"Although the slogan 'Believe the victim' has become popularized of late, it has no place in a criminal trial. To approach a trial with the assumption that the complainant is telling the truth is the equivalent of imposing a presumption of guilt on the person accused of sexual assault and then placing a burden on him to prove his innocence. That is antithetical to the fundamental principles of justice enshrined in our constitution and the values underlying our free and democratic society."

So wrote Ontario Superior Court of Justice Judge Anne Molloy this week when she acquitted three male Toronto police officers of charges of sexually assaulting a female officer in a hotel room, after a night of drinking at bars and a strip club. The complainant and the defendants agreed they had sex; the trial was about whether the sex could be proved to have been non-consensual, and therefore criminal.

At a time when violence against women is top of mind, and there's evidence that sexual assault allegations aren't always fully accepted or investigated, Judge Molloy no doubt knew that her verdict would displease many. So she did something unusual. She devoted a large part of that verdict to explaining the foundations of criminal law: defending the principle of the presumption of innocence, spelling out what proof beyond a reasonable doubt is, and asserting why these must be applied in criminal trials, even those involving an allegation of sexual assault.

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She was not doing this for the benefit of the lawyers in court that day. Her defence of the law was aimed at a much wider audience.

Taking away a person's liberty is the most extreme thing the state can do. That's why our criminal law is built on the presumption of innocence. If you're accused of a crime, you don't have to prove your innocence. You don't have to prove anything, or even testify in your own defence. The burden of proof is entirely on the Crown.

What's more, to secure a conviction, the Crown has to clear a very high legal hurdle: It must demonstrate that the accused is guilty "beyond a reasonable doubt." In a civil case, the standard of "balance of probabilities" – is one side just a bit more credible than the other? – is enough. But in a criminal case, where conviction can mean a record and prison, the judge or jury must believe that the evidence definitively proves the accused's guilt.

If the proof offered by the Crown isn't strong enough to leave the judge or jury sure of guilt – if there are doubts – then the verdict must be one of not guilty.

All of these protections tilt our justice system in favour of the accused, and they are designed to, with good reason. It's about protecting the individual against the overwhelming power of the state, and guarding against courts liable to be swayed by public opinion. It's an attempt to ensure that innocent people are not wrongly convicted, for any one of us could be that accused innocent.

We don't think many Canadians would wish to be tried under different legal principles. The system is not perfect – and a liberal society wisely does not aim for perfection. But it's considerably less imperfect than the alternatives.

Judge Molloy quoted the Supreme Court case which lays out the instructions to be given to a jury, and which a judge gives to herself, prior to reaching a verdict.

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"Even if you believe the accused is probably guilty or likely guilty, that is not sufficient. In those circumstances you must give the benefit of the doubt to the accused and acquit because the Crown has failed to satisfy you of the guilt of the accused beyond a reasonable doubt." And reasonable doubt, said the Supreme Court, "must not be based upon sympathy or prejudice. Rather, it is based on reason and common sense. It is logically derived from the evidence or absence of evidence."

In the case of the three accused officers, evidence, absence of evidence and doubts about the Crown's evidence led Judge Molloy to acquit. It wasn't that she entirely believed the men's story, and she said as much. But presumption of innocence means that the accused didn't have to definitively prove that they didn't do it. The Crown had to prove, beyond a reasonable doubt, that they did.

The prosecution did not fail because Judge Molloy was certain about exactly what happened that night. On the contrary, she acquitted the accused because the evidence presented by the Crown was not strong enough to leave her sure of what happened, or sure that what happened was the crime of non-consensual sex.

Hence the verdict: not guilty. Judges don't find people innocent, and the accused in this case didn't prove themselves innocent. But under a legal system that presumes innocence in the absence of a conviction, they didn't have to.

For many people, this will be an entirely unhappy conclusion. An allegation of rape was rejected. And while the case offered a definitive verdict, it did not provide definitive answers for everything that happened that night. But a criminal trial can't provide all the answers. Sometimes, the best it can do is to establish that much is unclear and uncertain. And if don't know for certain, you cannot convict.

After the verdict, one Toronto newspaper ran a picture of the accused on its front page, with a giant, one-word headline: "Scumbags." Maybe that's true. Maybe it isn't. But Judge Molloy, applying criminal law according to long-standing and necessary principles, wasn't asked to rule on their moral character, or whether they should remain police officers. Her job was to decide whether sufficiently persuasive evidence had been presented to find them, beyond a reasonable doubt, guilty of a crime. She could not.