NO. 08-964 
Supreme Court of the United States 
1111 East 60th Street 
   Counsel of Record 
Chicago, Illinois 60637 
1111 23rd Street, NW 
(773) 702-9563 
Apt 8d 
Washington, DC  20037 
(202) 558-6667
August 6, 2009  
Counsel for Amicus Curiae 

TABLE OF AUTHORITIES ...................................... iii 
INTEREST OF AMICUS CURIAE ............................  1 
STATEMENT OF CASE ............................................ 1 
SUMMARY OF ARGUMENT .................................... 8 
ARGUMENT .............................................................  12 
The Federal Circuit’s Approach  
Conflicts with the Statute ................... 12 
The Federal Circuit’s Approach  
Conflicts with this Court’s 
Precedent .............................................  14 
The Federal Circuit’s Approach  
Conflicts with Sound Policy ................ 15 
Sound Patent Law Need Not  
Tie a Patentable Invention  
to Some Physical Mode of Its 
Expression ................................. 15 
Strong Patent Protection  
Opens Technology Markets  
to Multiple Players and 
Facilitates Cooperation  
Among Them .............................  17 

Localized Solutions Offer the  
Best Means for Dealing with 
Particular Defects of the  
Patent System ........................... 19 
The Federal Circuit’s Approach Will 
Have a Profound Adverse Effect on the 
Public’s Ability to Benefit from Dr. 
Chakrabarty’s Own Research ............. 23 
CONCLUSION ......................................................... 26 

In re Alappat,  
33 F.3d 1526 (Fed. Cir. 1994) .......................... 6,  22 
In re Bilski,  
545 F.3d 943 (Fed. Cir. 2008) ................. 2, 6, 12-15 
Diamond v. Chakrabarty,  
447 U.S. 303 (1980) ..................................... passim 
Diamond v. Diehr,  
450 U.S. 175 (1981) .......................... 6, 9, 13-15, 26 
Funk Brothers Seed Co. v. Kalo Inoculant Co,  
333 U.S. 127 (1948) ....................................... 14, 15 
Gottschalk v. Benson,  
409 U.S. 63 (1972) ................................. 5,  6, 14, 15 
Graham v. John Deere, 
383 U.S. 1 (1966) ............................................ 16-17 
J.E.M. Ag Supply, Inc. v. Pioneer Hi-Bred Int’l, Inc., 
534 U.S. 124 (2001) ................................... 9, 14, 26 
In re Johnston, 
502 F.2d 765 (CCPA 1974) .................................... 6 
Parker v. Flook,  
437 U.S. 584 (1978) ....................................... 14, 15 
Picard v. United Aircraft Corp.,  
128 F.2d 632 (2d Cir. 1942) ................................. 17 
State Street Bank & Trust Co. v. Signature 
Fin. Group Inc.,  
149 F.3d 1368 (Fed. Cir. 1998) ........................ 6,  22 

35 U.S.C. § 100(b) ..................................................... 13 
35 U.S.C. § 101 .......................................... 9, 12, 13, 14 
35 U.S.C. § 102 .................................................... 13,  20 
35 U.S.C. § 103 .................................................... 13,  20 
35 U.S.C. § 112 .................................................... 13,  20 
35 U.S.C. § 122 .......................................................... 20 
Timothy Caulfield et al., Evidence and 
Anecdotes: An Analysis of Human Gene 
Patenting Controversies, 24 Nature 
Biotechnology 1091 (2006) .................................... 8 
Ian Cockburn et al., Pharmaceuticals and 
Biotechnologyin U.S. Industry in 2000 
Studies in Competitive Performance (David 
C. Mowery ed., 1999) ............................................. 5 
Richard A. Epstein & Bruce Kuhlik, Is There a 
Biomedical Anticommons, Regulation, 
Summer 2004, at 54 ........................................... 7-8 
Michael Heller and Rebecca Eisenberg, Can 
Patents Deter Innovation?  The 
Anticommons in Biomedical Research, 280 
Science 698, 700 (1998) ......................................... 7 

F. Scott Kieff, On Coordinating Transactions  
in Information: A Response to Smith’s 
Delineating Entitlements in Information
117 Yale L.J. Pocket Part 101 (2007) ............. 8, 19 
NIH: Moving Research from the Bench to the 
Bedside: Hearing Before the Subcomm. on 
Health of the H. Comm. on Energy and 
Commerce, 108th Cong. (2003), available at
/108-38.pdf (statement of Phyllis Gardner, 
Senior Associate Dean for Education and 
Student Affairs, Stanford University)  ................. 4 
Henry E. Smith, Intellectual Property as 
Property: Delineating Entitlements in 
Information, 116 Yale L.J. 1742 (2007)  ............. 19 
John P. Walsh et al., View from the Bench: 
Patents and Material Transfers, 309 Science 
2002 (2005) ............................................................ 8 

Dr. Ananda Chakrabarty is Distinguished 
University Professor in the College of Medicine’s 
Department of Microbiology and Immunology at the 
University of Illinois at Chicago.  He was the inventor 
of the bacterium at issue in this Court’s decision in 
Diamond v. Chakrabarty, 447 U.S. 303 (1980), which 
supported a broad definition of patent eligibility.  
Since that time, he has been a leading voice in the 
field of patent policy.  He has no direct stake in the 
outcome of this case and is primarily interested in 
ensuring that patent law develops in a way that best 
promotes innovation and competition.1 
Any patent application must go through two 
stages before actual patent rights are awarded by the 
Patent Office.  The first of these inquiries deals with 
“patent eligibility.”  That question determines what 
types of inventions can be considered for patent 
protection. Patent eligibility thus performs a 
gatekeeper function.  If an invention is not patent 
eligible, no other provision of the patent law can 
secure patent rights for that invention.  Patent 
eligible inventions are not, however, automatically 
Amicus has no financial interest in the outcome of this case. No 
counsel for a party authored this brief in whole or in part, and 
no counsel or party made a monetary contribution intended to 
fund the preparation or submission of this brief.  The Hoover 
Project on Commercializing Innovation at Stanford University’s 
Hoover Institution paid the actual printing and filing costs. 
Counsel for amicus curiae prepared this brief on a pro bono 
basis as part of their academic work in the field.   

entitled to protection.  Each such invention must 
thereafter be examined under a second, well-known 
set of requirements: novelty, non-obviousness, and 
disclosure.  These are more specific inquiries that ask 
whether or not the claimed invention merits the 
protection of the state by being a sufficient advance 
over the existing body of patented materials and by 
being supported by a sufficient disclosure to provide 
the public with notice and scientific teaching.   
In the decision below, the Federal Circuit held 
that the Patent Office properly rejected the 
applicants’ claimed process for managing legal and 
business risk.  The court’s sole ground was that the 
claimed process failed to meet the court’s newly 
announced and seriously restrictive test for patent 
eligibility.  Under the court’s “machine or 
transformation test,” a claimed process must be “tied 
to a particular machine or apparatus, or … 
transform[ ] a particular article into a different state 
or thing.” In re Bilski, 545 F.3d 943, 954 (Fed. Cir. 
2008) (en banc).   
This test threatens to transform patent law for 
the worse.  The key to modern technology lies in the 
assembly, organization and use of information of all 
sorts, kinds and descriptions.  The physical substrate 
in which it is contained is at best a mere technical 
detail that is under the Federal Circuit’s rule 
elevated to an end in itself, which only frustrates the 
great ends for which the patent law is designed.  Dr. 
Chakrabarty’s own research on advanced techniques 
for personalized medicine is placed at risk by the 
narrow definition of patent eligibility used in the 
Federal Circuit.   

In light of all the relevant information, the 
Federal Circuit’s approach must be rejected because 
it is in conflict with the statute, with the precedents 
of this Court, and with sound public policy. Of 
particular concern to Professor Chakrabarty is that 
affirming the decision below will place a dark cloud 
over the status of his own future research.  A broad 
reading of patent eligibility has played a central role 
in fostering both output from and competition within 
a range of technology industries.   
The course charted in the Federal Circuit 
marks an abrupt and unwarranted about-face from 
the bold decision in this Court’s 1980 Chakrabarty 
case. Over strong objections that living things were 
per se patent ineligible, this Court rejected the 
argument of the Patent Office that subject matter 
relating to living things was excluded from patent 
eligibility.  That case involved Dr. Chakrabarty’s 
patent application for a genetically engineered 
The  Chakrabarty decision’s strong affirmation 
of the broad scope for the patent system has been the 
fundamental pillar supporting the dramatic success 
of the United States’ biotechnology industry.  At the 
same time, the Chakrabarty decision is situated 
squarely in the middle of a host of this Court’s 
decisions relating to the patent eligibility of various 
business- and computer-related inventions, which 
have spurred huge technical advances in related 
Before the 1980 Chakrabarty decision, the 
United States, Europe, and Japan each had large 

biotechnology companies, often collectively called “Big 
Pharma,” which competed with rough parity with 
each other.   Each region has continued to be home to 
Big Pharma companies to this day.  All three regions 
have enjoyed access to comparable technological and 
capital resources.  But neither Europe nor Japan took 
the decisive step that the United States made 
through this Court’s Chakrabarty decision, which 
ignited the boom in basic biotechnology that 
continues to this day.  The rest of the world lags 
behind because the narrow vision of patent law that 
was adopted elsewhere led to the erection of various 
artificial roadblocks to effective patents, and 
resulting industrial development.  
This distinctive United States stance has paid 
huge dividends to this country in the 29 years after 
Chakrabarty.  Since 1980, the United States 
biotechnology industry has expanded so that Big 
Pharma companies are no longer the only significant 
players.  Their skills have been augmented by an 
expanding pool of small- and medium-sized 
companies that regularly numbers around 1,400 in 
its ranks.2  The pool is constantly turning over as 
some of these companies fail while others succeed 
spectacularly and fuel the appetite for more start-
NIH: Moving Research from the Bench to the Bedside: Hearing 
Before the Subcomm. on Health of the H. Comm. on Energy and 
Commerce, 108th Cong. 47 (2003), available at 
(statement of Phyllis Gardner, Senior Associate Dean for 
Education and Student Affairs, Stanford University) (detailing 
the differences between the smaller biotechnology companies 
and those in Big Pharma).   

ups, whose livelihood depends on their ability to 
develop some patentable technology. 
This unique growth in the United States’ 
biotechnology industry stems from the virtuous circle 
that the Chakrabarty  decision helped create.  The 
firms that have grown through their patented 
technologies in turn supply fresh resources to fund 
the basic biological research community.  That 
community in turn improves the knowledge of 
general scientific laws, which aids the formation of 
new commercial firms.  The general public benefits 
from the steady stream of new and better goods and 
services that have revolutionized vital industries 
such as healthcare.3  The broad account of patent 
eligibility has lowered the gates so that more can 
play, and in so doing it has spurred our biotechnology 
industry to be the most vibrant and competitive in 
the world. 
The key role played by a broad eligibility 
requirement is equally important within the field of 
business- and computer-related inventions, which 
encompasses the patent application filed by 
Petitioner in this case.   In the early 1970s, the 
United States’ software industry was devoid of 
meaningful patent protection because of the 
uncertainty created by this Court’s decision in 
Gottschalk v. Benson, 409 U.S. 63 (1972).  
3 Ian Cockburn et al., Pharmaceuticals and Biotechnology, in 
U.S. Industry in 2000 Studies in Competitive Performance 389-
92 (David C. Mowery ed., 1999) (reviewing relative performance 
of the U.S. biotechnology industry).   

While Benson’s holding was narrow, its impact 
was to leave all patents for computer software 
vulnerable to serious challenges.4  Unfortunately, the 
Benson approach controlled throughout the 1970s, 
until this Court’s decisions in Chakrabarty and 
Diamond v. Diehr, 450 U.S. 175 (1981), holding that 
software patents were not subject to per se exclusion, 
started to revive the market.  Indeed, it was only 
with In re Alappat, 33 F.3d 1526 (Fed. Cir. 1994) (en 
banc) and State Street Bank & Trust Co. v. Signature 
Fin. Group Inc., 149 F.3d 1368 (Fed. Cir. 1998) that 
the increased confidence in software patents 
translated into major infusions of investment capital. 
Yet these are the very decisions that the Federal 
Circuit has unwisely called into question in the 
instant case. Bilski, 545 F.3d at 990-92 (Newman, J., 
dissenting) (noting the majority’s break with these 
important precedents).  That window of reliable 
eligibility for business method and software patents 
has been closed over the past several months by the 
recent Federal Circuit cases including the en banc 
decision now before this Court.  That point raises real 
concern because the same patent system that creates 
the initial economic advantage to the first in the field 
also gives a strong encouragement for new firms to 
compete against its initial patent advantage by 
affording powerful patent protection to the next 
generation of new and useful inventions. 
4 For a discussion of the lead-up to Benson, and its impact, see In 
re Johnston, 502 F.2d 765, 772–774 (CCPA 1974) (Rich, J., 
dissenting) (noting normative problems with such a rule against 
software patents but pointing out the appellate court’s duty to 
follow this Court’s case law on the issue). 

It may seem at first blush that broad patent 
eligibility would lead to an unseemly deluge of 
patents.  But the ultimate success or failure of any 
patent in any field of technology must still be tested 
through a gauntlet of challenges that are both legal 
and economic.  On the legal side, an applicant will 
only receive a valid patent if it can carry the burden 
of preparing a sufficiently strong application 
containing claims that avoid the prior art.  On the 
economic side, the patentee can recover its initial 
investment only if it can successfully navigate the 
complex world of commercial transactions in the face 
of ever shifting technological and market landscapes.  
Restraints like these deter frivolous Patent 
Office and patent litigation filings whose sole purpose 
is to block other innovators from making their mark 
in the marketplace.  The empirical findings on the 
ground do not bear out all the gloomy talk about 
patent blockades, for private owners of valid patents 
do not act like Soviet-style bureaucrats who only 
prosper by blocking the gainful activities of others.  
Patents are wasting assets that can produce revenue 
only to the extent that they lead to production or 
licensing or both.5  
5 A popular trend in policy debates is to worry about a putative 
problem of a patent “anticommons” that might be created when 
there are too many valid patents in an area.  See Michael Heller 
and Rebecca Eisenberg, Can Patents Deter Innovation?  The 
Anticommons in Biomedical Research, 280 Science 698, 700 
(1998).  But the worries about an anticommons in the U.S. 
patent system are misplaced for several reasons, including the 
nature of the holder of the underlying assets, the nature of the 
licensing over those assets, and the flexibility private parties 
enjoy to bundle or divide both the assets and the licenses.  See 
Richard A. Epstein & Bruce Kuhlik, Is There a Biomedical 

A restrictive approach to patent eligibility 
embodies a dangerous view of industrial policy, 
because it puts the Patent Office in the business of 
picking winners and losers at the outset – by 
foreclosing patent examination on the merits for 
inventions that could well run the gauntlet of the 
second level challenges that face all patent 
applications. Broader eligibility rules avoid 
truncating the process by ruling out of bounds entire 
classes of useful inventions that have been routinely 
evaluated successfully on a case-by-case basis like all 
other inventions.   
The Court should reject the Federal Circuit’s 
new, restrictive approach to patent eligibility because 
it is in conflict with the statute, the precedents of this 
Court, and sound public policy.  The approach of the 
Federal Circuit decision now on review finds no 
support in the statute.  The statute speaks in broad, 
Anticommons, Regulation, Summer 2004, at 54 (discussing the 
incentives of private holders of wasting assets to negotiate 
towards productive use); F. Scott Kieff, On Coordinating 
Transactions in Information: A Response to Smith’s Delineating 
Entitlements in Information, 117 Yale L.J. Pocket Part 101, 106 
(2007) (discussing mechanisms by which holders of the assets 
and those seeking licenses can and do transact with each other). 
For empirical evidence against the Heller-Eisenberg hypothesis, 
see Timothy Caulfield et al., Evidence and Anecdotes: An 
Analysis of Human Gene Patenting Controversies, 24 Nature 
Biotechnology 1091 (2006) (reviewing data); John P. Walsh et 
al.,  View from the Bench: Patents and Material Transfers, 309 
Science 2002 (2005) (reporting empirical results that 
demonstrate that “access to patents on knowledge inputs rarely 
imposes a significant burden on academic biomedical research”).   

expansive terms when it holds that patent protection 
should extend to “any new or useful process, machine, 
manufacturer, or composition of matter, or any new 
and useful improvement thereof.” 35 U.S.C. §101 
(2006) (emphasis added). There are no sound policy 
reasons that should lead this Court to unduly limit 
the ordinary meaning of these terms, whose sole 
proper office is to exclude the coverage of ideas, 
natural laws and natural phenomena. 
The Federal Circuit’s narrow interpretation of 
patent eligibility disrupts this sensible scheme. It 
strikes first at excluding patents in the area of 
business methods and software, in direct conflict with 
this Court’s decision in Diehr.  Worse still, the 
Federal Circuit’s approach could easily cast a pall 
over all method claims in other areas of technology.  
Given the long established links between the 
eligibility rules for software and biotech, it is likely to 
spread its tentacles to biotech in particular, thereby 
undermining the huge boost that this Court’s decision 
in  Chakrabarty  gave to bioscience, which this Court 
blessed in its subsequent decision of J.E.M. Ag 
Supply, Inc. v. Pioneer Hi-Bred Int’l, Inc., 534 U.S. 
124 (2001).  
The Federal Circuit’s sharp break from 
established law is also bad policy.  It would cloister 
off large segments of the economy from the vibrant 
beneficial impact that patents have had in the United 
States in improving innovation and competition for 
both domestic and international markets.  That 
sudden and unexplained reversal of policy would by 
judicial fiat seriously frustrate the many investment-
backed expectations in existing patents, which could 

now be subject to challenge under far higher 
standards for patent eligibility than those under 
which the patents were granted.  In particular, it 
would place the research efforts of Professor 
Chakrabarty under a cloud by reducing the prospects 
for its successful commercialization. 
If left standing, the approach the Federal 
Circuit has taken in this case would likely engender 
other unfortunate consequences in the administration 
of patent law.  There is little doubt that many of the 
modern advances in areas of technology and finance 
are wrapped up in the creation, organization, and 
interpretation of information.  That information could 
be embodied in a wide number of different physical 
substrates, none of which is critical to its social utility 
or commercial success.  There is a major risk, should 
the decision below be affirmed, that inventors will 
now seek to recast their patent claims in ways that 
seize onto some inessential detail of the invention’s 
implementation in order to satisfy a “machine or 
transformation test” that is better suited to the 
nineteenth century than the twenty-first.  But those 
strategic maneuvers will only produce deadweight 
losses, as these physical elements will unduly limit 
the scope of claims and put greater pressure on the 
doctrine of equivalents than is now the case. 
Keeping the patent eligibility gates open is 
vital for information-intensive industries like 
healthcare and finance.  The spate of new inventions 
will have positive ripple effects on key actors in 
adjacent and complementary fields. Patents on 
business and science methods require disclosure of 
valuable information about risky undertakings, 

enabling patients, doctors, investors, and investment 
advisors to make more informed decisions. For 
example, investors would generally prefer for a hedge 
fund to disclose a risky derivatives scheme in a 
patent application than to keep it a trade secret. 
Patent transparency will also outperform mandatory 
disclosure regulation in getting valuable information 
into the public domain.  Direct regulation does not 
offer any benefit to the regulated firm remotely 
comparable to that of patent protection. 
No one doubts that there are a host of 
problems in the administration of patents, which 
should be addressed.  But these are often localized to 
specific areas or involve the administration of the 
patent system.  Patent eligibility is too blunt and too 
crude an axe to deal with these problems, for which 
much more laser-like fixes are appropriate. 
In the end, Amicus of course does not take a 
position on how this particular patent application 
should be examined under the long established 
substantive rules relating to the disclosure and the 
prior art.  But the looming tragedy if the Federal 
Circuit’s ruling is upheld is that nobody will ever find 
out, as a large swath of patent applications will be 
unceremoniously barred at the gates from even 
having a shot at competing in the commercial arena 
of patents.  

The Federal Circuit is improperly swinging the 
very blunt axe of the patent eligibility doctrine to 
excise from the patent system a huge swath of 
applications, many of which could well satisfy all of 
the substantive requirements for obtaining a patent.  
The court confessed to this charge when it wrote: 
“[w]hether a claim is drawn to patent-eligible subject 
matter under § 101 is a threshold inquiry, and any 
claim of an application failing the requirements of 
§ 101 must be rejected even if it meets all of the other 
legal requirements of patentability.” Bilski, 545 F.3d 
at 950.  But at no point does it offer reasons that 
support this radical surgery.  This Court should reject 
such an approach because it is inconsistent with the 
statutory language, the precedents of this Court, and 
sound public policy.   
The Federal Circuit’s Approach Conflicts 
with the Statute 
The Federal Circuit’s “machine or 
transformation” test has no basis in the relevant 
statutory language, which is both clear and broad 
with respect to the question of 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 therefor, 
subject to the conditions and 
requirements of this title. 35 U.S.C 
§ 101.   

The section provides an expansive list in ways that do 
not try to prejudge which inventions will make sense 
for science and commerce and which do not.  In case 
there were any doubt of the breadth intended by the 
word “process” in particular, the statute also 
expressly provides its own definition: “The term 
‘process’ means process, art or method, and includes a 
new use of a known process, machine, manufacture, 
composition of matter, or material.” 35 U.S.C § 100(b) 
(2006).  The combination of these two provisions in 
the statute creates a legal test that leaves the real 
limits on patentability to come from the other 
“conditions and requirements of this title.” 35 U.S.C 
§ 101.  The linguistic framework of the next two 
sections in the statute confirms Section 101’s broad 
reach.  Those sections are respectively titled 
“Conditions for patentability; novelty and loss of right 
to patent” and “Conditions for patentability; non-
obvious subject matter.” 35 U.S.C §§ 102-103 (2006).  
That is, the serious limits on patent claims are 
imposed by the sections of Title 35 that are outside of 
Section 101.  These substantive limits include the 
prior art rules of Sections 102 and 103, which are 
known as “novelty,” “statutory bar” (“loss of right”), 
and “nonobviousness,” as well as the disclosure rules 
set forth in Section 112, which are known as “written 
description,” “best mode,” “enablement,” and 
“definiteness.” See, 35 U.S.C § 112, ¶¶1-2 (2006).  
This Court has expressly agreed with this reading.  
As Judge Newman pointed out below in dissent, in 
Diehr, the Court explained that Section 101 is not an 
independent condition of patentability, but a general 
statement of subject matter eligibility.” Bilski, 545 
F.3d at 977 (Newman, J., dissenting) (citing Diehr
450 U.S. at 189-90).   

The Federal Circuit’s Approach Conflicts 
with this Court’s Precedent 
The Federal Circuit’s machine or 
transformation test directly conflicts with this Court’s 
well-established precedent, as Judge Newman also 
explained in depth in her dissent below.  Not only did 
this Court expressly reject the “machine or 
transformation” test in both Benson and Parker v. 
Flook, 437 U.S. 584 (1978),  this Court in 
ChakrabartyDiehr, and J.E.M. Ag Supply expressly 
embraced a very broad reading of Section 101 
eligibility to reach “anything under the sun made by 
man.”  Bilski, 545 F.3d at 977, 978-83 (Newman, J., 
dissenting) (providing detailed analysis of each case) 
(quoting Chakrabarty, 477 U.S. at 309 (citing S. Rep. 
No. 82-1979, at 5 (1952), reprinted in 1952 
U.S.S.C.C.A.N. 2394, 2399; H.R. Rep. No. 82-1923, at 
6 (1952))).   
The choice of those words was intended to 
allow the patent law to sweep broadly so as to 
embrace new forms of knowledge and technology that 
were unknown when they were incorporated in the 
1952 Act by Congress (largely drafted by Judge Giles 
Rich), which was intended to reverse some of the 
narrow decisions on patent eligibility that had grown 
up in the courts in the 1940s, such as Funk Brothers 
Seed Co. v. Kalo Inoculant Co., 333 U.S. 127 (1948).  
The patentee in that case had devised a method in 
which multiple strains of a particular bacterium 
where able to coexist in order to help a wide range of 
plants take nitrogen from the air.   

If the hostile attitude toward patents 
expressed in Funk Brothers had carried over to 
modern times, it is likely that the genetic revolution 
would have been long retarded.  It was just to avoid 
this cramped interpretation of the patent law that 
Congress enacted the current Section 101.  That work 
should not be undone by adopting a new rule that is 
inconsistent with the Chakrabarty line of cases 
The Federal Circuit’s Approach Conflicts 
with Sound Policy  
Sound Patent Law Need Not Tie a 
Patentable Invention to Some 
Physical Mode of Its Expression.   
As Judge Rader pointed out in dissent, below, a 
fundamental policy issue that seems to be overlooked 
by the Federal Circuit majority is the basic 
theoretical question of “why would [it make sense for] 
the expansive language of section 101 [to] preclude 
protection of innovation simply because it is not 
transformational or properly linked to a machine 
(whatever that means)?” Bilski, 545 F.3d at 1012 
(Rader, J., dissenting) (emphasis in original).  To be 
sure, as this Court has consistently held, it does 
make good sense to exclude from patent protection 
ideas, natural phenomena, and natural laws. Diehr
450 U.S. at 185) (citing Flook, 437 U.S. at 589, 
Benson, 409 U.S. at 67).  Indeed, these categories are 
already excluded by a basic application of the more 
substantive and more well known of patent law’s 
requirements: the novelty and non-obviousness rules 
would prevent patents on all three because they 
already exist, in nature; and the disclosure rules 

would prevent patents on at least abstract ideas 
because they are not able to be put to use if they are 
merely abstract.   
It might seem as though the patent system 
needs to be updated to deal with the new technologies 
of today and tomorrow.  It would be easy to conjure 
up the image of our Founding Fathers, dressed in 18th 
century fashions, unable to anticipate that the patent 
system they provided for in the Constitution would be 
applied to modern marvels like molecular biology or 
the internet. But the charge that the law must be 
updated to deal with new technologies is absurd 
when it comes to patents.  The entire patent system, 
with its core patentability requirements of novelty 
and nonobviousness, was designed to embrace 
unforeseen technologies.  As this Court pointed out in 
the Chakrabarty decision: “A rule that unanticipated 
inventions are without protection would conflict with 
the core concept of the patent law that anticipation 
undermines patentability.”  477 U.S. 315. 
Indeed, the rapid advance of technology is 
precisely a reason why fears about hyper 
proliferation of patenting in new fields are overblown.  
With new areas of technology come new reservoirs of 
prior art.  As this Court took pains to elaborate forty 
years ago in Graham, the ever-advancing state of the 
art fixes many of the problems with patents: 
Technology, however, has advanced – 
and with remarkable rapidity in the last 
50 years. Moreover, the ambit of 
applicable art in given fields of science 
has widened by disciplines unheard of a 

half century ago. It is but an 
evenhanded application to require that 
those persons granted the benefit of a 
patent monopoly be charged with an 
awareness of these changed conditions. 
The same is true of the less technical, 
but still useful arts. He who seeks to 
build a better mousetrap today has a 
long path to tread before reaching the 
Patent Office. Graham v. John Deere
383 U.S. 1, 19 (1966).  
Strong Patent Protection Opens 
Technology Markets to Multiple 
Players and Facilitates Cooperation 
Among Them.   
A broad reading of patent eligibility has played 
a central role in fostering both output from and 
competition within a broad range of technology 
industries.  As Judge Jerome Frank once put it, 
predictable patents can be the vital slingshots 
smaller innovative ‘Davids’ use to compete against 
large established ‘Goliaths.’ See Picard v. United 
Aircraft Corp., 128 F.2d 632, 643–644 (2d Cir. 1942) 
(Frank, J. dissenting).   
Getting an invention made and bringing it to 
market requires coordination among its many 
complementary users, including developers, 
managers, laborers, other technologists, financiers, 
manufacturers, marketers, and distributors.  Patents 
help achieve this socially constructive coordination by 
allowing those various actors to interconnect with 
each other like modules of a larger system.  The 

underlying mechanism depends in at least three 
fundamental ways on the expectation that patents 
will be available and enforced.   
First, the credible threat of a published 
patent’s right to exclude acts like a beacon in the 
dark, drawing to itself all those interested in the 
patented subject matter.  This beacon effect 
motivates those diverse actors to interact with one 
another and with the patentee, starting conversations 
among the relevant parties.  
Second, the widespread expectation that the 
patent will be enforced motivates each of these 
parties to reach agreements with one another over 
the use and deployment of the technology. That 
bargaining effect falls apart if the parties are unsure 
that the patent will be enforced; if the patent is seen 
as unlikely to be enforced, there is significantly less 
need to reach agreement ex ante. Thus the fear of 
uncertain enforcement creates a disincentive for the 
necessary parties to work together at the outset.  
This change in result is not a matter of indifference.  
The voluntary agreements entered into by the 
various firms are dense relationships that are 
tailored to the specific circumstances of each case.  A 
complex cooperative agreement could easily run 
hundreds of pages, all of which are calculated to 
maximize the gains from trade among the parties.  
Remove the patent system, and the gains from 
cooperation over technology will shrink.  And the 
increased reliance on trade secrets will deny the rest 
of the scientific and other communities the public 
disclosures in the patent that help direct competitors 

into fruitful areas of research, and customers, 
advisors, and regulators into fruitful areas of inquiry.   
Third, patent protection allows patentees and 
all other complementary users of the invention 
engaged in the coordination process to appropriate 
the returns to inputs (many of which economists term 
“rival” because use by one person deprives use by 
another) to developing and commercializing 
innovation – labor, lab space, unique business 
relationships, and so forth – without the law having 
to trace their relative contributions through either 
complex administrative procedures or complex 
litigation.  Instead patents form a platform on which 
coordination and development can take place. 6   
Localized Solutions Offer the Best 
Means for Dealing with Particular 
Defects of the Patent System. 
While patents are important for increasing 
access to new technologies as well as competition, 
Amicus recognizes that a number of problems can be 
associated with patents. These should be taken 
seriously and they are.  But using the tool of patent 
eligibility to solve them would make little sense 
because it would not help resolve problems that are 
far more localized.   
6 Henry E. Smith, Intellectual Property as Property: Delineating 
Entitlements in Information, 116 Yale L.J. 1742 (2007) 
(discussing modularity and information costs); F. Scott Kieff, On 
Coordinating Transactions in Information: A Response to 
Smith’s Delineating Entitlements in Information, 117 Yale L.J. 
Pocket Part 101 (2007) (discussing beacon and bargaining 
effects for facilitating coordination).   

Here are some examples of the basic 
proposition.  The constant concerns about the delay 
in processing patents or in the reliability of patent 
determinations are well known.  But patent eligibility 
is a vastly inferior device for dealing with these than 
a shift in budgetary allocations to the Patent Office or 
a change in the procedures whereby patents can be 
challenged either before the Patent Office or in court.   
At a more doctrinal level, designing the prior 
art rules to prevent patents from issuing for 
technological advances that are already in the public 
domain or in patents acquired by third parties serves 
to protect the reliance interests of third parties 
against a late-comer into the field.7  
Similarly, designing the publication rules of 35 
U.S.C. § 122(b) and the disclosure rules of 35 U.S.C. 
§ 112 to put the world on notice of patent claims soon 
after an application is filed mitigates similar 
opportunism concerns of third parties arising after a 
patent is filed.  
The rules of laches, implied license, and 
estoppel can further act to prevent unfair surprise by 
a lurking patentee who sits on his rights when others 
actively seek to develop their own inventions.   
Finally, good rules on licensing can increase 
the gains from trade by reducing the transaction 
costs needed to make voluntary agreements.  
7 This is the role played by the novelty, statutory bar, and 
nonobviousness requirements.  See 35 U.S.C. §§ 102-03. 

Closer to home, claims of sloppy patent control 
for business patents do not require throwing out the 
baby with the bathwater, as the other patent levers 
could result in sensible standards for nonobviousness, 
novelty, and disclosure that are appropriate to each 
We need not decide here which of these 
possible reforms is better handled by Congress and 
which by the Courts.  It is enough to say that neither 
the legislature nor the judiciary should select patent 
eligibility as the tool of choice to deal with any of the 
problems mentioned above or others that may arise 
in the future.  Targeted responses to specific 
problems dominate the blunderbuss approach of the 
Federal Circuit’s “machine or transformation” test.  
Patent eligibility purports to pick winners and losers 
at the outset, before any of the more discriminating 
tests for patentability ever kick in.  
Consider the specific rejection in this case of 
Petitioners’ claim to a process for managing legal and 
business risk because the process failed to meet the 
Federal Circuit’s unduly restrictive test for patent 
eligibility – the “machine or transformation test.” 
That technology addressed one critical problem that 
contributed to the recent financial crash which was 
attributable at least in part to the inability of even 
the best financiers on Wall Street to appreciate a host 
of legal and business risks, which are difficult to 
model and thus difficult to guard against.  The need 
for techniques to estimate the frequency and severity 
of so-called low probability events is critical to 
preventing a repetition of these massive dislocations.   

Against that backdrop, it belies reality for the 
Federal Circuit majority to insist that the ability to 
develop new programs and protocols to deal with 
these issues is not of the highest order of importance.  
Yet that court’s decision explicitly derogates from its 
own two earlier decisions, State Street Bank & Trust 
v. Signature Financial Group, Inc., 149 F.3d 1368 
(Fed. Cir. 1998), and In re Alappat, 33 F.3d 1526 
(Fed. Cir. 1994), which have afforded broader 
protection for business method and scientific patents. 
It shows deep inability to perceive the arc of modern 
technology to deny patent protection for the archaic 
reason that the proposed invention does not meet 
some nineteenth century test of physical 
Put differently, all modern understandings of 
risk take seriously that a true reduction (or increase) 
in risk leads to a significant change in overall social 
welfare.  There is no doubt that even the Federal 
Circuit’s cramped test treats as patent eligible a 
method of rescuing an innocent citizen who has been 
crushed by a freight train.  No sound policy reason 
countenances turning our back categorically on 
patent protection for those novel technologies that 
enable us to better manage the risk of collision in the 
first instance.  
In sum, many of the other areas of the patent 
system’s rules have been under consideration for 
change in recent debates before Congress and this 
Court.  And perhaps they should be changed.  But 
any sensible reform should come through the front 
door of a reasoned and focused debate about the 
merits and demerits of specific changes as they relate 

to each other and to the larger patent system.  Back 
door reform by way of a new judge-made limit on 
patent eligibility is the worst way to go. 
The Federal Circuit’s Approach Will Have 
a Profound Adverse Effect on the Public’s 
Ability to Benefit from Dr. Chakrabarty’s 
Own Research 
Professor Chakrabarty’s own research on 
infectious diseases and drug design and discovery 
gives ample testimony to the importance of the case 
that bears his name.  It is now well known that the 
effectiveness of a drug varies with each patient, 
whose genes often dictate whether a particular 
compound will reach its target and how it will act 
when it arrives.  One example involves the use of the 
drug Herceptin, a monoclonal antibody, in breast 
cancer patients.  Only some breast cancer patients, 
about 10 to 15%, will have the cancers expressing a 
gene, called HER 2, that Herceptin targets.  Thus 
HER 2-positive breast cancer patients in whom the 
gene is well expressed will be excellent recipients for 
Herceptin treatment.  In contrast, others with low-
level expression of the gene will derive little benefit 
from this drug.  Expression of genes can also dictate 
if a person infected with the AIDS virus HIV-1 will 
develop AIDS or not, because of the expression of a 
gene or genes that are involved in the entry of the 
virus to the CD4+ T cells.   
These general ideas are of course in the public 
domain.  But much hard work remains to translate 
them into useful inventions that will reduce human 
disease and suffering.  These innovative ideas in 

human genotypes and drug effectiveness have given 
rise to the fast emerging medical field of personalized 
medicine, where the efficacy of a drug is determined 
based on the genetic constitution of the patient.  The 
narrow definitions of patent eligibility adopted by the 
Federal Circuit could slow down the pace of progress. 
To determine the genetic constitution of each patient 
requires not only the knowledge of the sequence of 
the genomic DNA but also methodologies to 
determine which genetic variant may represent drug 
susceptibility or a lack of it.  Such methods may not 
involve any machine, or transformation of an article 
to another state or thing.  But it is virtually certain 
that they will require extensive literature searches, 
insightful analyses, logical deductions, and complex 
experimentation to determine if the target of a drug 
is properly expressed in the patient’s genome to make 
the drug functional and effective. 
Professor Chakrabarty’s current research lies 
at the intersection of these new fields in bioscience.  
It concerns the development of multi-disease-
targeting drugs, where a single candidate drug may 
be used in the treatment of a multitude of diverse 
diseases such as cancer, HIV/AIDS, malaria, and 
others.  No such drug currently exists.  Yet strong 
patent laws will speed their development.  Seven U.S. 
patents have been issued between 2006 and 2009 
relating to the fruits of Dr. Chakrabarty’s work on 
the development of candidate drugs and several other 
patents are pending.  Thus, there is no question of 
the patent eligibility of these drugs.  Yet there is 
ample reason to support Professor Chakrabarty’s 
worry that the highly restricted definition of patent 
eligibility by the Federal Circuit will prevent future 

patents on many aspects of personalized medicine.  
The baleful consequences of such a decision would be 
to greatly reduce progress in this field and the 
consequent development of new, innovative processes 
to determine drug efficacy in individual patients.   
This Court’s 1980 Chakrabarty decision 
declared “anything under the sun that is made by 
man” is the proper test for patent eligibility.  447 U.S. 
309.  That broad interpretation, not any stylized 
“machine or transformation test,” is the key to the 
full development of personalized medicine and other 
aspects of biomedical science.  The Federal Circuit’s 
decision to restrict patent eligibility of these 
important innovations will do much to prevent or 
delay such critical innovations from reaching the 
bedside or the market place.   

Amicus respectfully urges this Court to reject 
the “machine or transformation” test articulated by 
the Federal Circuit and reaffirm the broad rules for 
patent eligibility elucidated by this Court in 
ChakrabartyDiehr, and J.E.M. Ag Supply.  
Respectfully submitted,  
1111 East 60th Street 
   Counsel of Record 
Chicago, Illinois 60637 
1111 23rd Street, NW 
(773) 702-9563 
Apt 8d 
Washington, DC  20037 
(202) 558-6667 
August 6, 2009 
Counsel for Amicus Curiae 

I hereby certify that I have caused three true 
and correct copies of this BRIEF OF DR. ANANDA 
SUPPORT OF PETITIONERS to be served on this 6th 
day of August, 2009, by Federal Express, as well as 
one electronic copy by email, to the following:   
J. Michael Jakes  
Finnegan Henderson Farabow Garrett & 
Dunner, LLP  
901 New York Avenue, NW  
Washington, DC  20001-4413  
(202) 408-4000 
Attorneys for Petitioners, Bernard L. 
Bilski and Rand A. Warsaw  
Elena Kagan, Solicitor General 
United States Department of Justice  
950 Pennsylvania Avenue, N.W. 
Washington, DC  20530-0001 
(202) 514-2217 
Attorneys for John J. Doll, Acting Under 
Secretary of Commerce of Intellectual 
Property and Acting Director, Patent 
and Trademark Office  

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