Saturday, October 29, 2011

Quotes from Chapter Eight: Faith, Risk, and Rationality

I should be much more afraid of being mistaken and then finding out that Christianity is true than of being mistaken in believing it to be true. (Pascal, Pensées, 387/241, p. 143; in Christian Apologetics, p. 155)
...not to believe in Christianity, either as a committed unbeliever or as an agnostic, means to forfeit the benefits promised only to the believer (eternal life), should Christianity be true. Deciding not to choose has the same result as not believing in God. (Christian Apologetics, p. 159)
If Christianity is true, the prudential benefits for believing (eternal life) far exceed those offered by believing in atheism or any other worldview (finite pleasures). The prudential detriments of not believing if Christianity is true (loss of eternal life; gaining of hell) also far outweigh the detriments of not believing atheism or another other worldview if the non-Christian view is true (loss of some finite pleasures). Pascal is right to affirm that eternal bliss outweighs any finite good, and eternal loss is far worse than mere extinction. (Christian Apologetics, p. 161)
A prudential consideration of the Christian truth claim can, when offered wisely, invoke a healthy self-interest that encourages unbelievers to inquire into Christianity. (Christian Apologetics, p. 167)

Tuesday, October 25, 2011

More Apologetics Teaching

I am teaching on the origin of life at Crossroads Church of Denver this Sunday (October 30) at 9:00 and 10:30 AM. Here is my outline. I will be offering copies of Christian Apologetics for a discount also.

Douglas Groothuis, Ph.D., Professor of Philosophy, Denver Seminary

A Biblical View of the Origin of Life on Earth

I. Why Origins Matter

A. Knowing the source of something usually tells much about what it is

1. Food: Kroeger green beans are worse than any other brand

2. Automobiles: Dodge or Toyota

3. Wines, authors, drugs, and so on

B. Human origins

1. Naturalism: An impersonal, materialistic source (change and natural law) for nature, or:

2. Theism: A personal, moral, spiritual source for nature

II. The Origin of life: Two Major Worldviews in Conflict. Two stories of reality

1. Naturalism: all life arose and evolved through natural, unintelligent causes over long periods of time

a. Universe has always existed or came into being out of nothing for no reason or purpose (godless Big Bang)

Story: In the beginning were the particles and the laws of nature; these did all the arranging of matter and energy from the beginning until now. Chance and necessity

b. Abiogenesis: life from non-life without a designer

Story: On the ancient earth, lifeless matter somehow evolved into living matter according to chance and natural law

c. Speciation through natural selection (Darwinism)

Story: after the first reproducing life form came into existence, each generation varied from its predecessors sufficiently to generate all the species now in existence

d. Implication of a-c: Life has no design plan, no purpose, and no destiny

2. Christian theism

a. God created and designed the universe (Psalm 90:1-2; Genesis 1:1; John 1:1-5)

In the beginning was the Word, and the Word was with God and was God. All things were made through him

b. God created and designed all of life (Genesis 1); each thing created according to its “kind” (see also 1 Corinthians 15:35-41)

c. Allows for change within basic kinds, but claims that God has created and designed life and has left evidence of himself (Psalm 19:1-6; Romans 1:18-23)

13 For you created my inmost being;
you knit me together in my mother's womb.

14 I praise you because I am fearfully and wonderfully made;
your works are wonderful,
I know that full well. –Psalm 139:13-14

d. Implication: Life has a divine design plan, purpose, and destiny

III. Defending a Christian View of Origin of Life

A. How Christians address this:

1. Theistic evolution (Francis Collins, The Language of God, 2006; Tim Keller, The Reason for God, 2008). Darwinism explains biology: no need to appeal to intelligent causation (design)

a. Reason against this: Doesn’t fit Scripture. God has left evidence of his handiwork

b. Scientific evidence doesn’t support it

B. Intelligent design challenge to naturalism (broadly understood)

Designing intelligence is necessary to explain life and is evident in life’s forms. Naturalism cannot explain life adequately.

C. The case for intelligent design: inference to best explanation based on empirical evidence (not the Bible itself). Relies on no uniquely religious assumptions, but does have conclusions that point toward God.

1. Review: molecular machines: bacterial flagellum (First sermon in this worldview series)

Irreducible complexity cannot be explained by naturalism; it requires intelligence

2. Information argument (DNA). Film clip.10 minutes of “The Case for a Creator”

a. The cell has a tremendous amount of information in DNA

b. This information is not explained by any merely natural process (chance and natural law) because the information is highly specified and complex

The information in DNA and RNA is digital and the entire system is far more sophisticated than any computer we have designed.

“DNA is like a computer program, but far, far more advanced than any software we’ve ever created”—Bill Gates.

c. Therefore, a designing mind (an intelligent cause) is the best explanation for the information in the cell

3. Evidence for Darwinian natural selection (speciation) is inadequate

a. Evidence for micro-evolution (finch beaks) does not establish macro-evolution

b. There is no genetic mechanism to increase information required for adaptive mutations; most all mutations are harmful. (These genetic mechanism themselves are designed.)

c. There is no strong evidence for gradual Darwinian evolution in the fossil record. Rather: “sudden emergence and stasis” (Stephen Jay Gould, Darwinist, paleontologist)

IV. God, the Designer of Life

A. Naturalism fails to explain nature adequately: molecular machines, information in the cell, vast number of different species

B. Also fails to explain morality and resurrection of Jesus. See D. Groothuis, Christian Apologetics, chapters 15, 21

C. Intelligent design explains these facts logically, based on scientific evidence

D. Intelligent design points to the God of the Bible; although it does not tell us all we need to know about God. But gives good reason to investigate the biblical claims since nature does require a designer.

E. We learn the rest of God’s truth from the Bible (2 Timothy 3:15-16)

Recommended resources:


  1. Douglas Groothuis, Christian Apologetics: A Comprehensive Case for Biblical Faith (InterVarsity, 2011). See chapters 13-14 on Darwinism and design.
  2. Michael Behe, Darwin’s Black Box: The Biochemical Challenge to Evolution, 10 anniv. ed. (Free Press, 2006). A pivotal book for the Intelligent Design movement.
  3. Lee Strobel, The Case for a Creator (Zondervan, 2004).
  4. Jonathan Wells, Icons of Evolution (Moody, 2000). Images for Darwinism are bogus.
  5. Philip Johnson, Darwin on Trial (InterVarsity Press, 1993). Logical critique.
  6. William Dembski and Sean McDowell, Understanding Intelligent Design (Harvest House, 2008). Introductory, but excellent.
  7. Michael Denton, Evolution: A Theory in Crisis (Adler and Adler, 1986). Influential scientific and secular critique of Darwinism.
  8. Stephen Meyer, The Signature in the Cell (HarperOne, 2009). Magisterial defense of design of life. The best philosophy of science book I have read.


  1. Lee Strobel, “The Case for a Creator” (Illustra Media, 2006). The various scientific arguments for God from biology, physics, cosmology.
  2. “Unlocking the Mystery of Life” (Illustra Media, 2002). The evidence for God from biology.
  3. “The Privileged Planet” (Illustra Media, 2004). On the special design of the earth.
  4. “Expelled” with Ben Stein (2008). Shows how Darwinists persecute dissenters.
  5. Darwin’s Dilemma” (Illustra Media). On the Cambrian explosion, which Darwinists cannot explain.

Web pages: Access Research Network:; Discovery Institute:

Friday, October 21, 2011

Michele Bachmann on Obama's Big Mistake

Urbandale, Iowa – Republican presidential candidate Michele Bachmann issued the following statement in response to President Obama’s announcement to pull United States troops out of Iraq by the end of the year:

“Today’s announcement that we will remove all of our forces from Iraq is a political decision and not a military one; it represents the complete failure of President Obama to secure an agreement with Iraq for our troops to remain there to preserve the peace and demonstrates how far our foreign policy leadership has fallen. In every case where the United States has liberated a people from dictatorial rule, we have kept troops in that country to ensure a peaceful transition and to protect fragile growing democracies. We will now have fewer troops in Iraq than we have in Honduras – despite a costly and protracted war.

“President Obama’s decision represents the end of the era of America’s influence in Iraq and the strengthening of Iran’s influence in Iraq with no plan to counter that influence. We have been ejected from a country by the people that we liberated and that the United States paid for with precious blood and treasure. The administration claims that we got exactly what we needed, but today’s announcement demonstrates otherwise. The United States needed a working democratic partnership in Iraq and we should have demanded that Iraq repay the full cost of liberating them given their rich oil revenues. I call on the president to return to the negotiating table with Iraq and lead from the front and not from weakness in Iraq and in the world.”

I will be teaching on basic apologetics at Littleton Bible Chapel Sunday, October 23, at 6:30 PM. I will bring books to sell for $30. Hope to see you there.

Littleton Bible Chapel
6023 S Datura St.
Littleton 80130


We who preach the gospel must not think of ourselves as public relations agents sent to establish good will between Christ and the world. We must not imagine ourselves commissioned to make Christ acceptable to big business, the press, the world of sports or modern education. We are not diplomats but prophets, and our message is not a compromise but an ultimatum.--AW Tozer, "The Old Cross and the New."

Saturday, October 15, 2011

Sermon Outline for my message at Crossroads Church of Denver, October 16, 2011

Crossroads Church of Denver, October 16, 2011

Douglas Groothuis, Ph.D., Professor of Philosophy, Denver Seminary

A Short Course in Christian apologetics

I. Making Thinking a Sin (Marlene Winell, Leaving the Fold)

A. Intellectual challenges at the university

B. Wrong responses: critical thinking as sin

II. The Need for Defending Christianity as True, Rational, and Pertinent: Apologetics

A. Biblical case for rational spirituality (1 Peter 3:15-16; Jude 3; 2 Corinthians 10:3-5)

B. Defending objective truth of Christian worldview in humility and dependence on God (Luke 9:23-26)

C. Showing existential significance and consequence of Christianity

D. Being wise as serpent, innocent as a dove, bold as a lion (Matthew 10:16; Proverbs 28:1)

III. Making the Positive Case for Christianity

A. Commending the Christian Worldview

1. What is a worldview: set of assumptions about the basic make up of the world: ultimate reality, morality, human condition, and salvation

2. Christian worldview: creation, fall, redemption

The universe (originally good, now fallen and awaiting its divine judgment and restoration) was created and sustained by the Triune God, who has revealed himself in nature, humanity, conscience, Scripture, and supremely through the Incarnation for the purpose of salvation and judgment.

B. Giving the best explanation through a cumulative case

1. Best explanation: non-contradictory, factual, and livable

2. Cumulative case: combine arguments converging on God of the Bible

IV. The Three Circles of Evidence: Cosmology, Biology, and History

A. Cosmology: the universe is created, not eternal. The Big Bang cosmology. See Paul Copan and William Lane Craig, Creation Out of Nothing (Baker, 2004).

1. Scientific evidences for an absolute beginning of the universe out of

nothing. See Robert Jastrow, God and the Astronomers.

a. Einstein’s general theory of relativity (1917) contained an error (fudge factor), when corrected it predicted an expanding universe

b. In the 1920s, independent of each other, Belgian astronomer George Lemaitre and Russian mathematician Alexander Freidman corrected the error. This became the Freidman-Lemaitre model

c. In 1929, American astronomer Edwin Hubble detected the “red shift” in distant galaxies. Indicated that what was further away was moving at a greater speed. Evidence for expansion.

d. The detection of cosmic background radiation left over from initial condition of the universe.

e. Thermodynamics of the universe; second law of thermodynamics, entropy.

f. Upshot: everything be traced to an initial singularity: Barrow and Tipler: “At this singularity, space and time came into existence; literally nothing existed before the singularity, so, if the Universe originated in such a singularity, we would truly have a creation ex nihilo.” John Barrow and Frank Tipler, The Anthropic Cosmological Principle (Oxford: Oxford University Press, 1986), 442.

g. Alternative theories have failed: steady state and oscillating universe: lack empirical evidence and contravene known laws of physics.

B. Biology

1. Meet the bacterial flagellum

2. Universal joint, propeller, drive shaft, rotor, stator, bushings—all of which are needed for its function, none of which are expendable.

3. This is a biological motor attached to the back of a bacterium as seen through a high-powered microscope. Not built by any human.

4. Bacterial flagellum: only recently discovered to be a molecular machine. See Michael Behe, Darwin’s Black Box, 10th anniversary ed. (Free Press, 2006), 69-72. It exhibits the marks of design.

“Irreducible complexity”: the mousetrap principle. All the integrated parts are needed for fruitful function. It is very improbable that this was built up gradually through natural selection (a naturalistic explanation). See William Dembski, The Design Revolution, chapter 40.

5. Video clip from “The Case for a Creator” (Illustra Media) featuring Dr. Michael Behe, Dr. Scott Minnich.

6. Best explanation for molecular machines, such as the bacterial flagellum—design, not mindless nature

C. History and Jesus Christ

1. Christianity and history: God reveals himself in the actions of history (John 1:14)

2. Consider the New Testament

a. Transmission of the documents (textual criticism). Nearly 6,000 Greek manuscripts of the NT with little variation; better than any other ancient text

b. Original writings: by eyewitness or those who consulted them (Luke 1:1-4; John 20:30-31)

c. Synoptic Gospels written before about 70; entire NT before 100 AD.

d. Extra-biblical writers confirm some aspects of NT history

e. Miracles are possible if creation and design (theism is established)

3. The claims of Jesus Christ and their significance

a. Forgiven sins (Mark 2:1-14); give his life for sinners

b. Lord of the Sabbath (Mark 2:15-28)

c. One with the Father (John 10:30-31)

d. Crucified and resurrected Lord (1 Corinthians 15)

1. Known burial place; Empty tomb; many appearances; changed life of the disciples

2. Best explanation: simplest, explains the most: resurrection in space-time

4. The achievements of Jesus Christ best answers the human condition (John 10:10)

Jesus is the God whom we can approach without pride and before whom we can humble ourselves without despair.—Blaise Pascal, Pensées

V. Conclusion: Reason Enough to Rationally Believe

A. Christianity as objectively true, rational and personally pertinent

B. Christianity is a better explanation of reality than any other worldview

C. We should have confidence to present Christianity in the world of ideas (Romans 1:16-17)

Further reading

1. Francis Beckwith, et al, eds. To Everyone an Answer (InterVarsity Press, 2004). Essays by leading apologetics.

2. Craig Blomberg, The Historical Reliability of the Gospels (InterVarsity, 2007).

3. William Lane Craig, Reasonable Faith, 3rd ed. (Crossway, 2008).

4. William Dembski, The Design Revolution (InterVarsity, 2004).

5. Douglas Groothuis, On Jesus and On Pascal, both Wadsworth, 2003.

6. Douglas Groothuis, Christian Apologetics: A Comprehensive Case for Biblical Faith (InterVarsity Press, 2011).

7. The Discovery Institute (Intelligent Design):

8. J.P. Moreland, Scaling the Secular City (Baker, 1987).

9. James Sennett and Douglas Groothuis, editors, In Defense of Natural Theology (InterVarsity, 2005). More advanced work.

10. Lee Stroble, The Case for a Creator (Zondervan, 2004). See the DVD of the same name.

11. Lee Stroble, The Case for Faith (Zondervan, 2000).

12. Lee Stroble, The Case for Christ (Zondervan, 1998).

Saturday, October 08, 2011

Book Sales for Christian Apologetics

InterVarsity Press tells me that through September 11, 2011, Christian Apologetics has sold nearly 3,000 copies. That is quite good for a large, academic book.

Friday, October 07, 2011

My Outline for a Talk Tonight at The Word Conference

Douglas Groothuis, Ph.D., Professor of Philosophy

Denver Seminary,

Roots of Biblical skepticism on Campus

I. The Importance of the University

A. Charles Malik, A Christian Critique of the University

This great Western institution, the university, dominates the world today more than any other institution: more than the church, more than the government, more than all other institutions. All the leaders of government are graduates of universities, or at least of secondary schools or colleges whose

administrators and teachers are themselves graduates of universities. The same applies to all church leaders. How can you create economically without some technical training? But the technical schools which provide this training are some sort of mini-universities, and their administrators and instructors are

themselves graduates of colleges, universities or technical institutes. The professionals–doctors, engineers, lawyers, etc.–have all passed through the mill of the secondary school, the college and the university. And the men of the media are university trained, and some have undergone specialized, advanced instruction in communication and journalism.[1]

B. J. Gresham Machen (1881-1937)

False ideas are the greatest obstacles to the reception of the gospel. We may preach with all the fervour of a reformer and yet succeed only in winning a straggler here and there, if we permit the whole collective thought of the

nation or of the world to be controlled by ideas which, by the resistless force of logic, prevent Christianity from being regarded as anything more than a harmless delusion. Under such circumstances, what God desires us to do is

to destroy the obstacle at its root. [2]

II. Academic Culture Today

A. Secularization of the academy. See George Marsden, The Soul of the American University: From Protestant Establishment to Established Nonbelief (Oxford, 1996).

B. Academics are more secular than the general population

C. Worldview (philosophy of life)

1. Naturalism (philosophical materialism)

2. Postmodernism (Nonrealism)

D. Academic view of religion

1. Harmful or harmless delusion: naturalism

2. Relative, contingent social construction: postmodernism

3. The divided field of knowing

Faith, spirituality, subjective values (opinion)

Fact, rationality, science, objectivity (knowledge)[3]

III. Roots of Unbelief: Philosophical

A. Decline in natural theology

1. David Hume (1711-1776) skepticism about God (Dialogues on Natural Religion); unbelief in miracles (Enquiry on Human Understanding)

2. Immanuel Kant (1724-1804): God is unknowable, but a postulate of practical reason: “I have denied knowledge to make room for faith,” Critique of Pure Reason

B. Religion as a romantic ideal or feeling apart from reason (F. Schleiermacher, Soren Kierkegaard)

IV. Roots of Unbelief: Scientific Trends

A. Scientific revolution wrought by theists, many Christians: Newton, Galileo, Faraday, etc. See Rodney Stark, For the Glory of God (Princeton Univ. Press, 2004), chapter two

B. The Christian philosophical orientation to nature[4]

1. The physical universe is an objective reality, which is ontologically distinct from the Creator (Genesis 1:1; John 1:1).

2. The laws of nature exhibit order, pattern, and regularity, since they are established by an orderly God (Psalm 19:1-4).

3. The laws of nature are uniform throughout the physical universe, since God created and providentially sustains them.

4. The physical universe is intelligible because God created us to know himself, ourselves, and the rest of creation. (Genesis 1-2; Proverbs 8).

5. The world is good, valuable, and worthy of careful study, because it was created for a purpose by a perfectly good God (Genesis 1). Humans, as the unique image bearers of God, were created to discern, discover, and develop the goodness of creation for the glory of God and human betterment through work. The creation mandate (Genesis 1:26-28) includes scientific activity.[5]

6. Because the world is not divine and therefore not a proper object of worship, it can be an object of rational study and empirical observation.

7. Human beings possess the ability to discover the universe’s intelligibility, since we are made in God’s image and have been placed on earth to develop its intrinsic possibilities.

8. Because God did not reveal everything about nature, empirical investigation is necessary to discern the patterns God laid down in creation.

9. The intellectual virtues essential to carrying out the scientific enterprise (studiousness, honesty, integrity, humility, and courage) are part of God’s moral law (Exodus 20:1-17).[6]

C. Charles Darwin (1809 -1882), Origin of Species, 1859

1. Attempt to explain speciation apart from design

2. Natural selection (mutation and adaptation)

3. Theological agenda: the problem of evil in animals and humans

4. Result: methodological naturalism (metaphysical naturalism)

5. Richard Lewontin, prominent biologist

We take the side of science in spite of the patent absurdity of some of its constructs, in spite of its failure to fulfill many of its extravagant promises of health and life, in spite of the tolerance of the scientific community for unsubstantiated just-so stories, because we have a prior commitment, a commitment to materialism. It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is an absolute, for we cannot allow a Divine Foot in the door.[7]

V. Responding to the Challenge

A. Know the opposition (Acts 17:16-34; 2 Corinthians 10:3-5)

B. Out argue the opposition (1 Peter 3:15: Matthew 22:37-40). Next lecture.

1. Postmodernism: show that it self-destructs

2. Philosophy: defeat naturalism;: defend natural theology

3. Science: defend intelligent design, defeat Darwinism


  1. James Collins, God in Modern Philosophy. Greenwood Press Reprint; New edition, 1978.
  2. Stephen T. Davis, God, Reason, and Theistic Proofs. Grand Rapids, MI: Eerdmans, 1997.
  3. Douglas Groothuis, Truth Decay. Downers Grove, IL: InterVarsity Press, 2000.
  4. Doug Groothuis Blog: The Constructive Curmudgeon:
  5. Cornelius Hunter, Darwin’s God: Evolution and the Problem of Evil. Grand Rapids, MI: Brazos Books, 2002.
  6. Charles Malik, A Christian Critique of the University. Downers Grove, IL: InterVarsity Press, 1983.
  7. George Marsden, The Soul of the American University: From Protestant Establishment to Established Nonbelief . New York: Oxford, 1996.
  8. Ronald Nash, Faith and Reason. Grand Rapids, MI: Zondervan, 1988.
  9. Francis Schaeffer, How Shall We Then Live?The Rise and Fall of Western Culture Wheaton, IL: Crossway, 1976. See Doug Groothuis view at:
  10. Francis Schaeffer, The God Who is There, 30th anniv. ed. Downers Grove, IL: InterVarsity Press, 1998.
  11. John Sommerville, The Decline of the Secular University. New York: Oxford University Press, 2006.
  12. Rodney Stark, For the Glory of God. Princeton Univ. Press, 2004.
  13. Nancy Pearcey, Total Truth. Wheaton, IL: Crossway, 2004. See Doug Groothuis review at:

[2] "The Scientific Preparation of the Minister" was delivered September 20, 1912, at the opening of the one hundred and first session of Princeton Theological Seminary. It is found in the Princeton Theological Review, Vol. XI, No. 1, 1913, p. 1.

[3] For more on this dichotomy, see Francis Schaeffer, The God Who is There, 30th anniv. ed. (Downers Grove, IL: InterVarsity Press, 1998); Nancy Pearcey, Total Truth (Wheaton, IL: Crossway, 2004).

[4] See Douglas Groothuis, Christian Apologetics: A Comprehensive Case for Biblical Faith (Downers Grove: InterVarsity Press, 2011), 102-103.

[5] On the significance and depth of the creation mandate, see Francis Nigel Lee, “The Roots of Culture,” chap. 1, in Lee, The Central Significance of Culture (The Presbyterian and Reformed Publishing Company, 1976).

[6] On the presuppositions of science, see also J.P. Moreland, Scaling the Secular City (Grand Rapids, MI: Baker Books, 1987), pp. 198-201.

[7] Richard Lewontin, ‘Billions and Billions of Demons,” The New York Review, January 9, 1997, p. 31.

Thursday, October 06, 2011

Groothuis to Teach on Apologetics at Word Conference

I will be giving two talks at The Word Conference, held in Denver, October 7, 8. My talks will relate to the work in Christian Apologetics, and signed copies of the book will be available for purchase.

Another Good Reason to Defeat Obama

  • The Wall             Street Journal
  • OCTOBER 4, 2011, 10:48 P.M. ET

Washington Wants a Say Over Your Minister

The Supreme Court weighs whether the feds can decide which church employees are clergy and which aren't.


Today, the Obama administration will invite the Supreme Court to open a new front in the culture wars. Hosanna-Tabor Evangelical Lutheran Church and School v. EEOC concerns a commissioned minister, Cheryl Perich, who taught elementary school and led chapel devotions at a small Lutheran school outside Detroit. Ms. Perich became ill and was replaced in the classroom by a substitute. In the middle of the school year she sought to return and then, instead of attempting to work out the dispute through the church's reconciliation process, she threatened to sue.

As relations broke down, the church congregation voted to withdraw her "call" to the ministry, and she ceased to be eligible for her prior job. She sued under the Americans with Disabilities Act, with the support of the federal Equal Employment Opportunity Commission.

The federal statutes outlawing employment discrimination based on race, sex, age and disability contain no express exception for church employers. But for 40 years lower courts have applied a "ministerial exception," which bars the government from any role in deciding who should be a minister. Courts have reasoned that the separation between church and state protects the ability of churches to choose their own clergy just as it protects the state from any control by churches. The Supreme Court has never spoken to the issue.

But who counts as a minister? Cheryl Perich's duties included leading students in prayer and worship, but she also taught secular subjects, using ordinary secular textbooks. The sole disagreement in the lower courts was whether her job was sufficiently religious to be considered ministerial. The Supreme Court will consider, for the first time, how to make that determination.

But the Obama Justice Department has now asked the court to disavow the ministerial exception altogether. This would mean that, in every future case, a court—and not the church—would decide whether the church's reasons for firing or not hiring a minister were good enough.

But the government, including the judiciary, is not entitled under the First Amendment to decide what qualifications a minister should have, or to weigh religious considerations against others. Is a secular court to decide, for example, whether confining Catholic priests or Orthodox rabbis to males is a correct interpretation of scripture, or merely a vestige of outmoded and stereotypical bias?

James Madison famously declared that the civil magistrate is not a "competent Judge of Religious truth." Yet every discrimination claim about the hiring of a minister necessarily comes down to the question of whether the church had a bona fide religious reason for its decision. That places the courts squarely in the business of adjudicating the validity of a church's claims about its own religious practice.

The Justice Department's brief grudgingly concedes that there may be an exception for employees performing "exclusively religious functions," but this is an illusory protection. Every church officer—even the pope—performs at least some nonreligious administrative duties. If the government's position were accepted, the courts would be embroiled in disputes about the selection of clergy at all levels and in every denomination. This would be a radical reversal of our nation's long constitutional tradition.

In the colonial era, with an established Church of England, the government controlled who would preach the gospel. The royal governor of Virginia licensed ministers in the colony, and Madison's first known writing on religious liberty was a letter protesting the jailing of Baptist ministers for preaching without a license.

When the First Amendment declared that "Congress shall make no law respecting an establishment of religion," it meant that churches would support themselves and control themselves. And the separation of church and state is a two-way street: It protects the autonomy of religious institutions from governmental interference no less than it prevents advancement of religion by government power.

That tradition of church-state separation has continued to the present day. After the Civil War, for example, the framers of the 14th Amendment, which applied the Establishment Clause to the states, voted against legislation to subject churches to antidiscrimination laws, concluding this would violate the First Amendment. The Supreme Court has held (Bishop v. Amos, 1987) that religious organizations must be "free to select their own leaders, define their own doctrines, resolve their own disputes, and run their own institutions." Even EEOC guidelines a few years ago reaffirmed the ministerial exception.

Perhaps American churches should be more open to female clergy and more accommodating toward elderly pastors or disabled chaplains. But if the separation between church and state means anything, such changes must come from within.

As a lower court judge, Justice Sonia Sotomayor wrote: "Federal court entanglement in matters as fundamental as a religious institution's selection or dismissal of its spiritual leaders risks an unconstitutional trespass on the most spiritually intimate grounds of a religious community's existence." It is unfortunate that the Department of Justice does not see it that way.

Mr. McConnell is the director of the Constitutional Law Center at Stanford University. He wrote a friend-of-the-court brief in this case on behalf of major Protestant denomination