In Major League Baseball, Ryan Braun is a big name. He should be a bigger name, considering he was named National League Most Valuable Player in 2011, but he plays left field for the Brewers. Milwaukee is not Manhattan and if Braun had put up a .330/33 HR/111 RBI season for a Mets or Yankees team that won a franchise-record number of games he’d be a megastar.

On Thursday Ryan Braun blew up the twitter feed of anyone interested in MLB. And it all came down to where his pee was stored on a particular weekend last October.

In October 2011 a PED (Performance Enhancing Drug) tester asked Mr. Braun, 28, to pee in a cup. This he duly did. The tester, as it was a Saturday, didn’t bring it straight to a FedEx depot as he presumed it would be closed. Instead, he stored the sample in a basement fridge at his home.

The Brewers lost to the St. Louis Cardinals in the National League Championship Series. The Cardinals then, improbably, won the World Series against the Texas Rangers as the people of Milwaukee looked on, satisfied with their hometown team’s record season and their star, Ryan Braun.

All was then quiet in baseball.

That changed in December when it was announced that Braun, who had been named National League MVP in the meantime, had tested positive for a banned substance. Well, “announced” is not really correct. “Leaked” is the correct word. It was leaked, ESPN reported it, and that’s something we’ll come back to.

A positive test would require Braun, as a first-time offender, to serve a 50-game suspension. For anyone unfamiliar with the length of the MLB season (162 games) that’s the equivalent of a footballer being suspended for 12 Premier League games. It is significant.

Braun immediately and publicly pronounced his innocence: “I am completely innocent. This is B.S.”, he tweeted to the local newspaper, the Milwaukee Journal Sentinel. And he appealed the suspension.

In the meantime the debate started in earnest. Talking heads, media scribes, bloggers and tweeters all weighed in on the “Should we strip him of the MVP award?” debate. Some went all-in; others didn’t, taking a more circumspect approach in preferring not to come down on either side until the appeal was heard, ruled upon and an official announcement regarding a suspension actually made.

*As an aside, the world of fantasy baseball was thrown into chaos. Like Schrödinger’s Cat, Braun was now both suspended and not suspended. How low should he be dropped in the rankings? If he was using and he’s been caught, when he comes back after suspension will he be the same player now that he’ll have to stop ‘roiding up? Such were the musings of the armchair GMs of MLB.

In the shadows behind Braun lay MLB’s PED era, that period from the mid-90s until the late 00’s when offensive production went through the roof*. A proper testing policy had been put in place in 2006 with proper penalties. Since then, an assortment of players had tested positive for banned substances – hitters and pitchers; bit-part players and future Hall of Famers – nobody was immune. But a reigning MVP from a fairytale season who’d allegely tested positive during the playoffs? That was a punch in the gut.

* To the educated observer there were numerous reasons for this: a rash of new, smaller ballparks (owners loved to see home runs); the umpires calling a tiny strike zone; rumours about a secret change to a new baseball with a more lively core; the effects of expansion as a weaker level of competition needed time to find its natural balance. Oh, and drugs. Except perhaps not the ones you might think.

It rumbled on through the offseason.

After their amazing 2011 run when they had won the NL Central division for the first time and won a franchise record 96 games, Milwaukee lost their powerful and implausibly-proportioned first baseman, Prince Fielder – 5′ 11″ and over 20 stone in weight – to the Detroit Tigers and a $214m contract. Add the possible loss of Braun for a third of the 2012 season and the Brewers would be behind the 8-ball, to put it mildly.

And the person who leaked it sat quietly by.

The appeal went to arbitration. This process requires three parties: a representative from the Players’ Association (who will always side with the player appealing), a rep. from Major League Baseball (who will always side with the testers) and an independent arbitrator. This might seem on the surface to be a very odd system, placing all the weight on a single person’s shoulders. However, since either side is free to “fire” the arbitrator, it is in their interests to be scrupulously fair to both sides at all times.

Baseball’s arbitrator is a man called Shyam Das, and on Thursday night he made his decision: Ryan Braun would not serve a suspension.

The precise reason boiled down to what Das ruled to be a chain of custody problem with Braun’s sample, in particular its being stored in the tester’s basement fridge rather than a FedEx facility. To some, vindication of an innocent man. To others, Braun got off on a dubious “technicality” because at no stage had Braun’s legal team challenged the test result or the integrity of the sample itself.

And then MLB came out with an extraordinary official statement:

“Major League Baseball considers the obligations of the Joint Drug Prevention and Treatment Program essential to the integrity of our game, our Clubs and all of the players who take the field. It has always been Major League Baseball’s position that no matter who tests positive, we will exhaust all avenues in pursuit of the appropriate discipline. We have been true to that position in every instance, because baseball fans deserve nothing less.

“As a part of our drug testing program, the Commissioner’s Office and the Players Association agreed to a neutral third party review for instances that are under dispute. While we have always respected that process, Major League Baseball vehemently disagrees with the decision rendered today by arbitrator Shyam Das.”

From any perspective, this was stunning.

Major League Baseball was coming out in a very public manner against a decision that resulted from a process that it had campaigned for, had insisted upon after prolonged negotiation with the Players’ Association and had trumpeted in order to get the US Congress and other interfering parties off its back.

This boils down to something interesting, something that it’s not clear that MLB, the players, the baseball media or the fans understand. Drug testing isn’t perfect. It never will be. If it was, there would be a full body scanner that each player had to walk through as they walked out onto the diamond that would beep if they were juiced. But there isn’t such a machine, and as with all drug testing the testers will always trail the cheats as new drugs are developed, pushed and used.

Drug testing is about behavioural economics and incentivisation. That is to say, it’s not about catching every cheat, rather the priority is about creating an environment where fewer people cheat in the first place.

For some context, a quick history lesson. Until the very recent past there was no penalty imposed by MLB for using performance enhancing drugs. There wasn’t even any testing. Mark McGwire shattered the home run record in 1998 in an epic duel with Sammy Sosa, where McGwire’s 70 homers and Sosa’s 66 both smashed the 61 home runs that Roger Maris hit in 1961.

When a reporter saw a bottle of Androstenedione sitting in broad daylight in McGwire’s locker, not a steroid per se but the equivalent of a large neon sign saying “I AM USING STEROIDS AND I DON’T CARE IF YOU KNOW IT”, nothing was done. Nobody wanted to do anything. The cancellation of the 1994 World Series due to a players’ strike had caused huge damage to the game’s fanbase and the longball was bringing them back. MLB, the owners and the media wilfully suspended disbelief.

Other players saw this and made an obvious and understandable decision. “Juicing” was an open secret in the game but after McGwire and the Andro discovery it was very clear that there was no disincentive to load up on whatever drugs would make you stronger, faster and richer. We now know that all sorts of players used them, big guys and small guys, from minor leaguers to future Hall of Famers, pitchers and hitters alike.

Without testing in place, let alone penalties, there was every incentive for players to use PEDs and zero incentive to stay clean. So use them they did. The perception was that drugs would help you hit home runs or strike people out and that’s what people would pay money to see. And nobody would stop you.

What about peer pressure? The list of high profile players who publicly denounced the use of such drugs was small, really small, with only a single player, the now-retired Frank Thomas, willing to go on the record for George Mitchell’s controversial report into the use of performance enhancing drugs in MLB.

So, if one accepts that the goal of having testing and penalties isn’t about catching cheaters but instead changing the incentive system it’s clear from its Thursday statement that MLB doesn’t understand this. Its official reaction revealed a raw and barely-restrained desire to clap Ryan Braun in irons and have him publicly flogged. Shyam Das too, while they’re at it. But at what cost?

Ryan Braun doesn’t matter. He is one player among thousands. His being found guilty or innocent is ultimately of no consequence provided the system for doing so is seen to be above reproach. Getting off on a “technicality” will not do as much damage as the potential harm that could result from the initial leak that placed this all in the public eye combined with MLB forcefully condemning its own system.

There are always positive tests; some are confirmed and others are found to have been false positives. Others still are appealed, just like Braun, but it should all take place in private so that both the system and the people involved retain trust in each other. MLB should be taking action, quickly and in full view, to find out how the initial leak to ESPN happened in the first place.

Baseball Prospectus writer Jason Collette nailed it when he said that he didn’t recall MLB “vehemently disagreeing” with the initial leak of Braun’s (allegedly) positive test. Not a peep out of them was heard back then and that needs to change should any similar incident occur in the future.

MLB needs to see past Ryan Braun and look at the much bigger picture. That forest in the distance ain’t trees; it’s needles, with a load of ballplayers eyeing them up.