Utility and Biotechnology Patenting

Georgios I Zekos BSc(econ), JD, LLM, PhD

Associate Professor of Law

Riga Graduate School of Law

Riga, Latvia

[email protected]

Copyright © Georgios I Zekos 2006. First Published in Web Journal of Current Legal Issues.

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Contents

Bibliography

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Introduction

The Human Genome Project (“HGP”) identifies all the genes in the human and determines the sequence of base pairs for the entire human genome storing information in databases for further advancements in biotechnology. In other words the genome is the “complete set of genetic information of an organism”.

Deoxyribonucleic acid (“DNA”) is contained within the cells that make up all living things enclosing within a cell’s nucleus the code of the “information necessary to build the cells and tissue of an organism”.  The DNA double helix structure is governed by a process called complementation and the messenger RNA (“mRNA”) copies the DNA template and carries the DNA’s message outside of the cell’s nucleus. (Cooper 2000, pp 95-96) The overall notion of converting DNA to mRNA to protein is the central dogma of molecular biology. Tools such as recombinant DNA techniques, classical gene analysis, and gene mapping allow the isolation of the genes that encode particular proteins.  When a strand contains all the details necessary to explicate the sequence of bases on the other strand, this is known as complementation.  A gene is a small segment of DNA that can exist in various forms, called alleles. “Allelic variation causes heredity variation within a species. At the protein level, allelic variation becomes protein variation.” It is very common to clone cDNA through various recombinant techniques, and compile the cDNA into libraries for later use as probes to study which genes are expressed in particular tissues at any given time. A DNA sequence can also have non-coding regions, which do not play a role in protein synthesis, and regulatory regions, which mainly inform the gene when to start or stop the process of protein synthesis.

The entire collection of genetic material of a particular organism is known as its “genome.” Each cell in an organism contains a copy of the same genome, in the form of a set of structures called “chromosomes,” which are made up of DNA. Genetic sequence information is inherited through processes of reproduction. Within each gene typically are segments of DNA that encode protein chains (“polypeptides”) to be synthesized by the cell interspersed with non-coding segments of DNA.

The principal purposes of patent law are to recompense invention, encourage disclosure of inventions thus stimulating further advancements, and protect ideas in the public domain. Patentable subject matter includes “any . . . process, machine, manufacture, composition of matter or any new and useful improvement thereof” provided that it satisfies the statutory requirements of utility, novelty, and non-obviousness (Aronson v. Quick Point Pencil Co 440 U.S. 257, 262 (1979)).Research results on the functional characterization of genes have led many scientific organizations to seek patents claiming particular DNA molecules as having biological significance.

The patent system protects a patentee’s work-product from prospective infringers by preventing others from copying, making, using, offering for sale, or selling another’s work without consent. Most prospective gene patentees seek patent rights on genetic sequences, which lack intrinsic marketability or definite utility. Genetic research contributes to the development of many of today’s breakthrough pharmaceuticals and diagnostic tests.

The patent system significantly benefits society by expediting the discovery of new medications, technologies, and non-infringing improvements while decreasing consumer costs through the development of non-infringing substitutes. Biotechnology research is unveiling science at a more and more undeveloped level while patent law is becoming broader, thus threatening to remove fundamental building blocks of science from the public domain (Haseltine 2000)

Should DNA sequences be protected by patents? Is there a need to put an end to the international rush to patent DNA fragment sequences with no known function? Our analysis is based on USA law and examines the impact of utility on the patentability of biotechnology inventions.

 

Patentability of biotechnology

Knowledge is developed in a cooperative manner through the open disclosure of new knowledge and peer testing of that knowledge. The Patent Act provides that to be eligible for a U.S. patent, a claimed invention must constitute patentable subject matter and meet certain standards of utility, novelty, and non-obviousness. In addition, the applicant must provide an adequate disclosure of the invention and must file the application promptly after the commencement of certain activities deemed to place the public in possession of the invention (Summers 2003, pp 477-478). The discovery of every new and useful DNA molecule is contemporaneous with the act of reducing the molecule’s name and its structural formula to writing.  Courts have interpreted the patentable subject matter requirement of § 101 to exclude products of nature and discoveries in non-technological fields, such as pure mathematics and the liberal arts (Zekos 2004).

Under the prevailing Federal Circuit interpretation of the enablement requirement, a § 102 reference must disclose a method of making the claimed invention in any case where the method is not obvious to one with ordinary skill, but need not disclose a use for the claimed invention (Diamond v. Chakrabarty 447 U.S. 303). By comparison, the § 112 enablement requirement for a patent application is more stringent: a patent application must teach anyone skilled in the art both how to make and how to use the claimed invention (In re Donohue 766 F.2d  533).

The non-obviousness inquiry focuses on a comparison between the claimed invention and the relevant prior art. The non-obviousness requirement calls for a comparison between the prior art and the elements of the claimed invention from the perspective of one of ordinary skill in the art. Besides, patentability shall not be negatived by the approach in which the invention was made, even if the techniques used were routine in the art or automated (In re Payne 606 F.2d 303). The non-obviousness inquiry is a case-by-case analysis in which “the scope and content of the prior art are to be determined; differences between the prior art and the claims at issue are to be ascertained; and the level of ordinary skill in the pertinent art resolved” (Rai 2003, 1070).

If a claimed DNA molecule’s structural formula is neither disclosed nor suggested by the prior art, the invention may be considered non-obvious even though broad procedures leading to the making and use of the molecule are well-known and described in the prior art. Actually, this approach equates the disclosure of a new and non-obvious structural formula for a useful DNA molecule with the act of making “a new chemical . . . available as a basis for future research.” For instance, in In re Deuel (51 F.3d 1552, 1557) the Federal Circuit reviewed a § 103 rejection of claims directed to isolated and purified cDNA molecules encoding certain proteins known as heparin-binding growth factors (“HBGFs”). A DNA patent claim normally identifies the claimed DNA molecules by reciting their structural formulae; i.e., by disclosing and referring to the particular sequences of nucleotides that make up the molecules.

On the one hand, the raw sequence of the human genome is a natural manifestation of nature, not made by the human hand. On the other hand, the other format consists of the cloned or isolated and purified partial DNA fragments. The DNA fragments must be excised from the natural context of the human genome, isolated, purified, and cloned before scientists can study them. Since the sequenced gene fragments, like ESTs, do not exist in their natural state and are therefore “not nature’s handiwork,” they are “patentable subject matter under §101” (In re Bergstrom 427 F.2d 1394, 1397). Therefore, gene patentees can circumvent the “anything in nature” prohibition for patents (Amgen v. Chugai Pharm. 927 F.2d 1200). Today, computer searches characterizing genes based on probability replace experimental laboratory data.

Doctrinal support for the patentability of DNA under § 101 is grounded in the structural and functional distinctions between an isolated and purified DNA molecule, a chemical union constituting a “composition of matter”, and its naturally occurring, impure (i.e. less pure) counterpart (Parke-Davis & Co. v. H.K. Mulford Co. 189 F. 95, 103). New and useful methods of using DNA molecules are also eligible for patenting, under the § 101 subject matter category of “new and useful process.” Therefore, a new use for a DNA molecule may be patentable even if the DNA molecule itself is already well known and consequently un-patentable. The structural disclosure of DNA molecules in a patent application comports not only with the registry model of DNA discovery, but also with the § 101 patentable subject matter requirement.

The general rule is that the first to conceive the invention and reduce the invention to practice either “actually,” by building a working model or “constructively,” by filing a patent application is the first true inventor.

In Amgen, Inc. v. Chugai Pharmaceutical Co. (927 F.2d 1200) the court concluded that he had no conception until that date:

“Until Fritsch had a complete mental conception of [the claimed DNA molecule] and a method for its preparation, in which the precise identity of the sequence is envisioned, or in terms of other characteristics sufficient to distinguish it from other genes, all he had was an objective to make an invention which he could not then adequately describe or define.”

Hence, an inventor could not claim a date of invention earlier than his actual reduction to practice when a gene had been isolated.

The United States Patent and Trademark Office (“PTO”) initially rejected patent applications for DNA sequences on the premise that the claimed inventions lacked utility. There is a need to balance between protecting innovation and ensuring access to technology.

In the milestone case Diamond v. Chakrabarty (447 U.S. 303, 309) the Supreme Court affirmed a judgment which allowed the patent applicant’s claims for a human-made, genetically engineered bacterium capable of breaking down multiple components of crude oil. The Supreme Court has interpreted the four statutory classes of any process, machine, manufacture, or composition of matter to “include anything under the sun that is made by man.” Consequently, manifestations of nature, falling outside the scope of this definition, are not patentable. The court rejected the argument that Congress must explicitly authorize protection of new patentable subject matter. The bacterium in Diamond v. Chakrabarty had “markedly different characteristics from any found in nature” and the discovery was Chakrabarty’s invention not that of nature opening the door for patents grounded in genetic technology. Moreover, the bacterium was of the genus Pseudomonas providing separate hydrocarbon degradative pathways and this characteristic was not found in naturally occurring bacteria and was claimed to provide “more efficient and rapid oil-spill control.” The argument that a micro-organism was not patentable because it was analogous to a natural, physical phenomenon is rejected.

Manifestations of nature, such as the laws of nature, physical phenomena, and abstract ideas, are free to all and subsequently are not patentable but the Chakrabarty’s bacteria were not the “handiwork of nature,” but the result of human ingenuity and research. In re Deuel, the court reiterated an earlier opinion stating that in the absence of prior art suggesting the claimed DNA sequence, Deuel’s DNA sequence was non-obvious and, so, patentable because of the redundancy of the genetic code and the enormous number of sequences that could code for one protein. As long as the patentee can prevail over anticipation and obviousness, he/she can patent anything that does not occur in nature and so the question now is whether genes constitute a “manufacture” or a “composition of matter.”

Since Chakrabarty, the scope of patentable subject matter under § 101 has been extended to cover an ever widening range of biological materials that have been genetically altered, purified, or otherwise changed through human intervention into forms not found in nature. A DNA molecule excised from a living cell and stored in a saline solution, with no other DNA present, would be “isolated” and “purified” within the meaning of the patent claim, since water and salt are considered small molecules.

One of the strongest arguments opposing DNA sequence patenting is the assertion that such patenting hinders innovation rather than promoting it and so holders of DNA sequence patents have the capability to deprive researchers and physicians of any use of that sequence for diagnosis, treatment, or development of disease treatments. It is argued that granting patents in DNA area will compromise effective medical care and so a patent-holder’s ability to obstruct others from testing for the presence of a particular disease gene has increased concerns over the reasonable access to such tests and the quality of testing procedures. In other words, patients may be forced to pay the costs passed onto them, or look for less effective, less reliable, or possibly unconventional methods of treatment. Besides, to date, there are a number of predictive gene-testing options that are available or are being developed for diseases such as Tay-Sachs disease, cystic fibrosis, Huntington’s disease, Alzheimer’s disease, and predispositions to certain cancers and more others.

The growing trend towards the commercialization of research has led to the practice of promoting secrecy and hindering the exchange of information amongst researchers in biotechnology. It is true that information-sharing between laboratories seems to be inhibited by patents and licensing. In other word, until researchers acquire patent rights, publication of research findings, may be delayed and the commercialization of genetic research diminishes the collaborative efforts in scientific research.

DNA sequences are not only compositions of matter, but are also information and so it could be said that allowing the patenting of such useful information is a departure from the patent rules because the DNA sequences look less like new chemical entities than they do like new scientific information. It could be said that purified genes and isolated gene fragments are no dissimilar from naturally occurring sequences and as a result, because they exist in nature as naturally occurring manifestations fall outside the scope of patentable subject matter which means they are statutorily barred from patent protection. It could be argued that despite that a purified gene is similar to one naturally occurred the man’s work brought it in the purified condition which includes an inventory step that allows the reward of a patent.

DNA sequence patenting has been attacked on religious grounds based on the notion that genetic manipulation is the same as “playing God,” and that the fruits of such work should not be rewarded with patent control. As human knowledge increases, the area within human control begins to intrude upon God's territory.  It has to be taken into consideration that God has given the humans spirit in order to discover things and move from the material world into the spiritual world and so as long as the humans’ effort focused on the knowledge of life and not distortion of life patenting of new inventions are not against religion. On the other hand, granting patent rights in genetic material is synonymous to supplying property rights in life, which could lead to the exploitation of human beings as commodities. Patenting genetic material violates the “fundamental principle of morality that human beings not be used simply as a means to one's own ends”. (Pitcher 2003, 298). By patenting genes, one is reducing life to a commodity like any other inanimate object. By allowing patents on genetic material will lead to further injustice in the distribution of wealth in the world (Demaine and Fellmeth 2002, 440). DNA sequence patenting denies the benefits of biotechnological (“biotech”) research to under-developed countries to the advantage of a few industrialized nations but patenting an invention in one country does not prevent the use of that invention in another country.

In order to make useful progress in gene research, private sector investment incentives, including patenting, must exist (Lacy 1998, pp 801-802).  Without patent protection and the potential for commercial return, investors would be reluctant to invest in gene research. Patents encourage disclosure of information, and without patents, researchers would be required to rely on trade secret protections (Olsen 1997, pp 321-322). Patents result in the spreading of technological information to the scientific community for use as a basis for further research.  There is need to find a compromise that protects knowledge in the public domain and encourages further biotech research.

Utility In Biotechnology Patents

At the time of creation or discovery, an invention must be novel in order to be patentable and so an invention that is anticipated by the prior art is not novel. The invention disclosure must adequately enable one skilled in the art to make and use the invention without undue experimentation. The scientific information available about proteins, DNA, amino acids, and extrapolated EST functions renders the gene fragment obvious as soon as any sequencer splices up the gene. Under the proposed 35 U.S.C. § 102, prior art is limited to the following categories:

The U.S. presently validate applications for isolated genes and gene fragments, provided three utility criteria for patents are satisfied, specificity, substantiality, and credibility, narrowing patent claims as well as reduce the number of unsubstantiated applications (Patent Reform Act of 2005, H.R. 2795, 109th Cong. § 3 (2005)). USPTO defines “credible” as whether someone of ordinary skill in the art would believe the asserted utility based on the totality of evidence. Specific and substantial utility refers to usefulness for any particular, practical purpose excluding “throw-away,” “insubstantial,” or “non-specific” uses and refers to practical, real-world uses. Nevertheless, commercial viability of a product is not required to establish usefulness. The applicant must show that he/she really invented what he/she claims and that he/she possessed the claimed invention at the time of application. A patent is the quid pro quo for the public’s deriving an invention with substantial utility. Moreover, courts divide the utility requirement into three parts: general utility, specific utility, and moral utility. An invention has general utility if it is operable, or capable of doing something in general terms. An invention possesses specific utility if the invention provides a solution to a stated problem. Courts question whether an invention is valuable to society or if there is an absence of immoral purposes. It has to be taken into account that courts have enforced previously the utility requirement by demanding that inventors meet only a very low threshold for patentability. Furthermore, the utility requirement is effortlessly met for some types of inventions such as mechanical or electrical inventions but the utility requirement is often a “problem with chemical compounds and processes —predominantly pharmaceutical compounds” and biotechnology because in these fields, inventors synthesize compounds without a defined knowledge of how they may be used to achieve a practical working result. Consequently, a specific isolated and purified DNA sequence may have multiple prospective downstream uses that are unknown to the researcher.

A claimed invention must be “useful” to be patentable and the burden for proving utility is intrinsically higher for biological and chemical inventions because there is “no reliable way of predicting utility based upon chemical formulas alone” (Lemley 1997, 1007 n.78). In Lowell v. Lewis (15 F. Cas. 1018, 1019) the court broadly interpreted the needed utility requirement and required nothing more than a showing that the invention was not “frivolous or injurious to the well-being, good policy or sound morals of society.” On the other hand, the Supreme Court in Brenner v. Manson (383 U.S. 519, 534–35) rejected this de minimus standard in concluding that a chemical compound that only had utility as a potential object for use-testing did not satisfy the utility requirement. It has to be taken into account that use-testing are “objects upon which scientific research could be performed with no assurance that anything useful will be discovered in the end” (In re Fisher 421 F.3d 1365, 1373). There is a need for an invention to have some practical or substantial utility in order to be considered useful for patent purposes. A patent could not be a reward for the search, but compensation for its successful conclusion. Something that is not presently “useful” may become so some time in the future and so there is a need for a “substantial utility” standard and so there is no utility in a product with only a speculative use (Cross v. Iizuka 753 F.2d 1040, 1044). The grant of a patent is exchanged for the advantage derived by the public from an invention with substantial utility and the Court held that a claimed invention does not have patentable utility “unless and until . . . specific benefit exists in currently available form.” While the Brenner holding indicated the minimum degree of utility that a patent applicant must assert, it did not address the standard of proof required to demonstrate the asserted utility.

The case of In re Fisher (421 F.3d 1365, 1373) involved a patent application for ESTs generated from maize pooled leaf tissue. The utility claims asserted in that application included: serving as molecular markers for mapping the entire maize genome; identifying polymorphisms; restricting protein expression; and locating genetic molecules of other plants and organisms. The uses declared were non-specific because they applied in general to nucleic acids; thus, the utility requirement was not satisfied. Moreover, there was no known use for the proteins produced as final products resulting from processes involving the claimed ESTs and so because identifying a real-world use required further research, the substantial utility requirement was also not fulfilled. Fisher appealed to the Board of Patent Appeals and Interferences (“BPAI”) where the court upheld the examiner's final rejection. The U.S. Court of Appeals for the Federal Circuit reviewed the case using a “substantial evidence” standard adopting the real-world test for determining substantial utility as articulated by the PTO. Substantial evidence is such related evidence as a reasonable mind might accept as adequate to support a conclusion.  Additionally, the court stated that, for an invention to qualify as specific, “an application must disclose a use which is not so vague as to be meaningless.” Consequently, a claimed utility must provide a specific, well-defined benefit to society and the courts interpret the statutory term “useful” to require disclosure of at least one available practical benefit to the public.

The 2001 Guidelines reflect this determination by requiring the disclosure of at least one specific, substantial, and credible utility. If no such utility is disclosed or promptly perceptible from an application, the Office should reject the claim (2001 Guidelines, Comment 9, 66 Fed. Reg. 1,092, 1,094). A utility is “specific” if it is applicable to the subject matter claimed, rather than to the broad class of the invention. A claim to a DNA molecule for use as a “gene probe” is considered specific only if the application discloses a specific DNA target. A utility is “substantial” if it defines a “real world” context of use and is not a “throw away” utility. The use of a DNA molecule in assaying a material “which has a stated correlation to a predisposition to the onset of a particular disease condition” is considered substantial, while the use of a DNA molecule in assaying a material that itself has no disclosed specific and substantial utility is not. Examples of throw away utilities for a specific protein molecule would be using it as an animal food supplement or a shampoo ingredient and a utility is “credible” unless the logic underlying the assertion of utility would be considered seriously flawed or inconsistent with the asserted facts from the standpoint of one of ordinary skill in the art. Furthermore, the court held that “a claim directed to a polynucleotide disclosed to be useful as a ‘gene probe’ or ‘chromosome marker,’ as is the case here, fails to satisfy the specific utility requirement unless a specific DNA target is also disclosed.” An isolated and purified DNA molecule may meet the statutory utility requirement if it can be used to produce a useful protein or it hybridizes near and serves as a marker for a disease gene. As a result, a DNA molecule is not per se un-patentable for lack of utility, and each application claim must be examined on its own facts. The majority’s inflexible opinion in Fisher fails to address the research value that ESTs and other DNA sequences have within the biotech community and in his dissenting opinion, Judge Rader defended the utility of the claimed ESTs as research tools in studying and isolating other molecules. Rader analogized the claimed ESTs to a microscope because both are useful tools that lead scientists to a greater understanding of the corn genome and so both take a researcher one step closer to identifying and understanding a previously unknown and invisible structure. Judge Rader concluded that the majority erred in holding that “a research tool has a ‘specific’ and ‘substantial’ utility only if the studied object is readily understandable using the claimed tool—that no further research is required.” On the other hand, the PTO must distinguish between inventions that have expressly identified substantial utility and inventions whose asserted utility requires further research to identify or reasonably confirm. Labels such as “research tool,” “intermediate” or “for research purposes” are not helpful in determining if an applicant has identified a specific and substantial utility for the invention. Besides, the MPEP mainly explains that a claim for a DNA sequence patent must specify a particular DNA target but does not require disclosure of the particular function of the DNA target. While Brenner held that a chemical process that produced products of unknown function were unpatentable, in Fisher, the ESTs were not a process or method but products themselves. The asserted utility for those ESTs were to serve as research tools as probes and markers for specific DNA targets and not as methods or intermediates for producing those targets. Fisher's claimed EST's are beneficial to society.

Gene machines compare the gene fragments to a library of known ESTs, they only infer protein expression and function from the code, yielding largely theoretical information. Are isolated genes invented or discovered?  It is argue that isolated genes are not invented, but discovered.  The USPTO cannot reject a patent application based on the manner in which the invention was developed. An inventor can never invent a gene because genes existed since the beginning of time and are not new compositions. Genes are not novel because they are closer to being discoveries than new compositions. A gene patent covers an isolated, purified gene, not a naturally occurring gene that exists within the human body. The technical production of a gene could be a patentable invention but of course the role of genes in the human body cannot be invented or altered. The production of genes and the invention of their role for a new creature cannot be denied since biotechnology and nanotechnology advance.

One gene contains many ESTs, each of which can code for a functional protein and so one gene may code for several different protein functions. Hence, the inability to claim patent rights to an already patented gene fragment may deter other researchers from further investigating the same fragment. The high-speed search machines neither infer potential useful drugs or therapeutics nor investigate the potential interactions of ESTs with other sequences. As a result, the utility disclosure needed for patent protection may be inadequate, since a potential gene patentee may not fully understand the gene’s function.

Giving patent rights to a researcher who lacks a comprehensible understanding of the EST’s function would allow gene patentees to incorrectly benefit from future studies conducted with or related to the same EST. For instance, at the time of the application, HGS neither claimed nor contemplated an anti-viral utility for the CCR5 gene by describing its utility as a screening tool for receptor agonists and antagonists as well as for gene mutation detection and so through later research, the NIH determined that the gene played a role in the transmission of the AIDS virus and identified CCR5 as the docking mechanism on cell surfaces used by the virus to infect cells which means that HGS executed a licensing agreement with Praecis Pharmaceuticals for the development of a HIV therapy based on CCR5 regardless that the main invention does not made by HGS.

Can the utility requirement for patentability be used to curtail the number of patents issued on biotechnology inventions and research tools?  The utility requirement for patentability can curtail the number of patents issued on biotechnology inventions and research tools with the meaning that it will force inventor to patent the final invention and not merely abstract ideas with the expectation to finally arrive into the invention which means that this way of patenting disallow others from using the scientific knowledge to advance technology and knowledge. Utility presents a minimal requirement that the invention be capable of achieving a pragmatic result. Forman (2002) argues that more restrictive PTO guidelines will hamper the progress of biotechnology invention by delaying patent protection until later stages of invention resulting in less investment in high-risk research and development. The author argues that the utility requirement will force inventors to produce better inventions and it will lead in a more high risk research and development in order to get the patent and so all the money that will correspond to the use of the patent. USPTO issued examination guidelines that set forth a perhaps more restrictive view of utility than courts have formerly required. As a result the utility requirement ensures that the public receives an invention that is useful in exchange for the limited right to prohibit others from practicing the invention.  In other words, usefulness performs some function of certain benefit to society or achieves some practical utility.

Conclusions

Early patenting in the biotechnology innovation process is important to the continued growth and development of the industry.

The patentable value in biotechnology lies not in isolating a gene sequence, but further downstream once the gene’s function has been determined. The utility requirement should require an applicant for a gene patent to disclose the encoded protein along with the function of that protein. If a patent were allowed to issue on a claimed process, yielding a product with unknown utility, then the patent might include unknown areas of scientific development without providing the benefit to society, the substantial utility, that is at the heart of the quid pro quo that Congress had contemplated which means that there is a need to demonstrate a particular benefit from the patentee’s claimed invention. For instance, in pharmaceutical inventions the applicant must prove the practical utility or usefulness of the invention for which patent protection is sought and so applicants must provide adequate evidence to convince a person skilled in the specific art that the invention possesses the asserted utility.

Heightening the utility requirement makes sense for ESTs with a minimal disclosed utility given the application of techniques such as high-throughput sequencing. Nonetheless, the utility requirement should not preclude the patenting of research tools whose only function relates to the development or research of commercial applications. It has to be taken into consideration that some biotechnology firms only create research tools, and a market for those tools has developed and if research tools are not patentable, developers of those tools will use them in secret rather than disclosing them publicly. Without public disclosure of the tools, competing companies will waste considerable resources duplicating research in order to develop a beforehand invented tool.

Finally, it should not be allowed to patent merely abstract ideas which are simply science and so nature discovered by science cannot be transformed into merchandise. 

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