Thomson, while asserting Synod’s authority to make binding acts upon lower judicatories, argued that there were appropriate times for disobedience. The primary concern of the Presbytery of New Brunswick regarding the submission to Synod was that it could potentially result in submission to sinful acts, matters of conscience, which would be a violation of Christian Liberty, and that non-communion was an unjust consequence if submission were refused. They argued that in this system of Presbyterian government that Synod was advocating, Christian liberty would be violated because rulings were being made regarding indifferent matters. The Apology objected to synodical authority because of the possibility for Synod to require things that were unlawful. Thomson clarified that if synodical rulings required things that were unlawful, these would be void. If they required things that were lawful, but were not thought to be prudent, then submission was still required. If they made rulings on matters that were indifferent, then submission was required, because it would not be a violation of conscience.
Matters Of Sin
In proposition seven, The Apology argued that in order for church judicatories to assume the binding power of legislative authority, they must be infallible in their judgments. If this were not the case, then they could potentially make rulings that required an unlawful action or forbid lawful activity. In response to this, Thomson argued that even though a civil government could not claim omnipotence, it did not mean that they could not then legislate. The authors of The Apology were confusing the “abuse of any lawful authority” as an “argument against the just use of it.” In Thomson’s eyes, therefore, this was an invalid presupposition.
Under this heading, The Apology entered into a long discussion of active and passive obedience. The Apology objected to the idea that the church judicatories could forbid them to do things that in their own consciences must be done”
We ought to refuse active obedience to unjust sentences, but not passive, i.e. we must, according to their notions, neglect the performance of a duty, which God and conscience enjoins, because church-authority forbids it; if the case be so, then the church has power to oblige to sins of omission, but not of commission; then we ought to obey negative sinful commands, but not positive…To this shocking extremity does the legislative scheme necessarily lead its patrons; for if they allowed that sinful cannons were null and void in themselves, although passed by a majority of votes, and gave liberty to the minor party to judge for themselves, and to act according to their own judgment, without censure, their darling structure would crumble into deserved ruin.
Thomson disagreed with their interpretation of this argument. Thomson disagreed with their use of passive obedience, that when an authority made a ruling that was unlawful an individual was obligated to obey. Thomson argued that the historical understanding of passive obedience was “when in conscience we cannot obey the precept, we ought patiently to submit to the penalty.”
In proposition eight of The Apology, building upon the previous proposition, they argued that church judicatories might then require obedience to what could possibly be sinful. If this were the case, the Reformers and the dissenters from the Church of England could never have dissented,
If it be necessary to submit to erroneous sentences of churches, how then could the first reformers oppose the authority, and revolt from the jurisdiction, of the church of Rome? and how can the non-conformists, upon this plan, vindicate their opposing the canons of the church of England from the charge of schism? If any church hath a power of legislation about prudentials, they must by consequence have authority to judge and determine what are such, and to oblige to the observance of them, and the avoiding their contraries, under the penalties of non-communion. If the Presbyterians have this power, then certainly the Church of England have it also…Now how can we, according to the aforesaid scheme, justify our not submitting to the lawful authority of the church?
They assumed that absolute submission was necessary, even if the officers of the church were requiring something that was unlawful.
Answering these concerns, Thomson agued that if an authority were to legislate something that was contrary to Scripture, then it’s ruling would be illegitimate, “It’s only in matter of duty or what is lawful, that either authority is binding, and consequently neither require infallibility nor omnipotency.” According to Thomson, the “power of making rules” that officers of the church possessed did not obligate individuals to do what was “unlawful,” “such a rule is ipso facto, i.e. in itself null and void, in the sight of both God and man.”  If an authority could make erroneous rulings and it were possible to protest them, then the requirement for them to make infallible rulings was not necessary. If the officers of the church, which Thomson regarded as a “legitimate authority,” were to make a ruling that was not unlawful, then obedience was obligatory, even if the law were to be regarded as “unnecessary, or not the best expedient.” He later adds to this for clarification, even things “Clave errante, or supposing a mistake in the management of the key.” The reason for this was to avoid “anarchy and confusion” and it also “leaves every person possessed of all his sacred rights, privileges and liberties.”  Rather than this process being contrary to the protestation of the Reformation or the dissension from the Church of England, it gave a foundation for it. This process would protect the church from unnecessary division and also from requiring sinful obedience that would violate Christian liberty.
In addition to the possibility of sinful demands, the author’s of The Apology, however, were objecting to the Synod imposing indifferent things. They correlated their dissension to the acts of Synod with the dissenters from the Church of England and argued that if this same reasoning that Thomson was espousing was applied to the dissenters of Church of England and those of the Reformation, then their dissenting would be illegitimate. The dissenters of the Church of England, Thomson argued, would have never dissented if the things being imposed were in fact indifferent. Thomson then argued that they misunderstood the concept of Christian liberty and conscience. He argued that if something was indifferent, then there should be no burden upon the conscience. Thomson, however, argued that the nature of the dissenters of the Church of England was legitimate only because what they dissented from was considered sinful,
The votaries of the church of England do own the things, which they would impose upon us, to be indifferent in their nature; but we reckon them sinful, because we think they have no foundation in the Word of God, and yet are imposed as parts, and not mere external circumstances of religious worship; and therefore, until we be otherwise persuaded, we cannot in conscience comply. 
Mere “circumstantials” would be indifferent in their nature, but they were imposing elements of worship that had no foundation in the Word of God. The things that the Church of England imposed were thought to be sinful by dissenters. The difference between the two dissenting parties was that of circumstances verses elements of worship. Synod was imposing things indifferent in their nature, “but our brethren own in the tenor of this argument, that the things in debate between us and them, are indifferent in their general nature, which may be done without sin.” The difference between the argument against the Church of England and The Apology was that what is being imposed by Synod was acknowledged as not being sinful, but indifferent.
In proposition 4, in The Apology, they argued that liberty was granted to a believer on many issues for which Scripture was silent and for a church judicatory to make and enforce a ruling on a matter that was indifferent would be to violate Christian liberty. Synod was enforcing rules that were not found in Scripture and violated the liberty of the minority. They defined Christian Liberty as that which “contains in it a free use or disuse of things in their general nature indifferent, according to the best judgment we ourselves can form of their expediency or inexpediency, from the general direction of the divine word applied to our circumstances.” These things were left up to the individual to determine, not for the officers of the church. They argued that the majority had created these new laws, apart from Scripture, and threatened consequences against those who would disagree. They claimed that the church officers were stealing away the liberty that Christ had acquired for them.
In addition, in proposition five of The Apology, they argued that rules determined by church judicatories on things indifferent or on things silent in Scripture proposed an “encroachment” on “private judgment.” Surrendering private judgment was problematic if one’s private judgment saved him from guilt, “If every man must answer at last for his own actions, and the misguidance of others will not clear him from guilt, or guard him from punishment, in following them, it is but equal that he should judge for himself also.” He must be then able to follow his own judgment. Thomson argued that absent from their logic was that it would be just as harmful to go against one’s own liberty as it would to go against someone else’s. The Apology acknowledged that Presbytery may agree and determine issues. Thomson argued that this itself would be against liberty as they see it. No matter the determinations of Presbytery, someone’s liberty would be violated.
Thomson also argued that as a society, they voluntarily submit to voting about items that were indifferent. The very fact that items were brought to a vote presupposed that they could be determined by the whole and that the determination was not oppressive. Acts of the majority were to be ascribed to the whole by virtue of the vote of all. This act of voting itself about things indifferent was considered by Thomson to be a Christian liberty, “And doth not every member of that society or judicatory exercise his liberty, when he consents that the thing in debate be voted; and, as it were, declares, that he is willing that it be determined by vote of the whole society?” Thomson also argued that if an individual could determine the proper “use of his liberty,” then a church judicatory could safely determine the use of liberty for those they “represent and govern.” A multitude of officers was just that, which represented their respective churches, and could exercise the same wisdom as an individual to determine the use of their liberty.
© Tricia Howerzyl. All Rights Reserved.
 John Thomson, Government of the Church of Christ, 95.
 Ibid., 98.
 Ibid., 96.
 Ibid., 97-98.
 Ibid., 99.
 Ibid., 97.
 Ibid., 98.
 Ibid., 100-101.
 Ibid., 98.
 Ibid., 81.
 Ibid., 80.
 Ibid., 81.
 Ibid., 78.
 Ibid., 88.
 Ibid., 80.
 Ibid., 82.
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