1. The Language of genes Su Dong Kim Biointelligence Lab.
David D. Searls, Nature 420, (2002)
Su Dong Kim
Biointelligence Lab.
Interdisciplinary Program in Cognitive Science
Seoul National University
27 MAY 2003
(C) 2003, SNU Biointelligence Lab, 

2. (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, 

3. 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, 

4. The Chomsky hierarchy and formal language theory
(C) 2003, SNU Biointelligence Lab, 

5. 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, 

6. 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, 

7. (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, 

8. 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, 

9. 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, 

10. 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, 

11. 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,