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Congress has dealt a renewed blow to America's inventors and innovators by stripping another $100 million from the U.S. Patent and Trademark Office, an agency incapacitated by two decades of raids on the fees it collects.

Legislators siphoned the funds as part of the emergency spending bill drafted hastily to avert a shutdown of the government this month. The stopgap measure, which President Barack Obama signed into law Friday, cuts federal spending by $38 billion and quietly offset a fraction of that amount by draining more than $100 million in fee income from the patent office.

"They will be running on fumes," said former patent office director Q. Todd Dickinson, who now heads the American Intellectual Property Law Association, a Washington, D.C., trade group.

The patent office is meant to act as steward of the nation's newest technologies, granting protection to new ideas and products so their developers can commercialize them - and ultimately create jobs. The Harvard Business Review this year described the agency as the "biggest job creator you never heard of."

But beginning in the early 1990s, Congress got into a nearly two-decade habit of draining funds from the agency - which is structured to be self-supporting by charging fees without any taxpayer support - and using the funds to pay for other federal projects.

So just as patent applications have become increasingly complex because of the advance of technology, and as global technology competition exploded, the patent office finds itself underfunded and understaffed. Applications now languish so long that technologies can become obsolete before a patent is ruled upon. And the absence of patent protection in some cases allows infringers to steal new technologies, while legitimate inventions are unable to get licensed and start-ups are unable to get funding.

The patent office on Friday confirmed the latest diversion, which ensures it will remain underfunded until at least Oct. 1, when the next fiscal year begins. But the agency declined to comment on the impact of the latest setback.

Since 2009, the Journal Sentinel has documented how delays and dysfunction at the patent office have impeded U.S. competitiveness. Garage entrepreneurs and start-ups often suffer the greatest setbacks when they are unable to get patent protection for their ideas. The patent system has become even more relevant in a technological economy driven by the likes of eBay, Google and Amazon.

According to a Journal Sentinel analysis, patents awarded by the agency last year took nearly four years from application to issuance, on average, more than twice the agency's benchmark of 18 months.

The total number of applications awaiting a final decision remains stuck at 1.2 million, nearly unchanged from levels of the past three years. A study released last year by British patent authorities found that the United States wastes at least $6.4 billion each year in "forgone innovation" - legitimate technologies that cannot get licensed and start-ups that cannot get funding because of U.S. Patent Office problems.

The latest setback means the agency will be facing a deficit of nearly $1 million per working day.

"I don't see any way the pendency and backlog will significantly be reduced for the next six months," said Dickinson, who ran the agency from 1998 to 2001.

Dickinson predicts cutbacks, including:

• The chronically understaffed agency, which has aimed to hire 1,000 to 1,300 new examiners each year just to chip away at the backlog, is likely to continue to restrict hiring.

• Upgrades to its antiquated computer system, which obstructs the work of examiners, will be postponed.

• A plan to open satellite offices and ease overcrowding at its campus outside Washington could be delayed.

The latest diversion comes as key Senate and House leaders as well as the White House have started to extol the importance of the agency.

Those politicians champion a separate piece of legislation, called the America Invests Act of 2011, which is meant to "reduce backlogs of pending applications" at the patent office and improve the quality of the decisions by patent examiners, in the words of Sen. Patrick Leahy (D-Vt.), one of the key sponsors.

"We've got to improve this system significantly," Austan Goolsbee, the chairman of the White House Council of Economic Advisers, said in a presentation last month. "Patents are key. We've talked about a whole lot of ways we're going to win the future. We've got the greatest inventors in the world, and it's time we give them the help they need to bring the country where it needs to be."

The America Invests Act would grant the patent office authority for the first time to keep all the funds it collects. Even if Congress passes the legislation - it has rejected three previous attempts over the past four years - the agency wouldn't gain control over its finances until new fiscal year starts Oct. 1.

In 2009, the year Obama named former IBM executive David Kappos to head the patent office, Congress cut the agency's budget even as Kappos inherited a $200 million deficit and a hiring freeze.

Under a best-case scenario made before the latest congressional raid, Kappos predicted that the agency could reduce its backlog, and applicants' waiting times, to manageable levels by 2015.

The latest fee diversion, however, means that during nearly two decades of raids, Congress has now taken more than $900 million from a self-funded agency with a $2 billion annual budget that doesn't require a single penny of taxpayer funding.

David Smith, a Milwaukee patent attorney at the Michael Best & Friedrich law firm, said the ramifications of delays and backlogs go beyond individual inventors and ripple through the broader economy.

"If the patent system is allowed to become weak or slow and cumbersome," Smith said, "the incentive to manufacturers to invest in engineering and to produce new and better products is reduced, and we all lose."

More on patents To see previous stories in the "Patents Pending" series and explore an interactive timeline showing how the patent system has shaped American history, please see www.jsonline.com/patents.