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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.