Clark Glymour

We outline a cognitive and computational account of causal learning in children. We propose that children employ specialized cognitive systems that allow them to recover an accurate “causal map” of the world: an abstract, coherent representation of the causal relations among events. This kind of knowledge can be perspicuously represented by the formalism of directed graphical causal models, or “Bayes nets”. Human causal learning and inference may involve computations similar to those for learnig causal Bayes nets and for predicting with them. Preliminary experimental results suggest that 2- to 4-year-old children spontaneously construct new causal maps and that their learning is consistent with the Bayes-Net formalism.

“It ain't nuthin' until I call it.”Bill Guthrie, UmpireNumerous criticisms of Adolf Grünbaum's account of conventions in physics have been published, and he has replied to most of them. Nonetheless, there seem to me to be good reasons for offering further criticism. In the first place Grünbaum's philosophy seems to me at least partly an extrapolation of one aspect of the views on conventions developed by Reichenbach and others. Since I think many of the issues which Reichenbach attempted to settle in his various discussions of conventions in physics are genuine and important, and I also think that those aspects of his views on which Grünbaum has focused are among the least satisfactory, it seems important to suggest questions and answers about conventions in physics which may develop more satisfactory Reichenbachian themes. Secondly, Grünbaum's philosophy centers on a distinction, that between extrinsic and intrinsic properties and relations, which has never been made satisfactorily clear either by Grünbaum or by his critics. Until it is clarified we will remain unsure of just what he is claiming and why we should think it true or think it false. Finally, Grünbaum's replies to his critics, especially his most recent reply, [9], involve unusually important claims which fail to be buttressed by the arguments he gives. I have in mind such claims as that we can learn something important about the ontological status of properties and relations by examining descriptions of them, that on the most straightforward and literal interpretation, the general theory of relativity is inconsistent, and that the foremost advocates of geometrodynamics, Clifford and Wheeler, were and are enmeshed in contradiction. My own view is that all of these claims are dubious or false, but I shall be less concerned with establishing their falsity than with discrediting the arguments offered for them.

Through their transcript products genes regulate the rates at which an immense variety of transcripts and subsequent proteins occur. Understanding the mechanisms that determine which genes are expressed, and when they are expressed, is one of the keys to genetic manipulation for many purposes, including the development of new treatments for disease. Viewing each gene in a genome as a distinct variable that is either on or off, or more realistically as a continuous variable, the values of some of these variables influence the values of others through the regulatory proteins they express, including, of course, the possibility that the rate of expression of a gene at one time may, in various circumstances, influence the rate of expression of that same gene at a later time. If we imagine an arrow drawn from each gene expression variable at a given time to a gene variable whose expression it influences a short while after, the result is a network, technically a directed acyclic graph. For example, the DAG in Figure 1 is a representation of a system in which the expression level of gene G1 at time 1 ) causes the expression level of G2, which in turn causes the expression level of G3. The arrows in Figure 1 which do not have a variable at their tails are “error terms” which represent all of the causes of a variable other than the ones explicitly represented in the DAG. The DAG describes more than associations—it describes causal connections among gene expression rates. A shock to a cell—by mutation, heating, chemical treatment, etc. may alter the DAG describing the relations among gene expressions, for example by activating a gene that was otherwise not expressed, producing a cascade of new expression effects. Although “knockout” experiments can reveal some of the underlying causal network of gene expression levels, unless guided by information from other sources, such experiments are limited in how much of the network structure they can reveal, due to the sheer number of possible combinations of experimental manipulations of genes necessary to reveal the complete causal network. Recent developments have made it possible to compare quantitatively the expression of tens of thousands of genes in cells from different sources in a single experiment, and to trace gene expression over time in thousands of genes simultaneously. cDNA microarrays are already producing extensive data, much of it available on the web. Thus there are calls for analytic software that can be applied to microarray and other data to help infer regulatory networks. In this paper we will review current techniques that are available for searching for the causal relations between variables, describe algorithmic and data gathering obstacles to applying these techniques to gene expression levels, and describe the prospects for overcoming these obstacles

Of the many proposals for inferring genetic regulatory structure from microarray measurements of mRNA transcript hybridization, several aim to estimate regulatory structure from the associations of gene expression levels measured in repeated samples. The repeated samples may be from a single experimental condition, or from several distinct experimental conditions; they may be “equilibrium” measurements or time series; the associations may be estimated by correlation coefficients or by conditional frequencies (for discretized measurements) or by some other statistic. This paper describes two elementary statistical difficulties for all such procedures, no matter whether based on Bayesian updating, conditional independence testing, or other machine learning procedures such as simulated annealing or neural net pruning. One difficulty obtains if large numbers of cells are aggregated in a measurement of expression levels from a common population of cells; the other obtains if small numbers of cells are aggregated or if samples are separately aggregated over different populations of cells.

Reflectance spectroscopy is a standard tool for studying the mineral composition of rock and soil samples and for remote sensing of terrestrial and extraterrestrial surfaces. We describe research on automated methods of mineral identification from reflectance spectra and give evidence that a simple algorithm, adapted from a well-known search procedure for Bayes nets, identifies the most frequently occurring classes of carbonates with reliability equal to or greater than that of human experts. We compare the reliability of the procedure to the reliability of several other automated methods adapted to the same purpose. Evidence is given that the procedure can be applied to some other mineral classes as well. Since the procedure is fast with low memory requirements, it is suitable for on-board scientific analysis by orbiters or surface rovers.

The second edition of a unique introductory text, offering an account of the logical tradition in philosophy and its influence on contemporary scientific disciplines. Thinking Things Through offers a broad, historical, and rigorous introduction to the logical tradition in philosophy and its contemporary significance. It is unique among introductory philosophy texts in that it considers both the historical development and modern fruition of a few central questions. It traces the influence of philosophical ideas and arguments on modern logic, statistics, decision theory, computer science, cognitive science, and public policy. The text offers an account of the history of speculation and argument, and the development of theories of deductive and probabilistic reasoning. It considers whether and how new knowledge of the world is possible at all, investigates rational decision making and causality, explores the nature of mind, and considers ethical theories. Suggestions for reading, both historical and contemporary, accompany most chapters. This second edition includes four new chapters, on decision theory and causal relations, moral and political theories, “moral tools” such as game theory and voting theory, and ethical theories and their relation to real-world issues. Examples have been updated throughout, and some new material has been added. It is suitable for use in advanced undergraduate and beginning graduate classes in philosophy, and as an ancillary text for students in computer science and the natural sciences.

The use of ceteris paribus clauses in philosophy and in the sciences has a long and fascinating history. Persky (1990) traces the use by economists of ceteris paribus clauses in qualifying generalizations as far back as William Petty’s Treatise of Taxes and Contributions (1662). John Cairnes’ The Character and Logical Method of Political Economy (1857) is credited with enunciating the idea that the conclusions of economic investigations hold “only in the absence of disturbing causes”.1 His Leading Principles (1874) contains the classic example of a ceteris paribus law: “The rate of wage, other things being equal, varies inversely with the supply of labour”. Carines’ ideas were popularized by Alfred Marshall in his Principles of Economics (1890) where he argued for a methodology that involved holding disturbing causes “in a pound called Caeteris Paribus”. It is unclear when the notion of ceteris paribus laws made its appearance in the philosophical literature; but in the nineteenth century it is to be found in Mill’s System of Logic (1843), and in the twentieth century it gained prominence in the Hempel-inspired debates of the 1950’s over the role of general laws in historical explanations, albeit under other labels such as quasi-laws (Rescher) or grounded generalizations (Scriven).