With Thanksgiving kicking the end-of-year travel season into full gear, concerns over air travel safety have predictably resurfaced. The main issues this time surround the Transportation Security Administration’s (TSA) advanced imaging technology (AIT) machines—even though the agency has been rolling out these devices over the past few years—as well as the TSA-administered security pat-downs of passengers who refuse to submit to AIT screening.

Controversy has bubbled up this month on a number of fronts. Some question whether AIT, which uses millimeter wave and backscatter imaging technology to detect metallic and nonmetallic objects and substances, poses a health risk. Other major concerns are that AIT images are the equivalent of a virtual strip search, that the TSA stores these images and that the machines tend to malfunction.

The TSA denies all of these allegations but recently softened its stance on its latest approach to aviation security. In a statement posted to the TSA’s Web site on Sunday, agency administrator John Pistole noted that the TSA will work to make the procedures “as minimally invasive as possible” and that all security programs must undergo “a continual process of refinement and adjustment” as feedback is received from the public.

Yet Pistole also cited recent threats as the reason for the increased vigilance at airports. Earlier this month, a group known as Al-Qaeda in the Arabian Peninsula announced Operation Hemorrhage, a campaign to launch a series of smaller, low-cost attacks (the explosives on the cargo planes intercepted in Dubai and England cost $4,200 to make, the group says) against the U.S and its interests that disrupt commerce and perpetuate an “environment of security phobia.” (pdf)

To address health concerns that have been raised about the new scanning equipment, the TSA has said that the backscatter radiation doses for the individuals being screened, operators and bystanders “were well below the dose limits specified by the American National Standards Institute (ANSI).” The agency also says that the energy projected by millimeter wave technology is “thousands of times less than a cell phone transmission.” The TSA expects to deploy a total of 450 AIT units at airports across the U.S. by the end of this year.

Reactions to the pat-downs have added increased scrutiny of the TSA’s approach to tightening security. Some say the TSA has crossed a personal privacy boundary by authorizing pat-downs for any passengers who set off metal-detector alarms or opt out of using the AIT. High-profile protests have been initiated, including one by 15-minute YouTube hero John Tyner, who refused both to use the AIT and to submit to a pat-down on November 13. And Rep. John Mica, R-Fla., is calling for a review of the TSA’s pat-down procedures as well as the replacement of TSA workers with private contractors.

Far less visible are suggestions for practical alternatives to the TSA’s security policies. Scientific American asked Brian Michael Jenkins, a senior advisor at the RAND Corp. and a former member of the White House Commission on Aviation Safety and Security, for his perspective on the TSA’s latest moves and other options for tightening aviation security.