Johnson became a born-again Christian following a divorce, and later became an elder in the Presbyterian Church (U.S.A.). Johnson recounts that on sabbatical in England he sought, through prayer, inspiration for what he should do with the rest of his life, and then received an epiphany after he read Richard Dawkins' The Blind Watchmaker (1986) and Michael Denton's Evolution: A Theory in Crisis (1985). Johnson later said, "Something about the Darwinists' rhetorical style, made me think they had something to hide." Despite having no formal background in biology, he felt that could add insight into the premises and arguments: "I approach the creation-evolution dispute not as a scientist but as a professor of law, which means among other things that I know something about the ways that words are used in arguments." Since the publication of the first edition of Darwin on Trial in 1991, he has become a prominent critic of evolutionary theory.
Johnson popularized the term "intelligent design" in his book, Darwin on Trial. He remains one of the best known advocates for intelligent design, and is considered the founder of the intelligent design movement. He is a critic of methodological naturalism, the basic principle of science that restricts it to the investigation of natural causes for observable phenomena, and espouses a philosophy he has coined "theistic realism." He is the author of several books on intelligent design, science, philosophy, and religion, as well as textbooks on criminal law. He has appeared on various programs such as PBS's Firing Line and a Nova episode, "Judgment Day: Intelligent Design on Trial."
Since 2001, Johnson has suffered a series of minor right brain strokes. His rehabilitations have limited his public activities and participation in the debate on intelligent design, because of both their physical effects and Johnson's belief that they were signs from God urging him to spend more time with his faith and family and less in prideful debate. In 2004, he was awarded the inaugural "Phillip E. Johnson Award for Liberty and Truth" by Biola University, a private evangelical Christian college noted for its promotion of intelligent design. Johnson has two children and lives with his wife in Berkeley, California.
In 2006, Nancey Murphy, a religious scholar at Fuller Theological Seminary, stated she faced a campaign to get her fired after she expressed her view that intelligent design was not only poor theology, but "so stupid, I don't want to give them my time." Murphy, who accepts the validity of evolution, said that Johnson called a trustee in an attempt to get her fired and stated "His tactic has always been to fight dirty when anyone attacks his ideas." Johnson admits calling the trustee, but denies any responsibility for action taken against her. He said: "It's the Darwinists who hold the power in academia and who threaten the professional status and livelihoods of anyone who disagrees... They feel to teach anything but their orthodoxy is an act of professional treason." Murphy had previously criticized Johnson's book Darwin on Trial for being "dogmatic and unconvincing," primarily because "he does not adequately understand scientific reasoning."
During the 1990s, Johnson engaged in AIDS denialism, challenging the scientific consensus by claiming that HIV tests do not detect HIV, AIDS statistics are grossly exaggerated and that HIV is not the cause of AIDS. He wrote several articles about the subject, including a piece in Reason magazine. He was one of the 12 founding members of The Group for the Scientific Reappraisal of the HIV/AIDS Hypothesis and signatory to the group's letter to the editor of Science asserting that HIV is only tautologically associated with AIDS and that HIV tests are inaccurate.
Johnson has stated in an interview that he believed "the strength of America is not in its towers or in its battleships, it's in its faith. Of course, I said that, but I wasn't sure it was really true anymore. This isn't the same country we were in the previous decades." Johnson said the U.S. was "cringing in fear" of Muslim terrorists after September 11 attacks and that professors were afraid to discuss it "because they're afraid of what the Muslim students will do. They're afraid it won't keep the peace on campus. I never thought our country would descend to this level. We are afraid to search the truth and to proclaim it. We once knew who the true God was and were able to proclaim it frankly. But since about 1960 we've been hiding from that. We've been trying to pretend that all religions are the same."
Johnson is best known as one of the founders of the intelligent design movement, principal architect of the wedge strategy, author of the Santorum Amendment, and one of the ID movement's most prolific authors. Johnson is co-founder and program advisor of the Discovery Institute's Center for Science and Culture. Johnson has advocated strongly in the public and political spheres for the teaching of intelligent design as preferable to the teaching of evolution, which Johnson characterizes as "atheistic" and "falsified by all of the evidence" and whose "logic is terrible." In portraying the philosophy of science, and by extension its theories such as evolution as atheistic, Johnson argues that a more valid alternative is "theistic realism." Theistic realism asserts that science, by relying upon methodological naturalism, demands an a priori adoption of a naturalistic philosophy that wrongly dismisses out of hand any explanation that contains a supernatural cause.
Johnson rejects common descent and does not take a position on the age of the Earth. These concepts are a common theme in his books, including Darwin on Trial,Reason in the Balance: The Case Against Naturalism in Science, Law & Education (1995), Defeating Darwinism by Opening Minds (1997), and The Wedge of Truth: Splitting the Foundations of Naturalism (2000). Eugenie Scott wrote that Darwin on Trial "teaches little that is accurate about either the nature of science, or the topic of evolution. It is recommended neither by scientists nor educators." Working through the Center for Science and Culture Johnson wrote the early draft language of the Santorum Amendment, which encouraged a "Teach the Controversy" approach to evolution in public school education.
Nancy Pearcey, a Center for Science and Culture fellow and Johnson associate, credits Johnson's leadership of the intelligent design movement in two of her most recent publications. In an interview with Johnson for World magazine, Pearcey says, "It is not only in politics that leaders forge movements. Phillip Johnson has developed what is called the 'Intelligent Design' movement..." In Christianity Today, she reveals Johnson's religious beliefs and his criticism of evolution and affirms Johnson as "The unofficial spokesman for ID" The scientific community views intelligent design as unscientific, pseudoscience and junk science.
In its earliest days the intelligent design movement was called the 'wedge movement'. The wedge metaphor, attributed to Johnson, is that of a metal wedge splitting a log and represents using an aggressive public relations programme to create an opening for the supernatural in the public’s understanding of science. Johnson acknowledges that the goal of the intelligent design movement is to promote a theistic agenda as a scientific concept.
According to Johnson, the wedge movement, if not the term, began in 1992:
The movement we now call the wedge made its public debut at a conference of scientists and philosophers held at Southern Methodist University in March 1992, following the publication of my book Darwin on Trial. The conference brought together as speakers some key Wedge figures, particularly Michael Behe, Stephen Meyer, William Dembski, and myself.
Johnson describes the wedge movement as devoted to a "program of questioning the materialistic basis of science" and reclaiming the "intellectual world" from the "atheists and agnostics" that Johnson believes are synonymous with this "scientific materialist culture." He describes the "logic of our movement" as:
"The first thing you understand is that the Darwinian theory isn't true. It's falsified by all of the evidence, and the logic is terrible."
"...the next question that occurs to you is, 'Well, where might you get truth?' ...I start with John 1:1, 'In the beginning was the Word.' In the beginning was intelligence, purpose, and wisdom. The Bible had that right and the materialist scientists are deluding themselves."
"The next question is: Why do so many brilliant, well-informed, intelligent people fool themselves for so long with such bad thinking and bad evidence?" Johnson sees this as an issue of "turning away from" self-evident truth, the "sin question" and the need to prepare the way for acceptance of a Creator.
Johnson has been explicit about the Christian principles underlying his philosophy and agenda and that of the intelligent design movement. In speaking at the 1999 "Reclaiming America for Christ Conference," Johnson has described the movement thus:
I have built an intellectual movement in the universities and churches that we call "The Wedge," which is devoted to scholarship and writing that furthers this program of questioning the materialistic basis of science.
Now, the way that I see the logic of our movement going is like this. The first thing you understand is that the Darwinian theory isn't true. It's falsified by all of the evidence, and the logic is terrible. When you realize that, the next question that occurs to you is, "Well, where might you get truth?" ...I start with John 1:1, "In the beginning was the Word." In the beginning was intelligence, purpose, and wisdom. The Bible had that right and the materialist scientists are deluding themselves.
In summary, we have to educate our young people; we have to give them the armor they need. We have to think about how we're going on the offensive rather than staying on the defensive. And above all, we have to come out to the culture with the view that we are the ones who really stand for freedom of thought. You see, we don't have to fear freedom of thought because good thinking done in the right way will eventually lead back to the Church, to the truth-the truth that sets people free, even if it goes through a couple of detours on the way. And so we're the ones that stand for good science, objective reasoning, assumptions on the table, a high level of education, and freedom of conscience to think as we are capable of thinking. That's what America stands for, and that's something we stand for, and that's something the Christian Church and the Christian Gospel stand for-the truth that makes you free. Let's recapture that, while we're recapturing America.
— Johnson, How The Evolution Debate Can Be Won
The objective [of the wedge strategy] is to convince people that Darwinism is inherently atheistic, thus shifting the debate from creationism vs. evolution to the existence of God vs. the non-existence of God. From there people are introduced to 'the truth' of the Bible and then 'the question of sin' and finally 'introduced to Jesus.'
Johnson is one of the authors of the Discovery Institute's Wedge Document and its "Teach the Controversy" campaign, which attempts to cast doubt on the validity of the theory of evolution, its acceptance within the scientific community, and reduce its role in public school science curricula while promoting intelligent design. The "Teach the Controversy" campaign portrays evolution as "a theory in crisis."
In his 1997 book Defeating Darwinism by Opening Minds Johnson summed up the underlying philosophy of his advocacy for intelligent design and against methodological and philosophical naturalism:
If we understand our own times, we will know that we should affirm the reality of God by challenging the domination of materialism and naturalism in the world of the mind. With the assistance of many friends I have developed a strategy for doing this,...We call our strategy the "wedge".
Johnson has described the wedge strategy as:
"We are taking an intuition most people have [the belief in God] and making it a scientific and academic enterprise. We are removing the most important cultural roadblock to accepting the role of God as creator."
"Our strategy has been to change the subject a bit, so that we can get the issue of intelligent design, which really means the reality of God, before the academic world and into the schools."
"This isn't really, and never has been, a debate about science. It's about religion and philosophy."
"So the question is: 'How to win?' That's when I began to develop what you now see full-fledged in the 'wedge' strategy: 'Stick with the most important thing' —the mechanism and the building up of information. Get the Bible and the Book of Genesis out of the debate because you do not want to raise the so-called Bible-science dichotomy. Phrase the argument in such a way that you can get it heard in the secular academy and in a way that tends to unify the religious dissenters. That means concentrating on, 'Do you need a Creator to do the creating, or can nature do it on its own?' and refusing to get sidetracked onto other issues, which people are always trying to do."
When asked how best to raise doubts and question evolution with non-believers, Johnson responded:
What I am not doing is bringing the Bible into the university and saying, "We should believe this." Bringing the Bible into question works very well when you are talking to a Bible-believing audience. But it is a disastrous thing to do when you are talking, as I am constantly, to a world of people for whom the fact that something is in the Bible is a reason for not believing it.
You see, if they thought they had good evidence for something, and then they saw it in the Bible, they would begin to doubt. That is what has to be kept out of the argument if you are going to do what I to do, which is to focus on the defects in their [the evolutionist's] case—the bad logic, the bad science, the bad reasoning, and the bad evidence.
Johnson has been accused of being intellectually dishonest in his arguments advancing intelligent design and attacking the scientific community. Johnson has employed numerous equivocations regarding the term "naturalism," failing to distinguish between methodological naturalism (in which science is used to study the natural world and says nothing about the supernatural) versus philosophical naturalism (the philosophical belief that nothing exists but the natural world, and adopts as a premise the idea that there is no supernatural world or deities). In fact-checking Johnson's books Darwin on Trial and Defeating Darwinism by Opening Minds, one reviewer argued that almost every scientific source Johnson cited had been misused or distorted, from simple misinterpretations and innuendos to outright fabrications. The reviewer, Brian Spitzer, an associate professor of biology at the University of Redlands, described Darwin on Trial as the most deceptive book he had ever read.
Since Johnson is considered by those both inside and outside the movement to be the father and architect of the intelligent design movement and its strategies, his statements are often used to validate the criticisms leveled by those who allege that the Discovery Institute and its allied organizations are merely stripping the obvious religious content from their anti-evolution assertions as a means of avoiding the legal restrictions of the Establishment Clause, a view reinforced by the December 2005 ruling in the Kitzmiller v. Dover Area School District trial which found that intelligent design is not science and is essentially religious in nature. They argue that ID is an attempt to put a patina of secularity on top of what is a fundamentally religious belief and thus that the "Teach the Controversy" exhortation is disingenuous, particularly when contrasted to his statements in The Wall Street Journal and other secular media. Critics point out that contrary to the Discovery Institute's and Johnson's claims, the theory of evolution is well-supported and accepted within the scientific community, with debates regarding how evolution occurred, not if it occurred. Popular disagreement with evolutionary theory should not be considered as a reason for challenging it as a scientifically valid subject to be taught, they contend.
Critics of Johnson point to his central role in the Discovery Institute's carefully orchestrated campaign known as the wedge strategy. The wedge strategy, as envisioned by the Discovery Institute, is designed to leave the science establishment looking close-minded in the short term with a long-term goal being a redefinition of science that centers on the removal of methodological naturalism from the philosophy of science and the scientific method, thereby allowing for supernatural explanations to be introduced as science. Critics note that Johnson, as a principal officer of the Discovery Institute, often cites an overall plan to put the United States on a course toward the theocracy envisioned in the wedge strategy, and that the Discovery Institute as a matter of policy intentionally obfuscates its agenda. According to Johnson, "The movement we now call the wedge made its public debut at a conference of scientists and philosophers held at Southern Methodist University in March 1992."
—— (1975). Criminal Law: Cases, Materials, and Text on the Substantive Criminal Law in its Procedural Context. American Casebook Series. St. Paul, MN: West Publishing Company. LCCN75005083. OCLC1529179.
—— (1976). 1976 Supplement to Criminal Law: Cases, Materials, and Text on the Substantive Criminal Law in its Procedural Context. American Casebook Series. St. Paul, MN: West Publishing Company. LCCN77354635. OCLC2607013.
—— (1977). 1977 Supplement to Criminal Law: Cases, Materials, and Text on the Substantive Criminal Law in its Procedural Context. American Casebook Series. St. Paul, MN: West Publishing Company. LCCN77154398. OCLC3670876.
—— (1980). Criminal Law: Cases, Materials, and Text on the Substantive Criminal Law in its Procedural Context. American Casebook Series. With problems by the author and Myron Moskovitz (2nd ed.). St. Paul, MN: West Publishing Company. ISBN0-8299-2093-5. LCCN80014283. OCLC22560980.
—— (1985). Criminal Law: Cases, Materials, and Text. American Casebook Series. With problems by the author and Myron Moskovitz (3rd ed.). St. Paul, MN: West Publishing Company. ISBN0-3148-9682-1. LCCN85005079. OCLC12120243.
—— (1988). Goldenberg, Norman S., ed. Casenote Legal Briefs. Criminal Law: Adaptable to Courses Utilizing Johnson's Casebook on Criminal Law. Staff writers, Richard A. Lovich, Kemp Richardson. Beverly Hills, CA: Casenotes Pub. Co. ISBN0-8745-7093-X. LCCN89117347. OCLC20391227.
Arnold, Brian G.; Caves, Amy Melissa; Rose, Paul; Johnson, Phillip E. (2002). Blatt, Dana L., ed. West Group High Court Case Summaries. Criminal Law: Keyed to Johnson's Casebook on Criminal Law, 7th Edition. Eagan, MN: West Group. ISBN0-3141-4529-X. LCCN2003265465. OCLC56517350.
^Orr, H. Allen (May 30, 2005). "Devolution". The New Yorker (Condé Nast). Retrieved December 26, 2013. "Biologists aren't alarmed by intelligent design’s arrival in Dover and elsewhere because they have all sworn allegiance to atheistic materialism; they're alarmed because intelligent design is junk science."