So now we have the definitive word: Barry Bonds did test positive…just not for the substance everyone expected. T.J. Quinn of the New York Daily News broke the story when sources told him that Bonds failed a test in 2006 for amphetamines. The question is not if, but how and why. In the last 48 hours, I’ve been able to put together some of this information.

According to sources in Quinn’s story, Bonds tested positive for a “strong stimulant,” one that may have been the result of a supplement. While Bonds is unlikely to have taken the classic “greenie,” there are several amphetamine-like substances that have been found in legal supplements. Remember two things here: legal and banned are two different things, and an athlete is responsible for whatever he/she puts into his/her body.

Bonds, of course, will eternally be linked to BALCO. BALCO is not just known for steroids. In fact, many of the athletes who worked with Victor Conte and his lab used stimulants. The best known is modafinil, a drug originally designed to help with narcolepsy, and now prescribed for ADD. It is possible, though unlikely, that Bonds used this drug. It was not indicated at all in the research done in Game of Shadows. Modafinil is presumed to be on the MLB banned list, although the complete list is not publicly available. There are athletes that have requested Therapeutic Use Waivers for this drug in other sports, but again, it is not known to be used by legal waiver in baseball. (It’s worth noting that baseball has granted TUWs for substances such as testosterone. We don’t know why.)

Modafinil is hardly the only stimulant with a BALCO connection. Patrick Arnold, Conte’s source for THG, sells a legal supplement called AMP. It is legal and available. (In fact, I stopped by a GNC here in Indianapolis and saw it on the counter Thursday afternoon.) AMP was found to contain substances that were very much like amphetamines. In a May 2006 article, Amy Shipley of the Washington Post talked with Don Catlin, a steroid researcher who works with WADA and was involved in the BALCO case, about AMP. Catlin found that the active ingredient was not listed on the label. Methylhexaneamine, like many of Arnold’s substances, was a re-concocted version of a previously existing compound, this time one invented in the 1940s as a nasal decongestant. Catlin described the drug as similar to amphetamines and ephedrine.

Bonds is known to take supplements today, including ZMA, a supplement produced by SNAC, an offshoot of Conte’s infamous BALCO labs. This picture tells you all you need to know about SNAC. Yes, that’s Greg Anderson on the right. While there’s no evidence that Bonds used AMP, it is quite possible given the connections. Ergopharm, the producer of AMP and several other supplements, boasts of professional-athlete usage of their supplements. However, Ergopharm is not one of the supplement manufacturers whose products have been approved for usage in baseball or football. Under that policy, the National Science Foundation can “certify” or “bless” supplement manufacturers after inspecting their manufacturing facilities and testing their products.

Why would Bonds risk failing a drug test despite being under a level of scrutiny unlike any other athlete? The reason is unclear. Bonds could have taken a supplement that contained a banned substance, such as AMP. Again, Amy Shipley showed that some products that are available in stores may contain banned substances. (It should be noted that most of these products were immediately pulled from the market after Shipley’s story.)

Why would Bonds take these substances? One source suggested that it wasn’t performance enhancement, but weight management. Amphetamines and similar substances are often used in weight loss and weight management. The appetite-suppressant effect would have helped Bonds in two ways. First, his knees were under a lot of pressure carrying additional weight. The knee problems were part of a cycle–Bonds couldn’t work out with his normal intensity so he gained weight. When he gained weight, his knees hurt more. Add in that supplements like AMP are specifically designed to help “cut”–take off body fat and water weight–and there’s a twofold effect before we even get to possible performance enhancement.

While much of the coverage of this has been on the level, some of the reporting has been misleading. Most importantly, the Giants were aware of Bonds’ positive test. Teams are always conscious of positive tests, since things like additional tests and administrative needs would have to be communicated through the team. Saying that privacy rules would prevent Brian Sabean from knowing about Bonds’ test are laughable. While we’re on the topic of the additional tests, those are one more interesting data point. Since Bonds was not suspended, there was no second positive test, nor was there a positive test during that point for any other banned substance. Bonds may not have “played naked” during his comeback season in 2006, but he didn’t play juiced. That much we now know. Finally, the initial story of Bonds blaming the positive test on Mark Sweeney didn’t seem right. Bonds is nothing if not loyal, and needs to look no further than his friend Anderson to see the value of a shut mouth. Add in that Sweeney’s locker was not located near Bonds’ complex of lockers and the story just doesn’t fit the facts.

Things could hardly get worse for Bonds. He’s still in severe legal jeopardy, has the same physical challenges he faced last year with his knees, back and elbows, and faces the wrath of the pitchforked PED mob that now finally has a positive test to hang alongside Bonds’ effigy. He’ll live this year in the shadow of many things, Hank Aaron least of all.