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You missed a bit
Authored by: Ian Al on Friday, July 13 2012 @ 05:32 AM EDT
35 U.S.C. 121 Divisional applications. If two or more independent and distinct inventions are claimed in one application, the Director may require the application to be restricted to one of the inventions. If the other invention is made the subject of a divisional application which complies with the requirements of section 120 of this title it shall be entitled to the benefit of the filing date of the original application. A patent issuing on an application with respect to which a requirement for restriction under this section has been made, or on an application filed as a result of such a requirement, shall not be used as a reference either in the Patent and Trademark Office or in the courts against a divisional application or against the original application or any patent issued on either of them, if the divisional application is filed before the issuance of the patent on the other application. If a divisional application is directed solely to subject matter described and claimed in the original application as filed, the Director may dispense with signing and execution by the inventor. The validity of a patent shall not be questioned for failure of the Director to require the application to be restricted to one invention.
35 U.S.C. 120 Benefit of earlier filing date in the United States. An application for patent for an invention disclosed in the manner provided by the first paragraph of section 112 of this title in an application previously filed in the United States, or as provided by section 363 of this title, which is filed by an inventor or inventors named in the previously filed application shall have the same effect, as to such invention, as though filed on the date of the prior application, if filed before the patenting or abandonment of or termination of proceedings on the first application or on an application similarly entitled to the benefit of the filing date of the first application and if it contains or is amended to contain a specific reference to the earlier filed application. No application shall be entitled to the benefit of an earlier filed application under this section unless an amendment containing the specific reference to the earlier filed application is submitted at such time during the pendency of the application as required by the Director. The Director may consider the failure to submit such an amendment within that time period as a waiver of any benefit under this section. The Director may establish procedures, including the payment of a surcharge, to accept an unintentionally delayed submission of an amendment under this section.
35 U.S.C. 112 Specification. The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
35 U.S.C. 363 International application designating the United States: Effect. An international application designating the United States shall have the effect, from its international filing date under article 11 of the treaty, of a national application for patent regularly filed in the Patent and Trademark Office except as otherwise provided in section 102(e) of this title.
In other words, if the Director permits two or more independent and distinct inventions to be claimed in one application,the specification of each invention shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention. If the independent and distinct inventions are not clearly specified as such, then the patent becomes invalid. However, the part you highlighted merely says that the incorporation of more than one invention in a patent cannot be claimed as invalid for failure of the Director to require the application to be restricted to one invention

One way that the patent becomes invalid is highlighted by Diehr as noted in the Bilski opinion:
The application in Diehr claimed a previously unknown method for “molding raw, uncured synthetic rubber into cured precision products,” using a mathematical formula to complete some of its several steps by way of a computer. Diehr explained that while an abstract idea, law of nature, or mathematical formula could not be patented, “an application of a law of nature or mathematical formula to a known structure or process may well be deserving of patent protection.” Diehr emphasized the need to consider the invention as a whole, rather than “dissect[ing] the claims into old and new elements and then … ignor[ing] the presence of the old elements in the analysis.” Finally, the Court concluded that because the claim was not “an attempt to patent a mathematical formula, but rather [was] an industrial process for the molding of rubber products,” it fell within §101’s patentable subject matter.
If two or more independent and distinct process inventions are claimed in one application and the invented process steps for each invention are not clearly separated such that it 'enables any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same' then it is impossible to see each invention as a whole in order to find out whether each contains an inventive concept (see, Flook). Further, claims of infringement are impossible if it is not possible to identify which steps comprise the individual process invention as a whole.

---
Regards
Ian Al
Software Patents: It's the disclosed functions in the patent, stupid!

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