According to the article: "A wide-ranging surveillance operation by the Food and Drug Administration against a group of its own scientists used an enemies list of sorts as 
it secretly captured thousands of e-mails that the disgruntled 
scientists sent privately to members of Congress, lawyers, labor 
officials, journalists and even President Obama, previously undisclosed 
records show. ... What began as a narrow investigation into the possible leaking of 
confidential agency information by five scientists quickly grew in 
mid-2010 into a much broader campaign to counter outside critics of the 
agency’s medical review process, according to the cache of more than 
80,000 pages of computer documents generated by the surveillance effort. Moving to quell what one memorandum called the “collaboration” of the 
F.D.A.’s opponents, the surveillance operation identified 21 agency 
employees, Congressional officials, outside medical researchers and 
journalists thought to be working together to put out negative and 
“defamatory” information about the agency." ...
"The agency, using so-called spy software designed to help employers 
monitor workers, captured screen images from the government laptops of 
the five scientists as they were being used at work or at home. The 
software tracked their keystrokes, intercepted their personal e-mails, 
copied the documents on their personal thumb drives and even followed 
their messages line by line as they were being drafted, the documents 
show.        
The extraordinary surveillance effort grew out of a bitter dispute 
lasting years between the scientists and their bosses at the F.D.A. over
 the scientists’ claims that faulty review procedures at the agency had 
led to the approval of medical imaging devices for mammograms and colonoscopies that exposed patients to dangerous levels of radiation. A confidential government review in May by the Office of Special 
Counsel, which deals with the grievances of government workers, found 
that the scientists’ medical claims were valid enough to warrant a full 
investigation into what it termed “a substantial and specific danger to 
public safety.”" ...
"While federal agencies have broad discretion to monitor their employees’
 computer use, the F.D.A. program may have crossed legal lines by 
grabbing and analyzing confidential information that is specifically 
protected under the law, including attorney-client communications, 
whistle-blower complaints to Congress and workplace grievances filed 
with the government."         
The Rest of the Story
While the FDA claims that these efforts were intended only to prevent the release of confidential, proprietary information, it seems quite clear that the scope of the agency's spying efforts goes way beyond that narrow aim. The number of scientists who were monitored, the nature of the spy effort (including intercepting emails and tracking keystrokes in real-time), and the analysis of information that is protected under whistle-blower laws all indicate that the agency far exceeded its discretionary authority.
The most concerning aspect of the story is that it exposes an attempt on the part of the FDA to quell dissent by intimidating scientists from expressing disagreement with agency decisions that they felt put the safety of public at risk. In fact, an independent review confirmed that the concerns of these scientists about the approval of devices that exposed patients to dangerous levels of radiation were warranted: these devices represented “a substantial and specific danger to public safety.”
The integrity of science depends on the ability of scientists to express disagreement. In fact, most of the great scientific advances have come from scientists who have been willing to challenge conventional thinking. Quelling dissent destroys the integrity of the scientific process and ensures that agency decisions will be made on political, rather than scientific grounds.
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