It's interesting that this odd episode of early U.S. history got into the series YOU ARE THERE, because it really is an election rule problem that got out of hand.
When the Constitution was adopted, the rule for electing Presidents was that you nominate the candidates. He who got the highest votes was President, he who came in second was Vice President (and possible successor if the President died or resigned). This worked well from 1789 to 1793, through two Presidential elections only. Washington was the unanimous choice for President in 1789. Then it was decided to vote in the Vice President, and John Adams was chosen. Adams and Washington were fellow Federalists. The team were re-elected in 1792 (although, this time, there were a few other candidates). But Washington was determined to retire to his estate, and announced no third term (a tradition that lasted until 1940). Adams was nominated by the Federalists for President and his Vice President was fellow Federalist candidate Timothy Pinckney, a distinguished (and successful) Gemeral and diplomat. But now there was a rival political party - the Democrat-Republicans, led by Thomas Jefferson. He was nominated with Aaron Burr of New York for the two slots.
Enter Alexander Hamilton - Hamilton did not like Adams, but liked Pinckney. He manipulated the balloting of the Federalists, to try to get Pinckney elected as President instead of Vice President. It backfired badly. Adams won the Presidency over Jefferson, but by only three votes (his enemies would call him the "Three vote President" until he left office). Jefferson came in second, and was Adams' Vice President. Politics had driven a wedge between the portly Adams and his old chum from Monticello, and it would get worse in the next four years with the Vice President leading the opposition.
Came 1800. Adams was renominated President (despite the efforts of Hamilton) by the Federalists, with Charles Coatesworth Pinckney (Timothy's brother) as his running mate. Jefferson ran against them. Adams was swamped this time (the Federalists never were to win the Presidency again). However Jefferson's elation was quickly dashed. Somehow the balloting for him and his running-mate (Burr again) was both 60 electors. In short they were tied.
This should not have been a problem, as it was assumed that Burr was the running mate and would accept the Vice Presidency as what he was running for. But Burr had other ideas. Given the fluid state of the nature of the races for the President and Vice President in 1789 - 1796, with the Vice President getting a special vote in 1789 because Washington was unanimously elected (not being the man who came in second, as the Constitution said), and the Hamilton inspired 'free - for - all" in 1796, Burr could make a logically correct assumption that he could replace Tom as the ticket's President because he had just as many votes.
Jefferson never forgave Burr. Always suspicious of non-agrarian southerners, Jefferson liked allies in the Northeast who were pliable or second-rate (elderly, senile Governor George Clinton of New York was a better bet in later years - or seemed to be). Burr was acceptable because he was a good counter to the hated Hamilton in Federalist New York and New England. But Jefferson never was a close friend of his (unlike his friendships with fellow Virginians James Madison and James Monroe, or the one New Yorker he liked - Albert Gallatin). This trick of Burr's (although a permissible one, given the state of the rules) destroyed any further chance of a closer relationship.
Burr and his supporters now faced Jefferson and his supporters in the House of Representatives. The confrontation meant that the deciding group were the Federalists! Ironically now Jefferson could have used his old friendship with Adams but it was too strained. So the Federalist that he was now forced to rely on was his enemy Hamilton. Fortunately Hamilton did not like Burr either. Alexander went about from one delegation of Federalists to another holding them together and saying that if they had to make the choice choose Jefferson - Hamilton felt Burr too ambitious (possibly true, but possibly due to his personal feelings).
Burr lost as a result (one more reason for him to hate Hamilton - and one more step to Hamilton's death in that duel with Burr in Weehauken, New Jersey in 1804). Burr now was Jefferson's Vice President, and was affectively frozen out of all policy making by his chief (as well as all patronage in New York). Burr would be so disgusted he would even run for the Governorship of New York in 1804, and be defeated (again due to Hamilton - still another reason for him to hate Hamilton). Jefferson and Madison decided to make sure the mess could not reoccur: the eleventh amendment to the constitution was created in 1804 (just in time for the next election) that made specific nominations for President and Vice President on national tickets mandatory).
Burr would have his revenge on his chief - first by presiding over the Jefferson inspired impeachment of Associate Justice Chase of the Supreme Court in a manner fully partial to Chase (who the Senate acquitted as a result). Secondly he would be involved in the conspiracy with Wilkinson in the Western United States. Finally his own treason trial enabled Jefferson's other enemy, his dear cousin Chief Justice John Marshall to repay Aaron (on the Chase affair) by being partial to his defense over the prosecution's case. Aaron was acquitted much to Tom's humiliation.
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