Although the U.S. Patent and Trademark Office (PTO) has initially denied Apple a patent for some user interface elements of the popular iPod MP3 player--a revelation that may have initially come from someone at Microsoft--the issue has hardly been put to bed. If anything, it has only woken up and is starting to move around.

“The US patent process is often a lengthy one, involving much back and forth with the US patent office,” said Apple in a statement. “Apple will continue to pursue this patent application, as well as the many others covering iPod innovations.”

Industry analyst Roger Kay recently told MacWorld magazine said that even if Microsoft were to win a patent challenge from Apple, the chances of it having any significant effect on Apple’s future business are slim.  “I think that in practical terms, no judge will allow Microsoft to stop Apple’s iPod business from going forward,” said Kay, president of Endpoint Technologies Associates Inc. “I think that if Microsoft makes a narrow claim stick, the settlement will be a cross-licensing deal with little or no money changing hands.”

Additionally, open-source pioneer Bruce Perens recently told SYS-CON.TV that speaking of patents in general,  "the law must be fixed" so that Microsoft in particular is less able to control the patent process for software. (The full interview can be found here.) Perens comments come in the wake of the creation by the OSDL of a process in which it will attempt to monitor patents for open-source software.

Technology companies are familiar with a "first past the post" system in which the date of an application's filing is not as important as the actual development and use of the technology. But there is plenty of gray. It's very common for quite similar ideas to be presented independently, and the trick can be to determine which application among several competing ones actually describes a real product that will eventually be produced, how completely the patent application describes that products, and whether the idea was developed independently of existing patents owned by other companies.

Patent applications can be extremely complex, extremely simple, or fall somewhere in between the extremes, presenting a disorganized welter of information that is presented to various patent examiners, thereby making it difficult to determine precisely which specific product idea belongs to whom.

Patent disputes among chip manufacturers, among inventors and the companies for which they worked, and between rivals in almost every segment of the technology industry have been quite common over the years.

Microsoft’s Director of Intellectual Property Licensing, David Kaefer noted in a statement last week the two companies close relationship and that Microsoft does tend to license its patents to other companies. Often, a large company will attempt to surround a specific patent with others, to protect a core idea or to attack someone else's core idea.

Add to this the perception by many technology developers that the PTO lags behind indusry in its comprehension of the development and use of leading-edge products, and the picture is far from clear.