In December 2005, Judge John E. Jones III ruled that a Dover, Pennsylvania, school district could not tell its biology students about a book in the school library that explained the theory of intelligent design. The judge based his decision on the testimony of expert witnesses — two philosophers, Robert Pennock and Barbara Forrest — who argued that the theory of intelligent design is not scientific by definition.1 Since it is not scientific, the judge reasoned, it must be religious. As he put it in his ruling, “Since ID is not science the conclusion is inescapable that the only real effect of the ID Policy is the advancement of religion.”2 Therefore, he ruled, telling students about the theory of intelligent design would violate the establishment clause of the U.S. Constitution.
Many people have heard about the theory of intelligent design only from news reports about the Dover trial in 2005.3 Naturally, such reports about the trial and the judge’s decision have strongly influenced public perceptions of the theory. For many people, if they know anything at all about the theory, they know — or think they know — that intelligent design is “religion masquerading as science.”
I encounter this perception nearly every time I speak about the evidence for intelligent design, whether on university campuses or in the media. When I present the evidence for intelligent design, critics do not typically try to dispute my specific empirical claims. They do not dispute that DNA contains specified information, or that this type of information always comes from a mind, or that competing materialistic theories have failed to account for the DNA enigma. Nor do they even dispute my characterization of the historical scientific method or that I followed it in formulating my case for intelligent design as the best explanation for the evidence. Instead, critics simply insist that intelligent design “is just not science,” sometimes even citing Judge Jones as their authority.
Since Jones is a lower-level district judge who entered the trial with no apparent background in either science or the history and philosophy of science, and since he made several clear factual errors4 in his ruling, it would be easy to dismiss his opinion. Jones rendered this response all the more tempting by telling one reporter, apparently in all seriousness, that during the trial he planned to watch the old Hollywood film Inherit the Wind for historical background.5 Inherit the Wind is a thinly veiled fictional retelling of the 1925 Scopes “Monkey Trial.” But as historian of science Edward Larson has shown in his Pulitzer Prize-winning Summer for the Gods, the drama is grossly misleading and historically inaccurate. Clearly, Jones had little, if any, relevant expertise from which to make a judgment about the merits or scientific status of intelligent design.
His opinion, however, reflected a much broader consensus among scientific and academic critics of intelligent design. Indeed, it was later discovered that Jones lifted more than 90 percent of his discussion of “Whether ID Is Science” in his lengthy opinion virtually verbatim from an American Civil Liberties Union brief submitted to him before his ruling. The ACLU brief, in turn, recapitulated the most common reasons for challenging the scientific status of intelligent design based upon the testimony of the ACLU’s own expert witnesses.6 Thus, the Jones opinion and the witnesses who influenced it effectively expressed an entrenched view common not only among members of the media, but within the scientific establishment at large.
But why isn’t the theory of intelligent design scientific? On what basis do critics of the theory make that claim? And is it justified?
1. A Matter of Definitions?
As a philosopher of science, I’ve always thought there was something odd and even disingenuous about the objection that intelligent design is not scientific. The argument shifts the focus from an interesting question of truth to a trivial question of definition. To say that an idea or theory does or does not qualify as science implies an accepted definition of the term by which to make that judgment. But to say that a claim about reality “is not science” according to some definition says nothing about whether the claim is true — unless it can be assumed that only scientific theories are true. A definition of science does not, by itself, tell us anything about the truth of competing statements, but only how to classify them (whether as scientific or something else, such as philosophical, historical, or religious statements).
So, at one level, I regarded the debate about whether intelligent design qualifies as science as essentially a semantic dispute, one that distracts attention from significant questions about what actually happened in the past to cause life to arise. Does life exhibit evidence of intelligent design or just apparent design? Did life arise by undirected processes, or did a designing intelligence play a role? Surely such questions are not settled by defining one of the competing hypotheses as “unscientific” and then refusing to consider it.
At another level, the debate is tacitly about the basis of the theory itself. Since the term “science” connotes a rigorous experimental or empirical method for studying nature, denying that an idea is scientific implies that rigorous empirical methods played no role in its formulation. To emphasize this impression, many critics of intelligent design insist that the theory is not testable and, for this reason, is neither rigorous nor scientific.7 Because many people assume that only “the” scientific method produces justified conclusions, the charge that the theory isn’t science seems to justify dismissing it as merely a subjectively based opinion or belief. The objection “ID isn’t science” is code for “It isn’t true,” “It’s disreputable,” and “There is no evidence for it.”
That is why the claim that intelligent design is not science — repeated often and with great presumed authority — has led many to reject it before considering the evidence and arguments for it. I realized that in order to make my case — and open minds to the evidence in favor of it — I needed to defend the theory of intelligent design against this charge. To do so, indeed to defend any theory against this charge and to do so with intellectual integrity, requires one to navigate some treacherous philosophical waters. To claim that intelligent design is science implicitly invokes a definition of science — some understanding of what science is. But which definition?
Because of my background, I knew that historians and philosophers of science — the scholars who study such questions — do not agree about how to define science.8 Many doubt there is even a single definition that can characterize all the different kinds of science. In the philosophy of science this is known as the “demarcation problem,” the problem of defining science and distinguishing (or “demarcating”) it from “pseudoscience,” metaphysics, history, religion, or other forms of thought or inquiry.
Typically philosophers of science have tried to define science and distinguish it from other types of inquiry (or systems of belief ) by studying the methods that scientists use to study nature. But that’s where the trouble started. As historians and philosophers of science studied the methods that scientists use, they realized that scientists in different fields use different methods.
This, incidentally, is why historians and philosophers of science are generally better qualified to adjudicate the demarcation question than scientific specialists — such as inorganic chemists, for example. As they say of the catcher in baseball, the philosopher and historian of science has a view of the whole field of play, meaning he or she is less likely to fall into the error of defining all of science by the practices used in one corner of the scientific world. I already had some inkling of this from my work as a geophysicist. I was aware that historical and structural geology use distinct (if partially overlapping) methods. But as I delved into the demarcation question, I discovered that different sciences use a wide variety of methods.
Some sciences perform laboratory experiments. Some do not. Some sciences name, classify, and organize natural objects; some sciences seek to discover natural laws; others seek to reconstruct past events. Some sciences seek to formulate causal explanations of natural phenomena. Some provide mathematical descriptions of natural phenomena. Some sciences construct models. Some explain general or repeatable phenomena by reference to natural laws or general theories. Some study unique or particular events and seek to explain them by reference to past (causal) events.
Some sciences test their theories by making predictions; some test their theories by assessing their explanatory power; some test their theories by assessing both explanatory power and predictive success. Some methods of scientific investigation involve direct verification; some employ more indirect methods of testing. Some test theories in isolation from competing hypotheses. Some test theories by comparing the predictive or explanatory success of competing hypotheses. Some branches of science formulate conjectures that cannot yet be tested at all. Some sciences study only what can be observed. Some sciences make inferences about entities that cannot be observed. Some sciences reason deductively; some inductively; some abductively. Some use all three modes of inference. Some sciences use the hypothetico-deductive method of testing. Some use the method of multiple competing hypotheses.
This diversity of methods has doomed attempts to find a single definition (or set of criteria) that accurately characterizes all types of science by reference to their methodological practices. Thus, philosophers of science now talk openly about the “demise” of attempts to demarcate or define science by reference to a single set of methods.9
To say that an idea, theory, concept, inference, or explanation is or isn’t scientific requires a particular definition of science. Yet if different scientists and philosophers of science could not agree about what the scientific method is, how could they decide what did and did not qualify as science? And how could I argue that the theory of intelligent design is scientific, if I could not say what I meant by “science”? Conversely, how could critics of intelligent design assert that intelligent design is not science without articulating the standard by which they made this judgment? How could any headway in this debate be made without an agreed-upon definition?
I discovered that though it was difficult to define science by reference to a single definition or set of methodological criteria, it was not difficult to define science in such a way that either acknowledged the diversity of methodological practices or refused to specify which method made a discipline scientific. Such an approach allows science to be defined more broadly as, for instance, “a systematic way of studying nature involving observation, experimentation, and/or reasoning about physical phenomena.” So far, so good. The difficulty has come when scholars tried to equate science with a particular systematic method of studying nature to the exclusion of other such methods.
The situation was not hopeless, however. I discovered that although it was impossible to describe the rich variety of scientific methods with a single definition, it was possible to characterize the methodological practices of specific disciplines or types of science. This made sense. It was precisely the diversity of scientific methods that made defining science as a whole difficult in the first place. Focusing on a single established scientific method as the relevant standard of judgment eliminated the practical problem of deciding how to assess the scientific status of a theory without an established definition of science. Furthermore, from my own studies, I knew the methodological practices of the sciences directly relevant to the questions I was pursuing — the sciences that investigate the causes of particular events in the remote past. Stephen Jay Gould called these sciences the historical sciences.10 I knew that the inference to design followed from a rigorous application of the logical and methodological guidelines of these disciplines. If one carefully follows these guidelines in constructing a case for design, one is entitled to conclude there is a good (if definition-dependent) reason to regard intelligent design as a scientific — and, specifically, historically scientific — theory. In fact, there are several such reasons.
Reason 1: The Case for ID Is Based on Empirical Evidence
The case for intelligent design, like other scientific theories, is based upon empirical evidence, not religious dogma. Contrary to the claims of Robert Pennock,11 one of the expert witnesses in the Dover trial, design theorists have developed specific empirical arguments to support their theory. To name just one example, I have developed an argument for intelligent design based on the discovery of digital information in the cell.12 In addition, other scientists now see evidence of intelligent design in the “irreducible complexity” of molecular machines and circuits in the cell,13 the pattern of appearance of the major groups of organisms in the fossil record,14 the origin of the universe and the fine-tuning of the laws and constants of physics,15 the finetuning of our terrestrial environment,16 the information processing system of the cell, and even in the phenomenon known as “homology” (evidence previously thought to provide unequivocal support for neo-Darwinism).17 Critics may disagree with the conclusions of these design arguments, but they cannot reasonably deny that they are based upon commonly accepted observations of the natural world. Since the term “science” commonly denotes an activity in which theories are developed to explain observations of the natural world, the empirical, observational basis of the theory of intelligent design provides a good reason for regarding intelligent design as a scientific theory.
Reason 2: Advocates of ID Use Established Scientific Methods
The case for intelligent design follows from the application of not one, but two separate systematic methods of scientific reasoning — methods that establish criteria for determining when observed evidence supports a hypothesis. The primary method, the method of multiple competing hypotheses, may be used to justify an inference to intelligent design as the best explanation for the origin of biological information. This method is a standard method of scientific reasoning in several well-established scientific disciplines. Advocates of intelligent design have also developed another method that complements the method of multiple competing hypotheses.
In The Design Inference (and in subsequent works), William Dembski established criteria by which intelligently designed systems can be identified by the kinds of patterns and probabilistic signatures they exhibit. On the basis of these criteria, Dembski developed a comparative evaluation procedure—his explanatory filter18 — to guide our analysis and reasoning about natural objects and artifacts and to help investigators decide among three different types of explanations: chance, necessity, and design.19 As such, it constitutes a rigorous, systematic, evidence-based method for detecting the effects of intelligence, again suggesting a good reason to regard intelligent design as scientific in accord with common definitions of the term. In more recent work, Dembski has collaborated with Robert Marks to show that Darwinian evolution cannot generate new biological information, but rather, insofar as it is operative in biology, is itself inherently teleological and derivative of an intelligent source characterizable in precise information-theoretic terms.20
Reason 3: ID Is a Testable Theory
Most scientists and philosophers of science think that the ability to subject theories to empirical tests constitutes an important aspect of any scientific method of study. But for a theory to be testable, there must be some evidential grounds by which it could be shown to be incorrect or inadequate. And, contrary to the repeated claims of its detractors, the theory of intelligent design is testable. In fact, it is testable in several interrelated ways.
First, like other scientific theories concerned with explaining events in the remote past, intelligent design is testable by comparing its explanatory power to that of competing theories. Darwin used this method of testing in On the Origin of Species. In the presentation of the case for intelligent design in my book Signature in the Cell, I tested the theory in exactly this way by comparing the explanatory power of intelligent design against that of several other classes of explanation. That the theory of intelligent design can explain the origin of biological information (and the origin of the cell’s interdependent information processing system) better than its materialistic competitors shows that it has passed an important scientific test.
This comparative process is not a hall of mirrors, a competition without an external standard of judgment. The theory of intelligent design, like the other historical scientific theories it competes against, is tested against our knowledge of the evidence in need of explanation and our knowledge of the cause-and-effect structure of the world. Evaluations of “causal adequacy” guide historical scientific reasoning and help to determine which hypothesis among a competing group of hypotheses has the best explanatory power. Considerations of causal adequacy provide an experience-based criterion by which to test — accept, reject, or prefer — competing historical scientific theories. When such theories cite causes that are known to produce the effect in question, they meet the test of causal adequacy; when they fail to cite such causes, they fail to meet this test.21
Since empirical considerations provide grounds for rejecting historical scientific theories or preferring one theory over another, such theories are clearly testable. Like other historical scientific theories, intelligent design makes claims about the causes of past events, thus making it testable against our knowledge of cause and effect. Moreover, because experience shows that an intelligent agent is not only a known, but also the only known cause of specified, digitally encoded information, the theory of intelligent design passes two critical tests: the tests of causal adequacy and causal existence as the explanation for any observed occurrence of such information. Precisely because intelligent design uniquely passes these tests, I argue that it stands as the best explanation for the origin of DNA.
Finally, though historical scientific theories typically do not make predictions that can be tested under controlled laboratory conditions, they do sometimes generate discriminating predictions about what we should find in the natural world — predictions that enable scientists to compare them to other historical scientific theories. The theory of intelligent design has generated a number of such discriminating empirical predictions. These predictions not only distinguish the theory of intelligent design from competing evolutionary theories; they also serve to confirm the design hypothesis rather than its competitors.22
Reason 4: The Case for ID Exemplifies Historical Scientific Reasoning
There is another good, if convention-dependent, reason for classifying intelligent design as a scientific theory. Not only do scientists use systematic methods to infer intelligent design; the specific methods they use conform closely to established patterns of inquiry in the historical scientific disciplines — disciplines that try to reconstruct the past and explain present evidence by reference to past causes rather than trying to classify or explain unchanging laws and properties of nature. Indeed, the theory of intelligent design and the patterns of reasoning used to infer and defend it exemplify each of the four key features of a historical science.
A Distinctive Historical Objective
Historical sciences focus on questions of the form, “What happened?” or “What caused this event or that natural feature to arise?” rather than questions of the form, “How does nature normally operate or function?” or “What causes this general phenomenon to occur?”23 Those who postulate the past activity of an intelligent designer do so as an answer, or as a partial answer, to distinctively historical questions. The theory of intelligent design attempts to answer a question about what caused certain features in the natural world to come into existence — such as the digitally encoded, specified information present in the cell. It attempts to answer questions of the form “How did this natural feature arise?” as opposed to questions of the form “How does nature normally operate or function?”
A Distinctive Form of Inference
The historical sciences use inferences with a distinctive logical form. Unlike many non-historical disciplines, which typically infer generalizations or laws from particular facts (induction), historical sciences employ abductive logic to infer a past event from a present fact or clue. Such inferences are also called “retrodictive.” As Gould put it, the historical scientist infers “history from its results.”24 Inferences to intelligent design exemplify this abductive and retrodictive logical structure. They infer a past unobservable cause (in this case, an instance of creative mental action or agency) from present facts or clues in the natural world, such as the specified information in DNA, the irreducible complexity of certain biological systems, and the finetuning of the laws and constants of physics.25
A Distinctive Type of Explanation
Historical sciences usually offer causal explanations of particular events, not law-like descriptions or theories describing how certain kinds of phenomena — such as condensation or nuclear fission — generally occur. In historical explanations, past causal events, not laws or general physical properties, do the main explanatory work.26 To explain a dramatic erosional feature in eastern Washington called the Channeled Scablands, a historical geologist posited an event: the collapse of an ice dam and subsequent massive flooding. This and other historical scientific explanations emphasize past events as causes for subsequent events and/or present features of the world.
The theory of intelligent design offers such a distinctively historical form of explanation. Theories of design invoke the act or acts of an agent and conceptualize those acts as causal events, albeit ones involving mental rather than purely physical entities. Advocates of design postulate past causal events (or a sequence of events) to explain the origin of present evidence or clues, just as proponents of chemical evolutionary theories do.
Use of the Method of Multiple Competing Hypotheses
Historical scientists do not mainly test hypotheses by assessing the accuracy of the predictions they make under controlled laboratory conditions. Using the method of multiple competing hypotheses, historical scientists test hypotheses by comparing their explanatory power against that of their competitors. And advocates of the theory of intelligent design also use this method.
In sum, the theory of intelligent design seeks to answer characteristically historical questions, it relies upon abductive/retrodictive inferences, it postulates past causal events as explanations of present evidence, and it is tested indirectly by comparing its explanatory power against that of competing theories. Thus, the theory of intelligent design exhibits each of the main features of a historical science, suggesting another reason to regard it as scientific.
Reason 5: ID Addresses a Specific Question in Evolutionary Biology
There is another closely related reason to regard intelligent design as a scientific theory. It addresses a key question that has long been part of historical and evolutionary biology: How did the appearance of design in living systems arise? Both Darwin and contemporary evolutionary biologists such as Francisco Ayala, Richard Dawkins, and Richard Lewontin acknowledge that biological organisms appear to have been designed.27 Nevertheless, for most evolutionary theorists, the appearance of design is considered illusory, because they are convinced that the mechanism of natural selection acting on random variations (and/or other similarly unguided mechanisms) can fully account for the appearance of design in living organisms.28
In On the Origin of Species, Darwin sought to show that natural selection has creative powers comparable to those of intelligent human breeders. In doing so, he sought to refute the design hypothesis by providing a materialistic explanation for the origin of the appearance of design in living organisms. Following Aleksandr Oparin, chemical evolutionary theorists have sought to provide similarly naturalistic accounts for the appearance of design in the simplest living cells.
Is the appearance of design in biology real or illusory? Clearly, there are two possible answers to this question. Neo-Darwinism and chemical evolutionary theory provide one answer, and the competing theory of intelligent design provides the opposite answer. By almost all accounts the classical Darwinian answer to this question — “The appearance of design in biology does not result from actual design” — has long been considered a scientific proposition. But what is the status of the opposite answer? If the proposition “Jupiter is made primarily of methane gas” is a scientific proposition, then the proposition “Jupiter is not made primarily of methane gas” would seem to be a scientific proposition as well. The negation of a proposition does not make it a different type of claim. Similarly, the claim “The appearance of design in biology does not result from actual design” and the claim “The appearance of design in biology does result from actual design” are not two different kinds of propositions; they are two different answers to the same question, a question that has long been part of evolutionary biology and historical science. If one of these propositions is scientific, then it would seem that the other is scientific as well.29
Reason 6: ID Is Supported by Peer-Reviewed Scientific Literature
Critics of the theory of intelligent design often claim that its advocates have failed to publish their work in peer-reviewed scientific publications. For this reason, they say the theory of intelligent design does not qualify as a scientific theory.30 According to these critics, science is what scientists do. Since ID scientists don’t do what other scientists do — namely, publish in peer reviewed journals — they are not real scientists and their theory isn’t scientific either.
Critics of the theory of intelligent design made this argument before and during the Dover trial in support of the ACLU’s case against the Dover school board policy. For example, Barbara Forrest, a philosophy professor from Southeastern Louisiana State University and one of the expert witnesses for the ACLU, asserted in a USA Today article before the trial that design theorists “aren’t published because they don’t have any scientific data.”31 In her expert witness report in support of the ACLU, Forrest also claimed that “there are no peer-reviewed ID articles in which ID is used as a biological theory in mainstream scientific databases such as MEDLine.”32 Judge Jones apparently accepted such assertions at face value. In his decision, he stated not once, but five separate times, that there were no peer-reviewed scientific publications supporting intelligent design.33
But Dr. Forrest’s carefully qualified statement gave an entirely misleading impression. In 2004, a year in advance of the trial, I published a peer-reviewed scientific article advancing the theory of intelligent design in a mainstream scientific journal. The publication of this article evoked a huge backlash at the Smithsonian Institution, where the journal, The Proceedings of the Biological Society of Washington, was published. Moreover, controversy about the editor’s decision and his subsequent treatment spilled over into both the scientific and the mainstream press, with articles about it appearing in Science, Nature, the Wall Street Journal, and the Washington Post, among other places.34 Both Dr. Forrest and Judge Jones had every opportunity to inform themselves about the existence of at least one peer-reviewed scientific article in support of intelligent design.
In any case, as my institute informed the court in an amicus curiae brief, my article was by no means the only peer-reviewed or peer-edited scientific publication in support of the theory of intelligent design.35 By 2005, scientists and philosophers advocating the theory of intelligent design had already developed their theory and the empirical case for it in peer-reviewed scientific books published both by trade presses36 and by university presses.37 Michael Behe’s groundbreaking Darwin’s Black Box was published by the Free Press in New York. William Dembski’s The Design Inference was published by Cambridge University Press. Both were peerreviewed. In addition, design proponents have also published scientific articles advancing the case for intelligent design in peer-reviewed scientific books and anthologies published by university presses38 and in scientific conference proceedings published by university presses and trade presses.39 Advocates of intelligent design have also published work advancing their theory in peer-reviewed philosophy of science journals and other relevant interdisciplinary journals.40 Moreover, since the publication of my article in 2004, several other scientific articles supporting intelligent design (or describing research guided by an ID perspective) have been published in mainstream peer-reviewed scientific journals.41
Of course, critics of intelligent design may still judge that the number of published books and articles supporting the theory does not yet make it sufficiently mainstream to warrant teaching students about it. Perhaps.42 But that is a judgment about educational policy distinct from deciding the scientific status, or still less, the merits of the theory of intelligent design itself. Clearly, there is no magic number of supporting peer-reviewed publications that suddenly confers the adjective “scientific” on a theory; nor is there a tribunal vested with the authority to make this determination. If there were a hard and-fast numerical standard as low as even one, no new theory could ever achieve scientific status. Each new theory would face an impossible catch-22: for a new theory to be considered “scientific” it must have appeared in the peerreviewed scientific literature, but any time a scientist submitted an article to a peer-reviewed science journal advocating a new theory, it would have to be rejected as “unscientific” on the grounds that no other peer-reviewed scientific publications existed supporting the new theory.
Critics of intelligent design have actually used a similarly circular kind of argument to claim that ID is not science. Before 2004, critics argued that the theory of intelligent design was unscientific, because there were no published articles supporting it in peer-reviewed scientific journals (ignoring the various peer-reviewed books that existed in support of ID). Then once a peer-reviewed scientific journal article was published supporting intelligent design, critics claimed that the article should not have been published, because the theory of intelligent design is inherently unscientific.43 Indeed, critics accused the editor who published my article of editorial malfeasance, because they thought he should never have considered sending the article out for peer review in the first place.44 Why? Because, according to these critics, the perspective of the article should have immediately disqualified it from consideration. In short, critics argued that “intelligent design is not scientific because peer-reviewed articles supporting the theory have not been published” and that “peer-reviewed articles supporting intelligent design should not be published because the theory is not scientific,” apparently never recognizing the patent circularity of this self-serving, exclusionary logic.
Logically, the issue of peer review is a red herring — a distracting procedural side issue. The truth of a theory is not determined or guaranteed by the place of, or procedures followed, in its publication.45 Many great scientific theories were first advanced and published without undergoing formal peer review. Though modern peer-review procedures often do a good job of catching and correcting factual mistakes, they also can enforce ideological conformity, stifle innovation, and resist novel theoretical insights. Scientific experts can make mistakes in judgment and, being human, they sometimes reject good new ideas because of prejudicial attachments to older, more familiar ones. The history of science is replete with examples of established scientists summarily dismissing new theories that later proved able to explain the evidence better than previously established theories. In such situations, proponents of new theories have often found traditional organs of publication closed to them. Thus, it is neither surprising nor damning to intelligent design that currently many scientific journals are implacably opposed to publishing articles supporting the theory.
Yet if science is what scientists do, and if publishing peer-reviewed scientific books and articles is part of what scientists do that makes their theories scientific (as critics of ID assert), then there is another good, convention-dependent reason to regard intelligent design as scientific. The scientists who have developed the case for intelligent design have begun to overcome the prejudice against their ideas and have published their work in peer-reviewed scientific journals, books, conference volumes, and anthologies.46
So we see that the issue of whether intelligent design qualifies as a scientific theory depends upon the definition of science chosen to decide the question. But consideration of both common definitions of science and the specialized methodological practice of the historical sciences has shown that there are many good — if definition-dependent — reasons for considering intelligent design as a scientific theory.
Maybe there is some other, better definition of science that should be considered; perhaps some specific feature of a scientific theory that intelligent design does not possess, or some specific criterion of scientific practice that its advocates do not follow. Intelligent design meets the criterion of testability, despite what many critics of the theory asserted, but perhaps there are other criteria that it cannot meet. If so, then perhaps these definitional criteria establish a good reason for disqualifying intelligent design from consideration as science after all. Certainly, many critics of intelligent design have argued that the theory lacks many key features of a bona fide scientific theory — that it fails to meet criteria by which science could be defined and distinguished from non-science, metaphysics, or religion. In light of this, we need to examine why critics of the theory — including the judge in the Dover case — have insisted that, despite the arguments just outlined, intelligent design does not qualify as a scientific theory.
2. Intelligent Design and Explanation by Natural Law
Michael Ruse has argued that “there are no powers, seen or unseen, that interfere with or otherwise make inexplicable the normal working of material objects.”47 Since the scientific enterprise is characterized by a commitment to “unbroken regularity” or “unbroken law,”48 scientific theories must explain events or phenomena by reference to natural laws.49 And since intelligent design invokes an event — the conscious activity of a designing agent — rather than a law of nature to explain the origin of biological form and information, Ruse argued that it was scientifically “inappropriate.” Ruse also seemed to think that if an intelligent designer had acted during the history of life, then its actions would have necessarily violated the laws of nature, since intelligent agents typically interfere with the otherwise “normal workings of material objects.” Since, for Ruse, the activity of an intelligent designer violates the laws of nature, positing such activity — rather than a law — would violate the rules of science.
In response,50 I have pointed out that the activity of a designing intelligence does not necessarily break or violate the laws of nature. Human agents design information-rich structures and otherwise interfere with the “normal workings of material objects” all the time. When they do, they do not violate the laws of nature; they alter the conditions upon which the laws act. When I arrange magnetic letters on a metallic display board to spell a message, I alter the way in which matter is configured, but I do not alter or violate the laws of electromagnetism. When agents act, they initiate new events within an existing matrix of natural law without violating those laws.51
I have also pointed out that Ruse’s key demarcation criterion, if applied strictly, cut just as much against Darwinian and chemical evolutionary theories (as well as many other scientific theories) as it did against intelligent design. For example, natural laws often describe but do not explain natural phenomena. Newton’s law of universal gravitation described, but did not explain, what caused gravitational attraction. A strict application of Ruse’s second criterion would therefore imply that Newton’s law of gravity is “unscientific,” since it does not offer an explanation by natural law.
Many historical scientific theories do not offer an explanation by natural law. Instead, they postulate past events (or patterns of events) to explain other past events as well as presently observable evidence. Historical theories explain mainly by reference to events or causes, not laws. For example, if a historical geologist seeks to explain what caused the unusual height of the Himalayas, he or she will cite particular events or factors that were present in the case of the Himalayan mountain-building episode that were not present in other such episodes. Knowing the laws of physics that describe the forces at work in all mountain-building events will not aid the geologist in accounting for the contrast between the Himalayas and other mountain ranges. To explain what caused the Himalayas to rise to such heights, the geologist does not need to cite a general law, but instead to give evidence of a distinctive set of past events or conditions.52 Evolutionary theories, in particular, often emphasize the importance of past events in their explanations.53 Aleksandr Oparin’s chemical evolutionary theory, for example, postulated a series of events (a scenario), not a general law, in order to explain how the first living cells arose.
Of course, past events and historical scenarios are assumed to take place in a way that obeys the laws of nature. Moreover, our knowledge of cause-and-effect relationships (which we can sometimes formulate as laws) will often guide the inferences that scientists make about what happened in the past and will influence their assessment of the plausibility of competing historical scenarios and explanations. Even so, many historical scientific theories make no mention of laws at all. Laws at best play only a secondary role in historical scientific theories. Instead, events play the primary explanatory role.
The theory of intelligent design exemplifies the same style of scientific explanation as other historical scientific theories. Intelligent design invoked a past event — albeit a mental event — rather than a law to explain the origin of life and the complexity of the cell. As in other historical scientific theories, our knowledge of cause and effect (“information habitually arises from conscious activity”) supports the inference to design. A law (conservation of information)54 also helps to justify the inference of an intelligent cause as the best explanation. Advocates of intelligent design use a law (“since there is no informational ‘free lunch,’ the origin of complex specified information always requires intelligent input”) to infer a past causal event, the act of a designing mind. But that act or event explains the evidence in question. Though laws play a subsidiary role in the theory, a past event (or events) explains the ultimate origin of biological information.
But if explaining events primarily by reference to prior events, rather than laws, does not disqualify other historical scientific theories, including evolutionary theories, from consideration as science, then by the same logic it should not disqualify the theory of intelligent design either. Oddly, in a discussion of population genetics—part of the explanatory framework of contemporary Darwinian theory—Ruse himself noted that “it is probably a mistake to think of modern evolutionists as seeking universal laws at work in every situation.”55 But if laws can play no role or only a subsidiary role in other historical theories, then why was it “inappropriate” for a law to play only a supportive role in the theory of intelligent design?
Conversely, if invoking a past event, rather than a law, made intelligent design unscientific, then by the same token it should make materialistic evolutionary theories unscientific as well. Either way, Ruse’s key criterion for scientific status does not provide a basis for discriminating the scientific status of the two types of theories. Both are equivalent in their capacity to meet Ruse’s definitional standard.
3. Defeaters Defeated
I have been thinking about the “intelligent design isn’t science” objection for a number of years now. As I have done so, I have come to a radical conclusion: not only were there many good — if convention-dependent — reasons for classifying intelligent design as a historical scientific theory, but there were no good — that is, non-question-begging — reasons to define intelligent design as unscientific. Typically those who argued that “intelligent design isn’t science” invoked various demarcation criteria. I have encountered numerous such arguments. Critics claim that intelligent design does not qualify as a scientific theory because: (1) it invokes an unobservable entity,56 (2) it is not testable,57 (3) it does not explain by reference to natural law,58 (4) it makes no predictions,59 (5) it is not falsifiable,60 (6) it cites no mechanisms,61 and (7) it is not tentative.62
As I studied these arguments I discovered a curious pattern. Invariably, if the critics applied their definitional criteria—such as observability, testability, or “must explain by natural law”— in a strict way, these criteria not only disqualified the design hypothesis from consideration as science; they also disqualified its chief rivals — other historical scientific theories — each of which invoked undirected evolutionary processes.
Conversely, I discovered that if these definitional criteria were applied in a less restrictive way — perhaps one that took into account the distinctive historical aspects of inquiry into the origin of life — then these criteria not only established the scientific bona fides of various rivals of intelligent design; they confirmed the scientific status of the design hypothesis as well. In no case, however, did these demarcation criteria successfully differentiate the scientific status of intelligent design and its competitors. Either science was defined so narrowly that it disqualified both types of theory, or it was defined so broadly that the initial reasons for excluding intelligent design (or its competitors) evaporated. If one theory met a specific criterion, then so did the other; if one theory failed to do so, then its rival also failed — provided the criteria were applied in an evenhanded and non-question-begging way. Intelligent design and its materialistic rivals were equivalent in their ability to meet various demarcation criteria or methodological norms. Given this methodological equivalence, and given that materialistic evolutionary theories were already widely regarded as scientific, I couldn’t see any reason to classify intelligent design as unscientific. The defeaters didn’t work.
Because these “defeaters” are used against intelligent design all the time, it’s important to see why they fail. So, in what follows, I examine some additional demarcation arguments that are commonly used against intelligent design. (I will not provide an exhaustive demonstration of this equivalence since that would require a book-length argument the details of which only philosophers of science could endure. For those with the requisite endurance, however, various materials are available.)63
According to critics of intelligent design, the unobservable character of a designing intelligence renders it inaccessible to empirical investigation and, therefore, makes it unscientific. For example, in 1993 biophysicist Dean Kenyon was removed from teaching his introductory biology class at San Francisco State University after he discussed his reasons for supporting intelligent design with his students. His department colleagues believed their actions against him were justified because they believed that he had been discussing an unscientific theory with his class. Some of Kenyon’s colleagues argued that the theory of intelligent design did not qualify as a scientific theory because it invoked an unobservable entity, in particular, an unseen designing intelligence. In making this argument, Kenyon’s colleagues assumed that scientific theories must invoke only observable entities. Since Kenyon discussed a theory that violated this convention, they insisted that neither the theory he discussed, nor he himself, belonged in the biology classroom.64
Others who defended the action of the biology department, such as Eugenie Scott of the National Center for Science Education, used a similar rationale. She insisted that the theory of intelligent design violated the rules of science because “you can’t put an omnipotent deity in a test tube (or keep it out of one).”65 Molecular biologist Fred Grinnell has similarly argued that intelligent design can’t be a scientific concept, because if something “can’t be measured, or counted, or photographed, it can’t be science.”66
But was that really the case? Does a reference to an unobservable entity provide a good reason for defining a theory as unscientific? Does my postulation of an unobservable intelligence make my case for intelligent design unscientific?
The answer to that question depends, again, upon how science is defined. If scientists (and all other relevant parties) decide to define science as an enterprise in which scientists can posit only observable entities in their theories, then clearly the theory of intelligent design would not qualify as a scientific theory. Advocates of intelligent design infer, rather than directly observe, the designing intelligence responsible for the digital information in DNA.
But this definition of science would render many other scientific theories, including many evolutionary theories of biological origins, unscientific by definition as well. Many scientific theories infer or postulate unobservable entities, causes, and events. Theories of chemical evolution invoke past events as part of the scenarios they use to explain how the modern cell arose. Insofar as these events occurred millions of years ago, they are clearly not observable today. Darwinian biologists, for their part, have long defended the putatively unfalsifiable nature of their claims by reminding critics that many of the creative processes to which they refer occur at rates too slow to observe in the present and too fast to have been recorded in the fossil record. Furthermore, the existence of many transitional intermediate forms of life, the forms represented by the nodes on Darwin’s famous branching tree diagram, are also unobservable.67 Instead, unobservable transitional forms of life are postulated to explain observable biological evidence — as Darwin himself explained. But how is this different from postulating the past activity of an unobservable designing intelligence to explain observable features of the living cell? Neither Darwinian transitional forms, neo-Darwinian mutational events, the “rapid branching” events of Stephen Jay Gould’s theory of punctuated equilibria, the events comprising chemical evolutionary scenarios, nor the past action of a designing intelligence are directly observable. With respect to direct observability, each of these theories is equivalent.
Thus, if the standard of observability is applied in a strict way, neither intelligent design nor any other theory of biological origins qualifies as a scientific theory. But let’s consider the flip side. What if the standard of observability is applied in a more flexible and, perhaps, realistic way? What if science is defined as an enterprise that examines the observable natural world, but does not necessarily explain empirical observations by reference to observable entities?
Does it make sense to define science in this more flexible way? It does. Many entities and events posited in scientific theories cannot be observed directly either in practice, or sometimes even in principle. Instead, scientists often infer the existence of unobservable entities in order to explain observable events, evidence, or phenomena. Physical forces, electromagnetic or gravitational fields, atoms, quarks, past events, subsurface geological features, biomolecular structures — all are unobservable entities inferred from observable evidence. In 2008, under the border between France and Switzerland, European scientists unveiled the Large Hadron Collider. This supercollider will enable physicists to “look” for various elementary particles, including the elusive Higgs boson. None of the particles they hope to find are observable in any direct sense. Instead, physicists try to detect them by the energetic signatures, traces, or decay products they leave behind.
Scientists in many fields detect unobservable entities and events by their effects. They often infer the unseen from the seen. Nevertheless, such entities and events are routinely considered to be part of scientific theories. Those who argue otherwise confuse the event or evidence in need of explanation (which in scientific investigations is nearly always observable in some way) with the event or entity doing the explaining (which often is not).
The presence of unobservable entities in scientific theories creates a problem for those who want to use observability as a demarcation criterion by which to disqualify intelligent design from consideration as scientific. Many theories that are widely acknowledged to be scientific invoke unobservable entities. But if these theories, which include materialistic theories of biological origins, can invoke unobservable entities or events to explain observable evidence and still qualify as scientific, then why can’t the theory of intelligent design do so as well?
3.2 Testability Revisited
I earlier mentioned that the theory of intelligent design is testable by empirical means. But for years, I have talked to people — scientists, theologians, philosophers, lawyers, journalists, callers on talk shows — who purport to know that the theory of intelligent design cannot be tested.68 Sometimes these critics say that intelligent design is untestable because the designing intelligence is unobservable, thus combining two demarcation criteria, observability and testability. Other times these critics assert that intelligent design cannot be tested because they assume that ID advocates must posit an omnipotent deity. And yet other critics say that intelligent design is untestable because the actions of intelligent agents (of any kind) are inherently unpredictable, and testability depends upon the ability to make predictions.
These common objections to the testability and thus the scientific status of intelligent design have dissuaded many people from even considering evidence for intelligent design. So what should we make of these demarcation arguments against intelligent design? Do they provide a good reason for denying that intelligent design is a scientific theory? Do they show, despite the considerations we have offered to the contrary, that intelligent design cannot be tested? Let’s take a closer look.
3.3 Unobservables and Testability
Robert Pennock, one of the witnesses in the Dover trial, argued that the unobservable character of a designing intelligence precludes the possibility of testing intelligent design scientifically because, as he explained, “science operates by empirical principles of observational testing; hypotheses must be confirmed or disconfirmed by reference to . . . accessible empirical data.”69 Eugenie Scott also seemed to argue that intelligent design cannot be tested because it invokes an unobservable entity. In the article I cited above, in which she defended the actions of Kenyon’s detractors at San Francisco State, Scott also linked the criterion of observability to testability. After saying, “You can’t put an omnipotent deity in a test tube,” she went on to say: “As soon as creationists invent a ‘theo-meter,’ maybe then we can test for miraculous intervention. You can’t (scientifically) study variables you can’t test, directly or indirectly.”70
In this version of the argument, critics insist that the unobservable character of a designing intelligence renders the theory inaccessible to empirical investigation, making it both untestable and unscientific. So both “observability” and “testability” are asserted as necessary to scientific status and the converse of one (unobservability) is asserted to preclude the possibility of the other (testability). Superficially this version of the argument seems a bit more persuasive than demarcation arguments that simply invoke observability by itself to disqualify design. Yet it does not stand up to close inspection either.
In the first place, there are many testable scientific theories that refer to unobservable entities. For example, during the race to elucidate the structure of the genetic molecule, both double helix and triple helix models were considered, since both could explain the X-ray images of DNA crystals.71 Although neither structure could be observed directly, the double helix of Watson and Crick eventually won out because it could explain other observations that the triple helix model could not. The inference to one unobservable structure (the double helix) was accepted because it was judged to possess greater explanatory power than its competitor.
Claims about unobservables are routinely indirectly tested against observable evidence in scientific experiments. In many fields of science the existence of an unobservable entity or event is inferred from the positive outcome of testing for the consequences that would result if that hypothesized entity or event (i.e., an unobservable) were accepted as actual, or by the explanatory power the postulation of such an entity or event provides when contrasted with competing hypotheses. Thus, many sciences infer to the best explanation — where the explanation presupposes the reality of an unobservable entity or event — including theoretical physics, geology, molecular biology, genetics, cosmology, psychology, physical and organic chemistry, and evolutionary biology.
Secondly, the historical sciences, in particular, commonly use indirect methods of testing, methods that involve assessing the causal powers of competing unobservable events to determine which would, if true, possess the greatest explanatory power. Notably, Darwin defended the scientific status of his theory by arguing that an assessment of the relative explanatory power of his theory of common descent — a theory about the unobservable past — was a perfectly legitimate and acceptable method of scientific testing.72
Finally, intelligent design is testable in precisely this fashion — by examining its explanatory power and comparing it to that of competing hypotheses. The unobservable intelligence postulated by the theory of intelligent design does not preclude tests of its existence as long as indirect methods of testing hypotheses — such as evaluating comparative explanatory power — are recognized as scientific. If, however, science is defined more narrowly so that only the direct observation of a causal factor counts as a confirmatory test of a causal hypothesis, then neither intelligent design nor a host of other theories qualify as scientific.
Either way, the theory of intelligent design and various evolutionary theories of origins are equivalent in their ability to meet the joint criteria of observability and testability. If critics of intelligent design construe these criteria as forbidding both the indirect testing of hypotheses postulating unobservables and inferences to the existence of such unobservables if such tests are favorable, then both intelligent design and its competitors fail to be scientific. On the other hand, if critics construe these criteria to allow inferences to, and indirect testing of, unobservable entities and events, then both intelligent design and many competing evolutionary theories qualify as scientific theories. Either way, these criteria fail to discriminate between intelligent design and many other theories that are already accepted as scientific, and so they fail to provide a good reason for disqualifying intelligent design from consideration as a scientific theory. What is sauce for the goose is sauce for the gander.
3.4 Testability, Omnipotence, and the Supernatural
Robert Pennock argues that there is something else about the unobservable designing intelligence posited by intelligent design that makes it untestable. Specifically, Pennock claims that intelligent design is untestable because it invokes an unobservable supernatural being with unlimited powers. He argues that since such a being has powers that could be invoked to “explain any result in any situation,” all events are consistent with the actions of such a being. Therefore, no conceivable event could disprove the hypothesis of intelligent design. As Ken Miller asserts, “The hypothesis of design is compatible with any conceivable data, [and] makes no testable predictions.”73
This argument fails for two reasons. First, it misrepresents the theory of intelligent design. The theory of intelligent design does not claim to detect a supernatural intelligence possessing unlimited powers. Though the designing agent responsible for life may well have been an omnipotent deity, the theory of intelligent design does not claim to be able to determine that. Because the inference to design depends upon our uniform experience of cause and effect in this world, the theory cannot determine whether or not the designing intelligence putatively responsible for life has powers beyond those on display in our experience. Nor can the theory of intelligent design determine whether the intelligent agent responsible for information in life acted from the natural or the “supernatural” realm. Instead, the theory of intelligent design merely claims to detect the action of some intelligent cause (with power, at least, equivalent to those we know from experience) and affirms this because we know from experience that only conscious, intelligent agents produce large amounts of specified information. The theory of intelligent design does not claim to be able to determine the identity or any other attributes of that intelligence, even if philosophical deliberation or additional evidence from other disciplines may provide reasons to consider, for example, a specifically theistic design hypothesis.74
Pennock’s argument also fails because the theory of intelligent design is subject to empirical testing and refutation. Indeed, intelligent design actually makes a much stronger claim than the caricature of it he critiqued during the trial. Pennock critiques the hypothesis that “an omnipotent deity could explain the origin of life.” But the theory of intelligent design actually advocated differs from that hypothesis since it does not merely affirm that intelligence constitutes a possible explanation of certain features of life. Instead, it asserts that intelligent design constitutes the best explanation of a particular feature of life because of what we know about the cause-and-effect structure of the world — specifically, because of what we know about what it takes to produce large amounts of specified information. For this reason, the design hypothesis is not “compatible with any conceivable data” or observations whatsoever.
If it were shown, for example, that the cause-and-effect structure of the world were different than what advocates of intelligent design claim — if, for example, someone successfully demonstrated that “large amounts of functionally specified information do arise from purely chemical and physical antecedents,” then my design hypothesis, with its strong claim to be the best (clearly superior) explanation of such phenomena, would fail. Intelligent design would remain as a merely possible explanation (much as chance does now). But the claim that intelligent design provides the best (most causally adequate) explanation for the origin of biological information would be refuted. Similarly, if it could be shown that key indicators of intelligence — such as specified information — were not present in living systems, the basis of the design hypothesis in its present strong form would evaporate. Thus, Pennock and Miller incorrectly portray the theory of intelligent design as being consistent with any empirical situation. The theory of intelligent design is, in fact, testable — just as we have argued.
3.5 Testability and Predictability
When critics of intelligent design are confronted with refutations of a particular demarcation argument, they typically shift their ground and formulate other arguments either by invoking a different demarcation criterion or by applying the original criterion in a more demanding way. For example, after explaining how intelligent design can be tested and how it does make certain kinds of predictions, I commonly hear the objection that the theory of intelligent design is not scientific because it cannot make other kinds of predictions. Critics correctly point out, for example, that we cannot predict with complete accuracy what intelligent agents will do since, presumably, intelligent agents possess the capacity to act of their own free volition. Since ID invokes the action of an unpredictable intelligent agent, and since scientific theories must make predictions, theories invoking the activity of intelligent agents are not scientific — or so the argument goes.
Yet standard materialistic theories of evolution (whether chemical or biological) do not make predictions of this kind either. Specifically, evolutionary theory does not make predictions about the future course of evolution. It makes no prediction about the kind of traits or species that random mutations and natural selection will produce in the future. As Ken Miller notes, “The outcome of evolution is not predictable.”75 Even so, most evolutionary biologists think that these theories are scientific—and for good (if convention-dependent) reasons. Evolutionary theories provide explanations of past events and present evidence, and they make predictions about the patterns of evidence that scientists should find in their future investigations, for example, of the genome or the fossil record.
In the same way, the theory of intelligent design does not make predictions about when (or whether) the designing intelligence responsible for life will act in the future. Yet it does explain past events and present evidence, and it also makes discriminating predictions about the kind of evidence scientists should find in their future investigations.76 Thus, neither type of origins theory qualifies as scientific if the “ability to generate predictions” is treated as a condition of scientific status and interpreted in a strict way, though both types of theories qualify as scientific if this criterion is equated with scientific status and interpreted in a more flexible way. As I studied the various demarcation arguments against intelligent design, I repeatedly found this same pattern. Invariably, the criteria that supposedly showed that intelligent design is inherently unscientific either disqualified both intelligent design and its materialistic rivals, or if the criteria were applied more flexibly, legitimated both types of theories — provided, that is, that the criteria were not applied in a question-begging way. Again, what was sauce for the goose was sauce for the gander.
As this pattern became more pronounced with each of the definitional criteria examined, I became more convinced that there was no good reason to exclude intelligent design from consideration as a scientific explanation for the origin of biological information. Since — by convention — materialistic theories of biological origin were considered scientific, and since the theory of intelligent design met various criteria of scientific status just as well as these rival theories, it seemed clear that the theory of intelligent design, by the same conventions, must be considered scientific as well.
Consider the case of so-called junk DNA — the DNA that does not code for proteins found in the genomes of both one-celled organisms and multicellular plants and animals. The theory of intelligent design and materialistic evolutionary theories (both chemical and biological) differ in their interpretation of so-called junk DNA. Since neo-Darwinism holds that new biological information arises as the result of a process of mutational trial and error, it predicts that nonfunctional DNA would tend to accumulate in the genomes of eukaryotic organisms (organisms whose cells contain nuclei). Since most chemical evolutionary theories also envision some role for chance interactions in the origin of biological information, they imply that non-functional DNA similarly would have accumulated in the first simple (prokaryotic) organisms — as a kind of remnant of whatever undirected process first produced functional information in the cell. For this reason, most evolutionary biologists concluded upon the discovery of non-protein-coding DNA that such DNA was “junk.” In their view, discovery of the non-protein-coding regions confirmed the prediction or expectation of naturalistic evolutionary theories and disconfirmed an implicit prediction of intelligent design.
As Michael Shermer argues, “Rather than being intelligently designed, the human genome looks more and more like a mosaic of mutations, fragmented copies, borrowed sequences, and discarded strings of DNA that were jerry-built over millions of years of evolution.”77 Or as Ken Miller argues: “The critics of evolution like to say that the complexity of the genome makes it clear that it was designed. … But there’s a problem with that analysis, and it’s a serious one. The problem is the genome itself: it’s not perfect. In fact, it’s riddled with useless information, mistakes, and broken genes. … Molecular biologists actually call some of these regions ‘gene deserts,’ reflecting their barren nature.”78 Or as philosopher of science Philip Kitcher puts it, “If you were designing the genomes of organisms, you would not fill them up with junk.”79
ID advocates advance a different view of non-protein-coding DNA.80 The theory of intelligent design predicts that most of the non-protein-coding sequences in the genome should perform some biological function, even if they do not direct protein synthesis. ID theorists do not deny that mutational processes might have degraded or “broken” some previously functional DNA, but we predict that the functional DNA (the signal) should dwarf the nonfunctional DNA (the noise), and not the reverse. As William Dembski explained and predicted in 1998: “On an evolutionary view we expect a lot of useless DNA. If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function.”81 The discovery in recent years that non-protein-coding DNA performs a diversity of important biological functions has confirmed this prediction. It also decisively refutes prominent critics of intelligent design—including Shermer, Miller, and Kitcher — who have continued to argue (each as recently as 2008) that the genome is composed of mostly useless DNA.82
Contrary to their claims, recent scientific discoveries have shown that the non-protein-coding regions of the genome direct the production of RNA molecules that regulate the use of the protein-coding regions of DNA. Cell and genome biologists have also discovered that these supposedly “useless” non-protein-coding regions of the genome: (1) regulate DNA replication,83 (2) regulate transcription,84 (3) mark sites for programmed rearrangements of genetic material,85 (4) influence the proper folding and maintenance of chromosomes,86 (5) control the interactions of chromosomes with the nuclear membrane (and matrix),87 (6) control RNA processing, editing, and splicing,88 (7) modulate translation,89 (8) regulate embryological development,90 (9) repair DNA,91 and (10) aid in immunodefense or fighting disease92 among other functions. In some cases, “junk” DNA has even been found to code functional genes.93 Overall, the non-proteincoding regions of the genome function much like an operating system in a computer that can direct multiple operations simultaneously.94 Indeed, far from being “junk,” as materialistic theories of evolution assumed, the non-protein-coding DNA directs the use of other information in the genome, just as an operating system directs the use of the information contained in various application programs stored in a computer. In any case, contrary to the often-heard criticism that the theory makes no predictions, intelligent design not only makes a discriminating prediction about the nature of “junk DNA,” recent discoveries about non-protein-coding DNA also confirm the prediction that it makes.95 In the appendix to my book, Signature in the Cell, I describe several other discriminating predictions that the theory of intelligent design makes.96 Despite this, many continue to assert the falsehood that ID is not testable.
4. Methodological Naturalism, or How Dover Was Decided
In light of the preceding discussion about the specific failure of demarcation arguments, how is it that a federal court in 2005 was able to determine that ID is not science? By what definition did the judge in the now famous Kitzmiller vs. Dover case use to make this determination?
As it turned out, Judge Jones did a clever thing. He didn’t reject intelligent design as science because it failed to meet a neutral definition of science or some methodological norm. At the urging of the ACLU, he circumvented the whole demarcation problem by defining science as the exclusion of intelligent design — only he didn’t call it that. Instead, following the ACLU’s expert witnesses and brief, he called the exclusionary principle “methodological naturalism.”97 He then equated science with adherence to that principle and rejected intelligent design because it violated it.
But what is the principle of methodological naturalism? Methodological naturalism asserts that to qualify as scientific, a theory must explain all phenomena by reference to purely material — that is, nonintelligent — causes. As philosopher Nancey Murphy explains, methodological naturalism forbids reference “to creative intelligence” in scientific theories.98
So, did the judge find a demarcation criterion or methodological norm that could discriminate between intelligent design and materialistic theories of evolution? Clearly, he did. If science is defined as Judge Jones defined it, intelligent design does not qualify as a scientific theory. But should science be defined that way? Did the judge offer a good reason for excluding intelligent design from consideration as science?
He did not. Instead, he provided an entirely arbitrary, circular, and question-begging justification for the exclusion of design. I knew, as did many other philosophers of science, that demarcation arguments based upon neutral methodological norms such as testability could not justify a prohibition against intelligent causes in science. The judge in the Dover case supposedly offered a reason for this prohibition, but his reason turned out to be just a restatement of the prohibition by another name. According to Judge Jones, the theory of intelligent design cannot be part of science because it violates the principle of methodological naturalism. But that principle turns out to be nothing more than the claim that intelligent causes — and thus the theory of intelligent design — must be excluded from science.99 According to this reasoning, intelligent design isn’t science because it violates the principle of methodological naturalism. And what is methodological naturalism? It is a rule prohibiting consideration of intelligent design within science.
Thus, despite appearances to the contrary, Judge Jones did not offer a good reason — a theoretically neutral norm or definition of science — by which to justify the exclusion of intelligent design from science. Instead, he simply asserted a prohibition against the consideration of intelligent design, invoked the same prohibition by another name, and then treated it as if it were a reason — a methodological principle — justifying the prohibition itself.
Fortunately we don’t look to federal judges to settle great questions of scientific and philosophical import. Did life arise as the result of purely undirected material causes or did intelligence play a role?100 Surely a court-promulgated definition of science, especially one so logically problematic as methodological naturalism, does not answer that question.101
No doubt Judge Jones felt justified in offering such a thin and circular justification for his definition of science because he knew many scientists agreed with him. And, indeed, the majority of scientists may well accept the principle of methodological naturalism. So, if science is what scientists do, and if many or most scientists do not think that hypotheses invoking intelligent causes have a place in their theories, then perhaps intelligent design doesn’t qualify as a scientific theory after all. According to this line of thinking, Judge Jones did not impose an arbitrary definition of science. Instead, his ruling merely expressed a preexisting consensus about proper scientific practice from within the scientific community. As the judge himself wrote in the ruling, methodological naturalism is simply a “centuries-old ground rule” of science.102
So why shouldn’t scientists continue to accept methodological naturalism as a strict rule governing scientific practice? Maybe we should just accept this convention and move on. Of course, some scientists may decide to do exactly that. But if they do, it’s important to recognize what that decision would and would not signify about the design hypothesis. Scientists who decide to define explanations involving creative intelligence as unscientific cannot then treat the failure of such hypotheses to meet their definition of science as a tacit refutation of, or reason to reject, such hypotheses. Why? It remains logically possible that an “unscientific” hypothesis (by the criterion of methodological naturalism) might constitute a better explanation of the evidence than the currently best “scientific” hypothesis. In light of the evidence discussed in this essay and presented in my book Signature in the Cell, I would contend that, whatever its classification, the design hypothesis provides a better explanation than any of its materialistic rivals for the origin of the specified information necessary to produce the first life. Reclassifying an argument does not refute it.
In any case, there is no compelling reason for the currently dominant convention among scientists to continue. Conventions are just that. Without a good reason for holding them, they may do nothing more than express an unexamined prejudice and block the path of inquiry. When good reasons for rejecting conventions come along, reasonable people will set them aside — and there are now good reasons to set this convention aside.
First, scientists have not always restricted themselves to naturalistic hypotheses, contrary to the claims of one of the expert witnesses in the Dover trial. Newton, for example, made design arguments within his scientific works, most notably in the Principia and in the Opticks. Louis Agassiz, a distinguished paleontologist and contemporary of Darwin, also made design arguments within his scientific works, insisting that the pattern of appearance in the fossil record strongly suggested “an act of mind.” Defenders of methodological naturalism can claim, at best, that it has had normative force during some periods of scientific history. But this concedes that canons of scientific method change over time — as, indeed, they do. From Newton until Darwin, design arguments were a common feature of scientific research. After Darwin, more materialistic canons of method came to predominate. Recently, however, this has begun to change as more scientists are becoming interested in the evidence for intelligent design.
Second, many scientific fields currently posit intelligent causes as scientific explanations. Design detection is already part of science. Archaeologists, anthropologists, forensic scientists, cryptographers, and others now routinely infer intelligent causes from the presence of information-rich patterns or structures or artifacts. Furthermore, astrobiologists looking for extraterrestrial intelligence (SETI) do not have a rule against inferring an intelligent cause. Instead, they are open to detecting intelligence, but have not had evidence to justify making such an inference. Thus, the claim that all scientific fields categorically exclude reference to creative intelligence is actually false.
Even some biologists now contest methodological naturalism. Granted, many evolutionary biologists accept methodological naturalism as normative within their discipline. Nevertheless, biologists intrigued by the design hypothesis reject methodological naturalism because it prevents them from considering a possibly true hypothesis. Indeed, a central aspect of the current debate over design is precisely about whether methodological naturalism should be regarded as normative for biology today. Most evolutionary biologists say it should remain normative; scientists advocating intelligent design disagree. But critics of intelligent design cannot invoke methodological naturalism to settle this debate about the scientific status of intelligent design, because methodological naturalism is itself part of what the debate is about.
Third, defining science as a strictly materialistic enterprise commits scientists to an unjustified — and possibly false — view of biological origins. It is at least logically possible that a personal agent — a conscious goal-directed intelligence—existed before the appearance of the first life on Earth. Moreover, as evidenced by the work of William Dembski and Robert Marks, or by our explanation of how intelligent design functions as a historical science using the method of multiple competing hypotheses, there are now rigorous scientific methods by which the activity of intelligent agents can be inferred or detected from certain kinds of effects. Thus, if a personal agent existed before the advent of life on Earth, then it is also at least possible that the activity of such an agent could be detected using one of these methods. In light of this, prohibitions against the design hypothesis in investigations of the origin of life amount to an assumption that no intelligence of any kind existed or could have acted prior to that event. But this assumption is entirely unjustified, especially given the absence of evidence for a completely materialistic account of abiogenesis.
Finally, allowing methodological naturalism to function as an absolute “ground rule” of method for all of science would have a deleterious effect on the practice of certain scientific disciplines, especially the historical sciences.103 In origin of life research, for example, methodological naturalism artificially restricts inquiry and prevents scientists from exploring and examining some hypotheses that might provide the most likely, best, or causally adequate explanations. To be a truth-seeking endeavor, the question that origin of life research must address is not, “Which materialistic scenario seems most adequate?” but rather, “What actually caused life to arise on Earth?” Clearly, one possible answer to that latter question is this: “Life was designed by an intelligent agent that existed before the advent of humans.” If one accepts methodological naturalism as normative, however, scientists may never consider this possibly true hypothesis. Such an exclusionary logic diminishes the significance of claiming theoretical superiority for any remaining hypothesis and raises the possibility that the best “scientific” explanation (by the lights of methodological naturalism) may not, all things considered, be the best explanation at all.
Scientific theory evaluation is an inherently comparative enterprise. Theories that gain acceptance in artificially constrained competitions can claim to be neither “best” nor “most probably true.” At most such theories can be considered “the best, or most probably true, among an artificially limited set of options.” Openness to the design hypothesis would seem necessary, therefore, to any fully rational historical biology — that is, to one that seeks the truth, “no holds barred.”104 A historical biology committed to following the evidence wherever it leads will not exclude hypotheses a priori because of their possible metaphysical implications. Instead, it will employ only metaphysically neutral criteria — such as causal adequacy — to evaluate competing hypotheses. Yet this more open (and arguably rational) approach would now seem to affirm the theory of intelligent design as the best, most causally adequate, scientific explanation for the origin of the information necessary to build the first living organism.105
- Arnaud, Phillipe, Chantal Goubely, Thierry Pe’Lissier, and Jean-Marc Deragon. “SINE Retroposons Can Be Used In Vivo as Nucleation Centers for De Novo Methylation.” Molecular and Cellular Biology 20 (2000): 3434–41.
- Ayala, Francisco. “Darwin’s Revolution.” In Creative Evolution?! edited by J. Campbell and J. Schopf, 4–5. Boston: Jones and Bartlett, 1994.
- Bartel, David. “MicroRNAs: Genomics, Biogenesis, Mechanism, and Function.” Cell 116 (2004): 281–97. Behe, Michael. Darwin’s Black Box: The Biochemical Challenge to Evolution. New York: Free Press, 1996.
- ———. “Self-Organization and Irreducibly Complex Systems: A Reply to Shanks and Joplin.” Philosophy of Science 67 (2000): 155–62.
- Behe, Michael, and D. W. Snoke. “Simulating Evolution by Gene Duplication of Protein Features That Require Multiple Amino Acid Residues.” Protein Science 13 (2004): 2651–64.
- Bell, C., A. G. West, and G. Felsenfeld. “Insulators and Boundaries: Versatile Regulatory Elements in the Eukaryotic Genome.” Science 291 (2001): 447–50.
- Bridgman, Percy W. Reflections of a Physicist. 2nd ed. New York: Philosophical Library, 1955.
- Burgess-Beusse, B., C. Farrell, M. Gaszner, M. Litt, V. Mutskov, F. Recillas-Targa, M. Simpson, A. West, and G. Felsenfeld. “The Insulation of Genes from External Enhancers and Silencing Chromatin.” Proceedings of the National Academy of Sciences USA 99 (2002): 16433–37.
- Campbell, John Angus, and Stephen C. Meyer, eds. Darwinism, Design and Public Education. East Lansing: Michigan State University Press, 2003.
- Chen, Ling-Ling, Joshua N. DeCerbo, and Gordon G. Carmichael. “Alu Element-Mediated Gene Silencing.” EMBO Journal (2008): 1–12.
- Collins, Robin. “Evidence for Fine-Tuning,” in Neil Manson, ed. God and Design: The Teleological Argument and Modern Science. New York: Routledge, 2003.
- Craig, William Lane. “Barrow and Tipler on the Anthropic Principle vs. Divine Design.” British Journal for the Philosophy of Science 38 (1988): 389–95.
- ———. “God, Creation and Mr. Davies.” British Journal for the Philosophy of Science 37 (1986): 163–75. Darwin, Charles. On the Origin of Species by Means of Natural Selection. A facsimile of the first edition, published by John Murray, London, 1859. Reprint, Cambridge, MA: Harvard University Press, 1964.
- ———. Life and Letters of Charles Darwin, Including an Autobiographical Chapter. Edited by Francis Darwin. 2 vols. New York: Appleton, 1898.
- Davison, John A. “A Prescribed Evolutionary Hypothesis,” Rivista di Biologia/Biology Forum 98 (2005): 155–66. Dawkins, Richard. The Blind Watchmaker: Why the Evidence Reveals a Universe Without Design. New York: Norton, 1987.
- Dembski, William. “Intelligent Science and Design.” First Things 86 (1998): 21–27.
- ———. The Design Inference: Eliminating Chance Through Small Probabilities. Cambridge: Cambridge University Press, 1998.
- ———. ed. Mere Creation: Science, Faith and Intelligent Design. Downers Grove, IL:
- ———. “Specification: The Pattern That Signifies Intelligence.” Philosophia Christi (2005): 299–343. http://www.designinference.com/documents/2005.06.Specification.pdf.
- Dembski, William A., and Robert J. Marks II. “The Conservation of Information: Measuring the Information Cost of Successful Search.” Transactions on Systems, Man and Cybernetics, Part A. http://ieeexplore.ieee. org/xpl/RecentIssue.jsp?puNumber=3468/. Forthcoming.
- ———. “The Search for a Search: Measuring the Information Cost of Higher Level Search.” The International Journal of Information Technology and Intelligent Computing (2008). http://itic.wshe.lodz.pl/.
- Dembski, William A., and Michael Ruse, eds. Debating Design: From Darwin to DNA. Cambridge: Cambridge University Press, 2004.
- DeWolf, David K., John West, and Casey Luskin. “Intelligent Design Will Survive Kitzmiller v. Dover.” Montana Law Review 68 (2007): 7–57.
- DeWolf, David K., John G. West, Casey Luskin, and Jonathan Witt. Traipsing into Evolution: Intelligent Design and the Kitzmiller vs. Dover Decision. Seattle, WA: Discovery Institute Press, 2006.
- Discovery Institute. Brief of Amicus Curiae (Revised). In Kitzmiller v. Dover, 400 F.Supp. 707 (M.D.Pa. 2005), 17. http://www.discovery.org/f/646. Appendix A, http://www.discovery.org/f/647.
- Donnelly, S. R., T. E. Hawkins, and S. E. Moss. “A Conserved Nuclear Element with a Role in Mammalian Gene Regulation.” Human Molecular Genetics 8 (1999): 1723–28.
- Dunlap, K. A., M. Palmarini, M. Varela, R. C. Burghardt, K. Hayashi, J. L. Farmer, and T. E. Spencer. “Endogenous Retroviruses Regulate Periimplantation Placental Growth and Differentiation.” Proceedings of the National Academy of Sciences USA 103 (2006): 14390–395.
- Dunn, C. A., P. Medstrand, and D. L. Mager. “An Endogenous Retroviral Long Terminal Repeat Is the Dominant Promoter for Human B1,3-galactosyltransferase 5 in the Colon.” Proceedings of the National Academy of Sciences USA 100 (2003):12841–846.
- ENCODE Project Consortium. “Identification and Analysis of Functional Elements in 1% of the Human Genome by the ENCODE Pilot Project.” Nature 447 (2007): 799–816.
- Figueiredo, L. M., L. H. Freitas-Junior, E. Bottius, J.-C. Olivo-Marin, and A. Scherf. “A Central Role for Plasmodium Falciparum Subtelomeric Regions in Spatial Positioning and Telomere Length Regulation.” EMBO Journal 21 (2002): L815–24.
- Forrest, Barbara. Expert Witness Report. Kitzmiller v. Dover, 45. http://www2.ncseweb.org/kvd/ experts/2005_04_01_Forrest_expert_report_P.pdf.
- Forrest, Barbara, and Paul R. Gross. Creationism’s Trojan Horse: The Wedge of Intelligent Design. New York: Oxford University Press, 2004.
- Giles, Jim. “Peer-Reviewed Paper Defends Theory of Intelligent Design.” Nature 431 (2004): 114.
- Goh, S.-H., Y. T. Lee, N. V. Bhanu, M. C. Cam, R. Desper, B. M. Martin, R. Moharram, R. B. Gherman, and J. L. Miller. “A Newly Discovered Human Alpha Globin Gene.” Blood DOI 10.1182/blood-2005–03–0948.
- Gonzalez, Guillermo, and Jay W. Richards. The Privileged Planet: How Our Place in the Cosmos Was Designed for Discovery. Washington, DC: Regnery, 2004.
- Goodrich, J. A., and J. F. Kugel. “Non-coding-RNA Regulators of RNA Polymerase II Transcription.” Nature Reviews Molecular and Cell Biology 7 (2006): 612–16.
- Gould, Stephen J. “Evolution and the Triumph of Homology: Or, Why History Matters.” American Scientist 74 (1986): 60–69.
- Grawunder, U., M. Wilm, X. Wu, P. Kulesza, T. E. Wilson, M. Mann, and M. R. Lieber. “Activity of DNA Ligase IV Stimulated by Complex Formation with XRCC4 Protein in Mammalian Cells.” Nature 388 (1997): 492–95.
- Green, David G. “The Role of Translocation and Selection in the Emergence of Genetic Clusters and Modules.” Artificial Life 13 (2007): 249–58.
- Grinnell, Fred. “Radical Intersubjectivity: Why Naturalism Is an Assumption Necessary for Doing Science.” In Darwinism: Science or Philosophy? edited by Jon Buell and Virginia Hearn, 99–105. Richardson, TX: Foundation for Thought and Ethics, 1994.
- Han, Jeffrey S., Suzanne T. Szak, and Jef D. Boeke. “Transcriptional Disruption by the L1 Retrotransposon and Implications for Mammalian Transcriptomes.” Nature 429 (2004): 268–74.
- Henikoff, Steven. “Heterochromatin Function in Complex Genomes.” Biochimica et Biophysica Acta 1470 (2000): 01–08.
- Henikoff, Steven, Kami Ahmad, and Harmit S. Malik. “The Centromere Paradox: Stable Inheritance with Rapidly Evolving DNA.” Science 293 (2001): 1098–1102.
- Holden, Constance. “Random Samples.” Science 305 (2004): 1709.
- Hull, David L. Darwin and His Critics. Chicago: University of Chicago Press, 1973.
- Hyslop, L., M. Stojkovic, L. Armstrong, T. Walter, P. Stojkovic, S. Przyborski, M. Herbert, A. Murdoch, T. Strachan, and M. Lakoa. “Downregulation of NANOG Induces Differentiation of Human Embryonic Stem Cells to Extraembryonic Lineages.” Stem Cells 23 (2005): 1035–43.
- Janowski, Bethany, A., K. E. Huffman, J. C. Schwartz, R. Ram, D. Hardy, D. S. Shames, J. D. Minna, and D. R. Corey. “Inhibiting Gene Expression at Transcription Start Sites in Chromosomal DNA with Antigene RNAs.” Nature Chemical Biology 1 (2005): 216–22.
- Jones, Judge John E., III. Decision in Kitzmiller et al. v. Dover Area School Board. N0.04cv2688, 2005 WL 2465563, *66 (M.D.Pa. Dec. 20, 2005). http://www.pamd.uscourts.gov/kitzmiller/kitzmiller_342.pdf.
- ———. Kitzmiller et al. v. Dover Area School District. 400 F.Supp.2d 707, 745 (M.D.Pa. 2005).
- Jordan, I. K., I. B. Rogozin, G. V. Glazko, and E. V. Koonin. “Origin of a Substantial Fraction of Human Regulatory Sequences from Transposable Elements.” Trends in Genetics 19 (2003): 68–72.
- Judson, Horace Freeland. The Eighth Day of Creation: Makers of the Revolution in Biology. Exp. ed. Plainview, NY: Cold Spring Harbor Laboratory Press, 1996.
- Jurka, Jerzy. “Evolutionary Impact of Human Alu Repetitive Elements.” Current Opinion in Genetics and Development 14 (2004): 603–8.
- Kandouz, M., A. Bier, G. D. Carystinos, M. A. Alaoui-Jamali, and G. Batist. “Connexin43 Pseudogene Is Expressed in Tumor Cells and Inhibits Growth.” Oncogene 23 (2004): 4763–70.
- Kitcher, Philip. Living with Darwin: Evolution, Design, and the Future of Faith. New York: Oxford University Press, 2007.
- Klinghoffer, David. “The Branding of a Heretic.” Wall Street Journal, January 28, 2005, national edition, W11.
- Kondo-Iida, E., K. Kobayashi, M. Watanabe, J. Sasaki, T. Kumagai, H. Koide, K. Saito, M. Osawa, Y. Nakamura, and T. Toda. “Novel Mutations and Genotype–Phenotype Relationships in 107 Families with Fukuyama-Type Congenital Muscular Dystrophy (FCMD).” Human Molecular Genetics 8 (1999): 2303–9.
- Laudan, Larry. “The Demise of the Demarcation Problem.” In But Is It Science? edited by Michael Ruse, 337–50. Buffalo, NY: Prometheus, 1988.
- ———. Beyond Positivism and Relativism: Theory, Method, and Evidence. Boulder, CO: Westview, 1996. Lev-Maor, G., et al. “The Birth of an Alternatively Spliced Exon: 3′ Splice-Site Selection in Alu Exons.” Science 300 (2003): 1288–91.
- Li, Long-Cheng, S. T. Okino, H. Zhao, H., D. Pookot, R. F. Place, S. Urakami, H. Enokida, and R. Dahiya. “Small dsRNAs Induce Transcriptional Activation in Human Cells.” Proceedings of the National Academy of Sciences USA 103 (2006): 17337–342.
- Lipton, Peter. Inference to the Best Explanation. London and New York: Routledge, 1991.
Lönnig, Wolf-Ekkehard, and Heinz Saedler. “Chromosome Rearrangements and Transposable Elements.” Annual Review of Genetics 36 (2002): 389–410.
- Luskin, Casey. “Will Americans United Retract Their Demonstrably False Claims?” http://www.opposingviews.com/counters/will-americans-united-retract-theirdemonstrably-false-claims.
- Mariño-Ramírez, L., K. C. Lewis, D. Landsman, and I. K. Jordan. “Transposable Elements Donate LineageSpecific Regulatory Sequences to Host Genomes.” Cytogenetic and Genome Research 110 (2005): 333–41.
- Mattick, John S., and Michael J. Gagen. “The Evolution of Controlled Multitasked Gene Networks: The Role of Introns and Other Noncoding RNAs in the Development of Complex Organisms.” Molecular Biology and Evolution 18 (2001): 1611–30.
- Mattick, John S., and I. V. Makunin. “Small Regulatory RNAs in Mammals.” Human Molecular Genetics 14 (2005): R121–32.
- ———. “Non-coding RNA.” Human Molecular Genetics 15 (2006): R17–29.
- McKenzie, Richard W., and Mark D. Brennan. “The Two Small Introns of the Drosophila Affinidisjuncta Adh Gene Are Required for Normal Transcription.” Nucleic Acids Research 24 (1996): 3635–42.
- Medstrand, P., J. R. Landry, and D. L. Mager. “Long Terminal Repeats Are Used as Alternative Promoters for the Endothelin B Receptor and Apolipoprotein C-I Genes in Humans.” Journal of Biological Chemistry 276 (2001): 1896–1903.
- Meyer, Stephen C. Of Clues and Causes: A Methodological Interpretation of Origin of Life Studies. Ph.D. dissertation. Cambridge University, 1990.
- ———. “A Scopes Trial for the ’90s.” Wall Street Journal, December 6, 1993, A14.
- ———. “Open Debate on Life’s Origin.” Insight, February 21, 1994, 27–29.
- ———. “Laws, Causes and Facts: A Response to Michael Ruse.” In Darwinism: Science or Philosophy? edited by Jon Buell and Virginia Hearn, 29–40. Richardson, TX: Foundation for Thought and Ethics, 1994.
- ———. “The Return of the God Hypothesis.” Journal of Interdisciplinary Studies 11 (1999): 1–38. ———. “DNA and the Origin of Life: Information, Specification and Explanation.” In Darwinism, Design and Public Education, edited by John Angus Campbell and Stephen C. Meyer, 223–85. East Lansing: Michigan State University Press, 2003.
- ———. “The Cambrian Information Explosion: Evidence for Intelligent Design.” In Debating Design: From Darwin to DNA, edited by W. Dembski and M. Ruse, 371–91. Cambridge: Cambridge University Press, 2004.
- ———. “The Origin of Biological Information and the Higher Taxonomic Categories.” Proceedings of the Biological Society of Washington 117 (2004): 213–39.
- ———. Signature in the Cell: DNA and the Evidence for Intelligent Design. San Francisco: HarperOne, 2009.
- Miller, Kenneth R. Finding Darwin’s God: A Scientist’s Search for Common Ground Between God and Evolution. New York: HarperCollins, 1999.
- ———. Only a Theory: Evolution and the Battle for America’s Soul. New York: Viking, 2008.
- Minnich, Scott A., and Stephen C. Meyer. “Genetic Analysis of Coordinate Flagellar and Type III Regulatory Circuits in Pathogenic Bacteria.” In Design and Nature II:Comparing Design in Nature with Science and Engineering, edited by M. W. Collins and C. A. Brebbia, 295–304. Southampton: Wessex Institute of Technology, 2004.
- Morrish, Tammy A., Nicolas Gilbert, Jeremy S. Myers, Bethaney J. Vincent, Thomas D. Stamato, Guillermo E. Taccioli, Mark A. Batzer, and John V. Moran. “DNA Repair Mediated by Endonuclease-Independent LINE-1 Retrotransposition.” Nature Genetics 31 (2002): 159–65.
- Mura, M., P. Murcia, M. Caporale, T. E. Spencer, K. Nagashima, A. Rein, and M. Palmarini. “Late Viral Interference Induced by Transdominant Gag of an Endogenous Retrovirus.” Proceedings of the National Academy of Sciences USA 101 (2004): 11117–122.
- Murphy, Nancey. “Phillip Johnson on Trial: A Critique of His Critique of Darwin.” Perspectives on Science and Christian Faith 45 (1993): 26–36.
- Nagel, Thomas. “Public Education and Intelligent Design.” Philosophy and Public Affairs 36 (2008): 187–205. National Academy of Sciences. Science and Creationism: A View from the National Academy of Sciences. 2nd ed. Washington, DC: National Academy Press, 1999.
- Nelson, Paul, and Jonathan Wells. “Homology in Biology: Problem for Naturalistic Science and Prospect for Intelligent Design.” In Darwinism, Design and Public Education, edited by John Angus Campbell and Stephen C. Meyer, 303–22. East Lansing: Michigan State University Press, 2003.
- Pagano, A. M. Castelnuovo, F. Tortelli, R. Ferrari, G. Dieci, and R. Cancedda. “New Small Nuclear RNA Gene-like Transcriptional Units as Sources of Regulatory Transcripts.” PLoS Genetics 3 (2007): e1.
- Pardue, M.-L., and P. G. DeBaryshe. “Drosophila Telomeres: Two Transposable Elements with Important Roles in Chromosomes.” Genetica 107 (1999): 189–96.
- Peaston, E., A. V. Evsikov, J. H. Graber, W. N. de Vries, A. E. Holbrook, D. Solter, and B. B. Knowles. “Retrotransposons Regulate Host Genes in Mouse Oocytes and Preimplantation Embryos.” Developmental Cell 7 (2004): 597–606.
- Pennock, Robert. Expert Witness Report. Kitzmiller v. Dover. 400 F.Supp.2d 707 (M.D.Pa. 2005), 20. https://www.msu.edu/~pennock5/research/papers/Pennock_DoverExptRpt.pdf.
- Piehler, A. P., M. Hellum, J. J. Wenzel, E. Kaminski, K. B. Haug, P. Kierulf, and W. E. Kaminski. “The Human ABC Transporter Pseudogene Family: Evidence for Transcription and Gene-Pseudogene Interference.” BMC Genomics 9 (2008): 165.
- Powell, Michael. “Editor Explains Reasons for ‘Intelligent Design’ Article.” Washington Post, August 19, 2005, district edition. http://www.washingtonpost.com/wp-dyn/content/article/2005/08/18/AR2005081801680_pf.html.
- Ratliff, Evan. “The Crusade Against Evolution.” Wired, October 2004. http://www.wired.com/wired/archive/12.10/evolution.html.
- Riordan, Michael. “Stringing Physics Along.” Physics World 20 (2007): 38–39.
- Rubin, C. M., R. H. Kimura, and C. W. Schmid. “Selective Stimulation of Translational Expression by Alu RNA.” Nucleic Acids Research 30 (2002): 3253–61.
- Ruse, Michael. Darwinism Defended: A Guide to the Evolution Controversies. London: Addison-Wesley, 1982. ———. “A Philosopher’s Day in Court.” In But Is It Science? edited by Michael Ruse, 13–38. Buffalo, NY: Prometheus, 1988.
- ———. “Witness Testimony Sheet: McLean v. Arkansas.” In But Is It Science? edited by Michael Ruse, 287–306. Buffalo, NY: Prometheus, 1988.
- ———. “Darwinism: Philosophical Preference, Scientifi c Inference and Good Research Strategy.” In Darwinism: Science or Philosophy? edited by Jon Buell and Virginia Hearn, 21–28. Richardson, TX: Foundation for Thought and Ethics, 1994.
- Schueler, Mary G., Anne W. Higgins, M. Katharine Rudd, Karen Gustashaw, Huntington F. Willard, “Genomic and Genetic Definition of a Functional Human Centromere.” Science, 294 (2001): 109–15.
- Scott, Eugenie C. “Keep Science Free from Creationism.” Insight, February 21, 1994, 30.
- Scriven, Michael. “Truisms as the Grounds for Historical Explanations.” In Theories of History, edited by P. Gardiner. Glencoe, IL: Free Press, 1959.
- ———. “Explanation and Prediction in Evolutionary Theory.” Science 130 (1959): 477–82.
- ———. “Causes, Connections, and Conditions in History.” In Philosophical Analysis and History, edited by W. Dray, 238–64. New York: Harper & Row, 1966.
- ———. “Causation as Explanation.” Nous 9 (1975): 3–15.
- Shermer, Michael. Why Darwin Matters: The Case Against Intelligent Design. New York: Times/Holt, 2006 Skoog, Gerald. “A View from the Past.” Bookwatch Reviews 2 (1989): 1–2.
- Sober, Elliott “What Is Wrong with Intelligent Design?” Quarterly Review of Biology, 82 (2007): 3–8.
- Tam, O. H., A. A. Aravin, P. Stein, A. Girard, E. P. Murchison, S. Cheloufi, E. Hodges, M. Anger, R. Sachidanandam, R. M. Schultz, and G. J. Hannon. “Pseudogene-Derived Small Interfering RNAs Regulate Gene Expression in Mouse Oocytes.” Nature 453 (2008): 534–38.
- Thaxton, Charles, Walter L. Bradley, and Roger L. Olsen. The Mystery of Life’s Origin: Reassessing Current Theories. New York: Philosophical Library, 1984.
- Tremblay, A., M. Jasin, and P. Chartrand. “A Double-Strand Break in a Chromosomal LINE Element Can Be Repaired by Gene Conversion with Various Endogenous LINE Elements in Mouse Cells.” Molecular and Cellular Biology 20 (2000): 54–60.
- Van de Lagemaat, L. N., J. R. Landry, D. L. Mager, and P. Medstrand. “Transposable Elements in Mammals Promote Regulatory Variation and Diversification of Genes with Specialized Functions.” Trends in Genetics 19 (2003): 530–36.
- Vergano, Dan, and Greg Toppo. “‘Call to Arms’ on Evolution.” USA Today, March 23, 2005. http://www. usatoday.com/news/education/2005–03–23-evolution_x.htm.
- Voie, Albert. “Biological Function and the Genetic Code Are Interdependent,” Chaos, Solutions and Fractals 28 (2006): 1000–4.
- Von Sternberg, Richard. “On the Roles of Repetitive DNA Elements in the Context of a Unified GenomicEpigenetic System.” Annals of the New York Academy of Sciences 981 (2002): 154–88.
- Von Sternberg, Richard, and James A. Shapiro. “How Repeated Retroelements Format Genome Function.” Cytogenetic and Genome Research 110 (2005): 108–16.
- Wallis, Claudia. “The Evolution Wars.” Time, August 7, 2005. http://www.time.com/time/magazine/article /0,9171,1090909,00.html.
- Watanabe T., Y. Totoki, A. Toyoda, M. Kaneda, S. Kuramochi-Miyagawa, Y. Obata, H. Chiba, Y. Kohara, T. Kono, T. Nakano, M.A. Surani, Y. Sakaki, and H. Sasaki. “Endogenous siRNAs from Naturally Formed dsRNAs Regulate Transcripts in Mouse Oocytes.” Nature 453 (2008): 539–43.
- Wells, Jonathan. “Using Intelligent Design Theory to Guide Scientific Research.” Progress in Complexity, Information, and Design (November 2004): 3.1.2.
- ———. “Do Centrioles Generate a Polar Ejection Force?” Rivista di Biologia/Biology Forum 98 (2005): 37–62.
- Wilgoren, Jodi. “Politicized Scholars Put Evolution on the Defensive.” New York Times, August 21, 2005, national edition. http://www.nytimes.com/2005/08/21/national/21evolve.html.
- Worden, Amy. “Bad Frog Beer to ‘Intelligent Design’: The Controversial Ex-Pa. Liquor Board Chief Is Now U.S. Judge in the Closely Watched Trial.” Philadelphia Inquirer, October 16, 2005.
- West, John G., and David K. DeWolf. “A Comparison of Judge Jones’s Opinion in Kitzmiller v. Dover with Plaintiffs’ Proposed ‘Findings of Fact and Conclusions of Law.’”
- Wilson, Edward O. “Intelligent Evolution: The Consequences of Charles Darwin’s ‘One Long Argument.’” Harvard Magazine (November-December 2005): 29–33.
- Wilson, T. E., U. Grawunder, and M. R. Liebe. “Yeast DNA Ligase IV Mediates Non-Homologous DNA End Joining.” Nature 388 (1997): 495–98.