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Microsoft is not the real patent threat Linux and open source developers should be worried about, said Ubuntu founder Mark Shuttleworth. In fact, the software giant will itself be fighting against the software patents system within a few years, Shuttleworth predicted.

Shuttleworth was responding to a recent Fortune magazine interview in which senior Microsoft figures sent shockwaves through the software industry by declaring that Linux and other open source software violates 235 Microsoft patents.

But while Microsoft is using familiar tactics to put the fear into Linux users, Shuttleworth argued open source and Microsoft are ultimately on the same side of the software patent issue.

"I’m pretty certain that, within a few years, Microsoft themselves will be strong advocates against software patents," Shuttleworth wrote. "Microsoft is irrevocably committed to shipping new software every year, and software patents represent landmines in their roadmap which they are going to step on, like it or not, with increasing regularity."

Microsoft makes the "perfect target" for software patent lawsuits, and the company will pay more for such suits every year until they finally threaten its business, Shuttleworth said.

"Microsoft will lose a patent trench war if they start one, and I’m sure that cooler heads in Redmond know that," he wrote. "The real threat to Linux is the same as the real threat to Microsoft, and that is a patent suit from a person or company that is NOT actually building software, but has filed patents on ideas that the GNU project and Microsoft are equally likely to be implementing."

He said the most dangerous litigants are companies not themselves in the software business, small ventures or holding companies that get their principal revenue from patent licensing.

He singled out former Microsoft CTO Nathan Myhrvold and his company Intellectual Ventures, which is stockpiling patents at a rate that alarms large companies such as IBM and HP, as an example of such a potentially dangerous company.

But even such companies - sometimes known as "patent trolls", although Shuttleworth said he himself dislikes the term - are not themselves the real enemy. "They are only following the rules laid out in law, and making the most of a bad system," he wrote.

Rather, it is the patent system itself, which allows software patents to exist in the first place, that needs to be fixed, Shuttleworth argued. He said Ubuntu supports organisations such as the Foundation for a Free Information Infrastructure (FFII) and the Open Invention Network, which are attempting to do just that.

In the meantime, he said he expects Linux to be targeted by a "definitive" patent lawsuit within the next ten years.

"I'm certain someone will sue somebody else about Linux on patent grounds, but it's less likely to be Microsoft (starting a trench war) and more likely to be a litigant who only holds IP and doesn’t actually get involved in the business of software," he wrote.

In an interview with Fortune magazine a week ago, Brad Smith, Microsoft's general counsel, and Horacio Gutierrez, the company's vice president of intellectual property and licensing, said Microsoft wants distributors and users of open-source software to start paying royalties for the alleged patent violations.

"This is not a case of some accidental, unknowing infringement. ...There is an overwhelming number of patents being infringed," Gutierrez said.

Smith broke down the alleged patent violations during the Fortune interview, saying the Linux kernel violates 42 patents and the operating system's user interface violates a further 65. He went on to claim that the Open Office application suite violates 45 patents and open-source e-mail applications infringe on 15 more. Other open-source software applications infringe on 68 patents, Smith said.

Microsoft has been laying the groundwork for patent claims against Linux and open-source software for some time. Most notably, the company signed a Linux deal with Novell that indemnifies the company against Microsoft patent claims over Linux.

Two weeks ago Dell joined the deal, becoming the first hardware vendor to do so.

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