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In the recent decision, CSIRO v BASF Plant Science GmbH [2020] FCA 328, the Federal Court of Australia considered the allowability of amendments to patent specifications under s 102(1) of the Patents Act 1990, as amended by the ‘Raising the Bar’ Act[1]. In overturning a decision of the Commissioner of Patents, Beach J decided that BASF’s proposed amendments were impermissible because they claimed and disclosed matter that extended beyond the specification as filed. In so doing, the Court decided that the same strict test used by UK Courts should also be applied in relation to added matter in Australia.

The Background

At issue is a patent application filed by BASF Plant Sciences GmbH (BASF) entitled “Process for the production of polyunsaturated fatty acids in transgenic organisms”, which relates to genes from a species of unicellular algae that code for enzymes which can be employed for the recombinant production of polyunsaturated fatty acids (PUFAs) in plants. Specifically, the invention relates to a pathway for the synthesis of long-chain PUFAs, that involves a sequence of enzymatic reactions to convert shorter-chain PUFAs into commercially desirable long-chain PUFAs. The claims relate to isolating the genes for those enzymes in a species of unicellular algae, Ostreococcus lucimarinus, and introducing those genes into suitable oil-producing crops. Performing the invention enables the production of the valuable fatty acids in transgenic commercial crops.

CSIRO opposed BASF’s accepted application, and during the opposition proceedings BASF applied to amend its patent and introduce new dependent claims. The Australian Patent Office initially refused the proposed amendments on the basis that, as a result of the proposed amendments, the specification would not comply with the requirements of s 40(3). However, a second set of proposed amendments was submitted, which a Delegate of the Commissioner of Patents subsequently allowed. CSIRO then lodged an appeal to the Federal Court against that decision under s 104(7) of the Patents Act 1990.

The amendments

In a passage referred to by the parties as the “bridging paragraph”, the specification as filed stated that:

      “The invention, the subject of the present application, is directed to the following:

  • a CoA-dependent delta-6 desaturase having the substrate specificity of the delta-6 desaturase shown in SEQ ID NO:14 [referred to by Beach J as Feature A]and
  • the above CoA-dependent delta-6 desaturase which has a preference for conversion of alpha linolenic acid compared to linoleic acid [referred to by Beach J as Feature B].” (emphasis added)

The experts agreed that the words “the above” in the statement in the second bullet point of the bridging paragraph meant that this statement (i.e., the “conversion preference”) must be read together with the statement in the first bullet point of the bridging paragraph (i.e., the “substrate specificity”). In other words, the invention is directed to the claimed enzyme having the substrate specificity shown in amino acid “SEQ ID NO:14”, and having a certain conversion preference. The bridging paragraph is the only place in which a conversion preference is disclosed in the body of the specification of the application as filed. The invention described in each bullet point of the bridging paragraph is claimed in claims 1 and 2 respectively of the application as filed.

BASF removed the bridging paragraph and deleted corresponding claims 1 and 2 by amendment during prosecution and replaced it with a description that defines the invention as:

  • a process for the production of a substance of general formula I … wherein the process comprises the cultivation of (i) a host cell … or (ii) a transgenic non-human organism comprising … “an isolated polynucleotide comprising a nucleic acid sequence coding for a CoA-dependent delta-6 desaturase having at least 75% identity to a nucleotide sequence which codes for a polypeptide as shown in SEQ ID NO: 14” [referred to by Beach J as “Feature C”]; and
  • use of an isolated polynucleotide … (or vector, host cell, or transgenic non-human organism comprising said nucleic acid sequence) … for the production of an oil, lipid or fatty acid composition.

In light of the amendments to the bridging paragraph and the deletion of the corresponding claims, the application as accepted did not refer to Feature A, Feature B or Feature A combined with Feature B.

As Beach J noted at [130], Feature C captures a broader range of polypeptides than Feature A. That is, Feature A (substrate specificity of the Δ6-desaturase shown in SEQ ID NO:14) is a subset of Feature C (at least 75% identity to SEQ ID NO:14).

In a further round of post-acceptance amendments BASF sought to insert new dependent claims, to a process for production of, and use of, a CoA-dependent Δ6-desaturase:

a) having at least 75% identity to a nucleotide sequence which codes for a polypeptide as shown in SEQ ID NO:14 [Feature C]; and

b) that preferentially converts alpha linolenic acid compared to linoleic acid [Feature B].

The amendments also sought to introduce the following description after the consistory clause:

“According to an embodiment of the abovementioned process and use, the CoA-dependent desaturase preferentially converts alpha-linolenic acid compared to linoleic acid.” [Feature B]

CSIRO argued (at [166]) that the post acceptance amendments were not allowable as they would introduce a claim combining Feature C with Feature B, when the only disclosure of Feature B in the specification as filed was in the context of Feature A (a much narrower subset of Feature C) in the bridging paragraph.

Issues and Decision

Section 102(1) relevantly provides:

(1) An amendment of a complete specification is not allowable if, as a result of the amendment, the specification would claim or disclose matter that extends beyond that disclosed in the following documents taken together:

(a) the complete specification as filed;

(b) other prescribed documents (if any).

Beach J noted that that the Raising the Bar provisions were intended to mirror other jurisdictions, such as the UK and Europe, and that it was intended that Australian courts would have regard to the developments of case law in those jurisdictions when interpreting the Raising the Bar provisions. More specifically, he noted the intention disclosed in the explanatory memorandum to the Raising the Bar amendments that the operation ss40(2) and (3) as amended (which deal with sufficiency and support) be as close as practicable to that given to the corresponding provisions in the UK Patents Act and the European Patent Convention,

Beach J therefore commenced a review of the UK authorities and in coming to his decision, noted two “conceptual themes permeate the UK authorities”, namely “added matter” and “intermediate generalisation”.

In terms of the former, and with reference to several landmark UK decisions on added matter (including Bonzel[2]Richardson-Vicks[3], and European Central Bank[4]), it was noted that subject matter will be impermissible added matter “unless it is clearly and unambiguously disclosed in the application as filed”, having reference to what has been disclosed both explicitly and implicitly.

As to intermediate generalisations, it is useful to consider the EPO guidelines[5], which explain:

“…the content of the application as filed must not be considered to be a reservoir from which individual features pertaining to separate embodiments can be combined in order to artificially create a particular combination.

When a feature is taken from a particular embodiment and added to the claim, it has to be established that

  • the feature is not related or inextricably linked to the other features of that embodiment and
  • the overall disclosure justifies the generalising isolation of the feature and its introduction into the claim.

… it has to be ensured that the skilled person is not presented with information which is not directly and unambiguously derivable from the originally filed application, even when account is taken of matter which is implicit to a person skilled in the art using his common general knowledge”

In other words, the concept of “intermediate generalisation” requires that an amendment is not allowable if it takes a feature which is only disclosed in a particular context and seeks to introduce it into a claim deprived of that context.

Beach J found that there was “no good reason not to follow the UK authorities” to apply these analogous concepts for the purposes of construing the present form of s 102(1) of the Act.[6] In doing so, Beach J confirmed that, after Raising the Bar “the test is a strict one” in Australia, and that the concept of intermediate generalisation applies to s 102(1).

BASF argued that the relevant amendments, including the addition of new claims, were narrowing amendments. Beach J accepted this insofar as the comparison was with the accepted claims, however he noted that this did not resolve the issue of whether the amended specification would claim or disclose matter extending beyond that disclosed in the specification as filed.

BASF further argued that there was disclosure of Feature C in a particular paragraph of the specification as filed. However, Beach J decided that this paragraph could only be read in the context of the description of ‘the invention’ in the bridging paragraph. In this regard, Beach J considered that the bridging paragraph did not provide disclosure of a delta-6 desaturase with Feature B (the “conversion preference”) in the absence of Feature A (the “substrate specificity”).  As mentioned above, Justice Beach also considered that Feature A was not the same as the 75% homology requirement that BASF sought to introduce into the claims (Feature C).  This was because two enzymes can have different substrate specificities and still have 75% homology to each other at the DNA level.

Justice Beach concluded that BASF’s amendment sought to remove Feature B from the context in which it was disclosed in the application as filed (namely, in conjunction with Feature A) and introduce it into the specification and the claims deprived of that context.  The amendments generalised the originally disclosed technical information (applying Feature B in the broader context of Feature C, as opposed to Feature A), thereby introducing subject-matter extending beyond the content of the application as filed. This was an example of an impermissible intermediate generalisation.

As a result, BASF’s amendment was refused, and CSIRO’s appeal was upheld.


In the first Federal Court decision on “added matter” under the Raising the Bar Act, Beach J has confirmed that the test in Australia for added matter is strict, and that subject matter will be impermissibly added “unless it is clearly and unambiguously disclosed in the application as filed”. Importantly, until now it has not been clear whether the prohibition on “intermediate generalisation”, a familiar concept in European patent law, would be adopted in Australia. Beach J has confirmed that an intermediate generalisation is not permissible, where a feature which is only disclosed in a particular context (e.g. a particular example) is introduced into a claim deprived of that context.

At the time of filing a patent application, it is important to provide a full disclosure of your invention as adding subject matter later will not be allowable. It is also important to ensure that your patent application discloses your invention in terms that encompass all variants of the invention that you may later wish to claim.

Such limitations should also be borne in mind if seeking to limit granted claims in pre-litigation or litigation to avoid prior art brought to the attention of the patentee.

Shelston IP is well placed to advise its clients on how to best draft a patent specification to satisfy these important requirements and on related issues in a litigation context. If readers have any questions, please do not hesitate to contact any of our Shelston IP patent attorneys or lawyers.

[1] Intellectual Property Laws Amendment (Raising the Bar) Act 2012 (Cth) (the Raising the Bar Act)

[2] Bonzel v Intervention Ltd (No 3) [1991] RPC 553 (Bonzel)

[3] Richardson-Vicks Inc’s Patent [1995] RPC 568 (Richardson-Vicks)

[4] European Central Bank v Document Security Systems Inc [2007] EWHC 600 (European Central Bank)

[5] https://www.epo.org/law-practice/legal-texts/html/guidelines/e/h_v_3_2_1.htm

[6] Commonwealth Scientific and Industrial Research Organisation v BASF Plant Science GmbH [2020] FCA 328 at [214]

It seems the abolition of Australia’s second-tier patent system, the innovation patent, (as detrimental as this will be for Australian business) could be considered a high-profile distraction to divert attention away from new laws that will potentially render patents claiming chemical compounds, with reference to a structural formula, vulnerable to invalidation.

This issue relates to new laws that apply to Section 40(3A) of the Patents Act 1990, which was originally introduced in 2013 to remove the use of claims that refer to examples in a specification, i.e. omnibus claims. At that time, Section 40(3A) recited that “the claim or claims must not rely on references to descriptions or drawings unless absolutely necessary to define the invention”. More recently, the Intellectual Property Bill (Productivity Commission Response part 1 and other Measures) Bill 2018, expanded the scope of Section 40(3A) to cover claims referring to “drawings, graphics or photographs”.

Relevantly, Section 40(3A) does not refers to “parts” of the specification – it simply refers generally to “descriptions, drawings, graphics and photographs”. Thus, current Section 40(3A) appears to go beyond its initial purpose of removing the use of omnibus claims and potentially renders claims that include drawings, graphics and photographs unacceptable. This arguably includes frequently used chemical claims that refer to a structural formula as a graphic representation of the molecular structure of a chemical compound, or an X-ray diffraction pattern, i.e. drawings or graphics.

Currently, Section 40(3A) can only be considered during examination and, in our experience, the Patent Office is only enforcing it against claims that refer to parts of the specification. However, when the Intellectual Property Bill (Productivity Commission Response part 2 and other Measures) Bill 2019 comes into force, most likely at the end of November 2019, Section 40(3A) will become a ground for re-examination, opposition and revocation.

At the very least the new laws, as they relate to Section 40(3A), introduce considerable uncertainty as it is not clear how they will be interpreted judicially. The explanatory memorandum to the Bill is not helpful because it only considers Section 40(3A) as covering omnibus claims. Moreover, as there is a reasonable argument that reference to a structural formula in a claim is not absolutely necessary to define the invention because compounds can be defined by chemical names, future patentees of chemical compounds have a right to feel nervous. For this reason, it may be prudent for applicants of chemical compound applications to cover their most commercially relevant embodiments in independent claims that define a chemical compound by its IUPAC name, in addition to relying on claims that define a structural formula. Notwithstanding, that a claim that refers to a chemical structure is more succinct than one that refers to a long and potentially unclear chemical name.

Shelston IP will, of course, continue to monitor the introduction of the new laws and provide necessary updates.

Authored by Gareth Dixon, PhD