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[patentatt]

As I understood the original post, the question was not why printed matter was not argued, but rather why the case was not decided on the printed matter doctrine.  In my opinion, the printed matter doctrine would be a very weak basis for invalidating the claims.  Yes, there is an argument there, but it is pretty weak.  There isn't any question in my mind that the functionality of DNA is closely coupled to structure of the molecule.

To my knowledge, the Supreme Court has not has addressed the printed matter doctrine or any copyright-based limitation on patent eligibility (and Myriad is a likely candidate for Supreme Court review regardless of the CAFC decision).

Yet we know that the SC believes that some software inventions are patentable.

How do we know that?  The only reference to "software" in the majority opinion was not joined by Scalia, and therefore is not binding precedent.  Further, Bilski was decided by a bare majority, but the court's composition has changed with the addition of Justice Kagan and removal of Stevens.

Ultimately the case is going to be decided as a matter of public policy, and the goal will probably be to do as little harm elsewhere.   Hopefully, the courts will confine the printed matter doctrine playing in its current, tiny sandbox.

I agree that it's good policy to limit the printed matter doctrine (I would probably abolish it - if someone gets a monopoly on a nonobvious expression, who cares?  It's just another form of copyright.).  I just wonder why the ACLU and other parties have not even referenced the doctrine in their battery of arguments against Myriad.  Everyone here thinks that the argument is weak.  But I wonder whether the plaintiffs even considered the argument.

[Isaac]

Everyone here thinks that the argument is weak.  But I wonder whether the plaintiffs even considered the argument.

Why do you consider the argument worthwhile?  I'm sure there are other likely losing arguments that the ACLU did not bother with.  After all, we're currently second guessing the side that won at the district court level.

[patentatt]

Why do you consider the argument worthwhile?  I'm sure there are other likely losing arguments that the ACLU did not bother with.  After all, we're currently second guessing the side that won at the district court level.

Because I think that, if the judges are going to consistently apply the law, then they likely should invalidate the Myriad claims on printed-matter doctrine grounds.

In other words, I'm not persuaded by the counter-arguments:

1. DNA is not printed matter - it doesn't have to be printed matter, the doctrine doesn't depend on a particular medium
2. If you apply this to DNA, then you have to invalidate all chemical claims - DNA is not like all chemical compounds, DNA is an information-transmitting and message-encoding compound unlike virtually any other compound known in the universe
3. If you apply this to DNA, then you have to apply it to Beauregard and software claims - the status of software claims is totally in the air because the Supreme Court hasn't meaningfully addressed them in decades, and the few cases that do address them provide almost no meaningful guidance
4. your argument is just weak - this is just a generic gut-feeling argument that is not persuasive and is almost impossible to respond to

The best counter-argument, I think, is that the printed matter doctrine doesn't apply if there is a recited functional inter-relationship between the expression and the other claim elements - and here the claims recite that the expression codes for a protein.  Still, I think the argument is interesting and worth discussing (maybe I overstate its relevance).  Also, I don't that the Supreme Court has ever addressed or countenanced this "functional inter-relationship" prong of the CAFC's printed matter test.

I can imagine a lot of expressions having a structural interrelationship with machinery, without thinking that this should be a point of patentability: suppose I change the password on my computer to "zxczxcasdawefd."  Then I write a claim to a computer "wherein the computer is password protected so that the computer only allows access to users upon the entering of the password 'zxczxcasdawefd.'"  Suppose that "zxczxcasdawefd" (or the expression of your choice) is not known in the prior art.  Am I entitled to a patent now?  That seems to violate the spirit, if not the letter, of the printed matter doctrine.

I understand that the ACLU is an expert in First Amendment issues and not patent issues.  But if they, and the many other plaintiffs, are going to give the whole array of arguments against Myriad, including unprecedented arguments like the First Amendment one, I would have expected them to cite the printed matter doctrine, if they even considered it.

[Isaac]

The best counter-argument, I think, is that the printed matter doctrine doesn't apply if there is a recited functional inter-relationship between the expression and the other claim elements - and here the claims recite that the expression codes for a protein.

This is the only real argument to the merits.   Most of the other arguments simply point out the undesirable results from extending printed matter outside of its sand box.   

Still, I think the argument is interesting and worth discussing (maybe I overstate its relevance).  Also, I don't that the Supreme Court has ever addressed or countenanced this "functional inter-relationship" prong of the CAFC's printed matter test.

Maybe, but that's because the printed matter test has not been applied much beyond easy, writing on stuff type cases.  If we instead extend the doctrine to every case where shape and structure dictate function, I suspect that the doctrine would lose whatever current credibility it has now.   

Then I write a claim to a computer "wherein the computer is password protected so that the computer only allows access to users upon the entering of the password 'zxczxcasdawefd.'"  Suppose that "zxczxcasdawefd" (or the expression of your choice) is not known in the prior art.

That's exactly the type of invention that the printed matter doctrine does apply to.  But extending the printed matter doctrine to a cryptographic process for protecting the passwords to your computer goes to far IMO, even if you can make an internally consistent argument to do so.

[patentatt]

That's exactly the type of invention that the printed matter doctrine does apply to.  But extending the printed matter doctrine to a cryptographic process for protecting the passwords to your computer goes to far IMO, even if you can make an internally consistent argument to do so.

I appreciate your patient and understanding response.  But I have to respond to the above-quoted part of your post:

1. How does the printed matter doctrine apply?  My understanding is that the doctrine only applies if there is no functional inter-relation between the written matter and the rest of the claimed structure.  Here there is such a functional inter-relationship.  So it's not at all clear to me that the doctrine still applies.

2. If the doctrine applies to my password example, then why not to Myriad's DNA?

[Isaac]

That's exactly the type of invention that the printed matter doctrine does apply to.  But extending the printed matter doctrine to a cryptographic process for protecting the passwords to your computer goes to far IMO, even if you can make an internally consistent argument to do so.

I appreciate your patient and understanding response.  But I have to respond to the above-quoted part of your post:

1. How does the printed matter doctrine apply?  My understanding is that the doctrine only applies if there is no functional inter-relation between the written matter and the rest of the claimed structure.  Here there is such a functional inter-relationship.  So it's not at all clear to me that the doctrine still applies.

2. If the doctrine applies to my password example, then why not to Myriad's DNA?

I suspect you can give my answers to these questions yourself even if you don't agree them.

The difference between a computer with two different passwords is just non functional words.  The difference between two portions of DNA molecules is a difference in their chemical structures that we can describe in words.  The structure, and not merely our human readable description of the structure is what is responsible for the different behavior.
     
If simply being able to describe the difference in words were enough to render an invention unpatentable, then no improvement on an old invention would be patentable.

DNA molecules aren't simply loaded up with different information in the same way that you change the writing on pages in a book.  In a sense, all relative large molecules (for example pharms) are collections of atoms containing "information" of the sort you want to argue is subject to the printed matter doctrine.

If my arguments seem to be results driven, let me suggest that the printed matter doctrine itself is always applied in a results driven way. 

I find the doctrine to be similar to the merger doctrine in copyright law.  If the court takes an expansive view of what constitutes the "idea" you are communicating, then the court is more likely to find an idea-expression merger that renders your work not protectable by copyright.   At a lower level of abstraction, idea and expression are clearly distinct.  The problem is that for a new case with facts unlike those already decided, there is no way to determine what the proper level of abstraction.

Similarly, it seems clear that merely changing the password to a computer does not result in a patentable distinction, and I have no problem applying the printed matter doctrine to reach this result.   On the other hand, it is at least arguable that changing the programming on a computer to produce novel/non-obvious functionality does result in a patentable invention.   Someone else might use the printed matter doctrine to argue that a programmed general purpose computer is never patentable because software is printed matter.   But the difference in functionality between a computer program and a password is substantial IMO.

[ManOfManyBadIdeas]

Why do you consider the argument worthwhile?  I'm sure there are other likely losing arguments that the ACLU did not bother with.  After all, we're currently second guessing the side that won at the district court level.

Because I think that, if the judges are going to consistently apply the law, then they likely should invalidate the Myriad claims on printed-matter doctrine grounds.

In other words, I'm not persuaded by the counter-arguments:

You are missing two:
a) the claim is not drawn to the "information", but to the chemical structure. That's how it would be interpreted by a PHOSITA, therefore applying printed matter doctrine is improper as it requires improperly construing the claim.
b) you should be able to argue obviousness in any printed matter case; it's clear that you can't argue obviousness here, therefore it means that you can't apply printed matter.