Nested Balanced Incomplete Block Designs

If the blocks of a balanced incomplete block design (BIBD) with v treatments and with parameters (v; b1;r;k1) are each partitioned into sub-blocks of size k2, and the b2 =b1k1=k2 sub-blocks themselves constitute a BIBD with parameters (v; b2;r;k2), then the system of blocks, sub-blocks and treatments is, by de4nition, a nested BIBD (NBIBD). Whist tournaments are special types of NBIBD with k1 =2k2= 4. Although NBIBDs were introduced in the statistical literature in 1967 and have subsequently received occasional attention there, they are almost unknown in the combinatorial literature, except in the literature of tournaments, and detailed combinatorial studies of them have been lacking. The present paper therefore reviews and extends mathematical knowledge of NBIBDs. Isomorphism and automorphisms are defined for NBIBDs, and methods of construction are outlined. Some special types of NBIBD are de4ned and illustrated. A first-ever detailed table of NBIBDs with v⩽16, r⩽30 is provided; this table contains many newly discovered NBIBDs. © 2001 Elsevier Science B.V. All rights reserved

Methodological Fundamentalism: or why Batterman’s Different Notions of ‘Fundamentalism’ may not make a Difference

I argue that the distinctions Robert Batterman (2004) presents between ‘epistemically fundamental’ versus ‘ontologically fundamental’ theoretical approaches can be subsumed by methodologically fundamental procedures. I characterize precisely what is meant by a methodologically fundamental procedure, which involves, among other things, the use of multilinear graded algebras in a theory’s formalism. For example, one such class of algebras I discuss are the Clifford (or Geometric) algebras. Aside from their being touted by many as a “unified mathematical language for physics,” (Hestenes (1984, 1986) Lasenby, et. al. (2000)) Finkelstein (2001, 2004) and others have demonstrated that the techniques of multilinear algebraic ‘expansion and contraction’ exhibit a robust regularizablilty. That is to say, such regularization has been demonstrated to remove singularities, which would otherwise appear in standard field-theoretic, mathematical characterizations of a physical theory. I claim that the existence of such methodologically fundamental procedures calls into question one of Batterman’s central points, that “our explanatory physical practice demands that we appeal essentially to (infinite) idealizations” (2003, 7) exhibited, for example, by singularities in the case of modeling critical phenomena, like fluid droplet formation. By way of counterexample, in the field of computational fluid dynamics (CFD), I discuss the work of Mann & Rockwood (2003) and Gerik Scheuermann, (2002). In the concluding section, I sketch a methodologically fundamental procedure potentially applicable to more general classes of critical phenomena appearing in fluid dynamics

Evolution of Metabolic Networks: A Computational Framework

Background: The metabolic architectures of extant organisms share many key pathways such as the citric acid cycle, glycolysis, or the biosynthesis of most amino acids. Several competing hypotheses for the evolutionary mechanisms that shape metabolic networks have been discussed in the literature, each of which finds support from comparative analysis of extant genomes. Alternatively, the principles of metabolic evolution can be studied by direct computer simulation. This requires, however, an explicit implementation of all pertinent components: a universe of chemical reaction upon which the metabolism is built, an explicit representation of the enzymes that implement the metabolism, of a genetic system that encodes these enzymes, and of a fitness function that can be selected for. Results: We describe here a simulation environment that implements all these components in a simplified ways so that large-scale evolutionary studies are feasible. We employ an artificial chemistry that views chemical reactions as graph rewriting operations and utilizes a toy-version of quantum chemistry to derive thermodynamic parameters. Minimalist organisms with simple string-encoded genomes produce model ribozymes whose catalytic activity is determined by an ad hoc mapping between their secondary structure and the transition state graphs that they stabilize. Fitness is computed utilizing the ideas of metabolic flux analysis. We present an implementation of the complete system and first simulation results. Conclusions: The simulation system presented here allows coherent investigations into the evolutionary mechanisms of the first steps of metabolic evolution using a self-consistent toy univers