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At last, on April 12, 1633, Galileo appeared before the Commissary-General and the Procurator-Fiscal of the Inquisition. In answer to questions he said he supposed he was summoned on account of the book, which he admitted was written by him. When asked about the injunction laid on him in 1616, he clearly showed that he was only aware of Cardinal Bellarmine's admonition, which he claimed to have obeyed. On the further question of the strict command detailed in the minute on which, as we have seen, the case against him principally rested, he reiterated that if such a command had been issued he had forgotten it. He did not deny it, as he had promised complete submission, but he still maintained that he had not even acted contrary to the command "not to hold or defend" the opinions in question, but had actually shown that the arguments of Copernicus were weak and inconclusive.

He was detained in comfortable quarters belonging to the Procurator-Fiscal, and allowed to take exercise in the corridors, to have his meals sent in by Niccolini, and to have free correspondence with him. It is noteworthy, and does not agree with the ordinary ideas about Galileo's treatment by the Inquisition, that all previous prisoners since its foundation more than four centuries before had been straightway confined in the secret dungeons, from the beginning of their trial.

Three days later three counsellors of the Holy Office pronounced that Galileo had disobeyed the order of 1616, and did really hold and defend the obnoxious doctrines, but it was the practice to Omit no means of obtaining full admission from the prisoner himself. To ensure this, prior to his next appearance before the tribunal, the Commissary-General had a private interview with Galileo, and persuaded him to promise full confession, so that it should be possible for the Court, without weakening its reputation, to deal leniently with him. Accordingly, on April 30, Galileo appeared before the Court a second time, and made a statement that he had examined his book again carefully to see whether he had put the Copernican case too strongly, and found that in some of the arguments he had been carried away by pride in his own subtlety of reasoning in a false cause, and had put the false case too strongly, so that, contrary to his intention, it appeared to be true. He was then allowed to withdraw, but as he saw that the Court was not satisfied he returned and offered to add one or two more days to the Dialogues and to confute the doctrines to the best of his ability. He was then allowed to return to the Tuscan Embassy, to the delight of the Ambassador Niccolini.

On May 10 Galileo was summoned a third time, and produced a written confession of the truth of the minute of 1616, adding an appeal for clemency on the ground of his age and infirmity. He had evidently been persuaded once more, and perjured himself still further for the sake of peace. He thought that now the worst was over, though Niccolini was less sanguine.

On June 16 the Pope presided at a private meeting of the Congregation, and it was decided that Galileo should be tried, under threat of torture, as to his real convictions, should be made to recant before a plenary assembly of the Inquisition, and condemned to imprisonment at their pleasure: also that he should be forbidden to discuss the motion of the earth and the sun at all under pain of punishment as a relapsed heretic, and that his book should be prohibited. The decree was not at once made public, so that Niccolini put in a further plea for a speedy end to the trial, and was informed by the Pope that it was already ended, that Galileo would soon be sentenced, and that afterwards he would consult with Niccolini in order to minimise the distress Galileo would suffer. By way of letting him down gently, Niccolini only told Galileo that the trial would soon end, and that his book would be prohibited. This course was suggested by the Pope, who said things might possibly take a better turn.

On June 21 Galileo appeared before the judges once more. He stated in reply to questions that since he had been ordered to abandon them, he had not held the opinions of Copernicus as to the motion of the earth, and this he repeated when threatened with torture if he did not speak the truth. He signed his depositions and was detained somewhere in the Inquisition buildings till June 24. On June 22 he was summoned to receive sentence. The names of ten Cardinal Inquisitors were prefixed to the document read to Galileo, in which was recounted the whole gist of the proceedings of 1616, with its findings, including the famous minute, and an account of the admissions, forced and otherwise, made by the accused in the course of the further proceedings in the matter of the Dialogues. The successive steps were detailed showing how Galileo had first denied the accusations and defended himself, and then withdrawn his arguments and admitted his guilt, ultimately answering, under rigorous examination, "like a good Catholic". Then followed the actual sentence: Galileo being "vehemently suspected of heresy" for holding the doctrine of the motion of the earth, decreed contrary to Holy Scripture, has incurred grievous pains and penalties, but will be absolved if he will " abjure, curse, and detest the said errors and heresies, and every other error and heresy" in a prescribed form. But as a warning to himself and others, the book is to be prohibited by public edict, Galileo is to be formally imprisoned in the Inquisition at the judge's pleasure, and is to recite once a week for three years, by way of penance, the seven penitential psalms, the judges reserving the right to mitigate the penalties. Only seven of the ten Cardinal Inquisitors signed the decree, so that it does not seem to have been unanimous.

Galileo then knelt before the Inquisition, read aloud the prescribed form of abjuration, and signed it. This must have been the climax of the moral torture of the last ten months. We may acquit the Inquisition of having inflicted physical torture, and Galileo's actual imprisonment could only have been for the three days, June 21 to 24, and was probably not even in a dungeon. It seems as if a very little harshness of this kind at the beginning of the trial would have been enough to kill the old man, who was already ill, but he would then have escaped practically all the punishment intended. The moral bullying to which he was subjected is very, like the physical twisting of a boy's arm, until he admits that his tormentor is a "perfect gentleman," or some such obvious falsehood. So generally has the abjuration been regarded as compulsory perjury on the part of Galileo, that more than a century after his death a story was invented that immediately after his public denial of the earth's motion he muttered "Eppur si muove," but though doubtless he thought something of the kind, it is absolutely certain that the story is false.

True to his promise to Niccolini, the Pope substituted banishment to one of the Grand Duke's villas near Rome, for imprisonment in the Inquisition buildings, but we cannot acquit him of personal responsibility for much, if not all, of Galileo's previous suffering, responsibility not as Pope, for no "Ex Cathedrâ" pronouncement was made, and the doctrines were not condemned by the Church, but as a man who listened too readily to insinuations touching his dignity, and used his official position to avenge a fancied slight, not perceiving that it was not Galileo but his enemies that were really "scoring off him".

Galileo naturally was much depressed, not at the prohibition of his book, but at the personal proceedings which had impelled him to do such violence to his conscience. The sentence and abjuration were published as widely as possible, especially in Padua and Florence, and all the Papal officials who had favoured Galileo during the course of the proceedings were punished, including Castelli, Riccardi, and the Florentine Censor.

Galileo petitioned the Pope to allow him to return to Florence or its neighbourhood, and though this was not immediately granted, he was permitted to retire to Siena on June 30, and after further pressure exerted in his favour, to his villa at Arcetri on December 9, after an absence of nearly a year.