Half of all clinical trials ever completed on the medical treatments currently in use have never been published in the medical literature. Trials with positive results for the test treatment are about twice as likely to be published, and this applies to both academic research and industry studies

Does this throw out all the conclusions about vaccines, penicillin, and whatever else has been researched in this way?

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    This site is about debunking or proving notable claims. You question is not one. Now, if you could find an source claiming this throws out all the conclusions about vaccines, penicillin, and whatever else has been researched in this way that would be something - although still too broad IMO. – user22865 Sep 25 '17 at 7:17
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    Also, the implied statement is nonsensical -- when the clinical trial for a new medication produces negative results, the outcome isn't newsworthy to anyone except the company that now has to go back to the drawing board and figure out what went wrong. That's nothing sinister or unique to the pharma industry -- how many news articles have you read about the (probably hundreds of) failed design trials for new processor core architectures at Intel's R&D? How many crash test dummies Mercedes had to sacrifice until they finally had a new car design that satisfied safety standards? – Shadur Sep 25 '17 at 8:08
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    @Shadur I suggest you have a look at the work of Ben Goldacre and OpenTrials. The "hidden" trials do not concern only medications or drugs that don't get on the market, but also those that do, hiding possible side effects or overstating their effectiveness. – Federico Sep 25 '17 at 11:46
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    @shadur there are tons of reasons why failed experiments are super useful. Think about what happens when only marginally positive results for a molecule are published... it makes a perfectly ineffective medicine look as if it would be effective – Sklivvz Sep 25 '17 at 11:57
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    This almost seems like a conceptual question. I mean, yeah, tossing out scientific results obviously biases literature; repeat the jelly bean experiment enough, reporting only positive results, and the literature'll contain plenty of confirmation that jelly beans cause acne with ample replication. – Nat Sep 25 '17 at 12:25