•Science Education and Religion: Holding the Center
Jon Miller and Robert T. Pennock
Science Education and Secular Values: A Special Supplement to Religion in the News.  Summer/Fall. (2007, pp. 4, 9-10) [pdf]

•Investigating the Emergence of Phenotypic Plasticity in Evolving Digital Organisms
Jeff Clune, Charles Ofria, Robert T. Pennock
In Almeida e Costa, F., Rocha, L.M., Costa, E., Harvey, I. and Coutinho, A., Advances in Artificial Life.  Berlin: Springer.  (2007, pp. 74-83). [pdf]

Abstract: In the natural world, individual organisms can adapt as their environment changes. In most in silico evolution, however, individual
organisms tend to consist of rigid solutions, with all adaptation occurring at the population level. If we are to use artificial evolving systems as a tool in
understanding biology or in engineering robust and intelligent systems, however, they should be able to generate solutions with fitness-enhancing
phenotypic plasticity. Here we use Avida, an established digital evolution system, to investigate the selective pressures that produce phenotypic plasticity.
We witness two different types of fitness-enhancing plasticity evolve: static-execution-flow plasticity, in which the same sequence of actions produces
different results depending on the environment, and dynamic-execution-flow plasticity, where organisms choose their actions based on their environment. We
demonstrate that the type of plasticity that evolves depends on the environmental challenge the population faces. Finally, we compare our results
to similar ones found in vastly different systems, which suggest that this phenomenon is a general feature of evolution.

• Learning Evolution and the Nature of Science using Evolutionary Computing and Artificial Life
McGill Journal of Education (Vol. 42, No. 2, pp. 211-224, 2007) [pdf]

Abstract: Because evolution in natural systems happens so slowly, it is difficult to design inquiry-based labs where students can experiment and observe evolution in the way they can when studying other phenomena. New research in evolutionary computation and artificial life provides a solution to this problem. This paper describes a new A-Life software environment – Avida-ED – in which undergraduate students can test evolutionary hypotheses directly using digital organisms that evolve on their own through the very mechanisms that Darwin discovered.

• Biology and Religion.
In Ruse, Michael and David Hull (eds.) Cambridge Companion to Philosophy of Biology. Cambridge Univ. Press. (2007, pp. 410-428)

• How Not to Teach the Controversy about Creationism
In Jones, Leslie S. and Michael J. Reiss (eds.) Teaching About Scientific Origins While Taking Account of Creationism. Peter Lang Publishers. (2007, pp. 59-74) [pdf]

Abstract: The new common slogan one hears from creationists trying to get their views into the public schools is "teach the controversy" together with the curriculum proposals that schools should teach "arguments for and against evolution."  Creationists are using this kind of approach as an indirect way of bringing in standard Creation Science and Intelligent Design arguments without mentioning those terms explicitly.  This article examines this latest political strategy and the misleading rhetoric that it uses.  The Kitzmiller v. Dover Area School Board Federal court decision against teaching Intelligent Design also ruled against this strategy at the same time.

• Models, Simulations, Instantiations and Evidence: The Case of Digital Evolution.
Journal of Experimental and Theoretical Artificial Intelligence (Vol. 19, No. 1, 2007) [pdf]

Abstract: What is the difference between a simulation of X and simply another instance of X? Is there a point at which the ‘‘virtual reality’’ of a model becomes the real thing? This paper examines these questions using cases taken from recent developments in evolutionary engineering and artificial life research. By implementing the Darwinian mechanism and setting it to work on a design problem, scientists and engineers find that evolution not only can improve prior designs, but also produce novel technological solutions. Artificial life systems Tierra and Avida which operate at a higher level of abstraction than evolutionary engineering applications. I analyze simulation as a rational concept ‘‘S simulates R’’ and argue that it always includes some relevant property P, of R, that is captured but that there is always also some other that it omits, and that pragmatic factors fix what counts as relevant. The border between a simulation and an instance can change depending upon the context. I show that in one sense, evo-technology and artificial life simulate organic evolution, but in another relevant sense they are instances of evolution itself. Biologists can use such systems to experimentally test evolutionary hypotheses such as those involving the evolution of complex features and altruism. This analysis suggests lines for future research on broader questions about models classification and confirmation.

• God of the Gaps: The Argument from Ignorance and the Limits of Methodological Naturalism
In Andrew Petto & Laurie Godfrey (editors) Scientists Confront Intelligent Design and Creationism. W.W. Norton & Co. (2007, pp. 309-338.)

• Pre-Existing Conditions: Genetic Testing, Causation and the Justice of Medical Insurance.
In Rosamond Rhodes, Leslie Francis & Anita Silvers (eds.) Blackwell Guide to Medical Ethics. (Ch. 23, pp. 407-424, 2006)
[pdf of preprint]

Abstract: As tests that can identify genes associated with diseases proliferate faster than therapies, individuals face a problem: if they test positive for a disease gene they may find that prospective insurers say they have a "pre-existing condition" and deny them coverage on that basis. This paper explores the implications for the future of medical insurance of regarding genes in this manner, and examines some of the moral and conceptual difficulties. Looking simply at the level of causal interactions there is no reason to say that "the cause" of a disease is "genetic" and not "environmental." Thus, in a trivial sense, every disease may be said to have a pre-existing genetic component. I describe the CaSE model of the causal relation and show how it can help us understand the way tacit pragmatic assumptions are involved when we call something a "genetic disease." This lets us see where our moral choices lie. I propose that pre-existing conditions are not all equivalent from a moral point of view, and then, using a Rawlsian framework, argue that it would be unjust to deny access to insurance on the basis of genetic pre-conditions that are the result of life's lottery.

• The Premodern Sins of Intelligent Deisgn.
In Clayton, Phillip (ed.) Oxford Handbook of Science and Religion. Oxford University Press. (Ch 43. 2006) [pdf]

Abstract: With its metaphors of war and calls to martyrdom, the Intelligent Design (ID) Creationist movement is reigniting old animosities between religion and science. This article discusses several of the key religious controversies involving ID Creationism, especially the flaws in William Dembski's defense of ID.  It also rebuts his charge that science's naturalistic method is a "pre-modern sin" and shows how this is a problem not for science but for ID, which aims to resurrect occult explanations.   Contrary to Demski's claim, methodological naturalism is not a constraint upon the world but a constraint upon science. The difference between science and creationism is like the difference between seeing hurricanes and thunderstorms as natural disasters rather than as acts of God.

• Scientific Integrity and Science Museums.
Museums and Social Issues. (Vol. 1 No. 1. pp. 7-18, Spring 2006)

Abstract: Scientific epistemology—the goals and methods of science—carries with it an implicit ethical framework that can provide a basis for professional judgment and behavior and inform museums’ treatment of ethical dilemmas. This article reviews case studies of scientific ethical dilemmas within science museums and critically examines four operating models by which to approach such dilemmas. These include a business model, an entertainment model, and an education model. A proposed fourth model recommends that science museums view themselves as stewards of science, and it reinterprets the others in light of the underlying ethical framework and its corresponding “scientific virtues,” particularly scientific integrity. This approach will not solve all ethical questions but it will maintain a focus on the museum’s core values

• Of Swords and Smoking Guns
Science & Theology News (February 2006, p. 9)

• Expert Witness Report.  Kitzmiller et al v. Dover Area School District (2005)
[pdf]

• On Teaching Evolution and the Nature of Science
In Cracraft, J. and R. Bybee (eds.). Evolutionary Science and Society: Educating a New Generation. Biological Sciences Curriculum Study, Colorado Springs, CO. (pp. 1-12, 2005) [pdf]

• Determinism.
In Encyclopedia of Science, Technology, and Ethics. 4 volumes. Carl Mitcham (Ed.) Detroit: Macmillan Reference. (Vol. 2, pp. 511-513, 2005)

• Kin-Selection: The Rise and Fall of Kin-Cheaters
Sherri Goings, Jeff Clune, Charles Ofria, Robert T. Pennock.
In Pollack, Jordan, M. Bedau, P. Husbands, T. Ikegami and R. Watson (eds.) Artificial Life IX: Proceedings of the Ninth International Conference on the Simulation and SYnthesis of Living Systems. (pp. 303-308, 2004) [pdf]

Abstract: This reports on experiments that test hypotheses about the evolution of altruism.  Using the Avida digital evolution environment we test conditions under which self-sacrificing behavior towards members of one's kin group can evolve.  We also observe the subsequent evolution of kin-cheaters and examine circumstances in which these cheaters are then defeated.  This is part of on-going experiments involving experimental tests of group selection and the evolution of altruism.

• Bayesianism, Ravens and Evidential Relevance
Annals of the Japan Association for Philosophy of Science, Invited article. (Vol. 13, No. 1, 2004)

• DNA by Design?: Stephen Meyer and the Return of the God Hypothesis.
In Ruse, Michael and William Dembski (eds) Debating Design. New York: Cambridge University Press, (pp. 130 - 148, 2004)
[pdf]

• Critique of Philip Johnson.
In Parsons, Keith (ed.) The Science Wars: Debating Scientific Knowledge and Technology. Prometheus Press. (pp. 277-306, 2003)

• Creationism and Intelligent Design
Annual Review of Genomics and Human Genetics. (Vol. 4: 143-163, Sept. 2003) [pdf]

• The Evolutionary Origin of Complex Features
Richard E. Lenski, Charles Ofria, Robert T. Pennock, Christoph Adami
Nature (Vol. 423, 2003, pp. 139-145) [pdf]

• Research Funding and the Virtue of Scientific Objectivity
Academic Integrity (Vol. V. No. 2, Spring 2002, pp. 3-6)

• Should Creationism be Taught in the Public Schools?
Science & Education (Vol.11 no.2, March 2002, pp. 111-133)
[Available online]

• Whose God? What Science? Reply to Michael Behe
In Reports of the National Center for Science Education. (Vol. 21 No. 3-4 pp. 16-19, May-Aug. 2001)
[Available online]

• The Virtuous Scientist Meets the Human Clone
In New Ethical Challenges in Science and Technology, Sigma Xi Forum Proceedings. 2000. pp. 117-124.
[Available online]

• On Observing Evolution
In Society for the Study of Evolution/Society for Molecular Biology and Evolution. The Web of Life: Evolution in Action. Presentations at the National Association of Biology Teachers Annual Conferences. 1998-2000.

• Can Darwinian Mechanisms Make Novel Discoveries?: Learning from discoveries made by evolving neural networks.
Foundations of Science (Vol. 5 no. 2, pp. 225-238, 2000)

Abstract: Some philosophers of science have suggested that the development of scientific knowledge may be thought of as a kind of Darwinian process. The process of discovery, however, is one potentially problematic element of this analogy. In this paper I compare Herbert Simon’s attempt to simulate scientific discovery in a computer program (BACON) to more recent models that were not designed for that purpose, but which provide useful cases to help evaluate this aspect of the analogy, throwing light on the possibility of Darwinian discovery. One may think of the process of discovery as a special sort of problem-solving. If one then considers problem-solving abstractly, as a search through a space of possibilities, then there may be a kind of “logic of discovery” in the weak sense of heuristics that would narrow a search space. I describe two cases of discoveries made by evolving connectionist networks, which use a genetic algorithm to explicitly model Darwinian mechanisms. These cases are not susceptible to the criticism that the discoveries were somehow already “designed in.” I argue that the discovery process that the networks use fits Simon’s original abstract framework. This shows that Darwinian mechanisms can indeed make novel discoveries of complex, previously unknown patterns. This lends support to the evolutionary model of scientific development and leads to some interesting questions for evolutionary epistemology more generally. I consider the problem of the relation of the (non-teleological) evolutionary model to the apparent purposefulness of scientific investigation. Finally, I argue that that evolutionary model suggests there may be a kind of structure to discovery in science—a hierarchy of levels in the discovery process, for instance, whereby subsequent discoveries are affected by previous ones, and ways in which failures can transform into successes.

• Lions and Tigers and APES, Oh My!: Creationism vs. Evolution in Kansas
Science Teaching & The Search for Origin: Kansas Teach-In. AAAS Dialogue on Science and Religion. (2000)
[Available online]

• The Wizards of ID: Reply to Dembski
Metanexus (No. 089, Oct. 11, 2000) [Available online]

• Of Design and Desception: Kansas, Conflict & Creationism
Science & Spirit (Nov./Dec. 1999) [Also available online]

• Untitled—Reply to Phillip Johnson re: Tower of Babel
Books and Culture (Sept./Oct. 1999) [Available online]

• The Prospects for a Theistic Science
Perspectives on Science and Christian Faith (Vol. 50, No. 3, pp. 205-209, Sept. 1998)

• Death and Taxes: On the Justice of Conscientious Objection to War Taxes
(a) Journal of Accounting, Ethics & Public Policy (Vol. 1, No. 1, Winter 1998)
(b) Reprinted in Robert W. McGee (ed.) The Ethics of Tax Evasion. South Orange, NJ.: The Dumont Institute for Public Policy Research, pp. 124-142.
(c) Download PDF

Abstract: Resistance to paying war taxes that stems from a principled pacifism is not the same as tax-dodging and should be accommodated in the law by broadening the scope of Conscientious Objector (CO) status and by legislating a nonmilitary alternative fund so COs may redirect their tax money to peaceful uses. Using the religious example of the Society of Friends (Quakers) and various secular examples of pacifism I show that resisters' conscientious opposition to paying for war is of a kind with their conscientious refusal to carry arms. Their refusal to cooperate with military taxation is not disdain of the rule of law, but is a respectful form of civil disobedience. It is in the interest of justice for a liberal democracy to provide an option for conscientious objectors so they may satisfy their moral scruples without having to break the law.

• Evidential Relevance and the Grue Paradox.
Philosophy of Science (Japan) (Vol. 31, No. 1, May 1998) [pdf]

Abstract: Goodman's Grue Paradox may be intransigent as a version of the problem of induction, but may be resolved within the more limited context of confirmation theory in which our task is to explicate the basic notion of evidential relevance. Although the green and grue hypotheses are equivalently confirmed if we follow Goodman's use of the Hempelian instance confirmation relation, there are asymmetries than can be exploited if we adopt an "ontic" confirmation theory that uses a causal notion of evidential relevance. I sort out a variety of interpretive confusions about the intended content of the definition of grue and show how the causal approach resolves each in a way that is not paradoxical.

• Creationism's War on Science.
Environmental Review (Vol. 5, No. 2, pp. 7 - 16, February 1998)

• Is a Necessity-and-Sufficiency Account of Causation Contradictory?
In Paul Weingartner, Gerhard Schurtz & Georg Dorn (eds.) The Roles of Pragmatics in Contemporary Philosophy. Kirchberg am Wechsel: The Austrian Ludwig Wittgenstein Society. Vol. 2, pp. 753-757, 1997.

• Naturalism, Creationism and the Meaning of Life: The Case of Phillip Johnson
Revisited
Creation/Evolution (Vol. 16, No. 2, pp. 10-30, Winter 1996)

• Inappropriate Authorship in Collaborative Scientific Research
Public Affairs Quarterly: (Vol. 10, No. 4, pp. 379-393, October 1996)

Abstract: National scientific societies have cited "inappropriate authorship" of scientific papers as one sort of ethical misconduct they are concerned about, but there has been little discussion of what it involves or what to do about it. I analyze varieties of improper authorship and show that they involve failure to respect ethical principles of truthfulness, responsibility and justice. One can do little to prevent willful misconduct of this sort, but many of the ethical problems arise not because of unethical behavior of scientists, but because of the vague and conflicting authorship conventions currently available for differentiating researcher contributions. I propose and defend alternative attribution strategies that may help mitigate this sort of problem.

• Reply to Johnson - Johnson's Reason in the Balance
Biology & Philosophy (Vol. 11, No. 4, pp. 565-568, 1996)

Abstract: This replies to Johnson's response to the previous article. It also updates that article by discussing Johnson's 1995 book Reason in the Balance, that appeared a year after the above article was accepted for publication.

• Naturalism, Evidence and Creationism: The Case of Phillip Johnson
Biology and Philosophy (Vol. 11, No. 4, pp. 543-559, 1996)

Abstract: Phillip Johnson claims that Creationism is a better explanation of the existence and characteristics of biological species than is evolutionary theory. He argues that the only reason biologists do not recognize that Creationist's negative arguments against Darwinism have proven this is that they are wedded to a biased ideological philosophy-Naturalism-which dogmatically denies the possibility of an intervening creative god. However, Johnson fails to distinguish Ontological Naturalism from Methodological Naturalism. Science makes use of the latter and I show how it is not dogmatic but follows from sound requirements for empirical evidential testing. Furthermore, Johnson has no serious alternative type of positive evidence to offer for Creationism, and purely negative argumentation, despite his attempt to legitimate it, will not suffice.

• Epistemic and Ontic Theories of Explanation and Confirmation
Philosophy of Science-Japan (Vol. 28:31-45, 1995)

Abstract: This paper reviews some recent work on issues connecting the theories of scientific explanation and confirmation. Beginning with Harman and Hempel and continuing with Salmon, Miller, Pennock and Ruben, I consider different explications of the explanatory relation that could be used in an Inference to the Best Explanation (I.B.E.) confirmation theory. Causal theories of explanation are currently the most promising and I discuss the strengths of an I.B.E. theory based upon an objective "ontic" view of explanation like Salmon's over an "epistemic" causal view such as Miller's. Finally I show how a causal theorist can address two purported weaknesses of the causal approaches that arise from Humean and Sellarsian arguments.

• Death of the Self: Changing Medical Definitions in Japan and the U.S.
Obirin Review of International Studies (Vol. 7:109-125, 1995)

Abstract: Recently proposed legislation in the Japanese Diet regarding transplantation of organs has led to renewed debate on what should be the medical definition of death. Although the United States and most Western nations have moved to a neocortical brain death criterion, Japan retains the whole-body (heart and lungs) criterion, and significant opposition remains in Japan to the proposed change. This paper reviews the history of changes in the definition of death in the West and discusses a central philosophical argument in favor of the brain-death criterion based upon a thought experiment which shows that irreversible termination of mental life constitutes death of the self. I claim that this core notion of the person applies in the Japanese case as well, and then argue that some purportedly special characteristics of the Japanese notion of self do not undermine this conclusion.

• Moral Darwinism: Ethical Evidence for the Descent of Man
Biology & Philosophy, (Vol. 10: 287-307, 1995)

Abstract: Could an ethical theory ever play a substantial evidential role in a scientific argument for an empirical hypothesis? In The Descent of Man, Darwin includes an extended discussion of the nature of human morality, and the ethical theory which he sketches is not simply developed as an interesting ramification of his theory of evolution, but is used as a key part of his evidence for human descent from animal ancestors. Darwin must rebut the argument that, because of our moral nature, humans are essentially different in kind from other animals and so had to have had a different origin. I trace his causal story of how the moral sense could develop out of social instincts by evolutionary mechanisms of group selection, and show that the form of Utilitarianism he proposes involves a radical reduction of the standard of value to the concept of biological fitness. I argue that this causal analysis, although a weakness from a normative standpoint, is a strength when judged for its intended purpose as part of an evidential argument to confirm the hypothesis of human descent.

• Marshall Nirenberg invents an experimental technique that cracks the genetic code
Great Events in History: Science and Technology. U.S.A.: Salem Press (1991)

• Oldham and Mohorovicic determine the general structure of Earth's interior
Great Events in History: Science and Technology. U.S.A.: Salem Press (1991)

• Evolution — Once More, With Feeling (Review Essay)
Dual review of George Levine’s Darwin Loves You and David Sloan Wilson’s Evolution for Everyone.)  American Scientist.  (Vol. 95, November-December, pp. 528-531, 2007) [Online link] [pdf]

• Explaining Bioethics to Others (Review Essay)
Dual review of Bryant, Baggot la Velle, and Searle's Bioethics for Scientists and Miller and Humber’s The Nature and Prospect of Bioethics.
Quarterly Review of Biology. (Vol. 79, No. 3, pp. 295-296,  Sept. 2004)

• Lindberg and Numbers' When Science and Christianity Meet
Trends in Ecology and Evolution (Vol. 19, No. 1, pp. 8 – 9, January 2004)

• A Bridegwater Treatise for the 21st Century (Review Essay)
Review of Michael Ruse, Darwin and Design: Does Evolution Have a Purpose?
Science (Vol. 301, p. 1051, 22 Aug 2003) [pdf]

•Bowler on Science and Religion (Review Essay)
Review of Peter Bowler's Reconciling Science and Religion: The Debate in Early Twentieth-Century Britain.
Endeavour (Vol. 27, No. 3, pp. 101-102, September 2003) [pdf]

• Johnson's Defeating Darwinism (Review Essay)
Reports of the National Center for Science Education (Vol. 17, No. 6, pp. 36-38, Nov/Dec 1998)

• Dunbar's The Trouble with Science
Quarterly Review of Biology: (Vol. 73, No. 1, pp. 61, March 1998)

• Reynolds & Tanne's The Social Ecology of Religion
Quarterly Review of Biology: (Vol. 71, No. 3, pp. 394-395, September 1996)

• Ethical Theory Applied to the Scientific Enterprise (Review Essay)
- (i) Erwin, Gendin & Kleiman's Ethical Issues in Scientific Research
- (ii) Shrader-Frechette's Ethics of Scientific Research
- (iii) Penslar's Research Ethics: Cases & Materials
American Scientist (March/April:179-180, 1996)

• David-Hillel Ruben. Explaining Explanation
Philosophy of Science (Vol. 61(1): 146-147, 1994)