Neurophysiology

Contains reports on two research projects.Bell Telephone Laboratories, Inc.National Institutes of Health (Grant B-1865-(C3))National Institutes of Health (Grant MH-04737-02)The Teagle Foundation, Inc.U.S. Air Force (Aeronautical Systems Division) under Contract AF33(616)-778

Neurophysiology

Contains reports on two research projects.Teagle Foundation, IncorporatedNational Institutes of HealthBell Telephone Laboratories, Incorporate

Neurophysiology

Contains reports on one research project.National Science FoundationOffner Electronics, IncorporatedTeagle FoundationBell Telephone Laboratories, Incorporate

Neurophysiology

Contains reports on eight research projects.Bell Telephone Laboratories, Inc.Teagle Foundation, Inc.National Science Foundation (Grant GP-2495)National Institutes of Health (Grants MH-04737-04)National Institutes of Health (NB-04985-01)U. S. Air Force. Aeronautical Systems Division (Contract AF 33(615)-1747)U. S. Air Force. Cambridge Research Laboratories (Contract AF19(628)-3807)U. S. Air Force. Electronic Systems Division (Contract AF19(628)-4147)National Aeronautics and Space Administration (Grant NsG-496

Neurophysiology

Contains reports on three research projects.Bell Telephone Laboratories, IncorporatedTeagle FoundationNational Science FoundationOffner Electronics, Incorporate

Genome-based peptide fingerprint scanning

We have implemented a method that identifies the genomic origins of sample proteins by scanning their peptide-mass fingerprint against the theoretical translation and proteolytic digest of an entire genome. Unlike previously reported techniques, this method requires no predefined ORF or protein annotations. Fixed-size windows along the genome sequence are scored by an equation accounting for the number of matching peptides, the number of missed enzymatic cleavages in each peptide, the number of in-frame stop codons within a window, the adjacency between peptides, and duplicate peptide matches. Statistical significance of matching regions is assessed by comparing their scores to scores from windows matching randomly generated mass data. Tests with samples from Saccharomyces cerevisiae mitochondria and Escherichia coli have demonstrated the ability to produce statistically significant identifications, agreeing with two commonly used programs, peptident and mascot, in 86% of samples analyzed. This genome fingerprint scanning method has the potential to aid in genome annotation, identify proteins for which annotation is incorrect or missing, and handle cases where sequencing errors have caused framing mistakes in the databases. It might also aid in the identification of proteins in which recoding events such as frameshifting or stop-codon read-through have occurred, elucidating alternative translation mechanisms. The prototype is implemented as a client/server pair, allowing the distribution, among a set of cluster nodes, of a single or multiple genomes for concurrent analysis

Neurophysiology

Contains reports on seven research projects.Bell Telephone Laboratories, IncorporatedNational Institutes of HealthTeagle Foundation, IncorporatedUnited States Air Force (WADD Contract AF33(616)-7783

Neurophysiology

Contains a report on a research project

The Algorithmic Origins of Life

Although it has been notoriously difficult to pin down precisely what it is that makes life so distinctive and remarkable, there is general agreement that its informational aspect is one key property, perhaps the key property. The unique informational narrative of living systems suggests that life may be characterized by context-dependent causal influences, and in particular, that top-down (or downward) causation -- where higher-levels influence and constrain the dynamics of lower-levels in organizational hierarchies -- may be a major contributor to the hierarchal structure of living systems. Here we propose that the origin of life may correspond to a physical transition associated with a shift in causal structure, where information gains direct, and context-dependent causal efficacy over the matter it is instantiated in. Such a transition may be akin to more traditional physical transitions (e.g. thermodynamic phase transitions), with the crucial distinction that determining which phase (non-life or life) a given system is in requires dynamical information and therefore can only be inferred by identifying causal architecture. We discuss some potential novel research directions based on this hypothesis, including potential measures of such a transition that may be amenable to laboratory study, and how the proposed mechanism corresponds to the onset of the unique mode of (algorithmic) information processing characteristic of living systems.Comment: 13 pages, 1 tabl