Appendix D: Philonomy and Covenant Theology

Introduction

This book has been written from within a particular confessional home. I am a Baptist who holds to the 1689 London Baptist Confession and the covenant theology articulated by our forebears, men like Nehemiah Coxe, whose Discourse of the Covenants has so profoundly shaped my understanding of how the old and new covenants relate. This covenantal framework is not incidental to my reading of Scripture; it informs every chapter you have read.

And yet I have tried to write a book that can serve Christians from other confessional traditions. The philonomic method (the careful analysis of case laws to identify general equity) does not require agreement on every point of covenant theology before it can be employed. A Presbyterian, a Reformed Baptist, a Continental Reformed believer, or even a thoughtful Dispensationalist may find the form/function distinction useful, may appreciate the mapping of case laws to the Decalogue, and may employ the checklist in Chapter 5 without first resolving our differences about infant baptism or the precise nature of the old covenant.

This appendix exists for those who want to understand the covenantal framework that shapes my own reading. Some readers will share this framework and find in it a confirmation of what they already believe. Others will disagree, perhaps sharply, and that is well. My hope is not that you adopt my covenant theology, but that you understand it well enough to evaluate where it shapes my conclusions and where the philonomic method can operate independently of these commitments.

Here, then, is an explanation of 1689 Federalism and its relationship to philonomy. I offer it not as a conversion tract but as an honest disclosure of theological conviction. Take what is useful. Test what seems questionable. And may we all be those who search the Scriptures daily to see whether these things are so (Acts 17:11).

What Is 1689 Federalism?

The term “1689 Federalism” refers to the covenant theology held by the framers of the Second London Baptist Confession (1689). While the 1689 Confession shares much language with the Westminster Confession (1646) and the Savoy Declaration (1658), including the crucial affirmation of general equity in 19.4, it diverges in its understanding of the covenants, particularly in chapters 7 and 8.

The clearest exposition of this position in the seventeenth century came from Nehemiah Coxe, whose Discourse of the Covenants (published posthumously in 1681) articulated what has come to be called Baptist covenant theology or 1689 Federalism.

It is worth noting that Coxe did not labor in isolation. He explicitly deferred to John Owen on the covenant question, and Owen’s monumental exposition of the Epistle to the Hebrews provides the theological architecture on which much of the Baptist covenantal position rests. Owen supplied both the ontological ground for understanding the judicial laws – “all the judgments relating unto civil things were but an application of the moral law to their state and condition” (Vol. 2, Exercitation IV.6) – and the epistemological test for identifying what persists: the formal-reason test of Hebrews 7:4, which asks whether both the subject-matter and the underlying rationale of a command remain constant across redemptive-historical epochs. Coxe built the covenantal architecture; Owen provided the judicial-law-as-explication framework that gives that architecture its hermeneutical potency for the question of general equity. Together, they furnish philonomy with both its covenantal home and its interpretive method.

The Core Distinction

The fundamental difference between 1689 Federalism and Westminster/Presbyterian covenant theology concerns the relationship between the old covenant (the Mosaic covenant) and the covenant of grace.

The Westminster Position holds that the covenant of grace has been administered in different ways throughout history. Under the old covenant, it was administered through promises, prophecies, sacrifices, and ordinances that pointed to Christ. Under the new covenant, it is administered through the preaching of the Word, the sacraments of baptism and the Lord’s Supper, and the Spirit’s application of redemption. But it is one covenant of grace throughout, administered in different forms to the same spiritual people of God. Presbyterians have captured this elegantly: “one covenant in two administrations.”

The 1689 Federalist Position holds that the old covenant (Mosaic covenant) was not the covenant of grace in another administration but a distinct covenant with a distinct people, operating alongside the covenant of grace but not identical to it. The covenant of grace was revealed and promised under the old covenant, but it was not formally made until the new covenant. The Mosaic covenant served to prepare for, point toward, and ultimately give way to the new covenant, which is the covenant of grace in its fullest expression. If Presbyterians speak of “one covenant in two administrations,” Baptists might better say: “one promise, progressively revealed, ultimately sealed.” The promise of salvation through the Seed of the woman was given from the beginning, unveiled in ever-greater clarity through the patriarchs, prophets, and types, and finally sealed in the blood of the new covenant when Christ declared, “It is finished.”

The 1689 Confession puts it this way:

“This covenant [of grace] is revealed in the gospel; first of all to Adam in the promise of salvation by the seed of the woman, and afterwards by farther steps, until the full discovery thereof was completed in the New Testament; and it is founded in that eternal covenant transaction that was between the Father and the Son about the redemption of the elect; and it is alone by the grace of this covenant that all the posterity of fallen Adam that ever were saved did obtain life and blessed immortality, man being now utterly incapable of acceptance with God upon those terms on which Adam stood in his state of innocency.” (1689 LBCF 7.2-3)

Notice the careful phrasing. The covenant of grace was revealed progressively but finds its full discovery in the New Testament. The old covenant saints were saved by the grace of this covenant (that is, by the covenant of grace revealed in promise), but they were not under the new covenant administration that we now enjoy.

The Old Covenant as a Distinct Covenant

Scripture teaches that the old covenant and the new covenant are genuinely distinct. The prophet Jeremiah, speaking of the new covenant, makes this explicit:

“Behold, the days are coming, declares the LORD, when I will make a new covenant with the house of Israel and the house of Judah, not like the covenant that I made with their fathers on the day when I took them by the hand to bring them out of the land of Egypt, my covenant that they broke, though I was their husband, declares the LORD.” (Jeremiah 31:31-32)

The new covenant is “not like” the old. It is contrasted with the covenant made at the exodus: the Sinai covenant, the Mosaic economy. The author of Hebrews develops this contrast extensively:

“For if that first covenant had been faultless, there would have been no occasion to look for a second. For he finds fault with them when he says: ‘Behold, the days are coming, declares the Lord, when I will establish a new covenant with the house of Israel and with the house of Judah, not like the covenant that I made with their fathers on the day when I took them by the hand to bring them out of the land of Egypt. For they did not continue in my covenant, and so I showed no concern for them, declares the Lord.’” (Hebrews 8:7-9)

The “fault” of the old covenant was not in its laws but in its inability to provide what the new covenant provides: regenerate hearts, the law written on the mind and heart, the forgiveness of sins, and the knowledge of God given directly to all covenant members. As Hebrews continues:

“For this is the covenant that I will make with the house of Israel after those days, declares the Lord: I will put my laws into their minds, and write them on their hearts, and I will be their God, and they shall be my people. And they shall not teach, each one his neighbor and each one his brother, saying, ‘Know the Lord,’ for they shall all know me, from the least of them to the greatest. For I will be merciful toward their iniquities, and I will remember their sins no more.” (Hebrews 8:10-12)

The old covenant could not guarantee regeneration. Its membership included believers and unbelievers, circumcised in body but not always in heart. Its sacrifices pointed forward but could not actually take away sins. “In speaking of a new covenant, he makes the first one obsolete. And what is becoming obsolete and growing old is ready to vanish away” (Hebrews 8:13).

This is the sharp discontinuity that 1689 Federalism affirms. The old covenant has vanished. It is obsolete. Not merely its ceremonies, but the covenant itself has given way to something better.

Seed Laws and Typological Expiration

The Apostle Paul’s argument in Galatians illuminates why certain categories of Mosaic law have definitively expired. Speaking of the Abrahamic promises, Paul writes:

“Now the promises were made to Abraham and to his offspring. It does not say, ‘And to offsprings,’ referring to many, but referring to one, ‘And to your offspring,’ who is Christ.” (Galatians 3:16)

And again:

“There is neither Jew nor Greek, there is neither slave nor free, there is no male and female, for you are all one in Christ Jesus. And if you are Christ’s, then you are Abraham’s offspring, heirs according to promise.” (Galatians 3:28-29)

Here is the hermeneutical key that I mentioned in the Introduction: laws designed to preserve the genealogical line until the Seed arrived have fulfilled their purpose now that the Seed has come. The seed laws (regulations governing land inheritance, tribal boundaries, levirate marriage, and the preservation of Israel as a distinct people) were never unjust. They were purposeful. But their purpose was typological. They pointed forward to Christ and the ingathering of all nations into Abraham’s family by faith.

With the substance come, the shadows fade. “For Christ is the end of the law for righteousness to everyone who believes” (Romans 10:4).

Galatians 4 and the Pedagogical Purpose

Paul develops this further in Galatians 4, using an analogy that reveals the guardian function of the Mosaic economy:

“Now I say that the heir, as long as he is a child, does not differ at all from a slave, though he is master of all, but is under guardians and stewards until the time appointed by the father. Even so we, when we were children, were in bondage under the elements of the world. But when the fullness of the time had come, God sent forth His Son, born of a woman, born under the law, to redeem those who were under the law, that we might receive the adoption as sons.” (Galatians 4:1-5 NKJV)

The old covenant was a guardian, a tutor, a temporary steward over minor children. It was not itself the inheritance but the custodian of those waiting for the inheritance. Now that the heir has come of age, now that the Son has appeared and accomplished redemption, the guardian role has ended. We are no longer under the pedagogue (Galatians 3:25).

This does not mean the law was bad. A good guardian serves a good purpose. But it does mean the covenant has changed. The formal arrangement that governed Israel (land, temple, priesthood, sacrificial system, tribal structure, seed laws) has passed away. Its pedagogical purpose has been accomplished.

Why Does Covenant Theology Matter for Applying Mosaic Law?

You may be wondering why any of this matters for the practical question of how to apply Mosaic case laws today. Is this not theological abstraction far removed from the question of restitution for theft or the responsibilities of property owners?

Not at all. How you understand the covenants profoundly affects how you read and apply the law.

The Problem of Naive Continuity

Some approaches to Mosaic law assume a kind of naive continuity: the laws were given by God, they are still Scripture, therefore they are still binding in their original form. This sounds pious but ignores the massive covenantal transition that Scripture itself announces.

If the Mosaic covenant is simply an administration of the covenant of grace, one might be tempted to import its forms more directly. If circumcision and baptism are simply different signs of the same covenant, if Israel and the church are the same people under different management, then the laws given to Israel might seem more immediately transferable to the church today.

But Scripture does not support this reading. The land promises were typological, pointing to heavenly rest (Hebrews 4). The priesthood was typological, pointing to Christ’s perfect mediation (Hebrews 7). The sacrifices were typological, pointing to Christ’s once-for-all atonement (Hebrews 10). The temple was typological, pointing to God’s dwelling with His people in Christ and the Spirit (John 2:19-21; 1 Corinthians 3:16).

If so much of the Mosaic economy was typological and has been fulfilled, we cannot simply import the laws wholesale. We must ask the harder question: What was bound to the covenant form, and what reflects God’s enduring moral character?

The Problem of Naive Discontinuity

On the other hand, some approaches assume that because the old covenant has passed away, nothing from it remains binding. This is the antinomian error. It forgets that the moral law summarized in the Ten Commandments reflects God’s eternal character, not merely a temporary arrangement. It ignores the apostles’ ongoing use of Mosaic law for moral instruction (Romans 13:8-10; 1 Corinthians 9:9; Ephesians 6:1-3). It treats the case laws as irrelevant antiquities rather than Scripture given for our instruction.

“All Scripture is breathed out by God and profitable for teaching, for reproof, for correction, and for training in righteousness” (2 Timothy 3:16). All Scripture, including Exodus 21 and Deuteronomy 22.

The 1689 Federalist Solution

1689 Federalism offers a way through this dilemma. It maintains:

The Mosaic covenant has expired as a covenant. We are not under it. Its formal administration (its ceremonies, its sacrificial system, its priesthood, its national structure) has passed away. The new covenant is not another phase of the old but something genuinely new.
God’s moral character has not changed. The moral law reflects who God eternally is. It was revealed through the Mosaic economy, but it was not created by that economy. “The law is holy, and the commandment is holy and righteous and good” (Romans 7:12). This does not become false because the covenant has changed.
The case laws were expositions of the moral law. As Chapter 2 argued, the judicial statutes function as worked examples of the Decalogue. They showed what obedience and violation look like in concrete circumstances. This expository function does not depend on the covenant remaining in force; it depends on the moral law remaining in force.
The form has expired; the function often endures. This is the key insight. The form of the law (oxen treading grain, flat roofs, specific restitution amounts) belonged to Israel’s circumstances. But the function (just compensation for laborers, safety for visitors, proportionate remedy for theft) reflects moral reality that transcends any covenant.

The 1689 Federalist can affirm moral continuity precisely because he maintains covenantal discontinuity. We are not trying to smuggle the Mosaic covenant back into force. We are recognizing that God’s character does not change with covenantal transitions. The wisdom revealed through the case laws remains wisdom even after the covenant that contained them has expired.

How Philonomy Works Within 1689 Federalism

Let me now explain more directly how the philonomic method relates to 1689 Federalist covenant theology.

The Mosaic Covenant Has Expired

Philonomy begins by acknowledging what Scripture teaches: the Mosaic covenant, as a covenant, has been fulfilled and superseded. We are not under it. We do not attempt to reinstate it. We do not pretend we are Israel or that America (or any other nation) can become a new Israel.

This is not a grudging admission but a joyful confession. The new covenant is better. It provides what the old could not. “For since the law has but a shadow of the good things to come instead of the true form of these realities, it can never, by the same sacrifices that are continually offered every year, make perfect those who draw near” (Hebrews 10:1). The shadow has given way to the substance. Thanks be to God.

God’s Character Has Not Changed

But the expiration of the covenant does not mean the expiration of moral truth. God is still God. What was righteous then is righteous now, because righteousness is grounded in God’s unchanging nature, not in temporary covenantal arrangements.

“The grass withers, the flower fades, but the word of our God will stand forever.” (Isaiah 40:8)

“Jesus Christ is the same yesterday and today and forever.” (Hebrews 13:8)

The case laws revealed moral wisdom embedded in historical circumstances. The circumstances have changed; the wisdom has not. When God legislated that a laborer must share in the fruit of his labor (Deuteronomy 25:4), He was not merely accommodating ancient agricultural practice. He was revealing something true about justice, something that reflects His own character. That truth does not expire with the covenant.

Case Laws Reveal Abiding Moral Truth

This is why the apostles continued to reason from the case laws for moral instruction. Paul did not say, “Deuteronomy 25:4 was for Israel, so it no longer teaches us anything.” He said, “It was written for our sake” (1 Corinthians 9:10). The original setting was agricultural; the principle is universal. The form was for Israel; the function is for all who seek to understand what justice requires.

The philonomic method, developed fully in Chapter 5, is simply a disciplined way of making this distinction. When we analyze a case law, we follow seven steps:

Wooden Literalism: What elements cannot transfer at all? The specific geographic, institutional, technological, or economic features bound to ancient Israel.
Presuppositions: What does the text assume about authority, relationships, justice, and human nature? Surface all assumptions exhaustively before categorizing.
Separate Form from Function: Based on the presuppositional analysis, distinguish what is culturally bound from what is morally foundational.
Remove Expired Categories: Is any aspect of this law sacrificial, geographically bound, seed-related, typological, or tied to theocratic mechanisms?
Find Commandment Domain: Which domain of the Decalogue does this law address?
Map to Commandment: Which specific commandment does this case law expound?
Explain How Case Elaborates Commandment: What does this law teach us about the commandment it expounds?

For laws with multi-epoch attestation and debatable form/function boundaries, an enhanced step (Step 4b) draws on John Owen’s formal-reason test to track the underlying rationale across redemptive-historical epochs. Owen argued that when “not only the subject-matter, but the formal reason of the command is the same” across epochs, the command is “of natural equity, and unalterable.” But when the subject-matter persists while the formal reason varies, the specific form does not carry permanent moral force. This diachronic precision tool reflects 1689 Federalism’s sensitivity to the progressive unfolding of revelation across covenantal history – it takes seriously that what God commanded in one epoch may serve a different purpose than what appears superficially similar in another.

This is not reimposing the Mosaic covenant. It is reading Scripture carefully to discern what God has revealed about justice through the laws He gave to Israel.

The Threefold Division of the Law

The traditional Reformed distinction between moral, ceremonial, and judicial law remains useful within 1689 Federalism, though it requires careful handling.

The moral law (summarized in the Decalogue) reflects God’s eternal character and is binding in all times and places. The 1689 Confession affirms this unequivocally: “The same law that was first written in the heart of man continued to be a perfect rule of righteousness after the fall, and was delivered by God upon Mount Sinai in ten commandments” (19.1). The moral law was not invented at Sinai; it was publicly delivered there in summary form.

The ceremonial law governed Israel’s worship: sacrifices, priesthood, temple, festivals, clean and unclean distinctions. These were typological, pointing to Christ. “For since the law has but a shadow of the good things to come” (Hebrews 10:1). With Christ’s coming, these have been fulfilled and abrogated. We do not offer animal sacrifices. We have a better High Priest.

The judicial law governed Israel’s civil and social life. The 1689 Confession says these laws “expired together with the state of that people, not obliging any now by virtue of that institution; their general equity only being of moral use” (19.4). The judicial laws have expired as binding statute; we cannot enforce them on the basis that God gave them to Israel. But their general equity remains morally instructive.

The challenge, of course, is that some laws contain mixed elements. The Sabbath commandment contains both moral and typological dimensions. Some judicial laws have ceremonial features woven into them. The philonomic method provides a way to analyze these complexities without pretending they are simpler than they are.

Not Reimposition but Discernment

Let me be clear about what philonomy does and does not claim.

Philonomy does not claim that the Mosaic judicial laws are still in force as laws. They expired with the covenant. They do not bind any nation today “by virtue of that institution” (1689 LBCF 19.4). We cannot point to a Mosaic statute and say, “This is law because God gave it to Israel.” Israel is not us. We are not Israel.

Philonomy does claim that the moral reasoning embedded in those laws reveals truths about justice that transcend their original context. These truths bind us not because they were given to Israel but because they reflect God’s unchanging character. They are examples of how God Himself applied His own moral law. As examples, they instruct.

This is not reimposition. It is discernment. We are not trying to bring back a defunct covenant. We are learning from Scripture what justice requires: justice that was revealed through the Mosaic economy but is not limited to it.

For Readers from Other Traditions

I write from within 1689 Federalism. You may not. Can the philonomic method still serve you?

I believe it can, and I want to explain how.

For Presbyterians and Westminster Confessionalists

If you hold to Westminster covenant theology, you likely view the old covenant as an administration of the covenant of grace. You affirm more continuity between the testaments than I do. You may see Israel as the church under a different administration.

And yet your confession also affirms that the judicial laws expired “not obliging any other now, further than the general equity thereof may require” (WCF 19.4). You, too, must distinguish between what was bound to Israel and what contains abiding moral instruction. You, too, must grapple with the form/function distinction.

The philonomic method offers a disciplined way to make this distinction. The checklist in Chapter 5 can be employed whether you believe the old covenant was an administration of the covenant of grace or a distinct covenant serving a preparatory purpose. The mapping of case laws to the Decalogue does not depend on resolving our covenantal differences.

Where our conclusions might differ: You may be more ready to see certain forms transferring directly. I may be more cautious about distinguishing what was typological or seed-related. But these are differences of application within a shared method. We both believe general equity exists. We both need a way to identify it.

For Continental Reformed Believers

The Three Forms of Unity (the Belgic Confession, the Heidelberg Catechism, and the Canons of Dort) represent a different confessional tradition than the English Puritan stream that produced Westminster and 1689. The Belgic Confession affirms the moral law’s continuing validity while acknowledging that “we still use the testimonies taken out of the law and the prophets to confirm us in the doctrine of the gospel” (Article 25).

The philonomic method aligns well with this emphasis. The case laws are “testimonies” that “confirm us” in understanding what righteousness requires. If you come from this tradition, you may find the form/function distinction a useful tool for reading those testimonies with precision.

For Dispensationalists

I confess that Dispensationalism is further from my own position than the traditions above. We disagree on more than covenant theology. And yet even within Dispensationalist circles, there are thoughtful believers asking how the Old Testament instructs the church.

The form/function distinction may be useful to you. If you believe Israel and the church are distinct programs, you already affirm discontinuity at the covenantal level. The question is whether there is moral continuity beneath that covenantal discontinuity. Philonomy says yes, not because we are Israel, but because God’s character does not change.

If a Dispensationalist can affirm that “all Scripture is breathed out by God and profitable for teaching” (2 Timothy 3:16), then the case laws are profitable. The philonomic method offers a way to extract that profit without confusing Israel and the church or collapsing the dispensations.

What Is Essential to Philonomy?

Let me distinguish between what is essential to the philonomic method and what is my particular covenantal commitment.

Essential to philonomy:

The Mosaic economy was a just society (the foundational premise)
Justice reflects God’s unchanging character
Case laws function as expositions of the moral law (the Decalogue)
The form/function distinction is hermeneutically necessary
General equity can be identified through careful textual analysis
Owen’s formal-reason test as a precision tool for ambiguous multi-epoch laws
New Testament teaching provides authoritative guidance for application

My particular covenantal commitment (1689 Federalism):

The old covenant was a distinct covenant, not an administration of the covenant of grace
The new covenant is the covenant of grace in its fullest expression
The Mosaic covenant has formally expired, though its moral content endures
Typological and seed-related laws have definitively passed away with Christ’s coming
The church is the new covenant community, not Israel continued

You may disagree with some or all of my covenantal commitments while still employing the philonomic method. If you believe the form/function distinction is valid, if you believe case laws expound the Decalogue, if you believe general equity exists and can be identified, then the method can serve you.

We may reach different conclusions about specific laws. A Presbyterian might apply a law more directly than I would. A Dispensationalist might be more cautious than either of us. But we can reason together from the same framework, testing our conclusions against Scripture and against one another’s exegesis.

An Invitation to Test the Method

Whoever you are, from whatever tradition, I invite you to test the philonomic method. Take a case law (perhaps one of the worked examples in Chapter 5) and work through the checklist yourself. Ask whether the form/function distinction illuminates the text. Ask whether the mapping to the Decalogue makes sense of the law’s moral logic. Compare your conclusions with mine.

If I have reasoned well, you will find the method helpful even where you adjust its conclusions for your covenantal framework. If I have reasoned poorly, I welcome correction. “Iron sharpens iron, and one man sharpens another” (Proverbs 27:17).

The goal is not that you become a 1689 Federalist Baptist (though you would be welcome). The goal is that we all grow in our understanding of God’s Word, that we love His law more deeply, and that we apply it more wisely in every sphere of life.

“Oh how I love your law! It is my meditation all the day” (Psalm 119:97).

May it be so for all of us, whatever our confessional home.

Conclusion: Unity in Love for God’s Law

The church of Jesus Christ has never been perfectly unified on questions of covenant theology. The Particular Baptists disagreed with the Presbyterians on these matters in the seventeenth century, and their heirs disagree still. These are not small matters. They affect how we read Scripture, how we administer the ordinances, and how we understand our relationship to the people of God in every age.

And yet there is a remarkable unity across these traditions on one crucial point: the general equity of God’s law remains instructive for the church in every age. Westminster, Savoy, and the 1689 Confession all affirm it. The Presbyterian and the Baptist, for all their disagreements, both believe that the case laws of Israel teach us something about justice, something that does not expire with the covenant that contained them.

Philonomy is an attempt to build on that shared conviction. It does not require you to resolve every covenantal question before proceeding. It offers a method (a disciplined, text-driven, confessionally grounded method) for identifying what abides and what has passed away.

I have written from within 1689 Federalism because that is my home, and I believe it is the biblical position. But I offer this method to the broader church as a gift to be tested. Use what is useful. Correct what is erroneous. And may we all grow in our love for the God who gave His law for our good and His glory.

“The law of the LORD is perfect, reviving the soul; the testimony of the LORD is sure, making wise the simple; the precepts of the LORD are right, rejoicing the heart; the commandment of the LORD is pure, enlightening the eyes; the fear of the LORD is clean, enduring forever; the rules of the LORD are true, and righteous altogether. More to be desired are they than gold, even much fine gold; sweeter also than honey and drippings of the honeycomb.” (Psalm 19:7-10)

Amen.