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 OF THE UNITED STATES PATENT AND 
TRADEMARK OFFICE, 
 Respondent. 
 
On Writ of Certiorari to the  
United States Court of Appeals 
for the Federal Circuit 
 
BRIEF OF AMICUS CURIAE  
AWAKENIP, LLC 
IN SUPPORT OF PETITIONERS 
JEFFREY R. KUESTER 
JOEL H. THORNTON 
THOMAS, KAYDEN, 
 Counsel 
of 
Record 
HORSTEMEYER & 
THE THORNTON FIRM 
RISLEY, L.L.P. 
P.O. Box 129 
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TABLE OF CONTENTS 
 
Page 
TABLE OF CONTENTS ........................................ i 
TABLE OF AUTHORITIES ................................ iii 
INTEREST OF AMICUS CURIAE ...................... 1 
SUMMARY OF ARGUMENT ...............................  3 
ARGUMENT ........................................................... 5 
I.  THE FEDERAL CIRCUIT HAS 
CREATED AN UNWORKABLE 
ABSTRACT IDEA TEST FOR 
DETERMINING PATENTABILITY 
THAT WILL UNDULY SUFFER LIKE 
THE VAGUE COPYRIGHT 
IDEA/EXPRESSION DICHOTOMY ......... 5 
II.  A BROAD, JUDICIALLY-MADE § 101 
TEST WILL PRECLUDE PATENTS 
AND STIFLE INNOVATION FOR 
NEW TECHNOLOGY IN THE 
UNPREDICTABLE FIELDS ................... 13 
A.  The Federal Circuit’s decision 
negatively affects 
biotechnologies, not simply 
business methods .......................... 13 
 
-i- 
 
 

TABLE OF CONTENTS 
(continued) 
Page 
B.  Sections 102, 103, and 112 of the 
Patent Act provide sufficient 
guidance for determining 
patentability in the 
unpredictable fields .......................  14 
III.  AMBIGUITY IN THE FEDERAL 
CIRCUIT’S NEW MACHINE-OR-
TRANSFORMATION TEST HAS 
ALREADY FOSTERED HARMFUL 
CONFUSION AND UNCERTAINTY 
IN THE CASE LAW AND USPTO 
APPEALS THAT HAVE FOLLOWED ... 18 
CONCLUSION ..................................................... 23 
 
 
-ii-  
 

TABLE OF AUTHORITIES 
 
CASES Page(s) 
Ariad Pharms., Inc. v. Eli Lilly & Co., 560 F.3d 
1366 (Fed. Cir. 2009) ............................... 16, 17 
Baker v. Seldon, 101 U.S. 99 (1879) ..................... 5 
Broderbund Software Inc. v. Unison World, Inc., 
648 F.Supp. 1127 (N.D. Cal. 1986) ................. 7 
Classen Immunotherapies, Inc. v. Biogen IDEC
304 Fed. Appx. 866 (Fed. Cir. 2008) . 13, 14, 17 
Classen Immunotherapies, Inc. v. Biogen IDEC
2006 WL 6161856 (N.D. Md. Aug. 16, 2006) 14 
Computer Assocs. Int’l v. Altai.,   
 
982 F.2d 693 (2d Cir. 1992) ..................... 7, 8, 9 
CyberSource Corp. v. Retail Decisions,  
 Inc., 620 F.Supp.2d 1068  
 
(N.D.Cal. 2009) ........................................ 20,  21 
Data East USA, Inc. v. Epyx, Inc., 862 F.2d 204 
(9th Cir. 1988).................................................. 9 
DealerTrack, Inc. v. Huber, 2009 WL 2020761 
(C.D.Cal. 2009) .............................................. 21 
Diamond v. Diehr, 450 U.S. 175 (1981) ....... 11, 22 
Ex parte Atkin, 2009 WL 247868 (B.P.A.I. Jan. 
30, 2009) ......................................................... 20 
Ex parte Barnes, 2009 WL 164074 (B.P.A.I. Jan 
22, 2009) ......................................................... 20 
Ex parte Competitive Techs., Inc., Appeal No. 
2009-005519 (B.P.A.I. July 30, 2009) ........... 16 
Ex parte Cornea-Hasegan, 89 U.S.P.Q.2d 1557 
(B.P.A.I. 2009) ............................................... 19 
Ex parte Gutta, 2009 WL 112393 (B.P.A.I. Jan. 
15, 2009) ................................................... 19, 20 
 
-iii- 
 
 

TABLE OF AUTHORITIES 
(continued) 
 
Gates Rubber v. Brando Chem., 9 F.3d 823  
 
(10th Cir. 1993).............................................. 10 
Gottschalk v. Benson, 409 U.S. 63 (1972) .......... 22 
Harper & Row Publishers, Inc. v. Nation 
Enterprises, 471 U.S. 539 (1985) ..................... 5 
In re Alappat, 33 F.3d 1526  
 
(Fed. Cir. 1994) ...................... 18, 19, 20, 21, 22 
In re Bilski, 545 F.3d 943  
 
(Fed. Cir. 2008) ............................ 18, 19, 20, 21 
In re Comiskey, 554 F.3d 967 (Fed. Cir. 2009) .. 19 
In re Comiskey, 89 U.S.P.Q.2d 1641 
 
 (Fed. Cir. 2009) ............................................. 19 
Lab. Corp. of Am. Holdings v. Metabolite Labs., 
Inc., 548 U.S. 124 (2006) ................... 11, 15, 16 
Mazer v. Stein, 347 U.S. 201 (1954) ..................... 5 
Nichols v. Universal Pictures Co.,  
 
45 F.2d 119 (2d Cir. 1930) ............. 6, 10. 11, 12 
Peter Pan Fabrics, Inc. v. Martin Weiner Corp.
274 F.2d 487 (2d Cir. 1960) ............................. 6 
Plains Cotton Co-op v. Goodpasture Computer 
Serv., Inc., 807 F.2d 1256 (5th Cir.) cert. 
denied, 484 U.S. 821 (1987) ............................ 7 
Warner-Jenkinson Co., Inc. v. Hilton Davis 
Chemical Co., 520 U.S. 17 (1997) ........... 10, 11 
Wavetronix LLC v. EIS Elec. Integrated Sys., 
2009 WL 2245213 (Fed. Cir. 2009) ............... 20 
Whelan Assocs., Inc. v. Jaslow Dental Lab., Inc.
797 F.2d 1222 (3d Cir. 1986) ........................... 6 
 
-iv- 

TABLE OF AUTHORITIES 
(continued) 
 
STATUTES 
17 U.S.C. § 101 ...................................................... 6 
17 U.S.C. § 102(b) ................................................. 5 
35 U.S.C. § 101 .................................. 14, 15, 16, 23 
35 U.S.C. § 102 ........................................ 12, 14, 16  
35 U.S.C. § 103 ........................................ 12, 15, 16  
35 U.S.C. § 112 ........................................ 13, 15, 16 
 
OTHER AUTHORITIES 
Federal Trade Commission hearings, The 
Evolving IP Marketplace the Operation of IP 
Markets, 6 Monday, May 4, 2009 ................. 17 
H.R.Rep. No. 1476, 94th Cong., 2d Sess. 54, 
reprinted in 1976 U.S.C.C.A.N. 5659 ............. 6 
Pub.L. No. 96-517, § 10(a), 94 Stat. 3028 (1980) . 6 
Steven R. Englund, Note, Idea, Process, or 
Protected Expression?: Determining the Scope 
of Copyright Protection of the Structure of 
Computer Programs, 88 MICH. L. REV. 866, 
867-73 (1990) ................................................... 7 
 
 
-v- 



INTEREST OF AMICUS CURIAE 
 
Pursuant to Supreme Court Rule 37, AwakenIP, 
LLC (hereinafter "AwakenIP") submits this brief as 
amicus curiae in support of Petitioners Bernard L. 
Bilski,  et al.1  All parties have consented to the 
filing of amicus curiae briefs with this Court. 
AwakenIP provides intellectual property 
consulting services that help maximize the value of 
intellectual assets.  Furthermore, through its new 
blog website at AwakenIP.com, it attempts to 
reignite broader recognition of the full value of 
intellectual property.  Much criticism has been 
levied against the usefulness of intellectual property 
and its place in our new economy, but there are 
those among us who continue to recognize the 
wisdom of maintaining strong intellectual property 
protection for worthwhile contributions that 
“promote the progress of science and useful arts.” 
While there has always been a need to 
distinguish and properly limit the scope of protection 
for worthwhile contributions, the pendulum of 
protection has been swinging in the direction of 
weaker protection for a number of years.  It is time 
for the pendulum to begin swinging in the other 
direction, or the value of innovation and creativity 
will eventually disappear.  It is time for intellectual 
                                                 
1 Pursuant to Supreme Court Rule 37.6, counsel for amicus 
curiae  certifies that no counsel of either party authored the 
brief in whole or in part and that no person or entity other than 
the named amicus curiae or its counsel has made a monetary 
contribution to the preparation or submission of this brief. 
 


property and those who recognize our vital need for 
it to wake up. 
AwakenIP is very interested in the outcome of 
the case before the Court and is concerned that the 
Court of Appeals for the Federal Circuit obfuscated 
Congressional intent by rigidly construing § 101 of 
the Patent Act and imposing ambiguous and 
arbitrary requirements on patent seekers. 
 
 
 
 
 


SUMMARY OF ARGUMENT 
 
 
1.  The Federal Circuit’s decision held that a 
process that is not tied to a particular 
machine or fails to transform a particular 
article is not patentable.  This test requires 
courts and examiners at the United States 
Patent and Trademark Office (USPTO) to 
distinguish abstract ideas from processes that 
satisfy the machine-or-transformation test.  
This task of distinguishing abstract ideas from 
protectable subject matter suffers from the 
same vagaries that plague the copyright 
idea/expression dichotomy.  The Federal 
Circuit’s decision threatens to transform 
patentable subject matter analysis from a 
once bright-line rule to a complicated and 
unworkable analysis that currently haunts 
copyright law. 
 2.  The Federal Circuit’s machine-or-
transformation test resonates negative 
implications across fields beyond business 
methods.  For instance, courts have 
experienced difficulty in applying the rigid 
test to unpredictable fields such as 
biotechnology.  Moreover, existing 
patentability guidelines proscribed by sections 
102, 103, and 112 of the Patent Act provide 
clear and adequate direction for determining 
patentability in the unpredictable fields.  In 
fact, courts have recognized the importance of 
sections 102, 103, and 112 in evaluating 
 


patent applications in the unpredictable 
fields. 
 
 
3.  The Federal Circuit’s machine-or-
transformation test has created superfluous 
confusion among lower courts and the 
USPTO.  Consequently, the Federal Circuit 
has disrupted long-settled court precedent.  As 
such, this Court should resolve the pending 
action in favor of Petitioners. 
  
 


ARGUMENT 
 
I.  THE FEDERAL CIRCUIT HAS CREATED 
AN UNWORKABLE ABSTRACT IDEA 
TEST FOR DETERMINING 
PATENTABILITY THAT WILL UNDULY 
SUFFER LIKE THE VAGUE COPYRIGHT 
IDEA/EXPRESSION DICHOTOMY  
 
  The machine-or-transformation test is forcing 
the well-defined concepts of patentable subject 
matter toward the complex abstract idea analysis 
that has frustrated copyright attorneys for decades.  
Specifically, following the Federal Circuit’s decision, 
the task of relegating protected elements and 
abstract elements in computer program patent 
infringement claims will soon mirror the baffling 
and multifarious procedures of computer program 
copyright analysis. 
It is a fundamental principle of copyright law 
that copyright protection does not extend to an idea, 
only to the expression of the idea.  See  17 U.S.C. § 
102(b);  Mazer v. Stein, 347 U.S. 201, 217 (1954); 
Baker v. Seldon, 101 U.S. 99 (1879).  In recent years 
the limitation on ideas has developed into the 
“idea/expression dichotomy.”  As this Court stated in 
Harper & Row Publishers, Inc. v. Nation Enterprises
quoting the Second Circuit’s analysis, 
“idea/expression dichotomy strike[s] a definitional 
balance between the First Amendment and the 
Copyright Act by permitting free communication of 
facts while still protecting an author's expression.” 
471 U.S. 539, 556 (1985). 
 


Computer programs are regulated under the 
same laws, and no special exceptions exist. 
 
 
Legislative history specifically states that copyright 
laws protect computer programs only “to the extent 
that they incorporate authorship in programmer’s 
expression of original ideas, as distinguished from 
the ideas themselves.”  See H.R.Rep. No. 1476, 94th 
Cong., 2d Sess. 54, reprinted in 1976 U.S.C.C.A.N. 
5659, 5670.  Confirming this principle, a definition of 
the term “computer program” was added to 17 U.S.C. 
§ 101 as an amendment to the 1976 Copyright Act.  
See Pub.L. No. 96-517, § 10(a), 94 Stat. 3028 (1980). 
Through years of analyzing the idea/expression 
dichotomy, the courts have struggled with 
attempting to define what is protected under 
copyright law and what is simply an abstract idea 
regarding computer programs.  Judge Learned Hand 
noted that “[n]obody has ever been able to fix that 
boundary, and nobody ever can.” Nichols v. 
Universal Pictures Co., 45 F.2d 119, 121 (2d Cir. 
1930).  Thirty years later Judge Hand concluded 
“[o]bviously, no principle can be stated as to when an 
imitator has gone beyond copying the ‘idea,’ and has 
borrowed its ‘expression.’”  Peter Pan Fabrics, Inc. v. 
Martin Weiner Corp., 274 F.2d 487, 489 (2d Cir. 
1960).  Instead, no bright line test exists and 
“[d]ecisions must therefore inevitably be ad hoc.”  Id.  
 In 1986, the Third Circuit in Whelan Associates, 
Inc. v. Jaslow Dental Laboratory, Inc., tried in vain 
to utilize the idea/expression dichotomy with 
software programs.  797 F.2d 1222, 1237 (3d Cir. 
1986).  The court was tasked with determining 
which aspects of a computer program were ideas and 
 


which were expression.  Id. at 1234.  The court 
observed “the purpose or function of a utilitarian 
work would be the work’s idea, and everything that 
is not necessary to that purpose or function would be 
part of the expression of the idea.”  Id. at 1236.  This 
attempt to simplify an already impossible 
examination with an even more complicated series of 
tests was immediately criticized by subsequent 
courts and even the academic community at large.  
See Broderbund Software Inc. v. Unison World, Inc.
648 F.Supp. 1127, 1133 (N.D. Cal. 1986); Plains 
Cotton Co-op v. Goodpasture Computer Serv., Inc.
807 F.2d 1256, 1262 (5th Cir.) cert. denied, 484 U.S. 
821 (1987); See generally Steven R. Englund, Note, 
Idea, Process, or Protected Expression?: Determining 
the Scope of Copyright Protection of the Structure of 
Computer Programs, 88 MICH.L.REV. 866, 867-73 
(1990). 
Seeing the Whelan court’s failed attempt, in 1992 
the Second Circuit created the abstraction-filtration-
comparison test in Computer Associates 
International v. Altai as an attempt to clarify some 
of the confusion surrounding the idea/expression 
dichotomy for computer program protection.  982 
F.2d 693, 707 (2nd Cir. 1992).  According to the 
Second Circuit, Whelan's approach of separating idea 
from expression in computer programs "relies too 
heavily on metaphysical distinctions" and "a 
satisfactory answer to this problem cannot be 
reached by resorting, a priori, to philosophical first 
principals."  Id. at 706.  The Altai case involved a 
copyright infringement claim where the defendant 
 


enlisted clean room programmers2 to produce code 
designed to operate like the plaintiff’s code.  Id. at 
700.  The Second Circuit implemented a new 
substantial similarity test to determine whether the 
defendant had infringed the plaintiff’s protected 
expression, as opposed to permissibly using the 
unprotectable ideas.  Id. at 701.  That is, the court 
applied the abstraction-filtration-comparison test, 
which offers one way to determine which aspects of 
the computer program involve ideas and which are 
expressions.  Ultimately, no copyright infringement 
was found as a result in that case. 
It is instructive to appreciate the complexity that 
is involved in distinguishing protectable subject 
matter from abstract ideas in the copyright context 
under this test. First, the abstraction step of the 
abstraction-filtration-comparison test requires that 
“a court should dissect the allegedly copied 
program’s structure and isolate each level of 
abstraction contained within it.”  Id. at 707.  The 
implementation begins with the lowest level of 
abstraction, the physical code, and ends with the 
highest level of abstraction, the program’s ultimate 
function.  Id.   
Once the levels of abstraction have been 
determined and separated, the filtration step is then 
used to separate protectable expressions from non-
protectable material.  Id.  A “successive filtering 
method” is first implemented to “examine the 
structural components at each level of abstraction.” 
On a per level basis, particular inclusions are 
                                                 
2 Programmers with no direct access to the original code. 
 


determined to be “[an] ‘idea’ or . . . dictated by 
considerations of efficiency, so as to be necessarily 
incidental to that idea.”  Id.  Courts must consider 
the “structural content of an allegedly infringed 
program for elements that might have been dictated 
by external factors.”  Id. at 710.  Courts must also 
consider elements dictated by efficiency through 
examining “‘whether the use of this particular set of 
modules is necessary efficiently to implement that 
part of the program’s process’ being implemented.” 
Id. at 708.  If the court finds elements dictated by 
efficiency, then “the expression represented by the 
programmer’s choice of specific module or group of 
modules has merged with their underlying idea and 
is unprotected.”  Id.  Courts must then filter out 
unprotectable material that is determined to be “free 
for the taking and cannot be appropriated by a single 
author even though included in a copyrighted work”. 
 Id. at 710. 
Finally, the comparison step occurs once courts 
have filtered out “all elements of the allegedly 
infringed program which are ‘ideas’ or are dictated 
by efficiency or external factors, or taken from the 
public domain.” Id. at 710.  What remains is 
considered the “core of protectable expression.”  Id.  
This ‘core of protectable expression’ is then compared 
to the alleged infringing work to determine whether 
the defendant copied any aspect of the protected 
expression.  Id.  If all similarities in expression arise 
from external factors, elements of efficiency, or use 
of common ideas, then no substantial similarity can 
be found. Data East USA, Inc. v. Epyx, Inc., 862 F.2d 
204, 208 (9th Cir. 1988). 
 

10 
One year after the Altai decision, the Tenth 
Circuit reaffirmed the abstraction-filtration-
comparison test in Gates Rubber v. Brando 
Chemical.  9 F.3d 823, 830 (10th Cir. 1993).  The 
court in Gates Rubber divided the levels of 
abstraction into six categories:  “(i) the main 
purpose, (ii) the program structure or architecture, 
(iii) modules, (iv) algorithms and data structures, (v) 
source code, and (vi) object code.”  Id. at 835.  The 
imposition of abstraction levels allows for some 
generalities regarding filtering.  For example, the 
program’s purpose, the highest level of abstraction, 
will generally always be filtered out because it is 
simply an abstract idea.  Similarly, the object code, 
the lowest abstraction, if copied, will generally 
always lead to copyright infringement.  However, the 
intermediate levels require complex and ad hoc 
filtering examination. 
While the abstraction-filtration-comparison test 
likely constricted the unfixable boundary analogized 
by Judge Hand in Nichols, it is still far from 
concrete.  Furthermore, the additional levels of 
analysis provide even more opportunity for 
uncertainty.  In stark contrast, prior patent law has 
successfully steered clear of the complexities and 
vague procedures that have hindered copyright 
abstraction analysis.  Patents, on the other hand, 
have claims that are intended to provide just such a 
bright line.  Whereas the abstraction-filtration-
comparison test determines what is protected and 
what is an abstract idea for copyright infringement, 
a potential patent infringer need only construe the 
patent’s claims for notice of protected subject matter.  
As best stated in Warner-Jenkinson Co., Inc. v. 
 

11 
Hilton Davis Chemical Co., “[t]he presumption we 
have described . . . gives proper deference to the role 
of claims in defining an invention and providing 
public notice.”  520 U.S. 17, 33-34 (1997). 
The Federal Circuit’s decision threatens to 
transform patentable subject matter analysis from a 
once bright-line rule to a complicated and seemingly 
impossible analysis.  By requiring a process to meet 
its arbitrary machine-or-transformation test, the 
Federal Circuit has rejected this Court’s definition of 
patentable subject matter: “anything under the sun 
that is made by man” except “laws of nature, natural 
phenomena, and abstract ideas.”  Diamond v. Diehr
450 U.S. 175, 182, 185 (1981).  This test now 
requires District Courts, and even examiners at 
United States Patent and Trademark Office 
(USPTO), to determine whether a process passes the 
complex machine-or-transformation test.   
How can we possibly expect USPTO examiners 
and District Courts to distinguish abstract processes 
from process that satisfy the machine-or-
transformation test when this Court has noted its 
own struggles in examining this issue?  Dissenting  
from the Court’s dismissal in Laboratory Corp. of 
American Holdings v. Metabolite Laboratories, Inc.
Justice Breyer conceded the difficulty of defining 
non-patentable subject matter such as mental 
processes and abstract intellectual concepts.  548 
U.S. 124, 134 (2006).  Drawing this conclusion, he 
analogized those categories of subject matter to 
similar categories within copyright law.  Id.  To 
support his contention, Justice Breyer cited Nichols 
v. Universal Pictures Corp.:  “[W]e are as aware as 
 

12 
anyone that the line [between copyrighted material 
and non-copyrightable ideas], wherever it is drawn, 
will seem arbitrary.”  Id.  Further, Justice Breyer 
recognized that “all conscious human interaction 
involves a mental process” and as such “many a 
patentable invention rests upon its inventor’s 
knowledge of natural phenomena,” and “many 
‘process’ patents seek to make abstract intellectual 
concepts workably concrete.”  Id.  Much as copyright 
law’s approach to determining protectable material 
resides in a quagmire of uncertainty, Justice 
Breyer’s recognition reveals that a similar approach 
to patents would create similar confusion. 
In truth, words are themselves abstractions of 
reality, so it is logically futile, or at least immensely 
problematic, to attempt to use abstractions to define 
meaningful and workable distinctions between 
different types of abstractions, or between un-
protectable "fundamental principles" and protectable 
"applications" of those principles.  Indeed, the words 
"fundamental principle" and "application of a 
fundamental principle" can almost always be applied 
to the same claim terminology since there usually 
exist both higher and lower levels of abstraction in 
most situations, regardless of the context.  This 
Court is urged not to make the mistake of attaching 
additional words that beg further definitions, such 
as merely claiming a "result" or "effect," since such 
scope analyses are more appropriately handled 
under Title 35 U.S.C. § 102 novelty and §103 
obviousness.  Similarly, claims also should not be 
considered abstract simply because of their 
vagueness or lack of specificity since such analyses 
 

13 
are more appropriately handled under Title 35 
U.S.C. § 112.   
As such, the Federal Circuit’s holding creates a 
further undefinable standard that brings the once 
concrete patentable subject matter analysis an 
unfixable boundary similar to that between abstract 
idea and expression that currently haunts copyright 
law. Instead, the Court should stick very close to the 
statutory phrase "useful process" for evaluating the 
statutory subject matter question for processes.  This 
Court should leave behind all other abstractions of 
abstractions. 
 
II.  A BROAD, JUDICIALLY-MADE § 101 
TEST WILL PRECLUDE PATENTS AND 
STIFLE INNOVATION FOR NEW 
TECHNOLOGY IN THE 
UNPREDICTABLE FIELDS 
 
A.  The Federal Circuit’s decision 
negatively affects biotechnologies, 
not simply business methods 
It will be difficult to apply the machine-or-
transformation test to biotechnology inventions, 
where patentable subject matter challenges often 
allege preemption of a natural phenomena or law of 
nature.  In Classen Immunotherapies, Inc. v. Biogen 
IDEC, claims were directed to methods for 
determining an optimal immunization schedule by 
comparing the observed incidence of immune-
 

14 
mediated disorders in treatment groups subjected to 
different vaccination schedules. 304 Fed. Appx. 866, 
866 (Fed. Cir. 2008); Classen Immunotherapies, Inc. 
v. Biogen IDEC, 2006 WL 6161856 at *1 (N.D. Md. 
Aug. 16, 2006).   The Federal Circuit summarily 
applied its new machine-or-transformation test  to 
find the claims to be outside the scope of § 101.  
Classen, 304 Fed. Appx at 866.  Unfortunately, the 
court provided no framework for future analyses.  
This § 101 test is clearly incompatible with many 
biotechnology inventions, as they do not require 
machines (in the customary way of thinking about 
machines).  However, the claims do arguably involve 
a transformation.  Claim 1 of the Classen patent 
recites a “method . . . which comprises immunizing 
mammals in the treatment group of mammals with 
one or more doses of one or more immunogens.”  The 
immunization of a mammal clearly effects a 
transformation of a particular article (a mammal) 
into a different state (a state of induced immunity).   
Classen  is a good demonstration that the 
machine-or-transformation test fails to function in 
the unpredictable fields. 
 
B.  Sections 102, 103, and 112 of the 
Patent Act provide sufficient 
guidance for determining 
patentability in the unpredictable 
fields 
For an inventor to be entitled to a patent on a 
claimed invention, the inventor must, at the very 
least, meet the utility, novelty, non-obviousness, and 
disclosure requirements of sections 101, 102, 103, 
 

15 
and 112 of the Patent Act.  It is important to 
emphasize that the issue in this case is only whether 
a claimed invention is statutory subject matter 
under § 101.  
Recently, this Court considered addressing the 
merits of a § 101 dispute and clarifying what is 
patentable in Lab. Corp.  548 U.S. at 124.  This 
Court granted certiorari but dismissed the case 
before reaching the merits. Id.  Wishing to address 
the merits, three dissenting justices objected to the 
claimed process as being unpatentable.  Id.  at 133.  
Writing for the dissent, Justice Breyer stated:  “[The 
patent] embod[ies] only the correlation between 
homocysteine and vitamin deficiency that the 
researchers uncovered. In my view, that correlation 
is an unpatentable ‘natural phenomenon,’ and I can 
find nothing in [Lab. Corp.’s] claim 13 that adds 
anything more of significance.” Id at 137-138. 
Specifically, Lab. Corp.’s 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 homocysteine; and  
correlating an elevated level of total 
homocysteine in said body fluid with a 
deficiency of cobalamin or folate. 
Id at 129. 
Although Justice Breyer determined that Lab. 
Corp.’s claim 13 was unpatentable as being a 
“phenomenon of nature,” he conceded that 
categorizing non-patentable “phenomena of nature” 
 

16 
is difficult.  Id.  Considering then the difficulty of 
categorizing non-patentable “phenomena of nature,” 
it stands to reason that Justice Breyer’s thoughtful 
concern as to the patentability of Lab. Corp.’s claim 
13 may be misplaced. 
In  Lab. Corp., there was a specifically tailored 
use derived from the phenomena by the creativity of 
man.  This was why the lower courts and  the 
USPTO affirmed the validity of the claim, 
illustrating further that the issue of patentability is 
better dealt with through novelty, obviousness and 
written description inquiries.  In addition, the patent 
owner, Competitive Technologies, Inc., subsequently 
initiated reexamination in the USPTO.  Id. at 128; 
Ex parte Competitive Technologies, Inc., Appeal No. 
2009-005519 (B.P.A.I. July 30, 2009).  Upon 
reexamination of the patent, the Board of Patent 
Appeals and Interferences (BPAI) reversed the 
examiner’s § 103 rejection.  Ex parte Competitive 
Technologies, Inc., Appeal No. 2009-005519. 
 
Determining that the claims are patentable under § 
103, this decision by the BPAI provides evidence 
that  sections 102, 103, and 112 of the Patent Act 
provide sufficient guidance for determining 
patentability in the unpredictable fields. 
In  Ariad Pharms., Inc. v. Eli Lilly & Co., the 
Federal Circuit found that the claims were invalid 
for violating the written description requirement of § 
112.  560 F.3d 1366, 1376 (Fed. Cir. 2009).  Ariad 
Pharms and Classen together demonstrate that 
reviewing patentability through §§ 102, 103, and 112 
provides clearer guidance than a § 101 analysis.  
That is, the Federal Circuit provided clear standards 
for reviewing written description and enablement 
 

17 
standards in Ariad Pharms but failed to articulate 
the application of the machine-or-transformation 
test to unpredictable arts in Classen.  This Court 
faces the question of whether a judge-made test is 
appropriate, or for that matter necessary, in light of 
other statutory tests that are clear, articulate, and 
well established, especially in the unpredictable arts 
where scientific advances are, by definition, 
unpredictable and likely to suffer from rigidly 
applied tests. 
Finally, the timing delay implications for ad hoc 
determinations of statutory subject matter can be 
particularly harmful for biotechnology inventions.  
In hearings by the Federal Trade Commission on 
Intellectual Property in the Marketplace, Assistant 
Vice Chancellor for Intellectual Property & Industry 
Research Alliances Carol Mimura stated that “in the 
area of early-stage patents . . . these [biotechnology] 
patents are very crucial to the success of start-up 
companies that are spawned from university 
research.”  Federal Trade Commission hearings, The 
Evolving IP Marketplace:  The Operation of IP 
Markets, 6 Monday, May 4, 2009.  The patent 
application in the present case was filed in 1997. 
Twelve years have transpired, and the ad hoc 
analysis continues.  When patents are so important 
to the growth of entire industries, the determination 
of patent eligibility—a gateway question—must be 
clear.   
  
 

18 
III.  AMBIGUITY IN THE FEDERAL 
CIRCUIT’S NEW MACHINE-OR-
TRANSFORMATION TEST HAS 
ALREADY FOSTERED HARMFUL 
CONFUSION AND UNCERTAINTY IN 
THE CASE LAW AND USPTO APPEALS 
THAT HAVE FOLLOWED 
  The Federal Circuit’s decision held that 
processes not transforming a particular article must 
be tied to a particular machine.  In re Bilski, 545 
F.3d at 954.  However, the Federal Circuit declined 
to offer guidance on what is meant by “particular 
machine,” including the question of whether reciting 
particular software suffices to tie a process to a 
particular machine.  Id. at 962.   
Prior to the Federal Circuit’s decision, it had 
been well-settled law that a computer programmed 
with particular software was patentable subject 
matter.  In re Alappat, 33 F.3d 1526, 1545 (Fed. Cir. 
1994).  In the front-page holdings, the Federal 
Circuit expressly “abrogated” Alappat by name.  In 
re Bilski, 545 F.3d at 943.  However, the only 
negative treatment offered in the body of the opinion 
was directed toward Alappat’s role in establishing 
the “useful, concrete and tangible result” test, from 
which the Federal Circuit now departs.  Id. at 959.  
No mention was made regarding Alappat’s guidance 
on machines particularized by programming, despite 
Judge Newman’s dissent urging the majority to 
clarify what exactly was being abrogated.  Id. at 994.  
The majority simply left the question to future cases.  
Id. at 962. 
 

19 
 
The Federal Circuit again declined to provide 
clarity in In re Comiskey.  554 F.3d 967 (Fed. Cir. 
2009).  Faced with an arbitration system 
implemented with various software modules and a 
database, the court held that “under the broadest 
reasonable interpretation” the system represented a 
machine.  Id. at 981.  However, the Federal Circuit 
panel nevertheless remanded to the USPTO for 
determining whether the system claims were 
statutory as machines.  Id. at 971.  Dissenting from 
the en banc decision, Judge Moore sharply criticized 
the majority for remanding the case on this issue 
since  In re Bilski, in her opinion, did not affect 
whether machine claims were statutory under 
Alappat.  In re Comiskey, 89 U.S.P.Q.2d 1641, 1650 
(Fed. Cir. 2009). 
The result of this ambiguity has been confusion 
and conflict in the USPTO and lower courts, with 
rampant uncertainty for American inventors.  The 
USPTO still seems to regard particularized software 
as sufficiently particularizing a machine for § 101 
purposes.  In Ex parte Cornea-Hasegan, the Board of 
Patent Appeals and Interferences considered a 
method for routing computations to either software 
or specialized hardware, based on which of the two 
would be best suited for the task.  89 U.S.P.Q.2d 
1557, 1558 (B.P.A.I. 2009).  The BPAI rejected the 
claims for merely reciting a “processor” because a 
general purpose processor is not patentable when 
programmed in an “unspecified manner.”  Id.  at 
1560-61.  Subsequent BPAI decisions reiterated that 
claims reciting a general purpose processor are 
unpatentable unless they specify the manner of 
programming with particularity.  See, e.g.,  Ex parte 
 

20 
Gutta, 2009 WL 112393 (B.P.A.I. Jan. 15, 2009); Ex 
parte Barnes, 2009 WL 164074 (B.P.A.I. Jan 22, 
2009).  Additionally, in Ex parte Atkin, the BPAI 
established that sufficient particularity may exist 
when referring to the patent specification via means-
plus-function language.  2009 WL 247868 at *9 
(B.P.A.I. Jan. 30, 2009). 
Fissures have also emerged at the district court 
level as judges attempt to decipher the new 
landscape.  In March of 2009, the Northern District 
of California granted summary judgment in an 
infringement action involving a process for detecting 
credit card fraud in online transactions. 
 
CyberSource Corporation v. Retail Decisions, Inc.
620 F.Supp.2d 1068, 1071, 1081 (N.D.Cal. 2009).  
Judge Patel viewed Bilski as abrogating more than 
those portions of Alappat that laid the foundation for 
State Street’s “useful, concrete and tangible result” 
test.  Id. at 1080-81.  Indeed, she viewed all portions 
of  Alappat as abrogated entirely, including the 
software question which the Federal Circuit’s 
decision in In re Bilski expressly deferred to future 
cases.  Id. at 1080-81. 
This view has carried a weight inordinate to a 
lone California district court ruling.  Judge Patel 
was shortly thereafter invited to sit by designation 
on the Federal Circuit bench, authoring the panel 
decision for Wavetronix LLC v. EIS Electronic 
Integrated Systems.  2009 WL 2245213 (Fed. Cir. 
2009).  Judge Patel’s views on In re Bilski and 
Alappat may thus have more in common with the 
direction in which the Federal Circuit is headed.  
 

21 
Even so, Judge Patel’s neighboring district gave 
little deference to this CyberSource view three 
months later.  In DealerTrack, Inc. v. Huber, the 
Central District of California granted summary 
judgment against the patentee in an infringement 
action involving an automated credit approval 
process for automotive dealers.  2009 WL 2020761 at 
*1 (C.D.Cal. 2009).  The court correctly noted that 
Bilski declined to adopt any new broad exclusion 
over software, and that it has been well-settled law 
that “a general purpose computer in effect becomes a 
special purpose computer once it is programmed to 
perform particular functions pursuant to 
instructions from program software.”  Id. at *3 
(citing  In re Alappat, 33 F.3d 1526, 1545 (Fed. Cir. 
1994)). 
The Central District of California acknowledged 
the  CyberSource court’s holding that a process 
performed “over the Internet” does not satisfy the 
“machine” rubric of Bilski.  Id.    But  the  court 
rejected the view that particularized programming 
on a general purpose computer is no longer 
patentable subject matter.  Id. at *4.  The court’s 
determination of invalidity was expressly based on 
the finding that DealerTrack’s patent did not specify 
the programming with sufficient particularity to 
meet the discussed Alappat standard.  Id. 
None of the present uncertainty is proper in light 
of the plain language of § 101 and subsequent 
legislative treatment of the statute, nor is it 
necessary to meet the policy considerations behind 
this Court’s precedent upon which the Federal 
Circuit relied.  At each step of the way in the Federal 
 

22 
Circuit’s analysis, the question of preempting 
abstract ideas and other fundamental principles was 
presented as the underlying Supreme Court concern.  
See  Diamond v. Diehr, 450 U.S. 175, 187 (1981) 
(“[the inventors] do not seek to pre-empt the use of 
that equation”); Gottschalk v. Benson, 409 U.S. 63, 
72 (1972) (“the patent would wholly pre-empt the 
mathematical formula”). 
In broad terms, the preemption question is 
already addressed by code sections pertaining to 
anticipation, obviousness, and overbreadth.  In the 
specific field of software, it is addressed by Alappat 
and its requirement that only particular software 
can render patentable a process performed by 
general purpose computers.  By requiring inventors 
to claim with particularity the “how and why” of 
their software-driven inventions, other practitioners 
remain free to practice non-infringing methods of 
achieving the same result.  Any underlying abstract 
ideas are not monopolized or removed from the 
public domain.  At the same time, the patentee is 
rewarded with limited-term protection for 
contributing a particularly innovative means for 
achieving the result to the public knowledge. 
The Federal Circuit may be wary of emerging 
technologies and unsure as to whether the USPTO 
can successfully adapt to avoid issuing patents for 
inventions that are anticipated, obvious, or overly 
broad.  However, the BPAI decisions discussed supra 
illustrate that the USPTO is fully versed in Alappat 
guidance and equipped to bar those patents that do 
not claim the “hows and whys” with particularity 
sufficient to avoid preemption.   
 

23 
If the problem is a lag between the emergence of 
new technologies and the sources with which 
subject-matter experts may search prior art, then 
the solution is more resources for the subject-matter 
experts to shorten this lag.  The Federal Circuit’s 
chosen alternative, fabricating a new restrictive § 
101 standard, treats the skin rash with amputation.  
Matters are made even worse when ambiguity and 
silence leave questions as to what exactly has been 
amputated.   
CONCLUSION 
 
Between the conflicting views of the BPAI and 
lower courts and the ambiguity of the new exclusive 
test from the Federal Circuit, the owners of tens if 
not hundreds of thousands of patents now sit in 
limbo regarding the legal status of their intellectual 
property.  Businesses and individual inventors are 
clouded by uncertainty as to whether they would 
receive the protection needed to recoup investment 
in new innovation.  Without the finality provided by 
the customary presumption of patent validity, 
opportunities for sale or licensing diminish as the 
limited window of each patent’s protection dwindles.  
Legal practitioners have no way to advise clients 
when rigid-yet-ambiguous new § 101 rules place a 
question mark atop wide swaths of the patent 
landscape, and America’s leadership in global 
innovation suffers as a result. 
Neither the plain language of § 101 nor the cited 
Supreme Court precedent support the new, exclusive 
Federal Circuit standard.  Further, other statutory 
tools are readily available to protect the policy 
 

24 
concerns of overly broad preemption.  This Court 
should therefore rely on those tools and quiet the 
confusion and uncertainty imposed by the Federal 
Circuit’s decision below by reversing that decision. 
 
Respectfully submitted, 
JOEL H. THORNTON 
 Counsel 
of 
Record 
THE THORNTON FIRM 
P.O. Box 129 
Rome, GA  30162 
706-266-6836 
 
JEFFREY R. KUESTER 
THOMAS, KAYDEN, 
HORSTEMEYER & RISLEY, 
L.L.P. 
600 Galleria Parkway SE 
Suite 1500 
Atlanta, GA  30339 
(770) 933-9500 
  
 

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