Commissioner of Agriculture, horticulturalist, and political ally of Attorney General Edward Bates, Isaac Newton was first appointed chief clerk in the Patent Office's Bureau of Agriculture in 1861.

In May 1862, Congress authorized the appointment of a commissioner of agriculture to oversee the dissemination of information about agriculture and samples for planting. "It was natural for Lincoln to promote to the position the Patent Office clerk who had looked after agricultural matters, Isaac Newton—a Quaker with a farm of his own in Pennsylvania. Newton soon had a chemist, an entomologist, a statistician, and most important of all, the versatile Scottish-born botanist William Saunders, working beside him," wrote historian Allan Nevins.1 Lincoln’s interest in scientific agriculture influenced his selection of Isaac Newton as commissioner of agriculture. Historian Gabor S. Boritt wrote: “He was not a well know agriculturist and as a department chief alternately showed both ability and blundering. He proved to be a controversial political figure, too. All the same, he soon had a botanist, a chemist, an entomologist, and a statistician working for him – all very able persons. He also started an agricultural library and a museum.”2

Newton himself inspired less admiration. "He was an ignorant, credulous old gentleman, quite rotund about the waistband, with snow-white hair and a mild blue eye," wrote Ben Perley Poore.3 Washington chronicler Margaret Leech wrote that “Newton was a stupid old fellow. …But he was honest and kind, and he befriended Mrs. Lincoln, preventing, he told John Hay, ‘dreadful disclosures.’”4 Newton employed New Yorker Simeon Draper as his agent in threatening James Watt with imprisonment and reimbursing him with a bribe to key his confidences.

Newton was a gossipy Quaker and a spiritualist who became a friend of Mary Todd Lincoln and introduced her to some of Washington's other spiritualists. Two of them were hired in the Bureau of Agriculture at Mrs. Lincoln's request. According to historian Margaret Leech, he was so stupid "he once made requisition for two hydraulic rams, because he had been told they were the best sheep in Europe. But he was honest and kind, and he befriended Mrs. Lincoln, preventing, he said, dreadful disclosures."5 Newton helped engineer the cover-up of gardener John Watt's blackmail of Mrs. Lincoln. Presidential aide John Hay recorded in his diary of February 13, 1867 an interview he had with "Father Newton":

"he launched off in his buzzing way about Mrs. Lincoln how imprudent she was—how he protected & watched over her & prevented dreadful disclosures; how at one time when Watt had entered into a conspiracy to extort 20,000 from the President by using three letters of Mrs Lincoln, he sent for [Simeon] Draper who went to Watt in his greenhouse on 14th Street & told him he was come to take him to Fort Lafayette, with much bluster & great oaths as Simeon's wont; how Watt fell on his literal marrow bones & begged, & gave up the letters & the conspiracy got demoralized & came down, down, to 1500 dollars which was paid, and the whole ting settled. 'Oh,' said the old fellow, 'that lady has set here on this here sofa & shed tears by the pint a begging me to pay her debts which was unbeknown to the President. There was one big bill for furs which give her a sight of trouble—she got it paid at last by some of her friends—I don't know who for certain—not Sim Draper for he promised to pay it afore Cuthbert but after Lincoln's death he wouldn't do it."6

Bates recorded in his February 3 1862 diary: "Certainly friend Newton does hear more gossip than anyone I know."7 On February 25, 1863 he added: "At night, Mr. Newton and Mr. Sargent called to see me, and Mr. N (as usual) had secrets to tell—He took me aside to say he must have a talk with me, but now—saying only that he had just had a long private talk with the P. partly about me—that the P. assured him that he had full and unabated confidence in Me."8 On May 23 1863, Bates wrote: "Today Isaac Newton told me, as a great secret, that Gen. [Henry Halleck] was a confirmed opium—eater— as he is very credibly informed.."9 Bates recorded in his February 28,1864 diary: "Friend Newton is full of news. He tells me today, that a secret pamphlet has been gotten up (he thinks, by the machinations of Secy. [John Usher] and Senator [Samuel] Pomeroy) levelled agst. Mrs. L. in reference to the infamous [John] Watt scandal. He expects to get a copy tomorrow; and if it turn out to be what he supposes, thinks it will produce an explosion."10

On the night President Lincoln was assassinated, it was Newton who brought word to the White House, according to doorkeeper Thomas Pendel: "Probably about twenty minutes before eleven o'clock, I stepped up to the door in answer to another ring at the bell. Who should be there but Isaac Newton, the Commissioner of Agriculture….I admitted him inside the door, and at once closed it. He was a bosom friend of President Lincoln. I was thoroughly acquainted with him, and I knew to whom I was talking. He said to me, 'They have shot the President. And the bullet', he said, 'has entered the left side of his head'. I immediately hurried upstairs, leaving him on the inside, and went to Captain Robert Lincoln's room."11

Newton's Quaker connections were also important to the White House. It was Newton who served as the bearer of a message of support in 1863 from noted Quaker Eliza Gurney: "I feel inclined to give the assurance of my continued hearty sympathy in all thy heavy burdens and responsibilities and to express, not only my own earnest prayers, but I believe the prayers of many thousands whose hearts thou has gladdened by thy praiseworthy and successful effort 'to burst the bands of wickedness, and let the oppressed go free'…"12

President Lincoln wrote Mrs. Gurney on October 26, 1862: "I am glad of this interview, and glad to know that I have your sympathy and prayers. We are indeed going through a great trial—a fiery trial. In the very responsible position in which I happen to be placed, being a humble instrument in the hands of our Heavenly Father, as I am, and as we all are, to work out his great purposes, I have desired that all my works and acts may be according to his will, and that it might be so, I have sought his aid—but if after endeavoring to do my best in the light which he affords me, I find my efforts fail, I must believe that for some purpose unknown to me, He wills it otherwise. If I had had my way, this war would never have been commenced; If I had been allowed my way this war would have been commenced; If I had been allowed my way this war would have been ended before this, but we find it still continues; and we must believe that He permits it for some wise purpose of his own, mysterious and unknown to us; and though with our limited understandings we may not be able to comprehend it, yet we cannot but believe, that he who made the world still governs it."13