There are big problems in medicine, but they’re not silly conspiracy theories. While colorful quacks like to pretend that drug companies have hidden the truth about vitamin pills curing cancer, the reality is much more nerdish and interesting.

I’m a doctor, and a geek, and I write about problems in science. Since publishing a book on problems in medicine, I’ve received an instant and rather lurid attack from PhRMA, the drug-industry body. Much more strangely, in the very same week, I’ve had GSK, one of the biggest pharmaceutical companies in the world, sign up to the campaign I cofounded at alltrials.net. GSK has committed to providing the very same thing that PhRMA denounces me for requesting: the results of all their clinical trials.

Most people are amazed that such a campaign is even necessary. It seems obvious that doctors and patients need to see the results from all the clinical trials that have ever been conducted on a treatment in order to make informed decisions about which will work best for them. Sadly, this doesn’t happen.

The best available evidence comes from a systematic review, which looks at all the dozens of studies that have ever been conducted on the problem of “missing results.” I hope I’m a trustworthy person, but working from this kind of systematically collected evidence means there is no danger of my “cherry-picking” the research I prefer. The systematic review evidence on missing results shows that, for the treatments we use today, our best estimate is that half of all trials haven’t been published; trials with flattering results are twice as likely to be shared. This is an issue with academic trials, as well as industry sponsored research.

As a result, the well of medical evidence is definitively poisoned. For all that drug-company sales reps, and TV adverts, and covertly paid advocates might all influence doctors (and the systematic review evidence shows that they do), all this marketing flim-flam can easily be ignored by any good doctor. When the evidence on what works is systematically distorted, when trial results are withheld, then nobody—not even the best doctor in the world—can truly know which treatment is best.

This presents such huge problems for informed decision making, which are obvious to even the most casual observer, and the issue of missing trials could not possibly survive informed public scrutiny. This is why a battle has been waged to pretend that the problem doesn’t exist, helped along by a series of “fake fixes” that have delivered little more than false reassurance.

A series of websites, or “registries,” were set up so that the existence of trials could be posted publicly, allowing everyone to spot which ones went missing after they finished—but they weren’t used. So, in 2005, the International Committee of Medical Journal Editors announced that it would only published trials that were properly “registered,” and everyone rejoiced. But a paper published in the Journal of the American Medical Association showed that many years after this promise, half of all published trials weren’t properly registered, and a quarter weren’t registered at all. This is hardly surprising, given the huge incentives for academic journals to take positive and industry-sponsored papers.

Then in 2007, a law was passed, saying all trials in the U.S. on currently available treatments must post their results to clinicaltrials.gov within a year of completion. Everyone rejoiced, again, claiming the problem was fixed. But nobody audited to see if the rules were followed, and we found in 2012 that four out of five trials had ignored the law. Despite very poor compliance, no fine has ever been levied for failure to comply with this law.

This is just the beginning of the story, before we go anywhere near the saga of how trials can be subtly flawed by design, to the point that they’re no longer “fair tests” of a treatment; or the brand-new story of how we need full clinical study reports on medical trials, because the brief reports in published academic papers can be incomplete or misleading.

I’m not interested in a few anecdotes about bad people doing the wrong thing. Our failure to implement the simple aspirations of evidence based medicine is something much bigger than that, and much more fascinating. This story combines science, of course, but also policy, the culture of medicine, human nature, and above all, a vast ecosystem of systems failures, rather than bad people.

We need industry—it makes good drugs, and there is no medicine without medicines. But that doesn’t give it a free pass, and the flaws that worry me are all fixable. They don’t involve drug companies “hiding the cure for cancer,” and there is no succor for quacks here, because flaws in aircraft design don’t prove the existence of magic carpets. But there is a problem with our plane, and we should be allowed to talk sensibly about it in public, without anyone having a tantrum, since we have failed—as doctors, academics, regulators and industry—to fix these problems behind closed doors.

More than anything, we need to remember that this is not an abstract academic game. In medicine, distorted evidence maps directly onto the very real world of human suffering, pain, and death. That stuff matters.