"Having never been patted down before, I understand completely the concerns people have," Isakson told Channel 2 political reporter Lori Geary. Isakson said he's concerned about the pat-downs because they are so random.
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"This is basically a probable cause search and one of the concerns I raise with the administrator is you've got to have probable cause to apply a probable cause search," said Isakson.
Isakson's flight came just days after he questioned Transportation Security Administrator John Pistole during a commerce committee hearing.
"If you have an indication on the full-body screen that there is something that's not right, that's probable cause to search somebody," Isakson told Geary.
The Georgia Republican said it's a delicate balance of security versus personal privacy, adding, "It's also understandable that somebody would be concerned with a physical pat-down as close to vital areas as you can get. But those vital areas happen to be the areas that the underwear bomber tried to use to blow up a plane."
Isakson said he understands why some travelers have concerns over the images from the full-body scanners. Isakson told Geary he's seen a new technology the TSA is testing in the field that distorts those images.
"As far as the person watching the screen, they see a stick figure. They don't see a body. Then around the area of concern, there's a red box," said Isakson.
"I'm sure they'll get the bugs out of that system and when that system is in place, it will address 99.9 percent of the concerns, either about the screen or the physical pat down," added Isakson.
Isakson said there's no word on when that new technology will be available.