Superadditive correlation.

The fact that correlation does not imply causation is well known. Correlation between variables at two sites does not imply that the two sites directly interact, because, e.g., correlation between distant sites may be induced by chaining of correlation between a set of intervening, directly interacting sites. Such "noncausal correlation" is well understood in statistical physics: an example is long-range order in spin systems, where spins which have only short-range direct interactions, e.g., the Ising model, display correlation at a distance. It is less well recognized that such long-range "noncausal" correlations can in fact be stronger than the magnitude of any causal correlation induced by direct interactions. We call this phenomenon superadditive correlation (SAC). We demonstrate this counterintuitive phenomenon by explicit examples in (i) a model spin system and (ii) a model continuous variable system, where both models are such that two variables have multiple intervening pathways of indirect interaction. We apply the technique known as decimation to explain SAC as an additive, constructive interference phenomenon between the multiple pathways of indirect interaction. We also explain the effect using a definition of the collective mode describing the intervening spin variables. Finally, we show that the SAC effect is mirrored in information theory, and is true for mutual information measures in addition to correlation measures. Generic complex systems typically exhibit multiple pathways of indirect interaction, making SAC a potentially widespread phenomenon. This affects, e.g., attempts to deduce interactions by examination of correlations, as well as, e.g., hierarchical approximation methods for multivariate probability distributions, which introduce parameters based on successive orders of correlation.

Neural networks for determining protein specificity and multiple alignment of binding sites.

We use a quantitative definition of specificity to develop a neural network for the identification of common protein binding sites in a collection of unaligned DNA fragments. We demonstrate the equivalence of the method to maximizing Information Content of the aligned sites when simple models of the binding energy and the genome are employed. The network method subsumes those simple models and is capable of working with more complicated ones. This is demonstrated using a Markov model of the E. coli genome and a sampling method to approximate the partition function. A variation of Gibbs' sampling aids in avoiding local minima.

Gene-sized DNA molecules of the macronuclei in three species of hypotrichs: size distributions and absence of nicks. DNA of ciliated protozoa. VIII.

Macronuclear DNA s from three related hypotrichous ciliated protozoans were compared by agarose gel electrophoresis. Each was shown to be composed of DNA duplexes that yielded a unique pattern of bands overlying a continuous distribution of DNA sizes ranging from approximately 400 bp to approximately 20,000 bp. By EM, the number average molecular sizes for double-stranded DNA were 2,200 bp for Oxytricha sp., 2,514 bp for Stylonychia pustulata and 18,836 bp for Euplotes aediculatus. Contrary to previous reports we present evidence that the macronuclear DNA s in each of these three organisms lack single-stranded interruptions.

A model for replication of the ends of linear chromosomes.

Linear chromosomes possessing internal repeats of their terminal sequences can form intramolecular crossed-strand exchanges that allow replication of the chromosome ends. Evidence is discussed that such a mechanism may be utilized during replication of herpes simplex virus DNA and during replication of macronuclear DNA from the hypotrichous ciliate Oxytricha.