Chemical discovery as belief revision

In this paper we describe STAHLp, a system that constructs componential models of chemical substances. STAHLp is a descendent of Zytkow and Simon's (1986) STAHL system, and both use chemical reactions and known componential models in order to construct new chemical models. However, STAHLp employs a more unified and effective strategy for recovering from erroneous inferences, based partly on de Kleer's (1984) assumption-based method of belief revision. This involves recording the underlying source beliefs or premises which lead to each inferred reaction or model. Where Zytkow and Simon's system required multiple methods for detecting errors and recovering from them, STAHLp uses a more powerful representation and additional rules which allow a unified method for error detection and recovery. When given the same initial data, the new system constructs the same historically correct models as STAHL, but it has other capabilities as well. In particular, STAHLp can modify data it has been given if this is necessary to achieve consistent models, and then proceed to construct new models based on the revised data

Theory formation by abduction : initial results of a case study based on the chemical revolution

Abduction is the process of constructing explanations. This chapter suggests that automated abduction is a key to advancing beyond the "routine theory revision" methods developed in early AI research towards automated reasoning systems capable of "world model revision" — dramatic changes in systems of beliefs such as occur in children's cognitive development and in scientific revolutions. The chapter describes a general approach to automating theory revision based upon computational methods for theory formation by abduction. The approach is based on the idea that, when an anomaly is encountered, the best course is often simply to suppress parts of the original theory thrown into question by the contradiction and to derive an explanation of the anomalous observation based on relatively solid, basic principles. This process of looking for explanations of unexpected new phenomena can lead by abductive inference to new hypotheses that can form crucial parts of a revised theory. As an illustration, the chapter shows how some of Lavoisier's key insights during the Chemical Revolution can be viewed as examples of theory formation by abduction

Theory formation by abduction : a case study based on the chemical revolution

Abduction is the process of constructing explanations. This chapter suggests that automated abduction is a key to advancing beyond the "routine theory revision" methods developed in early AI research towards automated reasoning systems capable of "world model revision" - dramatic changes in systems of beliefs such as occur in children's cognitive development and in scientific revolutions. The chapter describes a general approach to automating theory revision based upon computational methods for theory formation by abduction. The approach is based on the idea that, when an anomaly is encountered, the best course is often simply to suppress parts of the original theory thrown into question by the contradiction and to derive an explanation of the anomalous observation based on relatively solid, basic principles. This process of looking for explanations of unexpected new phenomena can lead by abductive inference to new hypotheses that can form crucial parts of a revised theory. As an illustration, the chapter shows how some of Lavoisier's key insights during the Chemical Revolution can be viewed as examples of theory formation by abduction

Reverse Bayesianism and Act Independence

Karni and Vierø (2013) propose a model of belief revision under growing awareness—reverse Bayesianism—which posits that as a person becomes aware of new acts, consequences, or act-consequence links, she revises her beliefs over an expanded state space in a way that preserves the relative likelihoods of events in the original state space. A key feature of the model is that reverse Bayesianism does not fully determine the revised probability distribution. We provide an assumption—act independence—that imposes additional restrictions on reverse Bayesian belief revision. We show that with act independence knowledge of the probabilities of the new act events in the expanded state space is sufficient to fully determine the revised probability distribution in each case of growing awareness. We also explore what additional knowledge is required for reverse Bayesianism to pin down the revised probabilities without act independence

Josiah Parsons Cooke Jr.: Epistemology in the Service of Science, Pedagogy, and Natural Theology

Josiah Parsons Cooke established chemistry education at Harvard University, initiated an atomic weight research program, and broadly impacted American chemical education through his students, the introduction of laboratory instruction, textbooks, and influence on Harvard's admissions requirements. The devoutly Unitarian Cooke also articulated and defended a biogeochemical natural theology, which he defended by arguing for commonalities between the epistemologies of science and religion. Cooke's pre-Mendeleev classification scheme for the elements and atomic weight research were motivated by his interest in numerical order in nature, which reflected his belief in a divine lawgive

A beginner's guide to belief revision and truth maintenance systems

This brief note is intended to familiarize the non-TMS audience with some of the basic ideas surrounding classic TMS's (truth maintenance systems), namely the justification-based TMS and the assumption-based TMS. Topics of further interest include the relation between non-monotonic logics and TMS's, efficiency and search issues, complexity concerns, as well as the variety of TMS systems that have surfaced in the past decade or so. These include probabilistic-based TMS systems, fuzzy TMS systems, tri-valued belief systems, and so on

The computer revolution in science: steps towards the realization of computer-supported discovery environments

The tools that scientists use in their search processes together form so-called discovery environments. The promise of artificial intelligence and other branches of computer science is to radically transform conventional discovery environments by equipping scientists with a range of powerful computer tools including large-scale, shared knowledge bases and discovery programs. We will describe the future computer-supported discovery environments that may result, and illustrate by means of a realistic scenario how scientists come to new discoveries in these environments. In order to make the step from the current generation of discovery tools to computer-supported discovery environments like the one presented in the scenario, developers should realize that such environments are large-scale sociotechnical systems. They should not just focus on isolated computer programs, but also pay attention to the question how these programs will be used and maintained by scientists in research practices. In order to help developers of discovery programs in achieving the integration of their tools in discovery environments, we will formulate a set of guidelines that developers could follow

Does Changing the Definition of Science Solve the Establishment Clause Problem for Teaching Intelligent Design as Science in Public Schools? Doing an End-Run Around the Constitution

[Excerpt] When Charles Darwin published On the Origin of Species By Means of Natural Selection in 1859, it sparked some of the most contentious debates in American intellectual history, debates that continue to rage today. Although these debates have numerous political ramifications, the question posed in this paper is narrow: Does the Establishment Clause permit a particular assessment of current evolutionary theory – intelligent design (“ID”) – to be taught as science in American elementary and secondary public schools? This article shows that it does not. To understand current disputes over whether and how to teach the origins of life – including human life – in the science classes of public schools, it is necessary to understand both the legal and the scientific frameworks. I describe those general frameworks below in Part II. There I also show that Darwin’s theory of evolution meets the definition of science, an important step in showing that teaching evolution has a bona fide secular purpose as required by the Constitution. I also explain the relationship between Darwin’s theory and other explanations for the origins of life, such as creationism and classical versions of the design inference. I show, in particular, that neither creationism nor the design inference meets the definition of science, but belong rather to the religious domain. In Part III, I examine the origins of the conflict between evolutionary theory and creationism. That debate centered around two questions: May states constitutionally prohibit public schools from teaching evolution because its account of human origins is antithetical to the account set forth in the Book of Genesis? If not, does the Establishment Clause of the First Amendment permit a state to insist that its schools provide a balanced treatment of creationism and evolution when presenting human origins theories? Examining the historical development of the Establishment Clause in this context illuminates the question whether the current “teach the controversy” dispute is a historical product of the past controversies involving creationists. Answering that question helps determine whether efforts by ID proponents have a constitutionally impermissible religious purpose. In Part IV, I examine the modern theory of ID to determine whether it meets the definition of science. Again, answering that question helps to determine whether current efforts by ID proponents to “teach the controversy” have a secular purpose. I conclude that they do not, by showing that ID not only fails to meet the definition of science, but it also is linked to such famous proofs for the existence of God as St. Thomas Aquinas’ fifth proof, and Bishop Paley’s design inference. In Part V, I examine one school board’s solution to the constitutional problem – to change the definition of science. I conclude that the school board’s actions are unconstitutional to the extent they are attempting to inject proofs for the existence of God into public school science classes. And in Part VI, I draw some broad conclusions regarding the compatibility of theistic and scientific responses to origins of life inquiry

The use of phylogeny to interpret cross-cultural patterns in plant use and guide medicinal plant discovery: an example from Pterocarpus (Leguminosae)

The study of traditional knowledge of medicinal plants has led to discoveries that have helped combat diseases and improve healthcare. However, the development of quantitative measures that can assist our quest for new medicinal plants has not greatly advanced in recent years. Phylogenetic tools have entered many scientific fields in the last two decades to provide explanatory power, but have been overlooked in ethnomedicinal studies. Several studies show that medicinal properties are not randomly distributed in plant phylogenies, suggesting that phylogeny shapes ethnobotanical use. Nevertheless, empirical studies that explicitly combine ethnobotanical and phylogenetic information are scarce.In this study, we borrowed tools from community ecology phylogenetics to quantify significance of phylogenetic signal in medicinal properties in plants and identify nodes on phylogenies with high bioscreening potential. To do this, we produced an ethnomedicinal review from extensive literature research and a multi-locus phylogenetic hypothesis for the pantropical genus Pterocarpus (Leguminosae: Papilionoideae). We demonstrate that species used to treat a certain conditions, such as malaria, are significantly phylogenetically clumped and we highlight nodes in the phylogeny that are significantly overabundant in species used to treat certain conditions. These cross-cultural patterns in ethnomedicinal usage in Pterocarpus are interpreted in the light of phylogenetic relationships.This study provides techniques that enable the application of phylogenies in bioscreening, but also sheds light on the processes that shape cross-cultural ethnomedicinal patterns. This community phylogenetic approach demonstrates that similar ethnobotanical uses can arise in parallel in different areas where related plants are available. With a vast amount of ethnomedicinal and phylogenetic information available, we predict that this field, after further refinement of the techniques, will expand into similar research areas, such as pest management or the search for bioactive plant-based compounds