The Strongest Critics of Intelligent Design, in Their Own Words

This site argues that the order of the world points to its Maker. Because its motto is honesty, it also owes readers the strongest case against Intelligent Design (ID), made by the people best able to make it. Some of them are atheists. Several are Christians. One is a federal judge.

This article gathers six of the most serious critics and lets each speak in his or her own words: the court in Kitzmiller v. Dover (2005), the biologist Kenneth Miller, the biologist Nick Matzke, the philosopher Elliott Sober, Eugenie Scott of the National Center for Science Education and the geneticist Francis Collins. Each objection is stated at full strength, answered as well as the evidence allows, and graded. The article ends with a point that matters more than any single grade: the Orthodox faith does not stand or fall with the design argument.

In brief

The critics of ID raise five main objections. The Kitzmiller court held that ID is not science, while explicitly taking no position on whether its arguments are true. Miller and Matzke argued that the bacterial flagellum, ID's best-known example, is not irreducibly complex, since part of it works as a secretion system, and that its parts have relatives elsewhere in nature. Sober argued that ID cannot be tested, because nothing independent tells us what a designer would want. Scott argued that ID is a form of creationism that scientists do not use. Collins, a Christian, warned that faith built on gaps in knowledge "may be headed for crisis." Graded honestly, the critics win several points: irreducible complexity as a proof that the flagellum could not evolve has not held up, and ID has gained little scientific following. But no critic shows that the world has no Maker, and several (Miller, Collins, Scott) say outright that science cannot settle that question. The Orthodox faith rests on Christ risen and on God's self-revelation, not on any one inference from biology.

Thesis: The strongest critics of Intelligent Design succeed against some of its specific scientific claims, but none of their arguments touches the existence of God or the truth of the Christian faith, which never rested on those claims.

What is being criticized

Stephen Meyer of the Discovery Institute gives this definition: "the theory of intelligent design holds that there are tell-tale features of living systems and the universe - for example, the information-bearing properties of DNA, the miniature circuits and machines in cells and the fine tuning of the laws and constants of physics - that are best explained by an intelligent cause rather than an undirected material process."¹ Three things must be kept apart: ID as a proposed scientific research program, the older argument from design in natural theology, and the Christian faith itself. Most of the critics below are aiming at the first.

1. The court: Kitzmiller v. Dover (2005)

The objection at full strength

After a six-week trial over a Pennsylvania school board's ID policy, Judge John E. Jones III ruled: "we find that while ID arguments may be true, a proposition on which the Court takes no position, ID is not science. We find that ID fails on three different levels, any one of which is sufficient to preclude a determination that ID is science. They are: (1) ID violates the centuries-old ground rules of science by invoking and permitting supernatural causation; (2) the argument of irreducible complexity, central to ID, employs the same flawed and illogical contrived dualism that doomed creation science in the 1980's; and (3) ID's negative attacks on evolution have been refuted by the scientific community." He added that ID "has failed to gain acceptance in the scientific community, it has not generated peer-reviewed publications, nor has it been the subject of testing and research."²

The answer

The Discovery Institute answered that the court's science section was borrowed from the plaintiffs. Announcing a 2006 study he wrote with David DeWolf, John West said the judge "copied verbatim or virtually verbatim 90.9% of his 6,004-word section on whether intelligent design is science" from the plaintiffs' proposed findings.³ Judges commonly adopt proposed findings, so this criticism goes to the opinion's independence more than to its reasoning. The deeper reply is philosophical. Whether "science" can be defined so as to exclude any appeal to intelligence in nature is a dispute among philosophers that a court cannot settle by ruling (the site's article Is Intelligent Design Science or Creationism? sets out that debate in detail).

The ruling's own limits deserve notice. The judge wrote that "we do not question that many of the leading advocates of ID have bona fide and deeply held beliefs which drive their scholarly endeavors. Nor do we controvert that ID should continue to be studied, debated, and discussed."

Grade

{{very-strong: The Kitzmiller court ruled that ID is not science while expressly taking no position on whether ID's arguments are true.}} On the legal question the ruling stands. On the philosophical question of what counts as science, it is one voice in a live debate.

2. Kenneth Miller: the flagellum unspun

The objection at full strength

Miller, a biologist at Brown University, a Roman Catholic, and a witness for the plaintiffs at Dover, made the case against Michael Behe's flagellum argument in "The Flagellum Unspun" (2004). Some disease-causing bacteria use a type III secretory system (TTSS) built from proteins homologous to those at the base of the flagellum. Behe had argued that any precursor missing a part is "by definition nonfunctional." Miller answered: "Yet the TTSS is indeed fully-functional, even though it is missing most of the parts of the flagellum." His conclusion was sharp: with irreducible complexity collapsed, what remains of the design case is "the classic argument from ignorance, dressed up in the shiny cloth of biochemistry and information theory."⁴

Miller's critique was also theological. He called the movement's struggles "double failures": "rejected by science because they do not fit the facts, and having failed religion because they think too little of God."

The answer

Miller himself conceded a limit. To the reply that the TTSS "does not tell us how either it or the flagellum evolved," he answered: "This is certainly true." Meyer pressed the point. He argued that co-option faces at least three difficulties: the other twenty or so motor proteins, he says, are unique to the flagellum; the parts must be assembled in a precise order under genetic control; and sequence analyses he cited "suggest that the flagellar motor arose first and the pump came later."⁵

Grade

Miller wins the definitional point: a flagellum that contains a working subsystem is not irreducible in Behe's strict sense, and the claim that it could not evolve "even in principle" has not held. ID is right that no step-by-step pathway has been shown. Miller's theological point deserves an Orthodox hearing too: a God who appears only where explanations run out is not the God of the Creed, who is "Maker of Heaven and Earth and of all things visible and invisible."⁶ The full scientific debate is in Irreducible Complexity: The Bacterial Flagellum and Its Critics.

3. Nick Matzke: no such thing as "the" flagellum

The objection at full strength

In 2006 Mark Pallen of the University of Birmingham and Nicholas Matzke, then of the National Center for Science Education, answered the flagellum argument in Nature Reviews Microbiology. They described the ID claim as "essentially a modern re-working of the old creationist argument 'what good is half a wing?'" and stressed variety: "there is no such thing as 'the' bacterial flagellum." With thousands of different flagellar systems, "one is faced with two options: either there were thousands or even millions of individual creation events, which strains Occam's razor to breaking point, or one has to accept that all the highly diverse contemporary flagellar systems have evolved from a common ancestor." They argued that modelling the first flagellum "requires no great conceptual leap," since its modules are "fashioned from recycled parts that occur elsewhere in nature."⁷

The answer

The paper is candid about what it has not shown. Its authors note that a reduced core flagellum "is still a challenge to explain"; that although "at least nine core flagellar proteins share common ancestry with core components" of secretion systems, "the scientific community is divided on the nature of their common ancestor"; and that their abstract proposes only to "speculate as to how an experimental programme focused on this topic might look." Their dilemma also assumes that design means separate creation events. Design advocates reject that assumption; Casey Luskin, for example, writes that Jerry Coyne "assumes that ID is incompatible with common ancestry, which it isn't."⁸ The Christian doctrine of creation has never required each bacterial species to be made separately.

Grade

{{strong: The many kinds of bacterial flagella share core proteins, and several of those proteins are related to proteins in other bacterial systems.}} That is good evidence of common ancestry among flagella. A demonstrated evolutionary pathway to the first flagellum remains a proposal; the authors themselves only "speculate" about the experiments that might test it.

4. Elliott Sober: can design be tested?

The objection at full strength

Sober, a philosopher of biology at the University of Wisconsin, made what may be the most careful criticism. In "What Is Wrong with Intelligent Design?" (2007) he rejected two popular objections, that ID is unfalsifiable and that nature's imperfections refute it. His own objection is that testing is comparative, and that ID cannot make predictions that differ from evolution's without assumptions about the designer. "When scientific theories compete with each other, the usual pattern is that independently attested auxiliary propositions allow the theories to make predictions that disagree with each other. No such auxiliary propositions allow mini-ID to do this." He concluded: "In all its forms, ID fails to constitute a serious alternative to evolutionary theory."⁹

The answer

Meyer replies that the design inference does rest on independent knowledge: "we have positive experience-based knowledge of an alternative cause that is sufficient to have produced such effects. That cause is intelligence." Design theorists infer design, he writes, "because we know based upon our uniform experience that only intelligent agents produce these effects."¹⁰ That is a real answer about what kind of cause can produce information. It does not fully meet Sober's point, which concerns the designer's particular goals and abilities, the very things a theist says we know only in part.

Grade

Sober's objection is among the strongest against ID as a scientific rival to evolutionary theory. It has much less force against the classical argument from the existence and order of the world, which does not compete with any particular biological mechanism. It is also worth noting that Sober's paper rejects the popular "bad design" argument against a designer (see Is Intelligent Design a "God of the Gaps" Argument? for the related gaps debate).

5. Eugenie Scott: creationism by another name

The objection at full strength

Scott, the long-time executive director of the National Center for Science Education, argued with Matzke in the Proceedings of the National Academy of Sciences (2007) that "The content of ID is a subset of the claims made by the older 'creation science' movement," that "Historically, ID arose from efforts to produce a form of creationism that would be less vulnerable to legal challenges," and that "Scientists do not use ID to explain nature."¹¹

The answer

The origin of an argument does not decide its truth, and Meyer denies that ID's method or content is creationist. But the historical point is real, and the lack of uptake among working scientists is a fair measure of ID's success as a research program. Scott's most important words for Christians, though, came in a 1998 speech. Explaining why science must keep to natural causes, she said: "Properly understood, the principle of methodological materialism requires neutrality towards God; we cannot say, wearing our scientist hats, whether God does or does not act." She added: "Science is an equal opportunity methodology."¹²

Grade

Scott's history is largely accurate and her point about scientific uptake is fair. Her own principle, however, rules out the atheist use of science: by her account, science as a method cannot say whether God acts.

6. Francis Collins: a Christian critic

The objection at full strength

Collins, who headed the international team that mapped the human genome and who calls his own view "BioLogos," criticized ID as a believer. In The Language of God (2006) he warned: "Faith that places God in the gaps of current understanding about the natural world may be headed for crisis if advances in science subsequently fill those gaps."¹³ Debating Richard Dawkins in Time that year, he said: "I don't see that Professor Dawkins' basic account of evolution is incompatible with God's having designed it," and asked whether God might sensibly "use the mechanism of evolution without posting obvious road signs to reveal his role in creation."¹⁴ BioLogos states: "we believe that our intelligent God designed the universe, but we do not see scientific or biblical reasons to give up on pursuing natural explanations for how God governs natural phenomena."¹⁵

The answer

The design advocate Paul Nelson replied that Collins is inconsistent: Collins argues that human altruism cannot be explained by selfish genes and points to God, and "This mode of reasoning resembles exactly what Collins elsewhere derides as God-of-the-gaps thinking."¹⁶ In the same debate Collins himself pointed to the fine-tuning of physical constants as making a designer "a rather plausible explanation." So Collins does not reject design reasoning as such. He rejects resting faith on unexplained biological gaps.

Grade

Collins's warning is sound pastoral advice, and Nelson's charge of inconsistency has some force. Both write as Christians who confess God as Creator; their quarrel is about method. The site's article Can a Christian Accept Evolution? sets out the Orthodox range of views.

The scorecard

Critic	Main objection	Our grade
Kitzmiller court	ID is not science	Legally settled; philosophically debated
Kenneth Miller	The flagellum is not irreducibly complex	Strong against the strict claim; no full pathway shown
Nick Matzke	Flagella share parts and ancestry	Strong for common ancestry; origin still a model
Elliott Sober	ID cannot be tested against evolution	Strong against ID as a scientific rival; weak against natural theology
Eugenie Scott	ID is creationism that scientists do not use	Fair as history and as a measure of uptake
Francis Collins	Faith should not rest on gaps	Sound advice; applied unevenly

An Orthodox note: the design argument is not the foundation

None of these critics, and none of these grades, reaches the foundation of the Christian faith. The Church has always held that the created world speaks of its Maker: "For since the creation of the world His invisible attributes are clearly seen, being understood by the things that are made" (Romans 1:20, NKJV). The Book of Wisdom says that "by the greatness and beauty of the creatures proportionably the maker of them is seen" (Wisdom 13:5, Brenton).¹⁷

But St John of Damascus, summing up the Fathers in the eighth century, placed that knowledge in its proper rank. "God, however, did not leave us in absolute ignorance. For the knowledge of God's existence has been implanted by Him in all by nature. This creation, too, and its maintenance, and its government, proclaim the majesty of the Divine nature." Then he goes further: "by the Law and the Prophets in former times and afterwards by His Only-begotten Son, our Lord and God and Saviour Jesus Christ, He disclosed to us the knowledge of Himself as that was possible for us."¹⁸ Natural knowledge of God is real, but it is the porch. The house is the revelation of the Holy Trinity in Christ, received and lived in the Church.

That is why the Orthodox Christian can grade these critics honestly without anxiety. If Behe's flagellum argument fails, the Resurrection of Christ does not. If ID never becomes a successful research program, the Creed is not weakened by a word. "By faith we understand that the worlds were framed by the word of God" (Hebrews 11:3, NKJV). The site argues for design because the order of the world is real evidence, not because the faith needs it to survive.

The atheist conclusion that these critics are sometimes enlisted to support is false. Miller and Collins are believers who argue that evolution and God are compatible. Scott, a self-described nontheist, says that as scientists "we cannot say" whether God acts. Sober attacks ID's scientific standing, not the existence of God. The question whether the world has a Maker is answered by the existence and order of all things, by the moral law, and above all by the historical Resurrection; see Does God Exist? The Strongest Arguments for Theism Explained.

Objections to this article

"You concede too much. ID has answered every one of these critics."

ID has answered many, and those answers are given above. But honesty requires saying that the strict claim about the flagellum has not held, and that ID has not won the scientific community. Pretending otherwise would make the site's other arguments less credible.

"You concede too little. ID is simply creationism and should not be taken seriously."

The question whether the world bears marks of intelligence is one of the oldest in philosophy, and a court cannot close it. Even the Kitzmiller court said ID's arguments "may be true" and should "continue to be studied, debated, and discussed."

What we can say confidently

• The Kitzmiller court held that ID is not science and took no position on whether its arguments are true.
• Part of the bacterial flagellum is related to a working secretion system, so the strict claim that it could not evolve even in principle has not held.
• No detailed step-by-step pathway for the origin of the flagellum has been demonstrated.
• Bacterial flagella vary widely and share core proteins, which is evidence of common ancestry among them.
• ID has gained little following among working scientists.
• Several leading critics (Miller, Collins, Scott) state that science does not rule out God.

What remains disputed

• Whether design inferences can ever count as science (the demarcation debate).
• Whether the flagellum or the secretion system came first.
• Whether Meyer's "uniform experience" argument meets Sober's demand for independent auxiliary assumptions.
• How far the history of the ID movement bears on the merits of its arguments.

Conclusion

The strongest critics of Intelligent Design are worth reading in full. They have corrected real overstatements, and Christians should be grateful for that. A faith that leaned on the claim that the flagellum could never have evolved would be leaning on a reed.

The Orthodox faith has never leaned there. It confesses one God, the Father Almighty, and one Lord Jesus Christ, through whom all things were made, who was crucified, buried and rose on the third day. Creation proclaims its Maker to all who look; Christ reveals Him. The critics may win their arguments about bacteria, and the heavens still declare the glory of God.

Notes

1. Stephen C. Meyer, "A Scientific History - and Philosophical Defense - of the Theory of Intelligent Design," Discovery Institute PDF, https://www.discovery.org/m/2018/11/Scientific-History-Philosophical-Defense-Intelligent-Design-Stephen-Meyer.pdf, p. 2.
2. Kitzmiller v. Dover Area School District, 400 F. Supp. 2d 707 (M.D. Pa. 2005), Memorandum Opinion, 20 December 2005, slip op. at 64; later quotation at 137, https://www.pamd.uscourts.gov/sites/pamd/files/opinions/04v2688d.pdf.
3. Robert Crowther, "Study Shows Federal Judge Copied ACLU Text in Dover Intelligent Design Ruling," Discovery Institute, 12 December 2006, https://scienceandculture.com/2006/12/study_shows_federal_judged_cop/, reporting John G. West and David K. DeWolf, "A Comparison of Judge Jones' Opinion in Kitzmiller v. Dover with Plaintiffs' Proposed 'Findings of Fact and Conclusions of Law'" (2006).
4. Kenneth R. Miller, "The Flagellum Unspun: The Collapse of 'Irreducible Complexity'," in William A. Dembski and Michael Ruse, eds., Debating Design: From Darwin to DNA (Cambridge University Press, 2004), pre-publication text at http://www.millerandlevine.com/km/evol/design2/article.html. Miller's Catholic faith: Vatican Observatory review of Finding Darwin's God, https://www.vaticanobservatory.org/?p=171542.
5. Meyer, "A Scientific History" (see note 1), section on irreducible complexity, citing Minnich and Meyer (2004) and Saier (2004). Miller's concession: "The Flagellum Unspun" (see note 4).
6. Orthodox Church in America, "The Symbol of Faith," https://www.oca.org/orthodoxy/prayers/symbol-of-faith.
7. Mark J. Pallen and Nicholas J. Matzke, "From The Origin of Species to the origin of bacterial flagella," Nature Reviews Microbiology 4 (October 2006): 784-790, doi:10.1038/nrmicro1493.
8. Casey Luskin, "The Recurrent Laryngeal Nerve Does Not Refute Intelligent Design," Discovery Institute, 14 October 2010, https://scienceandculture.com/2010/10/the_recurrent_laryngeal_nerve_/.
9. Elliott Sober, "What Is Wrong with Intelligent Design?" The Quarterly Review of Biology 82, no. 1 (March 2007): 3-8; quotations as given in National Center for Science Education, "Sober explains what is wrong with 'intelligent design'," https://ncse.ngo/sober-explains-what-wrong-intelligent-design, and ScienceDaily, 23 February 2007, https://www.sciencedaily.com/releases/2007/02/070222155420.htm.
10. Meyer, "A Scientific History" (see note 1), p. 27.
11. Eugenie C. Scott and Nicholas J. Matzke, "Biological design in science classrooms," Proceedings of the National Academy of Sciences 104, suppl. 1 (2007): 8669-8676, doi:10.1073/pnas.0701505104 (abstract).
12. Eugenie C. Scott, "Science and Religion, Methodology and Humanism," excerpt from her 1998 Isaac Asimov Science Award acceptance speech, National Center for Science Education, https://ncse.ngo/science-and-religion-methodology-and-humanism-0.
13. Francis S. Collins, The Language of God (New York: Free Press, 2006), 93, as quoted in Paul Nelson's review (see note 16).
14. David Van Biema, "God vs. Science," Time, 5 November 2006 (debate between Richard Dawkins and Francis Collins), https://content.time.com/time/magazine/article/0,9171,1555132,00.html.
15. BioLogos, "How is Evolutionary Creation different from Evolutionism, Intelligent Design, and Creationism?" Common Questions, archived 2025, https://biologos.org/common-questions/how-is-biologos-different-from-evolutionism-intelligent-design-and-creationism.
16. Paul Nelson, "No God-of-the-Gaps Allowed: Francis Collins and Theistic Evolution," Christian Research Journal 30, no. 2 (2007), https://www.equip.org/articles/no-god-of-the-gaps-allowed-francis-collins-and-theistic-evolution/.
17. Wisdom of Solomon 13:5, Brenton Septuagint translation, https://ebible.org/eng-Brenton/WIS13.htm.
18. St John of Damascus, An Exact Exposition of the Orthodox Faith 1.1, trans. E. W. Watson and L. Pullan, NPNF2 vol. 9, https://www.newadvent.org/fathers/33041.htm.

Bibliography

Primary sources

• Kitzmiller v. Dover Area School District, 400 F. Supp. 2d 707 (M.D. Pa. 2005).
• The Holy Bible, New King James Version. Nashville: Thomas Nelson, 1982. Brenton, Lancelot C. L., trans. The Septuagint with Apocrypha: English. London: Samuel Bagster, 1851.

Orthodox and patristic sources

• John of Damascus. An Exact Exposition of the Orthodox Faith. Trans. E. W. Watson and L. Pullan. Nicene and Post-Nicene Fathers, Second Series, vol. 9. Buffalo: Christian Literature Publishing Co., 1899.
• Orthodox Church in America. "The Symbol of Faith."

Other scholarship (including scholars who disagree)

• BioLogos. "How is Evolutionary Creation different from Evolutionism, Intelligent Design, and Creationism?"
• Collins, Francis S. The Language of God: A Scientist Presents Evidence for Belief. New York: Free Press, 2006.
• Miller, Kenneth R. "The Flagellum Unspun." In Debating Design, ed. William A. Dembski and Michael Ruse. Cambridge: Cambridge University Press, 2004.
• Pallen, Mark J., and Nicholas J. Matzke. "From The Origin of Species to the origin of bacterial flagella." Nature Reviews Microbiology 4 (2006): 784-790.
• Scott, Eugenie C. "Science and Religion, Methodology and Humanism." NCSE, 1998 speech.
• Scott, Eugenie C., and Nicholas J. Matzke. "Biological design in science classrooms." PNAS 104, suppl. 1 (2007): 8669-8676.
• Sober, Elliott. "What Is Wrong with Intelligent Design?" The Quarterly Review of Biology 82 (2007): 3-8.
• Van Biema, David. "God vs. Science." Time, 5 November 2006.

Sources from the tradition discussed (Intelligent Design)

• Luskin, Casey. "The Recurrent Laryngeal Nerve Does Not Refute Intelligent Design." Discovery Institute, 2010.
• Crowther, Robert. "Study Shows Federal Judge Copied ACLU Text in Dover Intelligent Design Ruling." Discovery Institute, 2006.
• Meyer, Stephen C. "A Scientific History - and Philosophical Defense - of the Theory of Intelligent Design." Discovery Institute.
• Nelson, Paul. "No God-of-the-Gaps Allowed: Francis Collins and Theistic Evolution." Christian Research Journal 30, no. 2 (2007).