With the news that Alex Rodriguez's 211-game suspension was reduced to 162 games by Fredric Horowitz, the independent arbitrator on MLB's three-person review panel, we are forced to once again ask where these numbers come from. Given the protocol outlined in the Joint Drug Agreement's PED section—50 games for a first violation, 100 games for a second and a lifetime ban for a third— and the lack of a similarly clear guide in the Basic Agreement, it's a fair question.
In the years since his name was leaked as appearing on a list of players who failed what was supposed to be an anonymous test, Alex Rodriguez has not failed a drug test (and those years, 2001-2003, wouldn't count under the JDA, anyway). So, he did not violate the JDA via a positive test. The evidence presented against A-Rod was obtained from the very same unsavory characters MLB was investigating in South Florida, including Anthony Bosch himself. MLB even struck a deal with Bosch to indemnify him should shit get heavy for him. The league also purchased information. That is the case against A-Rod.
Whether that satisfies the "or otherwise violates the program through the use or possession" catchall language, is debatable. Evidence obtained from a friend of a friend of a friend who knows a guy is not quite what you're looking for when you want to put away Public Enemy No. 1., but let's assume it does satisfy the catch-all provision.
Let's assume that everything Bosch and Co. said was true and that A-Rod used Biogenesis to obtain and use PEDs over the course of several years. Although MLB would like to punish A-Rod for multiple violations, he was never caught, so all that could reasonably be meted out under the JDA is 50 games. Which, interestingly, is one more game than Horowitz's reduction. Whether intentional or not, the Basic Agreement does most of the heavy lifting.
Since 211 games—a de-facto lifetime ban—under the JDA is impossible based on these facts (there is no compounding violations for positive tests of multiple substances, the violation with the longest terms serves as the basis of a suspension) Selig and MLB played the just-cause game, the mother of all catch-alls. Article XII, section B of the Basic Agreement allows for discipline when MLB finds that a player's actions are materially detrimental or materially prejudicial to the best interests of baseball.
Here, from MLB's statement following the original 211-game suspension:
Rodriguez's discipline under the Joint Drug Prevention and Treatment Program is based on his use and possession of numerous forms of prohibited performance-enhancing substances, including Testosterone and human Growth Hormone, over the course of multiple years. Rodriguez's discipline under the Basic Agreement is for attempting to cover-up his violations of the Program by engaging in a course of conduct intended to obstruct and frustrate the Office of the Commissioner's investigation.
Bud Selig found that buying information, in a bungling attempt to silence an opposing voice and protect a legacy built on fraud was prejudicial to those best interests and picked an arbitrary number designed to keep Alex Rodriguez from ever playing again. It's no wonder Fredric Horowitz agreed with him.