I'll preempt the constitutional argument by saying that hasn't been made yet. You underestimate how strong such an argument has to be to succeed. What SCOTUS could clarify is Diamond v. Diehr. That still wouldn't be the end of our patent problems though.
Congress never passed a law allowing software patents, though. It was the courts (but only the lower courts, never the Supreme Court) which historically interpreted the old patent laws (written before the age of computers) to apply to software -- I don't know of any parts of Title 35 which cover software specifically. Congress could modify the law to explicitly allow software patents, but they haven't.
1. Is it good policy to allow software to be patentable, and
2. Does existing law allow for software to be patentable?
I am fairly agnostic on question one, and about three Juris Doctorates short of being able to answer question two, but it's the Supreme Court's job to answer question two without any regard whatsoever to question one.
This article appears to be arguing about question two based on his opinions on question one, which is like arguing that a cat is a handbag because you want to be able to take it as carry-on luggage.
There is extensive literature (a subset of "legal realism" which accounts strategically for judicial action) which claims that judges do in fact incorporate policy considerations in decision-making. Secondly, it's widely acknowledged that the court frequently and with considerable influence advises Congress to change the law. In that context, it might be fine & useful for this article to speak in policy terms to the Court.
This isn't unusual. Constitutional concepts like "reasonable search," "cruel and unusual punishment" similarly invite courts to make policy judgments.
Actually, that's exactly how the system works. Check and balances.
It's the pro-software-patent people who need to petition Congress. Anti-software-patent people should merely petition the executive branch to enforce the law as it stands.
That's not saying that SCOTUS would invalidate software patents, just the opposite. The SCOTUS discussion I've heard have turned on how invalidating software patents would be a fairly short step to invalidating all patents and there are too many interests involved to let that happen.
The argument in the supreme court debate I remember was essentially "software parents as a generic are absurd but tossing them out completely would be an earthquake that we don't want to play so we need a line that would allow some but not all software patents". Nothing turning on technicalities in the overall approach even if the solution they'd grope for would likely turn on said technicalities.
This supreme court is one of the most conservative of all time in terms of interpreting the law and limitation of its own power.
The solution can only come from the congress. The present supreme court will shy from setting a strong precedent. I don't think this is a bad thing. Relying on court to change the law is a sign of an unhealthy society who cannot control its elected representatives.
I wish I could upvote this wise advice ten times. even if patents made it to the top of the Supreme Court docket today and they justices interrupted their summer holidays tomorrow to consider the issue, a badly-thought-out case could just as easily end up extending patent terms to the 95 years that copyrights enjoy.
Unfortunately, a great deal of legal and political debate in the US currently looks like this: http://www.youtube.com/watch?v=yo3uxqwTxk0