF MONOGRAM BIOSCIENCES, INC.
AND GENOMIC HEALTH, INC. AS AMICI
CURIAE IN SUPPORT OF NEITHER PARTY
----------------- ♦ -----------------
NARINDER S. BANAIT
H. THOMAS ANDERTON, JR.
Counsel of Record
MONOGRAM BIOSCIENCES, INC.
TYLER BAKER
345 Oyster Point Blvd.
DANIEL R. BROWNSTONE
South San Francisco, CA 94080
STUART P. MEYER
(650) 624-4198
ROBERT R. SACHS
KATHLEEN DETERMANN
FENWICK & WEST LLP
GENOMIC HEALTH, INC.
801 California Street
301 Penobscot Drive
Mountain View, CA 94041
Redwood City, CA 94063
(650) 988-8500
(650) 556-9300
Counsel for Amici Curiae
================================================================
COCKLE LAW BRIEF PRINTING CO. (800) 225-6964
OR CALL COLLECT (402) 342-2831
i
QUESTIONS PRESENTED
1. Whether the Federal Circuit erred by holding
that a “process” must be tied to a particular machine
or apparatus, or transform a particular article into a
different state or thing (“machine-or-transformation”
test), to be eligible for patenting under 35 U.S.C.
§ 101, despite this Court’s precedent declining to limit
the broad statutory grant of patent eligibility for
“any” new and useful process beyond excluding
patents for “laws of nature, physical phenomena, and
abstract ideas.”
2. Whether the Federal Circuit’s “machine-or-
transformation” test for patent eligibility, which
effectively forecloses meaningful patent protection to
many business methods, contradicts the clear
Congressional intent that patents protect “method[s]
of doing or conducting business.” 35 U.S.C. § 273.
ii
TABLE OF CONTENTS
Page
INTEREST OF THE AMICI CURIAE ...................
1
SUMMARY OF ARGUMENT ................................
3
ARGUMENT ...........................................................
6
I. PATENTABLE PROCESSES CAN BE EI-
THER PHYSICAL OR NON-PHYSICAL .....
6
II.
THE FEDERAL CIRCUIT ERRED IN
HOLDING THAT A PROCESS MUST BE
TIED TO A PARTICULAR MACHINE OR
TRANSFORM A PARTICULAR ARTICLE
INTO A DIFFERENT STATE OR THING .... 10
A. The Federal Circuit Erred In Holding
That A “Process” Must Be Tied To A
Particular Machine Or Apparatus, Or
Transform A Particular Article Into A
Different State Or Thing (“Machine-
Or-Transformation” Test), To Be Eligi-
ble For Patenting Under 35 U.S.C.
§ 101 ....................................................... 10
B.
The Machine-Or-Transformation Test
Does Not Properly Distinguish Be-
tween Patent-Eligible And Patent-
Ineligible Subject Matter ...................... 12
C.
The Machine-Or-Transformation Test
Is Inconsistent With 35 U.S.C. § 101
And This Court’s Long-Standing Prec-
edent ...................................................... 13
iii
TABLE OF CONTENTS – Continued
Page
III. A PROPOSED FRAMEWORK FOR IDEN-
TIFYING PATENT-ELIGIBLE SUBJECT
MATTER ...................................................... 15
A. This Court Should Determine Whether
A Law Of Nature, Natural Phenom-
enon Or Abstract Idea Is Claimed And
Construe Those Terms In The Ordi-
nary English Sense ................................ 15
B. Diagnostic Claims Drawn To Methods
Of Predicting Response In A Patient Are
Patent-Eligible Because They Do Not
Describe A Fundamental Principle ......... 21
IV.
THE MACHINE-OR-TRANSFORMATION
TEST THREATENS TO STIFLE INNOVA-
TION IN PERSONALIZED MEDICINE .... 26
A.
Personalized Medicine Is A Growing
Field With A Tremendous Potential To
Help Patients ......................................... 26
B. Because The Machine-Or-Transformation
Test Endangers Funding For Person-
alized Medicine Companies, It Will
Undermine Personalized Medicine Com-
panies, Stifle Development And Ulti-
mately Harm Patients ........................... 31
CONCLUSION ....................................................... 33
iv
TABLE OF AUTHORITIES
Page
CASES
Arrhythmia Research Technology, Inc. v.
Corazonix Corp., 958 F.2d 1053 (Fed. Cir.
1992) ........................................................................ 11
Classen Immunotherapies, Inc. v. Biogen IDEC,
381 F. Supp. 2d 452 (D. Md. 2005), aff ’d,
2008 U.S. App. LEXIS 25661 (Fed. Cir. Dec.
19, 2008) .................................................................. 24
Cochrane v. Deener, 94 U.S. 780 (1876) ....................... 8
Diamond v. Chakrabarty, 447 U.S. 303 (1980).......... 14
Diamond v. Diehr, 450 U.S. 175 (1981) ................. passim
Funk Brothers Seed Co. v. Kalo Inoculant Co.,
333 U.S. 127 (1948) ........................................... 16, 25
Gottschalk v. Benson, 409 U.S. 63 (1972) .......... passim
In re Bilski, 545 F.3d 943 (Fed. Cir. 2008) ......... passim
In re Nuijten, 500 F.3d 1346 (Fed. Cir. 2007) ............ 11
Jacobellis v. Ohio, 378 U.S. 184 (1964) ..................... 16
KSR Int’l Co. v. Teleflex, Inc., 550 U.S. 398
(2007) ....................................................................... 14
Laboratory Corp. of Am. Holdings v. Metabolite
Labs. Inc., 548 U.S. 124 (2006) ................... 21, 24, 31
Parker v. Flook, 437 U.S. 584 (1978) ................. passim
Perrin v. United States, 444 U.S. 37 (1979) ............... 16
Prometheus Labs. v. Mayo Collaborative Servs.,
2008 U.S. Dist. LEXIS 25062 (S.D. Cal. Mar.
28, 2008) .................................................................. 24
v
TABLE OF AUTHORITIES – Continued
Page
Shepard v. United States, 544 U.S. 13 (2005) ........... 13
State Street Bank & Trust Co. v. Signature
Financial Group, Inc., 149 F.3d 1368 (Fed.
Cir. 1998) ................................................................. 12
Waxham v. Smith et al., 294 U.S. 20 (1935) ................ 8
STATUTES
35 U.S.C. § 100(b) ......................................................... 6
35 U.S.C. § 101 ................................................... passim
35 U.S.C. § 103 ........................................................... 14
35 U.S.C. § 273 ............................................................. 7
RULES
Supreme Court Rule 37 ................................................ 1
LEGISLATIVE MATERIALS
145 Congressional Record H11769 (daily ed.
Nov. 9, 1999) .............................................................. 7
OTHER AUTHORITIES
Julie E. Cohen and Mark A. Lemley, Patent
Scope and Innovation in the Software
Industry, 89 Cal. L. Rev. 1 (2001) ........................... 12
Genomics and Personalized Medicine Act of
2006 ......................................................................... 30
vi
TABLE OF AUTHORITIES – Continued
Page
C. Kongkaew, et al., Hospital admissions
associated with adverse drug reactions, Ann
Pharmacother 42(7):1017-1025 (2008) ................... 27
Oxford English Dictionary 6 (2d ed. 1989) ... 6, 7, 17, 18
B. Spear, et al., Clinical application of pharma-
cogenomics, Trends Mol. Med. 7(5):201-204
(2001) ....................................................................... 26
1
INTEREST OF THE AMICI CURIAE1
Personalized medicine is universally acknowl-
edged to hold enormous potential for treating
diseases, improving the quality of patients’ lives and
streamlining the drug discovery and development
process. Personalized medicine uses molecular diag-
nostic tests to correlate genetic and molecular
biomarkers with clinically useful disease charac-
teristics. The technology has already delivered
tremendous results for individual patients, and
current research efforts and clinical trials promise
significant future improvements in health care.
Personalized medicine companies are typically
small and rely on private investment capital to sus-
tain them through the lengthy and expensive re-
search, development and commercialization process.
Developing the tests is time consuming and ex-
pensive. Personalized medicine companies literally
flourish or fail based on their ability to build patent
portfolios protecting diagnostic correlations.
The success of personalized medicine in the
diagnosis and treatment of breast cancer has been
unexpectedly spectacular. Modern sophisticated mo-
lecular diagnostic tests allow providers to identify the
1 In accordance with Sup. Ct. R. 37, the Amici state that
this brief was not authored in whole or in part by counsel to a
party, and that no monetary contribution to the preparation or
submission of this brief was made by any person or entity other
than these Amici Curiae or their counsel.
2
30% of patients who have breast cancer tumors that
over-express human epidermal growth factor receptor
2 (HER2). These patients can be treated with
trastuzumab, an antibody that is more effective and
less toxic than traditional chemotherapy or radiation
therapy.
Monogram Biosciences, Inc. and Genomic Health,
Inc. are publically traded companies recognized as
world leaders in the emerging field of personalized
medicine. Monogram Biosciences currently offers the
HERmark® breast cancer diagnostic assay that accu-
rately quantifies HER2. HERmark® identifies pa-
tients likely to respond to trastuzumab with greater
precision than currently available tests. In addition,
Monogram offers five distinct HIV drug resistance
assays used to individualize the selection of antivirals
for HIV treatment. Monogram’s HIV assays provide a
direct measure of the patient’s virus’ ability to survive
in the presence of specific antiviral drugs and are
often the primary tests relied on by physicians to
determine which HIV drugs will be effective in a
specific patient.
Genomic Health currently offers the Oncotype
DX® assay that provides information on the
likelihood that a breast cancer patient will experience
(1) a recurrence of a tumor; and (2) a clinically
beneficial response to chemotherapy. In addition,
Genomic Health has completed validation of a colon
cancer prognostic assay which it expects to offer com-
mercially in 2010.
3
Essential
to
Amici is their ability to obtain
meaningful proprietary protection for their key
discoveries: diagnostic correlations. Amici expend
tremendous resources in obtaining tumor samples,
assaying the samples to discover correlations and
searching through and analyzing the results for
meaningful statistical significance that could identify
those correlations. There are literally hundreds of
unsuccessful attempts made for each identified
correlation.
Amici have an interest in ensuring that patent
claims to the discovered diagnostic correlations
remain patentable. Amici would have difficulty
in continuing with their mission of developing prod-
ucts for patients in the absence of meaningful patent
protection. The application of the machine-or-
transformation test as adopted by the Federal Circuit
to the diagnostic correlations forecloses the ability of
Amici to obtain commercially meaningful protection
for its discovery and products, and threatens the
future of the entire field of personalized medicine.
Patients can only suffer.
Amici will focus on the first question presented
as it relates to correlation claims often sought by
personalized medicine companies.
----------------- ♦ -----------------
SUMMARY OF ARGUMENT
The patent system creates incentives for research
into discovering correlations between biomarkers and
4
diseases to improve diagnostic tests thereby creating
a virtuous cycle progressing science to the benefit of
patients and society. The Federal Circuit’s require-
ment that all claims recite a “physical” step, such as a
machine or physical transformation step, jeopardizes
the future of research in personalized medicine
by making many biologically-based inventions un-
patentable under 35 U.S.C. § 101. In the end, fewer
personalized medicine avenues will be explored and
brought to market, and patients will suffer.
The Federal Circuit erred in holding that a
process must be tied to a particular machine or
apparatus or transform a particular article into a
different state or thing to be eligible for patent
protection under 35 U.S.C. § 101. The machine-or-
transformation test may work in a few cases for
determining whether a particular claim is patent-
eligible, but it results in “false negatives” for the
majority of cases. Specifically, it has been applied to
find some claims, such as those on the actual
diagnostic correlations, to be patent-ineligible. Amici
urge the Court to adopt a framework for patent-
eligible subject matter that accords with the existing
law, a framework that determines that non-physical
processes are patent-eligible, a framework that will
foster development of personalized medicine tech-
nologies.
Consistent with this Court’s precedent, Amici
propose that the Court articulate a framework that
considers as a threshold step whether a fundamental
principle (i.e., a law of nature, a phenomenon of
5
nature or an abstract idea) is claimed. For application
of the framework, the terms law of nature, natural
phenomenon and abstract idea should be construed in
the ordinary English sense each as a universal
principle having a central role in scientific practice
and each as being fundamental. If a law of nature,
natural phenomenon or abstract idea is not claimed,
the claimed subject matter describes a patent-eligible
process. If one of these is claimed, the Court should
turn its attention to secondary considerations such
as whether the patent claim entirely preempts
the law of nature, natural phenomenon or abstract
idea. Such a determination can take into account
whether the claimed method involves a machine-or-
transformation step, but not as the sole deter-
minative test for patentability. Amici believe that
once the Court sets forth a definitive test, the Court
will determine that claim 1 in Bilski’s application is
patent-eligible because it does not claim a law of
nature, natural phenomenon or abstract idea. Simi-
larly, the claims important to personalized medicine
companies, claims to the discovered correlations, will
be patent-eligible since they also do not involve laws
of nature, natural phenomena or abstract ideas.
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6
ARGUMENT
I. PATENTABLE PROCESSES CAN BE
EITHER PHYSICAL OR NON-PHYSICAL
35 U.S.C. § 101 provides the basis for patent-
eligibility:
Whoever invents or discovers any new and
useful process, machine, manufacture, or
composition of matter, or any new and useful
improvement thereof, may obtain a patent
therefore, subject to the conditions and
requirements of this title.
The statute states that there are four separate and
distinct categories of patentable subject matter,
namely: 1) processes, 2) machines, 3) manufactures or
4) compositions of matter. In addition, 35 U.S.C.
§ 100(b) provides a broad statutory definition for a
process to be used in 35 U.S.C. § 101:
The term “process” means process, art, or
method, and includes a new use of a known
process, machine, manufacture, composition
of matter, or material.2
According to the Oxford English Dictionary, a
“process” can be defined as:
2 The statutory provision on what constitutes patentable
subject matter has essentially been the same since 1793. Until
the Patent Act of 1952, the patent statutes used the word “art.”
The 1952 Act substituted the word “process.” To emphasize that
no change of meaning was intended, a process was defined as
“ . . . any process, art or method . . . ” 35 U.S.C. § 100(b).
7
A continuous and regular action or suc-
cession of actions, taking place or carried on
in a definite manner, and leading to the
accomplishment of some result; a continuous
operation or series of operations (The Oxford
English Dictionary 6 (2d ed. 1989)).
The term “process” thus does not have a special
meaning that would exclude non-physical processes
from patent eligibility under 35 U.S.C. § 101.
Nor is there any basis for concluding that the
Constitution imposes a requirement that non-
physical processes be excluded. According to this
Court, Congress has the authority to include non-
physical subject matter within the scope of patent-
eligible subject matter.3 In the encompassing
language as it used in § 101, Congress chose not to
limit patentable subject matter to only physical
subject matter; the only limitations are that the
subject matter be “new and useful.”4
3 See e.g., Gottschalk v. Benson, 409 U.S. 63, 72 (1972),
where the Court stated, “It may be that the patent laws should
be extended to cover these programs, a policy matter to which
we are not competent to speak.” See also, 35 U.S.C. § 273 and
145 Cong. Rec. H11769, at 11801 (daily ed. Nov. 9, 1999) (“Jt.
Conf. Report”), where, in discussing Title 35, Congress expressed
the intent that the patent laws may be drawn to physical as well
as non-physical limitations.
4 Other Amici extensively treat what it means for a process
to be “useful.” Accordingly, this brief will not repeat such
detailed analysis.
8
This Court has consistently and explicitly
refused to limit a process to the purely
physical. In Gottschalk v. Benson, 409 U.S.
63, 71 (1972), even as the Court was denying
the patentability of a method of converting
binary signals from one form to another,
citing Waxham v. Smith et al., 294 U.S. 20
(1935), the Court could not have more clearly
stated that a process need not have a
machine-or-transformation, a physical step,
to be patentable: It is argued that a process
patent must either be tied to a particular
machine or apparatus or must operate to
change articles or materials to a different
state or thing. We do not hold that no process
patent could ever qualify if it did not meet
the requirements of our prior precedents.
Gottschalk, 409 U.S. at 71. In Parker v. Flook, 437
U.S. 548, 589 n.9 (1978), the Court repeated and
strengthened this rationale:
The statutory definition of process is broad.
An argument can be made, however, that
this Court has only recognized a process as
within the statutory definition when it either
was tied to a particular apparatus or
operated to change materials to a “different
state or thing.” See Cochrane v. Deener, 94
U.S. 780, 787-788 (1876). As in Benson, we
assume that a valid process patent may issue
even if it does not meet one of these qual-
ifications of our earlier precedents. (internal
citations omitted)
9
Accordingly, the Court has consistently made it clear
that the process category of 35 U.S.C. § 101 should be
interpreted broadly to include all subject matter,
physical and non-physical.5 Other than the proscribed
categories of laws of nature, phenomena of nature
and abstract ideas (see, e.g., Gottschalk v. Benson, 409
U.S. 63 (1972); Parker v. Flook, 437 U.S. 584 (1978)
and Diamond v. Diehr, 450 U.S. 175 (1981)) all proc-
esses, both physical and non-physical, are patent-
eligible.
Amici would urge this Court to hold that
processes include all subject matter, physical and
non-physical.
5 Congress has also expressed its intent that a process
should include the physical as well as the non-physical. See, e.g.,
Jt. Conf. Report at 11801, where they indicate that they believe
that a process is not limited to the physical but should also
include the non-physical.
10
II. THE FEDERAL CIRCUIT ERRED IN
HOLDING THAT A PROCESS MUST BE
TIED TO A PARTICULAR MACHINE OR
TRANSFORM A PARTICULAR ARTICLE
INTO A DIFFERENT STATE OR THING
A. The Federal Circuit Erred In Holding
That A “Process” Must Be Tied To A
Particular Machine Or Apparatus, Or
Transform A Particular Article Into A
Different State Or Thing (“Machine-
Or-Transformation” Test), To Be Eligi-
ble For Patenting Under 35 U.S.C. § 101
Despite admonitions from the Supreme Court, in
Bilski, the Federal Circuit adopted the physical limi-
tation requirement of the machine-or-transformation
test as the sole test, effectively denying patentability
to much patent-eligible subject matter. Though the
Federal Circuit adamantly denied that the machine-
or-transformation step required a physical step,6 the
test it ultimately adopted clearly does require a
physical step. In articulating the ‘transformation’
prong of the machine-or-transformation test, the
Federal Circuit stated:
Purported transformations or manipulations
simply of public or private legal obligations
or relationships, business risks, or other
such abstractions cannot meet the test
6 In re Bilski, 545 F.3d 945, 963 (2008), see id., at 964,
where the Federal Circuit explicitly stated that it was rejecting
any notion of a physical steps test.
11
because they are not physical objects or
substances, and they are not representative
of physical objects or substances.7 (emphasis
added)
Thus, the Federal Circuit adopts a physical test at
the same time that it asserts that it is not adopting a
physical test.
Patent-eligible subject matter has been
traditionally limited only by whether the subject
matter is directed to a law of nature, a phenomenon
of nature or an abstract idea. Other than these
traditional categories of patent-ineligible subject
matter, the courts have been consistent in holding
that process steps are patentable despite the fact that
they lack a physical limitation, such as a machine-or-
transformation step.8 Indeed, attempting to distin-
guish between physical and non-physical steps will
lead to a futile effort in metaphysics and invite
practitioners to ‘game’ the system.9 Thus, the Federal
7 In re Bilski, 545 F.3d at 963.
8 See, e.g., Gottschalk v. Benson, 409 U.S. 63 (1972); Parker
v. Flook, 437 U.S. 584 (1978) and Diamond v. Diehr, 450 U.S.
175 (1981).
9 See, e.g., Arrhythmia Research Technology, Inc. v.
Corazonix Corp., 958 F.2d 1053 (Fed. Cir. 1992), where the
Federal Circuit found that the terms “determining” and “com-
paring” were physical process steps and that electrical signals
were inherently physical and In re Nuijten, 500 F.3d 1346 (Fed.
Cir. 2007), where the Federal Circuit determined that electrical
signals, while physical, were too transitory to fall within one of
the statutory categories for patentable subject matter. It is
unclear why the “transitory” nature of a signal is problematic,
(Continued on following page)
12
Circuit erred in holding that a process must be tied to
a particular machine or apparatus, or transform a
particular article into a different state or thing.
B. The Machine-Or-Transformation Test
Does Not Properly Distinguish Be-
tween Patent-Eligible And Patent-
Ineligible Subject Matter
There is quite a bit of patentable ground between
a process that is not limited by a physical step, such
as a machine-or-transformation step, and a process
that is. The machine-or-transformation test, by
requiring a physical limitation in the claims,
classifies all physical processes as patent-eligible
subject matter but misses much non-physical patent-
eligible subject matter that is acceptable under this
Court’s precedent. Namely, the test fails to identify
non-physical subject matter which is not a law of
nature, natural phenomenon or an abstract idea. As
an example, as Amici will discuss in section III(B)
below, claim 13 of U.S. Patent No. 4,940,658 (“ ’658”)
since many physical phenomena, such as chemical processes, are
equally transitory, but unquestionably patentable. See also State
Street Bank & Trust Co. v. Signature Financial Group, Inc., 149
F.3d 1368 (Fed. Cir. 1998), where the transitory nature of the
calculated net asset value was not a bar to patent eligibility. As
far as “gaming” the system, a clever patent practitioner will be
able to say the so-called “magic words” so that a claimed inven-
tion is drawn to some sort of a machine or has a physical trans-
formation step. See Julie E. Cohen and Mark A. Lemley, Patent
Scope and Innovation in the Software Industry, 89 Cal. L. Rev. 1
(2001).
13
patent claims non-physical subject matter which is
not a law of nature, natural phenomenon or an
abstract idea.
Thus, the machine-or-transformation test does
not adequately distinguish between patent-eligible
and patent-ineligible subject matter.
C. The Machine-Or-Transformation Test Is
Inconsistent With 35 U.S.C. § 101 And
This Court’s Long-Standing Precedent
The Federal Circuit erred in In re Bilski by creat-
ing a new and amorphous “machine-or-transformation”
test that is inconsistent with 35 U.S.C. § 101 and
long-standing Supreme Court precedent. As noted in
the dissenting opinions in Bilski, the majority’s novel
test raises more questions than it answers, and
indeed creates significant confusion. The Federal
Circuit’s interpretation of 35 U.S.C. § 101 uprooted
years of case law, which should only be done for the
most compelling reasons. “Considerations of stare
decisis have special force in the area of statutory
interpretation, for here, unlike in the context of
constitutional interpretation, the legislative power is
implicated, and Congress remains free to alter what
[the courts] have done.” Shepard v. United States,
544 U.S. 13, 23 (2005). “Where, as here, Congress has
not acted to modify the statute in the many years
since Diehr and the decisions of [the Federal Circuit],
the force of stare decisis is even stronger.” In re Bilski,
545 F.3d at 993 (Newman, J., dissenting) (citing
Shepard, 544 U.S. at 23). The Federal Circuit’s
14
majority decision in Bilski is based on a misguided
and novel reading of selected Supreme Court
quotations; it disrupts both settled precedent and
long-standing expectations concerning intellectual
property rights, and is bad public policy.
Recent Supreme Court precedent calls for judicial
flexibility in carrying out the Constitutional and
statutory mandates of the patent system. Indeed, the
Supreme Court recently rejected rigid Federal Circuit
precedent in KSR Int’l Co. v. Teleflex, Inc., 550 U.S.
398 (2007), when it overruled the “teaching, sug-
gestion, or motivation,” or TSM, test for analyzing
obviousness under 35 U.S.C. § 103. While recognizing
that the TSM test was developed to “resolve the
question of obviousness with more uniformity and
consistency,” the Supreme Court summarily rejected
the overly-rigid rule as “contrary to §103 and [its]
precedents.” Id. at 407. Unfortunately, the machine-
or-transformation test similarly seeks to achieve
consistency and predictability by supplanting the
broad and flexible Supreme Court precedent
governing patentability under § 101 (see Diehr, 450
U.S. at 185; Diamond v. Chakrabarty, 447 U.S. 303,
309 (1980); and Benson, 409 U.S. at 93), with a
narrow and rigid test. As KSR demonstrates, such an
effort to achieve predictability, even if well-intended,
is not reason enough to disregard controlling
precedent.
15
III. A PROPOSED FRAMEWORK FOR IDEN-
TIFYING PATENT-ELIGIBLE SUBJECT
MATTER
A. This Court Should Determine Whether
A Law Of Nature, Natural Phenom-
enon Or Abstract Idea Is Claimed And
Construe Those Terms In The Ordi-
nary English Sense
Amici propose a framework that considers as a
threshold step whether a fundamental principle (i.e.,
a law of nature, a phenomenon of nature or an
abstract idea) is claimed. If not, the claimed subject
matter describes a patent-eligible process. If a
fundamental principle is claimed, the patent claim
should be analyzed to determine if it entirely
preempts the fundamental principle. Such a deter-
mination can take into account whether the claimed
method involves a machine-or-transformation step,
but not as the sole determinative test for pat-
entability. For application of the test, the terms law of
nature, natural phenomenon and abstract idea should
be construed in the ordinary English sense as
universal having a central role in scientific practice
and as being fundamental.
As a threshold for the determination of whether
patent-eligible subject matter is present, Amici
propose an investigation of the ordinary English
meaning of the words law of nature, natural
16
phenomenon and abstract idea.10 Amici would propose
that the Court adopt a workable definition for each of
those terms which could be rationally applied by
practitioners.11 Consistent with the Court’s trend
towards reading words in an ordinary English way,12
10 Courts have never determined what exactly is included
within the terms “law of nature, natural phenomenon and
abstract idea” by construing the boundaries of those terms to
determine whether they do, in fact, have one of these
fundamental principles before them (see, e.g., Funk Brothers
Seed Co. v. Kalo Inoculant Co., 333 U.S. 127, 130 (1948)
(determining that bacterial qualities of non-inhibition were
phenomena of nature); Flook, 437 U.S. at 595 (determining that
a method of calculating is drawn to non-statutory subject
matter); Gottschalk, 409 U.S. at 68 (holding that a method of
binary conversion was so abstract as to not be patentable);
Diehr, 450 U.S. at 191 (holding that a claim to a process for
curing rubber which employed a mathematical equation did not
only entail an abstract mathematical formula and thus was
drawn to patentable subject matter). Amici believe that such an
approach, a sort of “ . . . know it when I see it . . . ” approach (see
Justice Potter Stewart’s statement in his concurrence in
Jacobellis v. Ohio, 378 U.S. 184 (1964) for example) has led to
much confusion. Amici do note that some justices of the
Supreme Court have cautioned against trying to define such
concepts as a law of nature, natural phenomenon or abstract
idea (see, e.g., Funk Brothers Seed Co., 333 U.S. at 133
(Frankfurter, J., concurring). But, we believe that a rational,
perhaps flexible, definition would be the best way to make the
process and analysis more meaningful.
11 Amici realize that the Courts have also been disposed to
consider thinking as patent ineligible. Amici believe the Court
should also adopt a position that claim language should be
construed, when possible, to avoid implicating the process of
thinking. The proposal is set forth below.
12 See, e.g., Perrin v. United States, 444 U.S. 37, 42 (1979).
17
Amici propose that each of the terms “law of nature,
natural phenomenon and abstract idea” should
incorporate the following elements:
1. That they are universal as defined in
terms of ordinary English and thus have
a central role in scientific practice; and
2. That they are fundamental, as defined
in terms of ordinary English.
For the terms “universal” and “fundamental,” Amici
would propose that the Court adopt the following
definitions:
A. Universal:
Something which is an absolute or general
concept regarded either as forming or having
an absolute, mental or nominal existence; a
universal proposition; a general term, notion
or idea. (The Oxford English Dictionary (2d
ed. 1989))
B. Fundamental:
Something which is a leading or primary
principle, rule, law, or article which serves as
the groundwork of a system; an essential
part. (The Oxford English Dictionary (2d ed.
1989))
18
For the terms “law of nature”, “phenomenon”, and
“abstract”, we would propose the following defini-
tions:
C. Law of Nature:
In the sciences of observation, a theoretical
principle deduced from particular facts,
applicable to a defined group or class of
phenomena, and expressible by the state-
ment that a particular phenomenon always
occurs if certain conditions are present. (The
Oxford English Dictionary (2d ed. 1989))
D. Phenomenon:
In scientific and general use, a thing that
appears, or is perceived or observed; an
individual fact, occurrence, or change as
perceived by any of the senses, or by the
mind; applied chiefly to fact or occurrence,
the cause or explanation of which is in
question. (The Oxford English Dictionary (2d
ed. 1989))
E. Abstract:
Refers to something that is withdrawn or
separated from material embodiment, from
practice, or from particular examples. Thus,
an abstract idea is an idea that is withdrawn
or separated from material embodiment,
from practice, or from particular examples.
(The Oxford English Dictionary (2d ed.
1989))
19
Accordingly, consistent with this Court’s precedent,13
Amici would propose that the terms “law of nature,”
“natural phenomenon” and “abstract idea” should be
defined as follows:
A. Law of Nature
A law of nature is, in the sciences of
observation, a theoretical principle deduced
from particular facts, applicable to a defined
group or class of phenomena, and expressible
by the statement that a particular phenom-
ena always occurs if certain conditions are
present. A law of nature has an absolute or
general concept regarded either as forming
or having an absolute, mental or nominal
existence; a universal proposition; a general
term, notion or idea. A law of nature is also a
leading or primary principle, rule, law or
article which serves as the groundwork of a
system, an essential part.
B. Phenomenon
of
Nature
A phenomenon of nature appears, or is
perceived or observed; an individual fact,
13 See, e.g., Gottschalk v. Benson, 409 U.S. 63 (1972); Parker
v. Flook, 437 U.S. 584 (1978); and Diamond v. Diehr, 450 U.S.
175 (1981), where this Court has consistently justified the
exclusion of patent-ineligible categories on the supposition that
they were fundamental principles, those containing a funda-
mental truth, an original cause, a motive, the basic tools of
scientific research, part of the storehouse of knowledge available
to all. Thus any set of working definitions should include these
ideas.
20
occurrence, or change as perceived by any of
the senses, or by the mind; applied chiefly to
fact or occurrence. A phenomenon of nature
has an absolute or general concept regarded
either as forming or having an absolute or
nominal existence; a universal proposition. A
phenomenon of nature is also a leading or
primary principle which serves as the
groundwork of a system, an essential part.
C. Abstract
Idea
An abstract idea is an idea that is withdrawn
or separated from material embodiment,
from practice, or from particular examples.
An abstract idea has an absolute or general
concept regarded either as forming or having
an absolute, mental or nominal existence; a
universal proposition; a general term, notion
or idea. An abstract idea is also a leading or
primary principle which serves as the
groundwork of a system, an essential part.
To determine whether claimed subject matter is
patent eligible, Amici propose this test with defini-
tions in mind:
1. As a threshold step, determine whether
a fundamental principle (i.e., a law of
nature, a phenomenon of nature or an
abstract idea) is claimed. If not, the
claimed subject matter describes a
patent-eligible process.
2. If a fundamental principle is claimed,
determine whether the patent claim
21
entirely preempts the fundamental
principle. The determination may take
into account whether the claimed
method involves a machine-or-trans-
formation step. If the claim does not
entirely preempt the fundamental prin-
ciple, then it claims patent-eligible
subject matter; if the claim does entirely
preempt the fundamental principle, then
it does not claim patent-eligible subject
matter.
With this test and these definitions in mind, Amici
now turn to a representative diagnostic claim, claim
13 of U.S. Patent No. 4,940,658.
B. Diagnostic Claims Drawn To Methods
Of Predicting Response In A Patient
Are Patent-Eligible Because They Do
Not Describe A Fundamental Principle
Amici will focus on how the machine-or-
transformation test could affect personalized
medicine companies, and claim 13 of U.S. Patent No.
4,940,658, the claim that was the subject matter of
Laboratory Corp. of Am. Holdings v. Metabolite Labs.
Inc., 548 U.S. 124 (2006), provides an excellent
vehicle to exemplify application of the proposed
framework.14 The claim is directed to a non-physical
14 Claim 13 recites: “A method for detecting a deficiency of
cobalamin or folate in warm-blooded animals comprising the
steps of: assaying a body fluid for an elevated level of total
(Continued on following page)
22
process, but non-physical processes are patentable, as
well.15
So, as a first step, the Court should consider
whether the process of correlating is drawn to a law
of nature, a natural phenomenon or abstract idea, as
Amici have defined these terms. Under the proposed
test, the ordinary English meaning of the words
“natural phenomenon” requires that the claimed
assay be universal and have a central role in
scientific practice. The scientific correlation of
homocysteine levels with a deficiency of cobalamin
describes a very narrow biological correlation, cer-
tainly not something universal and central to
scientific practice.16 In the human body, many
biological components, genes, proteins, tissues and
even entire organs, work together through very
complicated processes. Although the processes are
connected, they are very different, and, indeed, a
homocysteine; and correlating an elevated level of total
homocysteine in said body fluid with a deficiency of cobalimin or
folate.”
15 One could argue that the “assaying” step, among others,
does indeed require some sort of a physical step and requires a
machine, as a result. Amicus have chosen to focus on the issue
at hand, namely the “correlating” aspect of claim 13, and assume
that the step does not require an assay step.
16 Were one to analogize claim 13 to the Benson and Flook
claims, the difference would be that the claims in Benson and
Flook were, according to the Court, to the algorithm, per se.
Claim 13, on the other hand, is drawn to a very narrow
biological correlation. In any case, Amici would urge the Court
to use extreme caution in completely analogizing biological
claims to algorithm claims.
23
single disease or disorder can often be associated with
many different biomarkers in many different bio-
logical pathways. With so many different possible
markers, even for the same disease, a patent
monopoly on any one marker would not preclude
scientists from discovering other pathways.
Indeed, the patent monopoly provided by claim
13 (or any claimed biological correlation) would not
stifle innovation but would rather motivate others to
seek out similar correlations, perhaps even in related
biological pathways. Thus, claim 13 would not block
the basic tools of research but would foster research.
Similarly, in the specification of the ’658 patent, the
diagnostic process is explained in great detail,
including how the claimed correlation would be
applied to specific testing subjects, each of these
details show that the correlation is not universal and
central to the scientific process.
Under the proposed test, the ordinary English
meaning of the words “natural phenomenon” require
that the claimed assay additionally be fundamental,
thus a leading or primary principle, rule, law or
article which serves as the groundwork of a system,
i.e. an essential part. The correlation exists in some
human beings, perhaps as a product of evolution, and
as such, it could have been different. And, if it could
have been different, as evolution could have taken a
different path, it does not describe a leading or
primary principle, just an artifact of evolution. This is
key: the fact that it could have been different
demonstrates that it is not the groundwork for a
24
system or an essential part. As a result, claim 13, as a
correlation is not a fundamental principle and thus
does describe patent-eligible subject matter.17
In contrast, examples such as E=mc2, Newton’s
law of gravity, and phenomena of nature such as
water freezing or the aurora borealis would certainly
constitute laws of nature and natural phenomena in
the ordinary English meaning of the word. They each
describe an absolute or general concept regarded as
forming or having an absolute existence, and they are
each universal and central to scientific practice. Each
of these phenomena, and the principles behind them,
could also be considered as the groundwork of a
system, essential and fundamental, in other words.
Each of these principles, unlike claim 13 in Lab.
Corp. of Am. Holdings, very clearly fall into the
category of a fundamental principle and would be the
sort of patent-ineligible subject matter that would
constitute the basic tools of research, the common
knowledge of all.
17 Amici believe this argument can be extended to the
subject matter of all diagnostic claims. As examples, please see
the claims in U.S. Patent No. 6,680,302 drawn to methods of
optimizing therapeutic efficiency, the subject of Prometheus
Labs. v. Mayo Collaborative Servs., 2008 U.S. Dist. LEXIS 25062
(S.D. Cal. Mar. 28, 2008), as well as the claims in U.S. Patent
No. 5,723,283, claims drawn to a method of determining
whether an immunization schedule affects the incidence or
severity of a chronic immune-mediated disorder, the subject
matter of Classen Immunotherapies, Inc. v. Biogen IDEC, 381
F. Supp. 2d 452 (D. Md. 2005), aff ’ d, 2008 U.S. App. LEXIS
25661 (Fed. Cir. Dec. 19, 2008).
25
As an interesting point of contrast, since almost
anything and everything that is a result of nature
could be viewed as a natural phenomenon, this would
mean that the statutory proscriptions related to
patentability would apply to everything. Although
Justice Frankfurter was noting that an attempt to
define a law of nature would be futile, in Funk
Brothers Seed Co., 333 U.S. at 135, his concurring
opinion stated:
Everything that happens may be deemed
“the work of nature,” and any patentable
composite mixture exemplifies in its prop-
erties the “laws of nature.”
While Amici would agree with this statement on its
face, Amici would note that, since almost every
process is impacted by or based upon a law of nature,
arguments can be drawn for challenging any patent
based upon those grounds. The end result of this
reasoning is that nothing, or everything, is pat-
entable, and both results defy logic.
Amici urge the Court to adopt the two part test
setting forth the ordinary English definitions set
forth above. As applied according to that test and
those definitions, claim 13 of the ’658 patent are not
drawn to fundamental principles and describe patent-
eligible subject matter.
26
IV. THE MACHINE-OR-TRANSFORMATION
TEST THREATENS TO STIFLE INNOVA-
TION IN PERSONALIZED MEDICINE
A. Personalized Medicine Is A Growing
Field With A Tremendous Potential To
Help Patients
Personalized medicine refers to the tailoring of
medical treatment to the individualized charac-
teristics of each patient. The technology allows
physicians to make treatment decisions based on
molecular markers that signal the presence or risk of
developing a disease, potential outcome and likeli-
hood that the patient will respond to particular
therapies. Diagnostic correlations used to identify the
most effective treatment options for an individual
patient are critical to personalized medicine.
The use of diagnostic correlations to select the
optimal therapy for an individual patient translates
to improved and more cost-efficient health care for
all. There are two important issues in selecting a
treatment: efficacy and risk of side effects. On
average, a commercial drug works for only 50% of the
target population.18 Further, every drug and biological
therapeutic has undesirable side effects, some of
which can be predicted based on a patient’s drug
metabolism signature. Published estimates show that
approximately 5.3% of hospital admissions are
18 B. Spear, et al., Clinical application of pharma-
cogenomics, Trends Mol. Med. 7(5):201-204 (2001).
27
associated with adverse drug reactions (ADRs).19
Products marketed by personalized medicine com-
panies empower physicians with the ability to treat
patients with drugs that target the disease while
minimizing undesirable side effects. Personalized
medicine products thus spare the patients from
suffering through ineffective treatment regimes,
increase the probability of positive outcome and
decrease the health care costs.
The Oncotype DX® breast cancer assay, product
of research conducted by Genomic Health, can predict
the likelihood that a patient with early-stage, ER+
breast cancer will experience a recurrence of breast
cancer within 10 years and whether that patient will
benefit from adding chemotherapy to his/her hor-
monal therapy. The test is based on mRNA levels of
21 genes, and provides a continuous Recurrence
Score® (RS) result for each patient that places them
in a low, intermediate or high risk category. A patient
with a low RS will not significantly benefit from
adding chemotherapy, and may be treated with
hormonal therapy alone. Considering that about 20%
of patients are in this category, this represents a
substantial savings (approximately $1930.00 per
patient) to the health care system and benefit to
those patients who are spared the unnecessary
disruption and toxic effects of chemotherapy. On the
19 C. Kongkaew, et al., Hospital admissions associated with
adverse drug reactions, Ann Pharmacother 42(7):1017-1025
(2008).
28
other hand, a high RS signals that chemotherapy
should be added to the patient’s regimen. Used in
concert with other clinical factors, the Oncotype DX®
assay can aid physicians and patients in making
personalized and cost-efficient treatment decisions.
The selection and validation of the 21 genes, from
potentially thousands of genes, to use in this test and
development of RS from the expression levels was the
culmination of thousands of hours of research by
highly trained scientists at Genomic Health. The
selection of 21 genes whose mRNA should be
monitored was not the discovery of some mere
principle of nature, rather it was the identification
that certain arbitrary genes happen to be associated
with the risk of cancer. HERmark® is a proprietary
diagnostic of Monogram Biosciences that accurately
quantifies HER2 total protein expression in patients
with breast cancer. Preliminary data from three
cohorts of Herceptin-treated patients with metastatic
breast cancer who were identified as “HER2 positive”
by conventional assays suggesting that HERmark®
can identify patients who are likely to respond to
trastuzumab with greater precision than currently
available tests. To date, thousands of hours of re-
search have been involved in developing HERmark®.
The success of genomics in breast cancer is being
repeated in other cancers, as well as in other fields.
For example, about 40% of patients with metastatic
colon cancer are unlikely to respond to two key
therapies: cetuximab and panitumumab, because
these patients have certain KRAS gene mutations.
29
Current practice guidelines recommend that only
patients with the normal KRAS gene sequence be
treated with chemotherapy, resulting in potential
savings of approximately $604 million annually if all
patients are first stratified using the KRAS molecular
diagnostic.20
A patient’s genetic profile now allows physicians
to determine whether a patient will respond to a
particular therapy, and whether the risk of disease
for that patient justifies the expense and burden of
particular therapy. This information has the potential
to increase patient adherence to treatment regimens,
decrease costs and failure rates of drug clinical trials
by focusing on appropriate sub-classifications of
patients. It is no wonder, then, that the FDA has
recognized and encouraged the development of per-
sonalized medicine pharmacogenic information, and
nearly every major pharmaceutical project is in-
corporating information on genetic variation and
effects on the safety and effectiveness of the
candidate drug.21 The importance of supporting
further development of this technology has also been
recognized by the President’s Council on Science and
Technology (2008 Report on Priorities for Personalized
20 National Comprehensive Cancer Network Guidelines in
Oncology, Colon Cancer, v.2.2009 (available online at http://www.
nccn.org/professionals/physician_gls/PDF/colon.pdf ).
21 See, e.g., Guidance for Industry on Pharmacogenomic
Data Submissions (2005); Drug-Diagnostic Co-Development
Concept Paper (2005); 21 § C.F.R. 201.57.
30
Medicine), HHS (Personalized Health Care Initia-
tive,), the Legislature (Genomics and Personalized
Medicine Act of 2006 (Obama, S. 3822)) and rules and
comments put forth by many other professional, state
and federal health care organizations. In her written
testimony during Senate confirmation hearings, HHS
Secretary Kathleen Sebelius made the following
statement:
As a result of these contributions to im-
provement in the quality of care, per-
sonalized medicine represents a key strategy
on healthcare reform. The potential appli-
cation of this new knowledge, especially
when supported through the use of health
information technology in the patient care
setting, presents the opportunity for trans-
formational change.22
In sum, personalized medicine offers a model for
efficient and high quality health care.
22 Katheen Sebelius, written testimony given during Senate
confirmation hearings, April 2, 2009.
31
B. Because The Machine-Or-Transformation
Test Endangers Funding For Personal-
ized Medicine Companies, It Will Under-
mine Personalized Medicine Companies,
Stifle Development And Ultimately Harm
Patients
In his dissent in Lab. Corp. of Am. Holdings,
Judge Rader warns us of the consequences of
endangering funding for personalized medicine. He
characterized claim 13 of the ’658 patent as patent-
eligible and lamented that denying patent protection
for such a claim will undermine and discourage
future research for personalized medicine companies.
According to Judge Rader:
.
.
. this Court inadvertently advises in-
vestors that they should divert their unpro-
tectable investments away from discovery of
“scientific relationships” within the body that
diagnose breast cancer or Lou Gehrig’s
disease . . .
Given the long and expensive research, development
and commercialization cycles and relatively limited
resources of most personalized medicine companies,
the patent system is essential to protect and foster
innovation that, in turn, attracts financial investors.
Denying valuable patent protection for personalized
medicine companies will surely advise investors that
they should divert their unprotectable investments
away from personalized medicine and, as a result,
slow the progress of science and harm the interests of
human patients.
32
A strict requirement that a process be tied to a
particular machine or transform an article could
exclude much of the technology that drives today’s
information and knowledge-based economy from
patent protection, and prospectively hinder innova-
tion in fields of biotechnology, health sciences and
personalized medicine. The biotechnology industry
touches upon many essential aspects of the U.S.
economy, including pharmaceutical therapies, medi-
cal diagnostics, agricultures and industrial processes.
The biotechnology industry has registered a fast
growth since the early 1990s. For instance, their
revenues increased from $8 billion in 1992 to $39.2
billion in 2003. The job market forecast of biological
technicians is expected to grow by 28.2 percent be-
tween 2004 and 2014, and that of biological scientists
is projected to grow by 17.0 percent. In the health
care sector, the biotechnology industry has more than
370 therapeutic products currently in clinical trials
being studied to treat more than 200 diseases.
Because diagnostic correlating claims would not be
patentable with a strictly machine-or-transformation
step, the application of Bilski’s test threatens to
undermine the development of personalized medicine,
stem the progress of science and adversely affect the
health and quality of life of patients.
Personalized medicine helps patients, and holds
tremendous potential for improving their lives by its
ability to more precisely identify potential diseases
before they arise and select treatment options that
are specific to the individual. The key to this
33
capability is the discovery not of some “scientific
truth” or “law of nature” or even “natural phenom-
ena.” Rather, it is the discovery, like many medical
discoveries before now, of certain relationships –
“correlations.” The discovery of the correlations
should be patentable subject matter in order to
encourage and justify investments in the fledgling
industry.
Patents are essential to ensure further research
and development in personalized medicine and to
encourage and protect investment. Patent claims
directed to diagnostic correlations are the key to
progressing these goals. Patents and the protection
provided by them foster innovation as way leads on to
way, one discovery leading on to another, and as other
personalized medicine companies find other ways to
help other patients. Perhaps we will be telling this
story ages and ages hence: that we helped small
personalized medicine companies improve ourselves.
And that has made all the difference.
----------------- ♦ -----------------
CONCLUSION
Requiring, as does the Federal Circuit in Bilski,
that all claims recite a “physical” step, such as a
machine or physical transformation step, jeopardizes
the future of research in personalized medicine by
making many biologically-based inventions unpat-
entable under § 101. There is no support for the
machine-or-transformation test or the idea that only
physical processes should be patentable, and Amici
34
urge the Court to hold that all processes are patent-
eligible. Amici urge the Court to adopt a rational
framework for determining patent-eligible subject
matter that accords with the existing law, one that
involves determining, as a threshold step, whether a
fundamental principle (i.e., a law of nature, a
phenomenon of nature, or an abstract idea) is
claimed. The test should be simple and elegant and
the terms law of nature, natural phenomena and
abstract idea should be construed in an ordinary
English sense as universal and having a central role
in scientific practice and also as being fundamental.
Once the Court sets forth the test, Amici believe the
Court will determine that claims to the discovered
diagnostic corrections are patent-eligible, such as
claim 13 from the ’658 patent.
Patents to diagnostic correlations are essential to
personalized medicine companies to attract the fund-
ing necessary to bring new diagnostics to market.
Without adequate patent protection, personalized
medicine companies will suffer, new research will dry
up and new treatments will not become available to
patients.
Respectfully submitted,
NARINDER S. BANAIT
Counsel of Record
FENWICK & WEST LLP
801 California Street
Mountain View, CA 94041
(650) 988-8500
Counsel for Amici Curiae
Document Outline
- 22255 Brownstone II cv 02
- 22255 Brownstone II in 05
- 22255 Brownstone II br 04