Non-contact temperature assessment devices simply receive and measure natural infrared radiation (i.e., heat) from the skin. Some scanners may have laser pointers for aiming purposes but the lasers don't penetrate the skin. It is impossible for temperature scanners to cause injury to the brain or pineal gland.
That said, the scans do little to protect against actual spread of the virus, since most of that takes happens from infected people who are not yet sick or who may never become sick. These temperature checks are more for show than an effective public health measure.
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