The proper seat of Conscience is in the Understanding , and is no other thing , but this Reflect Act of our knowledge back upon our selves , dictating to us God's liking or disliking what we do , as good or evil : This ability is more or less , according to the suitable light God affords to our understanding , either inwardly or outwardly , whether natural or divine ; and is indeed to each man , the Rule of all other Rules God is pleased to govern him by ; for whether it be by natural Light or divine Revelation , still the utmost bounds of his Conformity lies in the knowledge and conception he hath of it , and of his duty in reference unto it . So that the information of the understanding is still the guide of the Conscience ; for when we become once convinced that this or that is Gods will , my understanding reflects back to my self , and tells me , This is my Duty in reference to it , and so comes in upon each man the obligation of that we call Conscience ; which is indeed so unavoidable a Reflection , suitable to the conviction and impression the understanding lies under , that no man hath power in himself , if he would to escape it ; Conscientiam non esse judicium theoreticum , quo verum à falso simpliciter discernitur , sed puncticum , quo particulariter illa cognitio applicatur ab homine ad illud , quod ipsi vel bonum , vel malum est , ut sit interna Regula , dirigens voluntatem : Ames . de cas. Consci . That there was at first in Adam a clear and perfect knowledge of God , and of himself , is not to be doubted ; and that there was this Reflect Act in Adams knowledge , that he fully viewed and beheld himself , and knew in what a happy estate God had made him , is also clear ; and that this exercise of his knowledge also , in a way of Conscience , he had to tell him , he was accepted of God , and did well in whatsoever he did ; but that equal reflection of mans Understanding , both towards good and evil , allowing the one , and condemning the other , was first introduced when he did eat of the Tree of knowledge of Good and Evil ; which was so called by anticipation , because by the sin committed in eating of it , Adam , who knew nothing before , neither in himself , nor any other Creature , but what was perfectly good , came to the miserable knowledge of good and evil . Evil , before he could not know ; for till he had sinned , there could be no such thing presented to his view ; but in that act of his sinning , he saw the greatest Evil , and the root of all other Evil ; what was Good also , by his fall he came to know in another manner than before ; for before he knew it only simply considered in it self , but now as it stood in a direct contrariety and opposition unto Evil. That perfect knowledge man had at the first so far retains , since the fall , its excellent nature , as to be a distinguisher between Good and Evil , and a constant witness for God in his soul , and by secret reference to what he was at first , tells him what he still ought to be : And this is the thing we call Conscince , which as it is the best thing left in man by far , since the fall , so 't is the noblest and worthiest thing the world hath left in it , and which above all others ought to be cherished and valued , as that whereby God is most acknowledged , each man in his own brest most quieted and settled , and mankind best enabled to live peaceably in society and converse together .

That it hath continued amongst men ever since the Fall , is plain , if we consider , that even in the darkest times of divine Knowledge , before any Law from God was written , this knowledge men had of themselves , in reference to God , was a Law unto them . Their natural light , derived to them from their first creation , dictating to them what they ought to do , and what not , and enabling them to pass a judgment upon themselves , of their due behaviour towards God ; and this the Apostle in the Epistle to the Romans calls Conscience , which will either excuse them , or accuse them in the great Judgment day , when the secrets of mens hearts shall be made known .

There be since mans fall two things eminently left in him ; A sence and knowledge of God , though remote , and that two ways : first , by Instinct in his very composition and constitution , God making him at first in his own Image : and secondly , by the use of his reason , in beholding the works of creation and providence , which he does daily behold , and converse with , and which do eminently preach God unto him ; the other thing is a sence of pleasing or displeasing God , by doing what his understanding tells him is good or ill , and this is to each man a Law ; so Paul in that place of the Romans tells us , That those that have not the Law written , are a Law unto themselves , and do by nature the things contained in the Law .

When afterwards men came to be under a law written , and the knowledge of Gods mind concerning man was more clearly revealed , every man came to have a larger view of his duty , and clearer reflection upon himself in reference to it , and so came to have a more enlightned Conscience , suitable to the enlargedness of his understanding in his walking before God .

This then being premised , that mans perfect knowledge which he had at first , does still retain a taste of , and a discerning principle between good and evil , and does enable a man to judge of himself , in reference to his pleasing or displeasing of God , by the one and the other ; and that every man hath more or less in him of that we call Conscience ; ( unless in some particular cases , whereby often endeavouring to resist and oppose Conscience , God in just judgment takes away the use of it ) and that Conscience is wholly regulated by the understanding , and the light thereof .

We will consider , First , That men do , and always have differed in their understandings and apprehensions , and so in their Consciences about divine things , and their duty to God . Secondly , what the grounds and reasons are , upon which men come to differ : And , Thirdly , How far men are to be tolerated , and indulged one by another , in such variety and difference of knowledge and conscience . For the first , we shall find it too obviously plain , so to have been in all times ; A man must have some ill will , either to himself or his Reader , that should spend much time in the proof of it . If we look into those early times , before any Law was written , though all men had one common instinct of God in their nature and being , and had the same outward Mediums of the knowledge of God , which were the works of Creation and Providence ; for there is no place where their Voice sounded not , yet doubtless the various Apprehensions of God , and of mans duty to him were very great ; some improving those common Rudiments of Divinity , to more reverent thoughts of a Deity , and a more sober virtuous way of living , by their natural light ; and others so far degenerating from them , as that when they know God , and might have known more of him , they glorified him not as God , but turned the glory of the true and incorruptible God into mock-Deities , of Birds and Beasts , and so came to be given up to all manner of Evil. Such who lived in those dayes , and were by dreams , visions , voices , and otherwise particularly enlightned , had other kind of apprehensions of God , and principles of Conscience suitable thereunto ; which yet could reach no further than themselves , nor be obliging to others farther than they could justifie those divine discoveries in their own nature , or by the credit of their own testimony gain belief , and perswade men thereunto .

When aferwards the Law came to be written in Stone , which was from the beginning written in the Heart , and was in truth no other than a transcript of the Law of Nature , and the Light thereof ; yet what great variety do we find in the Exposition of it , and what various Principles derived from it ? he is a great stranger to all Rabbinical Learning , who knows not the wide compass of the Jewish Debates and Controversies . And since the times of the largest and fullest Revelation of the Mind and Will of God in the days of the Gospel , do we not see , that knowledge hath multiplied Division ? What great variety of thoughts have arisen amongst men , not only concerning those more obscure Notions of the Order and Discipline of the Gospel Church , but of most of the other Doctrines and Truths of Religion ? And so general have the mis-apprehensions been , that have possessed men in these things , that sometimes we find in the Christian Church , Truth shut up , and thrust into a very narrow Corner ; and sometimes an Athanasius , and some very few opposing the torrent of mistakes , with which the generality of Christian understandings were possessed . And still the variety of mens Apprehensions have produced the same variety in several sorts of Consciences , and the effects of it . If we seriously ponder the reasons of these things , we shall find them to come under several heads , in the viewing of which , we may arrive at some satisfaction , in the second thing proposed , which is to know , how such uneven , disproportionate Thoughts , Opinions and Consciences come to be amongst men .

The first and great account that may be given of it , is this : An innate infirmity in the Soul of man since his fall , not to be able always to make a right judgment of things , but to receive various impressions in the understanding faculty ( by reason of the infirmity and imperfection of it ) according to all the several accidents and circumstances relating to its information , and the object 't is conversant about . Adam in his naming the Creatures , and what-else he did before the fall , was not capable of a mistake ; but man since lies very open to all delusion and deceit , being not able always to represent to himself in his understanding-faculty , all those things that should be known to make up a perfect judgment , nor if he could do so , were he able by the intrinsick strength of that faculty , perfectly and infallibly to judge of what should evidently appear before him ; nor lastly , to remain fixed in any determination , being not only subject to alter and change by seeing farther , and having more presented to his view than what he at the first knew , but also in his own nature now , become mutable and apt to change in his best and truest resolves : And from such a womb of infirmity , 't is not hard to conceive what various and differing thoughts may be born .

Secondly , The great variety there is of suitable means to operate upon such a weakness in the Soul , and to prevail over the Infirmity of mens understanding , to lead them in several Paths . This we shall easily find , if we consider the several postures and conditions mankind is settled in , as to Education , Company , Studies , and many such accidential matters , by which the minds of men are variously seasoned and engaged in their apprehensions ; and so come to have differing foundations laid of Conscience , according to impressions received thereby . And where ( as in most it is ) very weak and ordinary motives prevail , and no larger compass is taken to settle the judgment , than those accidential means that first prevail with us , yet as positive an obligation of Conscience ariseth from such things , as from any whatsoever ; there can be no perswasion so impotent , but may meet with some capacities , over which it may easily have dominion , and the bounds of such mens knowledge , though never so mean , must needs be a rule to the Conscience ; so that to imagine all mens Minds and Consciences should be the same , is to imagine all men to be educated a like , all Company to talk a like , and all Books to be written a like , and that all other things , that work upon the minds of men , should all concenter to inculcate the same thing .

Thirdly , Besides all this , there is an in-bred disposition in the Souls of men , according to the Bodies they dwell in , to apprehend and believe diversly of things , without any other outward help to such a variety ; some men being naturally prone to believe some things , and others to imbibe those of a contrary Nature ; and this is to be found without much difficulty , in the several constitutions and composures of men , where we shall find their thoughts and opinions holding great correspondence with , and bearing much proportion to their natural inclinations and tempers , and at several times several thoughts prevailing , according as the concommitant Humours of nature are predominant in them ; so that let a man but phylosophically view over the divers humors in mens Bodies , such as make men cholerick , flegmatick , or the like , and the wonderful mixture of those humors , in the various Temperament of them , and he will not be much to seek for the various Thoughts , Opinions and Consciences that are in the World ; and to force men out of these , through any door than that of the understanding , and means suited thereunto , is to force them out of their very nature and existence ; that Soul in man that was at first Lord over the Body , and could receive no sophistication from it , takes now a great tincture from thence , and savours much in all its operations of the vessel 't is kept in .

Lastly , Let us seriously ponder the wonderful variety there is in that inward divine illumination , afforded to men more or less , as God pleaseth , by which their judgments and consciences are in several measures settled and determined : As nothing can give us a clearer account of that variety there is in the World , in divine things , so nothing can be more prevailing upon us , to have compassion upon men severally informed and perswaded , than when we consider , God affordeth divine light severally to them , as he pleaseth , and gives it in what proportion , little or much , seems best to his Wisdom ; and by making men of several growths and statures in divine knowledge , does seem to let us know , he would have men of several sizes and attainments in that kind , to live quietly together in the World .

These things being able , in some measure , to discover to us the grounds of these disagreeing Principles we find amongst men , we will go on to the third and chief thing we have in pursuit by this discourse , which is a serious Enquiry , How far men are to be Tolerated one by another , whose Judgments and Consciences about Divine things are found to differ .

Conscience in it self considered ( being nothing else but the Understanding under such a kind of Exercise , as is before described ) is such a thing as can by no means come under any possibility of Force or Restraint , beyond its own Bounds , and is as much out of the reach of all humane Power , as the Soul it self is , and therefore is chosen of God to be the Witness , which he gives to himself amongst the Sons of men , of their due behaviour towards him , and is a thing neither in the power of others , nor in the man himself ; no man can point out what another shall believe , nor can he chuse out his own Belief ; but still the Understanding gives in its testimony by the Conscience , though in actings the Will may sometimes prevail against it . This is that which chiefly differs a man , as to his relativeness to God , from other Creatures , and is that whereby God keeps up his solemn claim of Soveraignity over us , in our own breasts , by such means as we can no way oppose nor avoid . This Dominion of God was never delegated to any substitute upon Earth , nor was there since the World began a judgment entrusted in any hands over the Consciences of men , nor was it indeed under a possibility to be , since no man , nor men , with the existence of humane Power , could ever come to know the state of another mans Conscience , nor the manifold Circumstances ( only open to a divine Eye ) relating to it ; and therefore does Paul himself to the Corinthians wholly disclaim the exercise of such a Power .

The simple actings therefore of Conscience abstractedly considered , are not capable of a forcible impression from without ; nor need any man fear the loss of liberty of Conscience in that sense of it , nor reckon himself under an obligation to any indulgence for it , since a donation of it from any , will with no more reality afford it to me , than a restraint from them will any way actually take it from me .

That which will ( as most proper and genuine to the present enquiry proposed ) come under consideration , will be , How far the products and effects of Conscience , in mens actings in pursuance of it , are to be indulged , and how far restrained ; and this will all come under two Heads :

First , How far men are to be suffered to do , or not to do those things which they say they are in Conscience obliged to do ?

Secondly , How far men are to be urged by commands to do such things which they say they are in Conscience obliged not to do ?

That a punctual clear Answer to these Questions will be a Travel of great peril undertaken , none that have any way versed themselves in such Controversies will deny , and therefore the better to secure our progress herein , it will be necessary chiefly and principally to reflect upon the Magistrate , and the Power he is entrusted withal ; this method will carry its own evidence sufficiently with it : If we consider the power that mankind hath over each other , is exercised by him , and that the success of this notion , and the influence both of freedom and restraint depends solely upon him , and that the power of Princes and Magistrates do actually bind and loose in matters of this nature ; I say , if we consider this , we shall soon make a discovery , that ( finding out what the Magistrate may do , and what he may not do in Religious affairs ) will give us a determination of this matter . In the prosecution of this , these several things shall be attempted :

First , To make it evident , that Magistracy is an Institution grounded upon the Light of nature , and how far he may and ought to proceed by that both negatively and positively in these things .

Secondly , That a Magistrate by becoming Christian receives no addition of Power to what he had before , only stands bound to an improved exercise of his Power , suitable to the light he then receives .

Thirdly , To discover some eminent mistaken extreams about the Magistrates Power in Religion , which have miserably involved us .

And Lastly , To shew how far the Magistrate , under the Gospel , should and ought to act about Religion , and wherein he is not to interpose his Power , the right stating whereof is the true and solid Foundation upon which all true Liberty of Conscience is built .