Yet throughout most of history, independent thinking was discouraged and often persecuted. The battle for independence of mind continued for centuries. In Freedom of Thought, J. Bury provides a dramatic survey of intellectual history, clearly and eloquently describing the struggle for intellectual freedom from ancient times to the beginning of the 20th century.
He guides the reader from the flowering of rational inquiry in early Greece, through the suppression of free thought during much of the Middle Ages, to the rediscovery of classical philosophy in the Renaissance, and finally to the growth of rationalism beginning with the Age of Reason in the 17th century.
The violation of the freedoms of thought, conscience and expression
But if the persecution is not so devised and carried out as to accomplish its end, then you have two evils instead of one, and nothing can justify this. From their point of view, the Emperors had good reasons for regarding Christianity as dangerous and anti-social, but they should either have let it alone or taken systematic measures to destroy it. If at an early stage they had established a drastic and systematic inquisition, they might possibly have exterminated it.
This at least would have been statesmanlike. But they had no conception of extreme measures, and they did not understand —they had no experience to guide them —the sort of problem they had to deal with. They hoped to succeed by intimidation. The later persecutions of A. It is particularly to be observed that no effort was made to suppress Christian literature.
The higher problem whether persecution, even if it attains the desired end, is justifiable, was not considered. The struggle hinged on antagonism between the conscience of the individual and the authority and supposed interests of the State. It was the question which had been raised by Socrates, raised now on a wider platform in a more pressing and formidable shape: what is to happen when obedience to the law is inconsistent with obedience to an invisible master? Is it incumbent on the State to respect the conscience of the individual at all costs, or within what limits?
The Christians did not attempt a solution, the general problem did not interest them. They claimed the right of freedom exclusively for themselves from a non-Christian government; and it is hardly going too far to suspect that they would have applauded the government if it had suppressed the Gnostic sects whom they hated and calumniated.
In any case, when a Christian State was established, they would completely forget the principle which they  had invoked. The martyrs died for conscience, but not for liberty. To-day the greatest of the Churches demands freedom of conscience in the modern States which she does not control, but refuses to admit that, where she had the power, it would be incumbent on her to concede it. If we review the history of classical antiquity as a whole, we may almost say that freedom of thought was like the air men breathed.
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It was taken for granted and nobody thought about it. If seven or eight thinkers at Athens were penalized for heterodoxy, in some and perhaps in most of these cases heterodoxy was only a pretext. They do not invalidate the general facts that the advance of knowledge was not impeded by prejudice, or science retarded by the weight of unscientific authority. The educated Greeks were tolerant because they were friends of reason and did not set up any authority to overrule reason. But this liberty was not the result of a conscious policy or deliberate conviction, and therefore it was precarious.
The problems  of freedom of thought, religious liberty, toleration, had not been forced upon society and were never seriously considered. When Christianity confronted the Roman government, no one saw that in the treatment of a small, obscure, and, to pagan thinkers, uninteresting or repugnant sect, a principle of the deepest social importance was involved. A long experience of the theory and practice of persecution was required to base securely the theory of freedom of thought. The lurid policy of coercion which the Christian Church adopted, and its consequences, would at last compel reason to wrestle with the problem and discover the justification of intellectual liberty.
The spirit of the Greeks and Romans, alive in their works, would, after a long period of obscuration, again enlighten the world and aid in re-establishing the reign of reason, which they had carelessly enjoyed without assuring its foundations. The first three are unthinkable, if he is a God worthy of the name; therefore the last alternative must be true.
Why then does evil exist? The inference is that there is no God, in the sense of a governor of the world.
This momentous decision inaugurated  a millennium in which reason was enchained, thought was enslaved, and knowledge made no progress. During the two centuries in which they had been a forbidden sect the Christians had claimed toleration on the ground that religious belief is voluntary and not a thing which can be enforced. When their faith became the predominant creed and had the power of the State behind it, they abandoned this view. This policy was adopted by Emperors and Governments partly on political grounds; religious divisions, bitter as they were, seemed dangerous to the unity of the State.
But the fundamental principle lay in the doctrine that salvation is to be found exclusively in the Christian Church. The profound conviction that those who did not believe in its doctrines would be damned eternally, and that God punishes theological error as if it were the most heinous of crimes, led naturally to persecution.
It was a duty to impose on men the only true doctrine, seeing that their own eternal interests were at stake, and to hinder errors from spreading. Heretics were more  than ordinary criminals and the pains that man could inflict on them were as nothing to the tortures awaiting them in hell. To rid the earth of men who, however virtuous, were, through their religious errors, enemies of the Almighty, was a plain duty.
Their virtues were no excuse. We must remember that, according to the humane doctrine of the Christians, pagan, that is, merely human, virtues were vices, and infants who died unbaptized passed the rest of time in creeping on the floor of hell. The intolerance arising from such views could not but differ in kind and intensity from anything that the world had yet witnessed.
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Besides the logic of its doctrines, the character of its Sacred Book must also be held partly accountable for the intolerant principles of the Christian Church. It was unfortunate that the early Christians had included in their Scripture the Jewish writings which reflect the ideas of a low stage of civilization and are full of savagery. It would be difficult to say how much harm has been done, in corrupting the morals of men, by the precepts and examples of inhumanity, violence, and bigotry which the reverent reader of the Old Testament, implicitly believing in its inspiration, is bound to approve.
It furnished an armoury for the theory of  persecution. The truth is that Sacred Books are an obstacle to moral and intellectual progress, because they consecrate the ideas of a given epoch, and its customs, as divinely appointed. Christianity, by adopting books of a long past age, placed in the path of human development a particularly nasty stumbling-block. It may occur to one to wonder how history might have been altered —altered it surely would have been—if the Christians had cut Jehovah out of their programme and, content with the New Testament, had rejected the inspiration of the Old.
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Under Constantine the Great and his successors, edict after edict fulminated against the worship of the old pagan gods and against heretical Christian sects. Julian the Apostate, who in his brief reign A. This was only a momentary check. Paganism was finally shattered by the severe laws of Theodosius I end of fourth century. It lingered on here and there for more than another century, especially at Rome and Athens, but had little importance. The Christians were more concerned in striving among themselves than in  crushing the prostrate spirit of antiquity.
The execution of the heretic Priscillian in Spain fourth century inaugurated the punishment of heresy by death. It is interesting to see a non-Christian of this age teaching the Christian sects that they should suffer one another. Themistius in an address to the Emperor Valens urged him to repeal his edicts against the Christians with whom he did not agree, and expounded a theory of toleration. Every faith should be allowed; the civil government should govern orthodox and heterodox to the common good.
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God himself plainly shows that he wishes various forms of worship; there are many roads by which one can reach him. No father of the Church has been more esteemed or enjoyed higher authority than St. Augustine died A. There was much  persecution, but it was not systematic.
There is reason to think that in the pursuit of heresy the Church was mainly guided by considerations of its temporal interest, and was roused to severe action only when the spread of false doctrine threatened to reduce its revenues or seemed a menace to society. He and his immediate successors are responsible for imagining and beginning an organized movement to sweep heretics out of Christendom. Languedoc in Southwestern France was largely populated by heretics, whose opinions were considered particularly offensive, known as the Albigeois.
They were the subjects of the Count of Toulouse, and were an industrious and respectable people. But the Church got far too little money out of this anti-clerical population, and Innocent called upon the Count to extirpate heresy from his dominion.