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Ever since Pan Am Flight 103 blew up over Lockerbie, Scotland, nearly 15 years ago, killing 270 people, terrorism experts have recognized the danger presented by a bomb in the belly of an aircraft.

Still, airport security tended to focus on what passengers were carrying onto the plane rather than on what they were checking as baggage. That left a gaping hole in the air safety net. But until the terrorist attacks on New York and Washington 16 months ago forced a top-to-bottom review of airline security, not much was done to reduce this danger. Prior to those attacks, only 5 percent of checked baggage was being screened for explosives in the U.S.

That has now changed. As of midnight last Tuesday, the Transportation Security Administration reported, 100 percent of all checked baggage is being screened at the nation’s 429 commercial airports. Ninety percent is being screened electronically and the rest is being handled by bomb-sniffing dogs, hand searches and passenger-bag matching.

The debut of screening all checked baggage for explosives has, so far at least, gone smoothly and has not resulted in excessive delays at the nation’s airports. The screening is just the latest piece of the layered security system that is being built to make flying safer. The TSA has hired 56,000 security screeners, as well as thousands of federal air marshals who anonymously patrol passenger flights. For an agency that didn’t even exist until November 2001, the TSA deserves a good deal of credit for meeting this deadline mandated by Congress.

That’s the good news. The not-so-good news is there still are plenty of gaping holes in transportation security, particularly away from the airports in the nation’s shipping, trucking and rail industries. Although Congress ordered better security as part of the 2001 USA Patriot Act, more than a year later many specific rules and regulations still aren’t finalized.

Disputes with unions over whether workers with criminal records should be given security clearance have delayed screening of port workers and truckers hauling hazardous materials. Using technology, such as satellite-tracking systems, to enhance trucking security has been hung up over who’s going to pay for it.

Meanwhile at the airports, the Immigration and Naturalization Service launched Operation Tarmac in the wake of the attacks. This nationwide probe into airport workers who have direct access to planes and other secure areas, the INS reported to Congress in June, resulted in audits of 190,000 employment eligibility verification forms at 1,900 airport businesses and arrests of more than 500 unauthorized immigrants.

In the latest sweep at O’Hare International and Midway airports in December, 25 restaurant and ramp workers, members of cleaning and service crews and truck drivers were arrested on criminal charges ranging from concealing criminal records to using fake IDs. Security clearances of another 523 workers were revoked pending further investigation.

Perhaps the best that can be said of security in the nation’s extensive and porous transportation networks is this: It’s better than it has been, but it’s not nearly as good as it must become to protect the nation.