Genomics and proteomics: a signal processor's tour

The theory and methods of signal processing are becoming increasingly important in molecular biology. Digital filtering techniques, transform domain methods, and Markov models have played important roles in gene identification, biological sequence analysis, and alignment. This paper contains a brief review of molecular biology, followed by a review of the applications of signal processing theory. This includes the problem of gene finding using digital filtering, and the use of transform domain methods in the study of protein binding spots. The relatively new topic of noncoding genes, and the associated problem of identifying ncRNA buried in DNA sequences are also described. This includes a discussion of hidden Markov models and context free grammars. Several new directions in genomic signal processing are briefly outlined in the end

The Sorcery of Context

There are countless one-word palindromes in the English language, many of them common, such as Mom, Dad, poop, boob, sees, racecar, level, and rotor, as well as the names Bob, Otto, Ava, and Hannah. At their most base level, one-word palindromes signify a concept, and the words themselves are palindromic more by coincidence than anything else; they sound perfectly natural when spoken. Slightly longer phrase palindromes, like a red-eyed era and to prefer pot are evasive as naturally uttered speech and in fact probably have been spoken by many yet recognized by few to no listeners or speakers

Definability by Horn Formulas and Linear Time on Cellular Automata

We establish an exact logical characterization of linear time complexity of cellular automata of dimension d, for any fixed d: a set of pictures of dimension d belongs to this complexity class iff it is definable in existential second-order logic restricted to monotonic Horn formulas with built-in successor function and d+1 first-order variables. This logical characterization is optimal modulo an open problem in parallel complexity. Furthermore, its proof provides a systematic method for transforming an inductive formula defining some problem into a cellular automaton that computes it in linear time

A Day in Linguistic History

The day begins like any other day. A few students straggle toward the Union in search of coffee and eggs. Delivery trucks come on the campus. At the entrance, the sign still reads SUSAN DOE UNIVERSITY FOUNDED 1894 NO SOLICITORS. This is it, the University, known affectionately by students and faculty as Sue Doe U

A Synchronology: the contemporary and other times

I curated this group exhibition in collaboration with Glasgow-based art's organisation The Common Guild. Drawing of the roster of highly significant contemporary artists with which TCG has worked over the past decade I selected a number of artworks that reflect on how time is marked and measured. These works often contested the restrictions of the conventional means of mapping and organising time, such as the clock, the calendar and the timeline. The artists included were: Robert Barry, Gerard Byrne, Phil Collins, Tacita Dean, Ruth Ewan, Sharon Hayes, Roman Ondak, Simon Starling and Corin Sworn. As a foil to the works made by this internationally renowned group of artists, which ranged from film and photography to conceptual statements and performance works, the exhibition also included a noted nineteenth-century timeline, Stephen Hawes' 'Synchronology of the Principal Events in Sacred and Profane History.' A series of events supported the show itself. These included a public discussion with Common Guild Director Katrina Brown and curator Kitty Anderson, and screenings of Tacita Dean's 'Event for a Stage' (a Scottish premiere of the work) and of Phil Collins' 'Baghdad Screen Tests'. In collaboration with Glasgow Film Theatre, the exhibition's closing was marked by a special screening of Stanley Kubrick's masterpiece 'Barry Lyndon,' selected and introduced by artist Gerard Byrne. The exhibition was well reviewed in The Skinny, Art Agenda and Art Monthly

Leigh Mercer, Palindromist

These seven words have earned Leigh Mercer a place among the logological immortals. Ask the man on the street for an example of a palindrome, and (if he knows what you are talking about) you will likely have this quoted back at you. (Or, perhaps, Madam, I\u27m Adam. ) But it is ironic that Mercer did not want to be remembered in this way; he chided me once in a letter (October 1971) ...I am writing again to make sure that you don\u27t think of me purely as a \u27drome man. I have had a number of hobbies, am only interested in ideas which only a few others care for..