Robert T. Pennock - Publications

[ Books | Anthologies | Articles | Book Reviews ]


“An Avida-ED digital evolution curriculum for undergraduate biology"
James J Smith; Wendy R Johnson; Amy M Lark; Louise S Mead; Michael J Wiser, Robert T. Pennock
Evolution: Education and Outreach. (2016, 9(1), 1-11; DOI 10.1186/s12052-016-0060-0) [onlline]

Abstract: We present an inquiry-based curriculum based on the digital evolution platform Avida-ED ( We designed an instructional sequence and lab book consisting of an introduction to Avida-ED and a set of three lessons focused on specific evolutionary concepts. These served to familiarize students with experimental evolution and Avida-ED. Students then developed independent Avida-ED research projects to test their own questions. Cur- riculum design and implementation occurred over the course or two semesters, with a pilot implementation in the first semester, followed by curriculum revision and full implementation in the second semester. The curriculum was implemented in an undergraduate Introductory Cell and Molecular Biology course at a major research university. Full implementation of the curriculum in semester two involved the use of Avida-ED mainly in the teaching lab in parallel with a bacterial antibiotic resistance experimental research stream, allowing students to draw connections between Avidian digital evolution and the evolution of antibiotic resistance in microbial populations. After carrying out the introductory exercises, students developed independent Avida-ED projects to test their own research questions, and presented their data to researchers in the NSF-funded BEACON Center for the Study of Evolution in Action. Preliminary results of our studies to assess the impacts of an Avida-ED curriculum indicate a positive effect on student learning of evolutionary concepts, particularly in increasing the level of complexity of student explanations about the random nature of mutation.

“Comparing Human and Automated Evaluation of Open-Ended Student Responses to Qustions of Evolution"
Michael J Wiser, Louise S Mead; James J Smith, Robert T. Pennock
Artificial Life 2016: Proceedings. (July, 2016) [pdf]

Abstract: Written responses can provide a wealth of data in understand- ing student reasoning on a topic. Yet they are time- and labor- intensive to score, requiring many instructors to forego them except as limited parts of summative assessments at the end of a unit or course. Recent developments in Machine Learning (ML) have produced computational methods of scoring writ- ten responses for the presence or absence of specific concepts. Here, we compare the scores from one particular ML program – EvoGrader – to human scoring of responses to structurally- and content-similar questions that are distinct from the ones the program was trained on. We find that there is substan- tial inter-rater reliability between the human and ML scoring. However, sufficient systematic differences remain between the human and ML scoring that we advise only using the ML scoring for formative, rather than summative, assessment of student reasoning.

“Developing a Scientific Virtue-Based Approach to Science Ethics Training"
Robert T. Pennock & Michael O'Rourke
Science and Engineering Ethics. (Jan 26, 2016) [online]

Abstract: Responsible Conduct of Research training typically includes only a subset of the issues that ought to be included in science ethics and sometimes makes ethics appear to be a set of externally imposed rules rather than something intrinsic to scientific practice. A new approach to science ethics training based upon Pennock’s notion of the scientific virtues may help avoid such problems. This paper motivates and describes three implementations—theory-centered, exemplar-centered, and concept-centered—that we have developed in courses and workshops to introduce students to this scientific virtue-based approach.


BooksBut Is It Science book coverALife 2013 Proceedings cover

  • Tower of Babel: The Evidence Against the New Creationism
    Cambridge, MA: The MIT Press - Bradford Books. 1999.  Paperback 2000.
    Reviews of Tower of Babel have appeared in over 50 publications.
  • Anthologies

  • Intelligent Design Creationism and its Critics: Philosophical, Theological & Scientific Perspectives
    Cambridge, MA: The MIT Press, December 2001.

  • R. T. Pennock and Michael Ruse (eds.) But Is It Science: The Philosophical Question in the Creation/Evolution Controversy
    U.S.A.: Prometheus Press, 2009.

  • C. Adami, D. Bryson, C. Ofria and R. T. Pennock (eds.) Proceedings of the 13th International Conference on Artificial Life The MIT Press (2012)
  • Articles

    • “Following Humbly where Nature Leads: How Scientists Embody Humility
    Slate. What Do We Know?  Essays and Opinions.  (Aug. 10, 2015) [pdf]

    • "Fostering a Culture of Scientific Integrity: Legalistic vs. Scientific Virtue-Based Approaches"
    Professional Ethics Report (2015, Vol. 28, No. 2, p. 1-3) [pdf]

    Abstract: Whereas deeply rooted cultural norms organically structure a society or a practice from within, responsible conduct of research (RCR) literature and training too often theorize and present research ethics in terms of quasi-legalistic external control.  I suggest an alternative that is explicitly centered instead on internal norms, specifically on scientific character virtues that embody both epistemic and ethical values. Scientific integrity is more than research integrity so it is useful to think in terms of a broader category of science ethics, which also encompassing the scientific virtues and other topics that may be linked to but are not directly a part of basic research.

    • "Modeling Evolution in the Classroom: The Case of the Fukushima Butterflies"
    Amy Lark, Gail Richmond, ROBERT T. PENNOCK 
    American Biology Teacher (2014, 76(7):450-454) [pdf]

    Abstract: New science standards and reform recommendations spanning grades K-16 focus on a limited set of key scientific concepts from each discipline that all students should know, but also emphasize the integration of these with science practices so that students learn not only the “what” of science but also the “how” and “why”. In line with this approach, we present an exercise that models the integration of fundamental evolutionary concepts with science practices. Students use Avida-ED digital evolution software to test claims from a study on mutated butterflies in the vicinity of the compromised Fukushima Daiichi Nuclear Power Plant complex subsequent to the Great East Japan Earthquake of 2011 (Hiyama et al., Scientific Reports 2 Article 570, 2012). This exercise is appropriate for use in both high school and undergraduate biology classrooms.

    • "Evolution and Computing"
    In J.B. Losos (ed.) The Princeton Guide to Evolution. Princeton: Princeton University Press. (2013, pp. 780-785) [pdf]

    Abstract: Shared principles between evolution and computing are opening up fruitful areas for research. This article discusses some unexpected connections between evolutionary biology and computer science, such as the core ideas of code, information, and function, and how these are leading to theoretical and practical ways that each is benefitting the other. It highlights the emerging field of evolutionary computation, giving a brief history and some examples of its utility not only for helping to solve basic research problems in biology and computer science, but also for applied design work in engineering..

    •"A Case Study in the De Novo Evolution of a Complex Odometric Behavior in Digital Organisms"
    Laura M. Grabowski, David M. Bryson, Fred C. Dyer, ROBERT T. PENNOCK and Charles Ofria 
    PLoS ONE (01/2013; 8(4):e60466) [pdf]

    Abstract: What is the definition of life? Artificial life environments provide an interesting test case for this classical question. Understanding what such systems can tell us about biological life requires negotiating the tricky conceptual boundary between virtual and real life forms. Drawing from Wittgenstein’s analysis of the concept of a game and a Darwinian insight about classification, I argue that classifying life involves both causal and pragmatic elements. Rather than searching for a single, sharp definition, these considerations suggest that life is a cluster concept with fuzzy boundaries and that there are multiple legitimate ways to make the notion precise for different scientific purposes. This pluralist, realist account avoids unnecessary border disputes by emphasizing how science negotiates such questions in relation to theory and evidence. I also discuss several objections to this approach, including a “moral hesitation” some have to allowing broader application of the concept of life to include artificial life.

    •"Are Pre-existing Condition Exclusion Clauses Just: Lessons from Causal and Ethical Considerations Regarding Genetic Testing"
    In R. Rhodes, M. P. Battin and A. Silvers (eds.) Medicine and Social Justice: Essays on the Distribution of Health Care (2nd edition)
    Oxford: Oxford University Press. (2012, pp. 387-399)

    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 updates my 2006 paper that explore 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.

    •"Ontogeny tends to recapitulate phylogeny in digital organisms"
    Jeff Clune, ROBERT T. PENNOCK, Charles Ofria and Richard Lenski 
    The American Naturalist, Vol. 180, No. 3 (July 2012)  E54-E63 [pdf]

    Abstract: Biologists have long debated whether ontogeny recapitulates phylogeny and, if so, why. Two plausible explanations are that (i) changes to early developmental stages are selected against because they tend to disrupt later development and (ii) simpler structures often precede more complex ones in both ontogeny and phylogeny if the former serve as building blocks for the latter. It is difficult to test these hypotheses experimentally in natural systems, so we used a computational system that exhibits evolutionary dynamics. We observed that ontogeny does indeed recapitulate phylogeny; traits that arose earlier in a lineage's history also tended to be expressed earlier in the development of individuals. The relative complexity of traits contributed substantially to this correlation, but a significant tendency toward recapitulation remained even after accounting for trait complexity. This additional effect provides evidence that selection against developmental disruption also contributed to the conservation of early stages in development.

    Clever Creatures: Case Studies of Evolved Digital Organisms.
    Laura M. Grabowski, David M. Bryson, Fred Dyer, ROBERT T. PENNOCK, and Charles Ofria 
    Advances in Artificial Life: ECAL 2011, pp. 276-283 (August 2011) [pdf]

    Abstract: We present in-depth analysis of three digital organisms— self-replicating computer programs—that evolved in three different experimental environments in the Avida platform. The ancestral environments required the evolv- ing organisms to use memory in different ways as they gathered information from the environment and made be- havioral decisions. Each organism exhibited a behavior or algorithm of particular interest: 1) simple step-counting odometer; 2) clever low-level computation; 3) pronounced modularity in both program structure and program functionality. We focus our analysis of the case study organisms on the structure and operation of the evolved algorithms that produce the individuals’ adaptive behaviors.

    On the Performance of Indirect Encoding Across the Continuum of Regularity.
    Jeff Clune, Kenneth O. Stanley, ROBERT T. PENNOCK, and Charles Ofria 
    IEEE Transactions On Evolutionary Computation, Vol. 15, No. 3, June 2011 [pdf]

    This paper investigates how an evolutionary algorithm with an indirect encoding exploits the property of phenotypic regularity, an important design principle found in natural organisms and engineered designs. We present the first comprehensive study showing that such phenotypic regularity enables an indirect encoding to outperform direct encoding controls as problem regularity increases. Such an ability to produce regular solutions that can exploit the regularity of problems is an important prerequisite if evolutionary algorithms are to scale to high-dimensional real-world problems, which typically contain many regularities, both known and unrecognized. The indirect encoding in this case study is HyperNEAT, which evolves artificial neural networks (ANNs) in a manner inspired by concepts from biological development. We demonstrate that, in contrast to two direct encoding controls, HyperNEAT produces both regular behaviors and regular ANNs, which enables HyperNEAT to significantly outperform the direct encodings as regularity increases in three problem domains. We also show that the types of regularities HyperNEAT produces can be biased, allowing domain knowledge and preferences to be injected into the search. Finally, we examine the downside of a bias toward regularity. Even when a solution is mainly regular, some irregularity may be needed to perfect its functionality. This insight is illustrated by a new algorithm called HybrID that hybridizes indirect and direct encodings, which matched HyperNEAT’s performance on regular problems yet outperformed it on problems with some irregularity. HybrID’s ability to improve upon the performance of HyperNEAT raises the question of whether indirect encodings may ultimately excel not as stand-alone algorithms, but by being hybridized with a further process of refinement, wherein the indirect encoding produces patterns that exploit problem regu larity and the refining process modifies that pattern to capture irregularities. This paper thus paints a more complete picture of indirect encodings than prior studies because it analyzes the impact of the continuum between irregularity and regularity on the performance of such encodings, and ultimately suggests a path forward that combines indirect encodings with a separate process of refinement.

    •"Negotiating Boundaries in the Definition of Life: Wittgensteinian and Darwinian Insights on Resolving Conceptual Border Conflicts"
    Synthese 2012, Vol. 185 No. 1 pp. 5-23. (Pubished online 15 Feb. 2011) [pdf]

    Abstract: What is the definition of life? Artificial life environments provide an interesting test case for this classical question. Understanding what such systems can tell us about biological life requires negotiating the tricky conceptual boundary between virtual and real life forms. Drawing from Wittgenstein’s analysis of the concept of a game and a Darwinian insight about classification, I argue that classifying life involves both causal and pragmatic elements. Rather than searching for a single, sharp definition, these considerations suggest that life is a cluster concept with fuzzy boundaries and that there are multiple legitimate ways to make the notion precise for different scientific purposes. This pluralist, realist account avoids unnecessary border disputes by emphasizing how science negotiates such questions in relation to theory and evidence. I also discuss several objections to this approach, including a “moral hesitation” some have to allowing broader application of the concept of life to include artificial life.

    Selective pressures for accurate altruism targeting: Evidence from digital evolution for difficult-to-test aspects of inclusive fitness theory.
    Jeff Clune, Heather Goldsby, Charles Ofria, and ROBERT T. PENNOCK 
    Proceedings of the Royal Society B (15 September, 2010) [pdf]

    Abstract: Inclusive fitness theory predicts that natural selection will favour altruist genes that are more accurate in targeting altruism only to copies of themselves. In this paper, we provide evidence from digital evolution in support of this prediction by competing multiple altruist-targeting mechanisms that vary in their accu- racy in determining whether a potential target for altruism carries a copy of the altruist gene. We compete altruism-targeting mechanisms based on (i) kinship (kin targeting), (ii) genetic similarity at a level greater than that expected of kin (similarity targeting), and (iii) perfect knowledge of the presence of an altruist gene (green beard targeting). Natural selection always favoured the most accurate targeting mechanism available. Our investigations also revealed that evolution did not increase the altruism level when all green beard altruists used the same phenotypic marker. The green beard altruism levels stably increased only when mutations that changed the altruism level also changed the marker (e.g. beard colour), such that beard colour reliably indicated the altruism level. For kin- and similarity-targeting mechanisms, we found that evolution was able to stably adjust altruism levels. Our results confirm that natural selection favours altruist genes that are increasingly accurate in targeting altruism to only their copies. Our work also emphasizes that the concept of targeting accuracy must include both the presence of an altruist gene and the level of altruism it produces.

    Early Evolution of Memory Usage in Digital Organisms.
    Laura M. Grabowski, David M. Bryson, Fred C. Dyer, Charles Ofria, and ROBERT T. PENNOCK 
    Proceedings of the International Conference on Artificial Life (August, 2010) [pdf]

    Abstract: We investigate the evolution of memory usage in environ- ments where information about past experience is required for optimal decision making. For this study, we use digital organisms, which are self-replicating computer programs that are subject to mutations and natural selection. We place the digital organisms in a range of experimental environments: simple ones where environmental cues indicate that a specific action should be taken (e.g., turn left to find food) as well as slightly more complex ones where cues refer to prior expe- rience (e.g., repeat the action indicated by the previous cue). We demonstrate that flexible behaviors evolve in each of these environments, often leading to clever survival strategies. Ad- ditionally, memory usage evolves only when it provides a sig- nificant advantage and organisms will often employ surpris- ingly successful strategies that do not use memory. However, the most powerful strategies we found all made effective use of memory.

    Should Students Be Able to Opt Out of Evolution? Some Philosophical Considerations.
    Evolution Education & Outreach (June, 2010) [online] [pdf]

    Abstract: One new development in the ongoing creationism/ evolution controversy has been the proposal to institute opt- out policies that would allow creationist parents to exempt their children from any instruction involving evolution. By way of an explanation of some of the philosophical issues at play in the debate over evolution and the nature of science, this article shows the educational folly of such policies. If evolution is taught properly, it should not be possible to opt out of it without opting out of biology. Moreover, if Intelligent Design creationist criticisms of evolution and scientific naturalism were taken as the basis for opting out, then the effect would be even more radical and would require opting out of science entirely.

    •The Postmodern Sin of Intelligent Design Creationism.
    Science & Education. (2010, Vol. 19, No. 6-8, pp. 757-778) [online] [pdf]

    Abstract: That Intelligent Design Creationism rejects the methodological naturalism of modern science in favor of a premodern supernaturalist worldview is well documented and by now well known. An irony that has not been sufficiently appreciated, however, is the way that ID Creationists try to advance their premodern view by adopting (if only tactically) a radical postmodern perspective. This paper will reveal the deep threads of postmodernism that run through the ID Creationist movement’s arguments, as evidenced in the writings and interviews of its key leaders. Seeing their arguments and activities from this perspective highlights the danger to science posed by both ID Creationism and radical postmodernism.

    HybrID: A Hybridization of Indirect and Direct Encodings for Evolutionary Computation.
    Jeff Clune, Benjamin E. Beckmann, ROBERT T. PENNOCK and Charles Ofria.  
    Proceedings of the 2009 Evolutionary Conference of Artificial Life (ECAL) Springer (2010) [preprint]

    Abstract: Evolutionary algorithms typically use direct encodings, where each element of the phenotype is specified independently in the genotype. Because direct encodings have difficulty evolving modular and symmetric phenotypes, some researchers use indirect encodings, wherein one genomic element can in- fluence multiple parts of a phenotype. We have previously shown that Hyper- NEAT, an indirect encoding, outperforms FT-NEAT, a direct-encoding control, on many problems, especially as the regularity of the problem increases. How- ever, HyperNEAT is no panacea; it had difficulty accounting for irregularities in problems. In this paper, we propose a new algorithm, a Hybridized Indirect and Direct encoding (HybrID), which discovers the regularity of a problem with an indirect encoding and accounts for irregularities via a direct encoding. In three different problem domains, HybrID outperforms HyperNEAT in most situations, with performance improvements as large as 40%. Our work suggests that hybridizing indirect and direct encodings can be an effective way to im- prove the performance of evolutionary algorithms.

    • Can’t Philosophers Tell The Difference Between Science and Religion?: Demarcation Revisited.
    Robert T. Pennock.  
    Synthese (April, 2009) [online]

    Abstract: In the 2005 Kitzmiller v Dover Area School Board case, a federal district court ruled that Intelligent Design creationism was not science, but a disguised reli- gious view and that teaching it in public schools is unconstitutional. But creationists contend that it is illegitimate to distinguish science and religion, citing philosophers Quinn and especially Laudan, who had criticized a similar ruling in the 1981 McLean v. Arkansas creation-science case on the grounds that no necessary and sufficient demarcation criterion was possible and that demarcation was a dead pseudo-problem. This article discusses problems with those conclusions and their application to the quite different reasoning between these two cases. Laudan focused too narrowly on the problem of demarcation as Popper defined it. Distinguishing science from religion was and remains an important conceptual issue with significant practical import, and philosophers who say there is no difference have lost touch with reality in a profound and perverse way. The Kitzmiller case did not rely on a strict demarcation criterion, but appealed only to a “ballpark” demarcation that identifies methodological naturalism (MN) as a “ground rule” of science. MN is shown to be a distinguishing feature of science both in explicit statements from scientific organizations and in actual practice. There is good reason to think that MN is shared as a tacit assumption among philoso phers who emphasize other demarcation criteria and even by Laudan himself.

    Using Avida-ED for teaching and learning about evolution in undergraduate introductory biology courses.
    Elena B. Spath, Tammy Long, Robert T. Pennock and Diane Ebert-May. 
    Evolution Education & Outreach. (Vol. 2, No. 3, pp. 415-428, 2009) [pdf]

    Abstract: Evolution is a complex subject that requires knowledge of basic biological concepts and the ability to connect them across multiple scales of time, space, and biological organization. Avida-ED is a digital evolution educational software environment designed for teaching and learning about evolution and the nature of science in undergraduate biology courses. This study describes our backward design approach to developing an instructional activity using Avida-ED for teaching and learning about evolution in a large-enrollment introductory biology course. Using multiple assessment instruments, we measured student knowledge and understanding of key principles of natural selection before and after instruction on evolution (including the Avida-ED activity). Assessment analysis revealed signif- icant post-instruction learning gains, although certain evolu- tionary principles (most notably those including genetics concepts, such as the genetic origin of variation) remained particularly difficult for students, even after instruction. Students, however, demonstrated a good grasp of the genetic component of the evolutionary process in the context of a problem on Avida-ED. We propose that: (a) deep understanding of evolution requires complex systems thinking.

    The Sensitivity of HyperNEAT to Different Geometric Representations of a Problem.
    Jeff Clune, Charles Ofria, and Robert T. Pennock.
    Genetic and Evolutionary Computation Conference (GECCO ‘09) Proceedings. New York: Association for Computing Machinery (2009) [pdf]

    Abstract: HyperNEAT, a generative encoding for evolving artificial neural networks (ANNs), has the unique and powerful ability to exploit the geometry of a problem (e.g., symmetries) by encoding ANNs as a function of a problem's geometry. This paper provides the first extensive analysis of the sensitivity of HyperNEAT to different geometric representations of a problem. Understanding how geometric representations affect the quality of evolved solutions should improve future designs of such representations. HyperNEAT has been shown to produce coordinated gaits for a simulated quadruped robot with a specific two-dimensional geometric representation. Here, the same problem domain is tested, but with different geometric representations of the problem. Overall, experiments show that the quality and kind of solutions produced by HyperNEAT can be substantially affected by the geometric representation. HyperNEAT outperforms a direct encoding control even with randomized geometric representations, but performs even better when a human engineer designs a representation that reflects the actual geometry of the robot. Unfortunately, even choices in geometric layout that seem to be inconsequential a priori can significantly affect fitness. Additionally, a geometric representation can bias the type of solutions generated (e.g., make left-right symmetry more common than front-back symmetry). The results suggest that HyperNEAT practitioners can obtain good results even if they do not know how to geometrically represent a problem, and that further improvements are possible with a well-chosen geometric representation.

    Evolving coordinated quadruped gaits using the HyperNEAT generative encoding.
    Jeff Clune, Benjamin E. Beckmann, Charles Ofria, and Robert T. Pennock.
    Proceedings of IEEE on Evolutionary Computing Special Section on Evolutionary Robotics.  (2009) [pdf]

    Abstract: Legged robots show promise for complex mobility tasks, such as navigating rough terrain, but the design of their control software is both challenging and laborious. Traditional evolutionary algorithms can produce these controllers, but require manual decomposition or other problem simplification because conventionally-used direct encodings have trouble taking advantage of a problem's regularities and symmetries. Such active intervention is time consuming, limits the range of potential solutions, and requires the user to possess a deep understanding of the problem's structure. This paper demonstrates that HyperNEAT, a new and promising generative encoding for evolving neural networks, can evolve quadruped gaits without manually decomposing the problem. Analyses suggest that HyperNEAT is successful because it employs a generative encoding that can more easily reuse phenotypic modules. It is also one of the first neuroevolutionary algorithms that exploits a problem's geometric symmetries, which may aid its performance. We compare HyperNEAT to FT-NEAT, a direct encoding control, and find that HyperNEAT is able to evolve impressive quadruped gaits and vastly outperforms FT-NEAT. Comparative analyses reveal that HyperNEAT individuals are more holistically affected by genetic operators, resulting in better coordination of the quadruped's legs. Overall, the results suggest that HyperNEAT is a powerful algorithm for evolving control systems for complex, yet regular, devices, such as robots.

    Cockroaches, Drunkards, and Climbers: Modeling the Evolution of Simple Movement Strategies Using Digital Organisms.
    Wesley R. Elsberry, Laura M. Grabowski, Charles Ofria, and Robert T. Pennock.
    Proceedings of IEEE Symposium on Artificial Life (ALIFE 2009) Symposium Series on Computational Intelligence. (2009, pp. 92-99) [pdf]

    Abstract: Even the simplest of organisms may exhibit low-level intelligent behaviors in their directed movements, such as in foraging. We used the Avida digital evolution research platform to explore the evolution of movement strategies in a model environment with a single local resource that diffuses to produce a gradient, which organisms have the ability to follow. Three common strategies that evolved, Cockroach, Drunkard, and Climber, exhibit how both environmental constraints and historical contingency play a role in the emergence of intelligent behaviors. The evolved programs are also suitable for use in controllers on robots.

    •How a Generative Encoding Fares as Problem-Regularity Decreases
    Jeff Clune, Charles Ofria and Robert T. Pennock
    In G. Rudolph et. al. (Eds.), Parallel Problem Solving in Nature. Berlin: Springer-Verlag (2008, pp. 358-367) [pdf]

    Abstract: It has been shown that generative representations, which allow the reuse of code, perform well on problems with high regularity (i.e. where a phenotypic motif must be repeated many times). To date, however, generative representations have not been tested on irregular problems. It is unknown how they will fare on problems with intermediate and low amounts of regularity. This paper compares a generative representation to a direct representation on problems that range from having multiple types of regularity to one that is com- pletely irregular. As the regularity of the problem decreases, the performance of the generative representation degrades to, and then underperforms, the direct encoding. The degradation is not linear, however, yet tends to be consistent for different types of problem regularity. Furthermore, if the regularity of each type is sufficiently high, the generative encoding can simultaneously exploit differ- ent types of regularities.

    •On the Evolution of Motility and Intelligent Tactic Response
    Laura Grabowski, Wesley Elsberry, Charles Ofria and Robert T. Pennock
    Genetic and Evolutionary Computation Conference (GECCO ‘08) Proceedings. New York: Association for Computing Machinery (2008, pp. 209-216) [pdf]

    Science Education and Religion in America in the 21st Century: Holding the Center
    Jon D. Miller and Robert T. Pennock.
    In Ariela Keysar & Barry A. Kosmin (eds.) Secularism & Science in the 21st Century. Institute for the Study of Secularism in Society and Culture (2008, pp. 9-32).
    • Excerpt reprinted in 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 Creationism: Intelligent Design and Beyond. W.W. Norton & Co. (2007, pp. 309-338.) [pdf]

    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) [pdf]

    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 ReportKitzmiller et al v. Dover Area School District (2005)

    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]

    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)

    Abstract: Bayesian confirmation theorists have proposed a variety of solutions to Hempel’s paradox of the ravens. I examine those of Suppes and Horwich and argue that they do not completely avoid counter-intuitive results about the relevance of data. The Bayesian explication of evidential relevance is also susceptible to the same relevance problems that infect Hypothetico-Deductivism. I explore a possible escape to the problem of old evidence, but conclude that it only leads to problems of the same sort—any datum can be relevant to any hypothesis in any circumstance. I argue that the Bayesian evidence relation is not sufficient or necessary to determine what counts as evidence. Such difficulties warrant pursuit of alternative explications of evidential relevance. I show how the raven’s paradox may be avoided by bringing in causal considerations.

    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)

    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
    (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) [pdf]

    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

    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) [pdf]

    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) [online, pdf]

    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) [pdf]

    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)


    Book Reviews & Essays

    Review of Charles Taliaferro and Jil Evans. The Image in Mind.
    Notre Dame Philosophical Reviews (April 1, 2012)  [Online link]

    Review of Wendy Wagner & Rena Steinzor (eds.) Rescuing Science from Politics.
     Isis  (Vol. 100, pp. 957-958, 2009).

    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?
    (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.
    (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)

    Created 11/15/95. Updated 8/22/2016.

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