All these honors bestowed upon Halley did not sit well with John Flamsteed. Despite his earlier liking of the young college student, soon, he considered him to be an enemy.
For the next few years, Edmund spent some time travelling and making observations. During this time, he observed a comet and worked with Giovanni Cassini trying to determine its orbit. In 1682, he returned to England and married Mary Tooke. That same year, his father also remarried, having lost his wife some 10 years previously.
The responsibilities of marriage placed a great financial strain on Halley, especially since his father’s new marriage cut into that support. Things went from bad to worse when in March 1684 his father disappeared and was discovered dead five weeks later, Edmund, then had to administer his father’s estate.
Shortly before the disappearance of his father, Edmund had been working on some research along with fellow Royal Society members; Christopher Wren and Robert Hooke. Halley had demonstrated that Kepler's third law implied the inverse square law of attraction, and now discussed with Wren and Hooke whether this implied elliptical orbits for planetary motion. Investigating the matter further, he visited Isaac Newton in Cambridge only to learn that Newton claimed to have solved the problem four years earlier, but could not find the proof among his papers.
Recognizing the greatness of Newton’s intellect, Halley urged Newton to allow him to write "Principia Mathematica" and to allow Halley to publish it.
Halley next sought an academic post. In 1691 he applied for the Savilian Chair of Astronomy at Oxford, which was currently vacant. However, the animosity he had generated in Flamsteed caused the Astronomer Royal to block this appointment.
Over the next several years, he continued to work for the Royal Society in a number of capacities. He edited "Philosophical Transactions", published some of the world’s first actuarial tables, and began making very careful studies of comets. In 1695, his friendship with Isaac Newton paid off when that man accepted the position of Master of the Mint and appointed him deputy controller of the mint at Chester.
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