When we put 23andMe CEO Anne Wojcicki on the cover of Fast Company’s November issue , we didn’t expect the FDA to yank the company’s $99 DNA test off the market a few weeks later. Yet there’s a reason we called Wojcicki “the most daring CEO in America”: Her company’s product challenges established conventions about medical practices, research, insurance, and more. So is that challenge at the heart of the FDA’s rebuke? Or did something more basic derail Wojcicki’s mission?

Anne Wojcicki Photo by Jeff Brown

Since the FDA shutdown, I’ve spoken with insiders at both the agency and 23andMe. I learned that there are significant philosophical differences between the two organizations. I also concluded that the break between them had as much to do with old-fashioned miscommunication as anything else.

There are three core points of dissonance between the FDA and 23andMe. The first is their level of faith in consumers. The FDA is tasked with protecting consumers, even from themselves. Among the objections the agency has to 23andMe is that DNA test results may provoke consumers to seek unnecessary treatments, self-medicate in dangerous ways, and take on needless anxiety about conditions for which there is no treatment. In contrast, 23andMe stresses that consumers are capable of managing their own medical care–and should have more information about it. The company highlights specific instances where customers’ DNA tests led to helpful, positive medical interventions. The FDA’s stated concerns at this stage revolve around hypotheticals, not observed cases of consumer-created medical mistakes.

The second core point of dissonance revolves around data. The FDA has been asking 23andMe for specific studies on the reliability and efficacy of its DNA test results as well as specific clinical analysis regarding health claims (for example, the risk of developing a condition that is associated with a genetic marker). 23andMe says it is working on satisfying those mandated requirements and admits it wishes its efforts were farther along. At the same time, 23andMe contends that the reliability of its test kits and data adheres to the highest standards, that its process matches that of a DNA test one would get through a physician. The fact that not all of its studies yet match the medical industry’s accepted clinical study procedures–and thus fail to meet FDA protocols–is, to 23andMe, not something that should be held against it.

The third core point of dissonance concerns education: What is the best way to prepare consumers for a future where DNA testing and information is more prevalent? 23andMe casts itself as a consumer-friendly way to provide useful information. If we are moving to a world where DNA sequencing is cheaper and used more frequently, then 23andMe contends it is preparing the way, introducing this new idea in a nonthreatening package. The FDA also sees this future coming: Around the same time 23andMe was curtailed, the agency approved a new gene sequencing technology from Illumina, the company that provides the back-end testing for 23andMe’s kits. What the FDA worries about is setting poor precedents for this coming wave. If any entity needs to be vigilant about creating appropriate standards for marketing health claims, it is the FDA.

Despite these three areas of tension, 23andMe and the FDA had been cooperating relatively smoothly. The FDA’s shutdown letter notes 14 meetings between the two entities–evidence that both sides have been trying to reach agreement. 23andMe launched more than five years ago, and the FDA allowed initial marketing of the DNA test kits, despite what it felt was incomplete data. Many promising medical devices and products are given leeway as real-world data builds.

What happened this fall was sparked less by philosophical or scientific differences than poor communication. Last spring 23andMe began to ramp up the marketing efforts behind its DNA kits. This included TV and video ads and a direct-marketing campaign. Given the long history of dialogue with the FDA, you might imagine that 23andMe would have sought feedback about these initiatives–to see if any concerns surfaced or tweaks were requested. Instead, 23andMe announced its plans to the FDA and proceeded independently. Perhaps the company did not want to set a precedent itself of having to get FDA approval for their marketing. In any case, the company charged ahead, heedless or unaware of the discomfort this created at the FDA.