The Language of genes Su Dong Kim Biointelligence Lab. David D. Searls, Nature 420, 211-217 (2002) Su Dong Kim Biointelligence Lab. Interdisciplinary Program in Cognitive Science Seoul National University 27 MAY 2003 (C) 2003, SNU Biointelligence Lab, http://bi.snu.ac.kr/

(C) 2003, SNU Biointelligence Lab, http://bi.snu.ac.kr/ Outline Introduction Mathematical linguistics and macromolecules Computational linguistics and genes Historical linguistics and evolution Literary linguistics and the genome (C) 2003, SNU Biointelligence Lab, http://bi.snu.ac.kr/

Introduction 1950s : ‘Modern era’ of Linguistics & Biology Linguistics Noam Chomsky Watson & Crick Universal Grammar Structure of DNA Formal Language Theory Molecular Biology (C) 2003, SNU Biointelligence Lab, http://bi.snu.ac.kr/

The Chomsky hierarchy and formal language theory (C) 2003, SNU Biointelligence Lab, http://bi.snu.ac.kr/

Mathematical linguistics and macromolecules Nucleic acid linguistics The language of RNA is at least context-free Natural languages seem to be beyond context-free Protein linguistics Grammar Operation Regular Concatenation Context-free Insertion Context sensitive Interleaving (C) 2003, SNU Biointelligence Lab, http://bi.snu.ac.kr/

Nucleic acid linguistics Grammar-style derivations of idealized versions of RNA structures : “She saw the man with telescope” a Stem b Branch c Pseudoknot d Attenuator (C) 2003, SNU Biointelligence Lab, http://bi.snu.ac.kr/

(C) 2003, SNU Biointelligence Lab, http://bi.snu.ac.kr/ Protein linguistics Protein domain arrangement and the Chomsky hierarchy a Context free ; Insertion b Context sensitive ; Interleaving (C) 2003, SNU Biointelligence Lab, http://bi.snu.ac.kr/

Computational linguistics and genes Computational biology string or words segment of a genome The Lexical Level Phonemes or Characters The Syntactic Level Grammar rules The Semantic Level Meaning The Pragmatic Level Context Colourless green ideas sleep furiously (C) 2003, SNU Biointelligence Lab, http://bi.snu.ac.kr/

History of gene-finding algorithms 1980s : The Lexical affair Oligonucleotide frequencies & periodicities Early 1990s : Lexical elements + Syntactic cast Gene grammar + general purpose parsor Advantages : alternative splicing & versatility Latter-day : Customized to a particular domain ‘Standard model’ gene structure hard-wired HMM (hidden Markov model) : GenScan & Genie HMM algorithm tRNA secondary structure Regular grammar Non-regular grammar (C) 2003, SNU Biointelligence Lab, http://bi.snu.ac.kr/

Historical linguistics and evolution Evolution of Languages & Species Different languages Different species Meme, cognates Gene, orthologues Glottochronology Evolutionary ‘Molecular clock’ Blending, Creolization Recombination, Mutation Noun + noun, Idioms Protein–protein interaction, Participation in Pathways (C) 2003, SNU Biointelligence Lab, http://bi.snu.ac.kr/

Literary linguistics and the genome Pfam protein domain of the yeast vs. the words in Romeo and Juliet Textual Criticism Bioinformatics (C) 2003, SNU Biointelligence Lab, http://bi.snu.ac.kr/