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The Complexity of Life in the context of Code Biology Jannie Hofmeyr Centre for Studies in Complexity and Dept. of Biochemistry, Stellenbosch University Complexity Forum, 23 Oct 2012 The major transitions of evolution Maynard Smith & Szathmáry (1995) Code Biology ? The increase in complexity during evolution Whole Organisation Complexity Parts A code establishes a conventional relation between two independent worlds World 1 (signs) World 2 (meanings) The highway code establishes a relation between Traffic signs Driving behaviours German legal code from the 15th century The Morse Code The codes of languages Sign language code The Consumer Code “An ingenious way to understand why people around the world live and buy as they do.” Codes are enabling constraints The Genetic Code Nothing? No more codes? 3.8 billion years Cultural Codes Yes, lots of them! Code Biology The Organic Codes Marcello Barbieri The Semantic Theory of Evolution (1985) The Organic Codes. An Introduction to Semantic Biology (2003) What is a code? A set of rules (a convention) that establishes a correspondence between two independent worlds Morse code (reversible, between equivalent entities) World of dots and dashes World of letters of the alphabet •— A B C D E —••• —•—• —•• • What is a code? A set of rules (a convention) that establishes a correspondence between two independent worlds Genetic code (irreversible, non-equivalent entities) World of ribonucleotide triplet sequences (codons) AUG GAC, GAU GAA, GAG GCA, GCC, GCG, GCU ACA, ACC, ACG, ACU World of amino acid sequences methionine aspartic acid glutamic acid alanine threonine A code consists of Two distinct worlds: Entities we call signs Entities we call meanings Arbitrary rules (a convention) that assign a meaning to each sign This does not imply randomness or irregularity All implemented by a code-user This does not imply only humans (mind, brain) DNA Copying mRNA Splicing code edited mRNA Genetic code protein An organic code • is a correspondence between two independent molecular worlds (messenger RNAs: nucleotide triplet sequences proteins: amino acid sequences) • requires molecular adaptors that bridge the two worlds (transfer-RNAs) • has a set of rules that guarantees biological specificity (the genetic coding rules) • is implemented by a molecular code-user (ribosomes, enzymes - the aminoacyl-tRNA transferases) The genetic code Punctuation marks Code is degenerative Phenylalanine (amino acid) Transfer-RNA the adaptor of the genetic code Adaptors are the “fingerprints” of organic codes anticodon Phenylalanine (amino acid) two different recognition sites no necessary connection between the two sites anticodon Phenylalanine (amino acid) What is connected to what is an arbitrary choice, that forms a natural convention anticodon The Organic Codes Code Adaptors World 1 World 2 Genetic tRNA DNA polypeptide Splicing snRNA pre-mRNA mRNA Signal transduction receptor for 1st msngr amplifier for 2nd msngr mediator in between 1st messengers 2nd messengers Compartment signal peptides cytosol destination compartment Cytoskeleton anchoring molecules (accessory proteins) microtubules cell shapes Adhesive cadherins cell-cell binding catenins (intracellular) modified histones transcription factors gene expression lectins (enzymes, antibodies) sugar epitopes on glycoconjugates cellular responses through signalling (Redies & Takeichi) Histone (Strahl and Allis) Sugar (Gabius) Sign (first messenger) Meaning (second messenger) 1st messenger 2nd messenger The role of codes in evolution Two fundamental processes underlie the evolution of life and replication) Catalysed assembly (replication and transcription) Copying Codified assembly (translation) Coding Copying creates organic information DNA → RNA Information can evolve (without changing meaning) Mater → Madre, Mère, Mutter, Mother, Moeder, Mamma Coding creates organic meaning UGG → tryptophan Meaning can evolve (without changing information) Broom in English: “an implement for sweeping” in Afrikaans: “the element bromine” Two fundamental processes underlie the evolution of life Relative novelties (modifies existing ent.) Copying Operates on individual molecules Variation changes information (sequence) Underlies evolution by natural selection Absolute novelties (new relationships) Coding Involves a collective set of rules Variation changes the meaning of a rule Underlies evolution by natural conventions Any new code establishes relationships that never existed before in the world. Natural conventions and biocomplexity A new organic code (natural convention), • by linking two previously independent molecular worlds, • opens a new relational space for evolution to explore, so • making an increase in complexity possible The number of organic codes in an organism is a new measure of its biocomplexity Take-home message Biological codes can explain the major transitions of evolution and the increase in the complexity of life during evolution.