Code Biology
A glossary of terms and concepts
by
Marcello Barbieri, Joachim de Beule, Jan-Hendrik Hofmeyr
Contents
Abduction
A category of logic introduced by Charles Peirce in addition to the Aris-totelian categories of ‘induction’ and ‘deduction’. It is the operation of ‘jumping to conclusions’, or ‘getting a result from incomplete data’.
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Adaptor
An object that provides a link between independent entities such as signs and
meanings.An adaptor is the physical structure that implements the rule of
a code. In the Morse code, for example, the adaptors are the neural circuits
that make connections in the brain between letters of the alphabet and groups
of dot and dashes. In protein synthesis, the adaptors are the transfers RNAs,
the molecules that establish a correspondence (or a mapping) between codons
(organic signs) and amino acids (organic meanings).
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Agent
An Agent is a ‘maker ’, more precisely an ‘artifact-maker ’. It is a system that
makes ‘artifacts’, where the term ‘artifact’ means any object that cannot be
formed spontaneously in Nature. A novel, a painting or a computer, for
example, are cultural artifacts. Genes and proteins are molecular artifacts
because they are manufactured by molecular machines. Making an artifact
means assembling it from components. A novel is assembled from words, a
protein is assembled from amino acids, a gene is assembled from nucleotides.
But the components of an artifact do not self-assemble spontaneously and it
is the ‘artifact-maker’ that arranges them in a specific order. This order, in
turn, must come from some other object and the job of the artifact-maker is
to assemble the components of an object (for example a protein) in the order
provided by another object (for example a gene). This means that an artifact-
maker is a system that makes use of objects that stand for other objects (for
example codons that stand for amino acids), and these are, by definition,
signs. An artifact-maker, therefore, is necessarily a semiotic system because
it creates an arbitrary link between the objects of two independent worlds
that are referred to as signs and meanings.
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Anthroposemiosis
It is the semiosis that takes place only in humans as distinct from ‘zoosemio-
sis’, the form that is typical of animals, and to ‘biosemiosis’, the form that
exists in all living creatures. According to some claims, there is also a form
of semiosis in the physical world which is referred to as ‘physiosemiosis’ (or
‘pansemiosis’), but there is no scientific evidence in support of this view.
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Apoptosis
It is a form of cell death that is not caused by accidental injuries or old age
but by active cell suicide. This is induced by the activation of specific sui-
cide genes, and it is a universal mechanism of embryonic development, one
that is used to shape virtually all organs of the body. The key point is that
suicide genes exist in all cells and the signalling molecules that switch them
on and off are of many different types. This means that the recognition of a
signalling molecule and the activation of the suicide genes are two indepen-
dent processes. There simply is no necessary connection between them and
the only realistic solution is that the link is established by the rules of an
Apoptosis code, i.e., a code that determines which signalling molecules switch
on the apoptosis genes in which tissue.
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Arbitrariness
In science, arbitrariness means independence from physical necessity. Codes
and conventions, for example, are arbitrary because their rules are not dic-
tated by the laws of physics. In the case of the genetic code, it is has been
proven beyond doubt that any codon can be associated with any amino acids,
just as any group of dots and dashes can be associated with any letter of the
alphabet. The genetic code, in short, is a real code because it does have the
essential feature that defines any code: the arbitrariness of the coding rules.
It must be underlined, however, that this point has raised streams of objec-
tions, all claiming that arbitrariness is a myth because there are all sorts of
regularities in the genetic code. In reality, a few simple cases are enough to
deflate this argument. In the Morse code, for example, the most frequent
letters of the alphabet are associated with the simplest combinations of dots
and dashes, but nobody would dream to conclude that the Morse code is
not made of arbitrary rules because of that regularity. In any language there
are countless regularities, and yet arbitrariness exists even in the number
and the type of letters that make up an alphabet. Regularities, in short, are
perfectly compatible with arbitrariness. What they are not compatible with
is randomness, but arbitrariness should not be confused with randomness.
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Artifacts
Artifacts are all objects that cannot be formed spontaneously in Nature. For
a long time it has been assumed that artifacts are necessarily cultural prod-
ucts, i.e., that only man can produce them. In reality genes and proteins too
are artifacts because they are manufactured by molecular machines. Primor-
dial nucleic acids and primordial polypeptides did appear spontaneously on
the primitive Earth, but could not evolve into the first cells because sponta-
neous molecules do not have biological specificity. They evolved instead into
primitive molecular machines, and it was these machines and their products
that eventually gave origin to the first cells. The crucial point is that genes
and proteins with the same sequence cannot be reproduced indefinitely by
spontaneous reactions. This can be achieved only by manufacturing pro-
cesses that stick monomers together in the order provided by a template.
Only this operation can guarantee biological specificity, and it was therefore
the appearance of ‘molecular machines’, i.e., of ‘artifact-makers’, or ‘agents’,
that produced the specific molecular artifacts that we call genes and proteins.
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Autonomy
In biology it is a form of relative independence from the environment, and
it is achieved when living systems acquire the ability to store materials and
energy for later use. It is also achieved when they acquire a greater degree of
complexity in the course of evolution, because this allows them to increase
the number and the quality of their interactions with the outside world.
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Biolinguistics
It is a research field dedicated to studying language as any other attribute
of our species, and more specifically, as an organ of the mind/brain. In
the editorial of the first issue of the journal Biolinguistics (2007) the editors
Cedric Boeckx and Kleanthes Grohmann stated that there is both a weak
and a strong sense to the term ‘biolinguistics’. The weak sense refers to
the fact that linguists are seriously engaged in “discovering the properties of
grammar, in effect carrying out the research program Chomsky initiated in
Syntactic Structures (1957)”. The strong sense refers to “attempts to pro-
vide explicit answers to questions that require the combination of linguistic
insights and insights from related disciplines (evolutionary biology, genetics,
neurology, psychology, etc.).” They underlined that Eric Lenneberg’s book,
Biological Foundations of Language (1967), was an outstanding example of
research in biolinguistics in the strong sense.
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Biosemiotics
The synthesis of biology and semiotics that today we call ‘biosemiotics’
was developed independently in two fields that lie at the opposite ends of
academia. The first origin took place in molecular biology as a result of
the discovery of the genetic code (the name “molecular biosemiotics” was
coined by Marcel Florkin in 1974 precisely to designate the study of semio-
sis at the molecular level). The second origin took place in the humanities
and was masterminded by Thomas Sebeok in two distinct stages. In 1963,
Sebeok extended semiosis from human culture to all animals and founded
the new research field of ‘zoosemiotics’ (Sebeok 1963). More than 20 years
later, he made a second extension from animals to all living creatures and
called it ‘biosemiotics’ (Anderson et al. 1984, Sebeok and Umiker-Sebeok
1992, Sebeok 2001). These two ‘birthplaces’ of biosemiotics have nurtured
two different concepts of semiosis that still divide the field into two opposite
schools. In biology, the existence of a real genetic code is proof enough that
semiosis exists at the molecular level, and this implies that organic semiosis
is defined by coding. In the humanities, the dominant view is the Peircean
concept that semiosis is always an interpretive process, and this implies that
Peircean semiosis is defined by interpretation. We have therefore two types
of semiosis, one based on coding and one based on interpretation, and each
of them represents phenomena that undoubtedly exist in Nature. There is
ample evidence that animals are capable of interpreting the world, and this
clearly means that Peircean (or interpretive) semiosis is a reality. But it is
also evident that the rules of the genetic code do not depend on interpretation
because they have been the same in all living creatures and in all environ-
ments ever since the origin of life. The division between the two schools
of biosemiotics is precisely about this point. According to the ‘biological’
school, the two types of semiosis are both present in Nature and represent
two distinct evolutionary developments. According to the Peircean school,
instead, interpretive semiosis is the only type that has existed on Earth ever
since the origin of life.
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Brain
The nervous system is made of three types of neurons: (1) the sensory neu-
rons transmit the electrical signals produced by the sense organs, (2) the
motor neurons deliver electrical signals to the motor organs (muscles and
glands), and (3) the intermediate neurons provide a bridge between them. In
some cases the sensory neurons are directly connected to the motor neurons,
thus forming a reflex arch, a system that provides a quick stimulus-response
reaction known as a reflex. In a few cases, therefore, intermediate neurons
can be dispensed with, but most animals use them extensively, and what we
observe in evolution is that brains increased their size primarily by increasing
the number of the intermediate neurons. The evolution of the brain, in other
words, has largely been the evolution of the intermediate brain, a process
during which the intermediate neurons started processing the signals that
they were transmitting, and that opened up a whole new world of possibili-
ties. In practice, the processing evolved in two great directions and produced
two very different outcomes. One was the formation of neural networks that
give origin to feedback systems and provide a sort of ‘automatic pilot’ for
any given physiological function. The other was the generation of feelings
and instincts. The first processing was totally unconscious and was carried
out by a component of the intermediate brain that can be referred to as the
cybernetic brain. The second processing was adopted by another major com-
ponent of the intermediate brain that can be referred to as the instinctive
brain. The intermediate brain, in short, evolved from a primitive reflex-arch
system and developed two distinct types of neural processing, one completely
unconscious and the second controlled by instincts.
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Brain as a modelling system
The brain produces what we are used to call feelings, sensations, perceptions,
mental images and so on, but it is convenient to have also a more general
term that applies to all of them. Here we follow the convention that all prod-
ucts of brain processing can be referred to as brain models. The brain, in
other words, uses the signals from the sense organs to generate models of the
world. A visual image, for example is a model of the information delivered
by the retina, and a feeling of hunger is a model obtained by processing the
signals sent by the sense detectors of the digestive apparatus. The brain can
be described in this way as a modelling system, a concept that has been
popularized by Thomas Sebeok and has acquired an increasing importance
in semiotics (Sebeok and Danesi, 2000). The term was actually coined by
Juri Lotman, who described language as the ‘primary modelling system’ of
our species (Lotman, 1991), but Sebeok underlined that language evolved
from animal systems, and should be regarded as a secondary, if not a ter-
tiary, modelling system. The distinction between primary, secondary and
tertiary modelling systems has become a matter of some controversy, so it
is important to be clear about it. Here we use those terms to indicate the
modelling systems that appeared at three different stages of evolution and
were the results of three different types of brain processing.
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Brain’s first modelling system
This is the system that appeared when the primitive brain managed to pro-
duce feelings and sensations. These entities can be divided into two major
classes because the sense organs deliver information either about the outside
world or about the interior of the body. The first modelling system consists
therefore of two types of models, one that represents the environment and
one that carries information about the body. Jakob von Uexkll (1909) called
these two worlds Umwelt and Innenwelt, names that express very well the
idea that every animal lives in two distinct subjective universes. We can say
therefore that Innenwelt is the model of the internal body built by the in-
stinctive brain, and that Umwelt is the model of the external world built by
the cybernetic brain of an animal. The brain as we know it, came into being
when the primordial brain split into instinctive brain and cybernetic brain,
and these started producing the feelings and sensations that make up the first
modelling system of all triploblastic animals (vertebrates and invertebrates).
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Brain’s second modelling system
Some animals (like snakes) stop chasing a prey when this disappears from
sight, whereas others (like mammals) deduce that the prey has temporarily
been hidden by an obstacle and continue chasing it. Some can even learn to
follow the footsteps of a prey, which reveals a still higher degree of abstrac-
tion. This ability to ‘interpret’ the signals from the environment, is based
on a new type of neural processing that makes use of memory, learning, the
ability to ‘generalize’ and in many cases also the faculty to ‘jump to con-
clusions’ (abduction). All together these operations produce a model of the
world that vastly expands the potentialities of the primitive brain and rep-
resents a second modelling system, a system that appeared when part of the
cybernetic brain became an ‘interpretive brain’.
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Brain’s third modelling system
The last major novelty in brain’s history was the origin of language in our
species, and that too required a new macroevolution, a new type of neural
processing that went far beyond the reach of the interpretive brain because
it was capable of coping with mental operations involving symbols. This is
why it is legitimate to say that language represents a third modelling system.
There have been, in conclusion, three major transitions in the evolution of
the brain and each of them gave origin to a new type of neural processing
that was, to all effects, a new modelling system.
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Code
A code is a set of rules that create a correspondence between two independent
worlds. The Morse code, for example, is a correspondence (or a mapping)
between the letters of the alphabet and groups of dots and dashes. The
highway code is a correspondence between signals and driving behaviours.
A language is a correspondence between words and objects. The genetic
code is a correspondence between triplets of nucleotides, called codons, and
amino acids. What is essential in all codes is that the coding rules are not
dictated by the laws of physics. They are arbitrary in the sense that they
are independent from physical necessity and this implies that they can be
established only by natural or by cultural conventions.
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Code Biology
Code Biology is the study of all codes of life, from the genetic code to the
codes of culture. The genetic code appeared on Earth at the origin of life, and
the codes of culture arrived almost 4 billion years later, at the end of life’s
history. According to official (textbook) science, these are the only codes that
exist in Nature, and if this were true we would have to conclude that codes are
extraordinary exceptions that appeared only at the beginning and at the end
of evolution. In reality, various other organic codes (codes between organic
molecules) have been discovered in the last 25 years, and it seems likely that
many more will come to light in the future. The existence of many organic
codes in Nature, however, is not only a new experimental fact. It is one of
those facts that have extraordinary theoretical implications. The first is that
all great events of macroevolution were associated with the appearance of new
organic codes, and this gives us a completely new description of the history of
life. The second great implication is about the mechanisms of evolution. The
discovery that there are two fundamental molecular mechanisms at the basis
of life, copying and coding, means that there are two distinct mechanisms
of evolutionary change: evolution by natural selection, based on copying,
and evolution by natural conventions, based on coding. The experimental
discoveries and the theoretical implications of the organic codes make of
Code Biology an entirely new field of research and an autonomous academic
discipline, the real new frontier of biology.
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Codemakers
(see Molecular machines)
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Codepoiesis
Before the origin of the genetic code, the ancestors of the first cells were
engaged in the process of evolving coding rules and contained therefore a
code generating system. After the origin of the genetic code, however, the
situation changed dramatically. No other modification in coding rules was
tolerated and the system in question became a code conservation system.
Another part of the system, however, maintained the potential to evolve
other coding rules and behaved as a new code generating, or code exploring,
system. In the early Eukarya, for example, the cells had a code conservation
part for the genetic code, but also a code exploring part for the splicing code.
This tells us something important about life. The origin of the first cells
was based on the ability of the ancestral systems to generate the rules of
the genetic code, and the subsequent evolution of the cells was based on
two complementary processes: one was the generation of new organic codes
and the other was the conservation of the existing ones. Taken together,
these two processes are the two sides of a biological phenomenon that can be
referred to as ‘codepoiesis’. What is common to all living systems is either
the generation or the conservation, or both, of organic codes, and this gives
us an entirely new definition of the cell that can be expressed in this way:
“the cell is a codepoietic system, i.e., a system that is capable of creating
and conserving its own codes”. This definition accounts for the two most
important events of evolution. [1] The ability to create coding rules accounts
for the origin of the genetic code and of all the other codes that followed. [2]
The ability of the cell to conserve its own codes accounts for the fact that the
organic codes are the great invariants of life, the entities that are conserved
while everything else is changing.
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Coding
(see Copying and coding)
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Coding semiosis
Semiosis requires the existence of four distinct entities—signs, meanings, code
and codemaker—because signs cannot exists without meanings and the re-
lationship between them is necessarily based on the rules of a code, which
in turn implies an agent that produces them, i.e., a codemaker. Semiosis,
in other words, is necessarily based on coding, but this does not mean that
it is based exclusively on coding. In the course of evolution, some animals
have acquired the ability to interpret the world, and interpretation is cer-
tainly a form of semiosis, since it makes use of signs and meanings, but it is
not based on coding alone because it also requires memory, learning, mental
representations and probably some form of ‘abduction’. For the first three
thousand million years of evolution, the Earth has been inhabited exclusively
by single cells, and these are capable of coding and decoding the world but
do not make representations and therefore cannot interpret them. In order
to distinguish the semiosis of single cells from that of animals it is convenient
to use terms that qualify them and to this purpose the two types are referred
to as coding semiosis and interpretive semiosis.
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Computable entities
(see Nominable entities)
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Convention
A convention or conventional code is a code that is shared among two or
more agents. Coordination always relies on a convention. The highway code
is an example of a convention that allows car drivers to coordinate their
driving behavior. Language is also a convention and is the result of coordi-
nation between humans. Conventions can be dictated by a central authority
(e.g. the government), but the vast majority of conventions are the result of
conventionalization processes. In particular, the conventions that character-
ize theMajor Transitions are the result of evolution by natural conventionalization.
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Conventionalization
Conventionalization is any process in which a convention or shared code is
established between several agents. One well studied mechanism of conven-
tionalization in semiotic dynamics is the process in which individual agents
adapt their codes through individual learning in order to align and make
coordination between them possible. However, conventionalization does not
necessarily require that individual agents can learn or adapt their codes. It
is also possible that codes are hardwired into agents but that different codes
come into existence by differential reproduction, so that offspring of agents
possibly employ different codes and a variety of coding behaviors exists at
the population level. Those agents in the population that are better aligned
may then have a selective advantage over other agents, so that learning takes
place at the population level (see also natural conventionalization).
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Conventional signs
(see Signs, Peirce model of semiosis, and Conventions)
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Coordination
Coordination occurs when the combined (coding) behavior of two or more
interacting agents gives rise to a global or collective phenomenon. Coordi-
nation thus always involves two levels of organization: a microscopic level of
interacting agents and a macroscopic level at which the effect of their coor-
dination can be observed. Furthermore, in order for coordination to occur,
the agents must conform to a convention or shared code. For instance, a col-
lection of cells may coordinate into a multi-celled body provided that each
cell fulfills (conforms to) it’s function in the whole, that is, differentiates into
the appropriate cell-type during development and responds appropriately to
signals coming from other cells during life-time etc. As another example,
car drivers may coordinate into a crash-free flow of traffic provided that all
drivers conform to some highway code, e.g. drive on the left side of the road
etc. Humans coordinate through culture and language. From an evolutionary
perspective, coordination may increase the combined fitness of the coordinat-
ing agents. The Major Transitions are extreme forms of coordination to the
degree that novel, irreducible agencies arise at the macroscopic level. In this
case the degree to which agencies at the microscopic level must conform to
the convention that supports coordination is such that they sometimes even
have to commit suicide (see apoptosis).
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Copying and Coding
Copying and coding are mechanisms that work at two distinct levels in every
living system. Copying operates at the individual level of the molecules and
coding at the collective level of the whole system. None of them is reducible
to the other because they are complementary mechanisms. They evolved
in parallel in the history of life just as individual words and rules of gram-
mar evolved in parallel in the history of language. There are, furthermore,
other two important differences between copying and coding. One is the fact
that copying produces either exact copies or slightly different versions of the
copied molecules, which means that natural selection produces new objects
by gradually modifying preexisting ones. Natural selection, in other words,
creates only relative novelties, not absolute ones. In the case of coding, in-
stead, the situation is totally different. The rules of a code are not dictated
by physical necessity, and this means that they can establish relationships
that have never existed before in the Universe. Natural conventions, in short,
have the potential to create absolute novelties. Another difference between
copying and coding is that they involve two different entities. A variation in
the copying of a gene changes the linear sequence, i.e., the information of that
gene. A variation in a coding rule changes instead the meaning of that rule.
The great difference that exists between copying and coding, and therefore
between natural selection and natural conventions, comes from the difference
that exists between ‘information’ and ‘meaning’. There are, in short, three
major differences between copying and coding: (1) copying acts on individ-
ual molecules whereas coding acts at the collective level, (2) copying modifies
existing objects whereas coding brings new objects into existence, and (3)
copying is about biological information whereas coding is about biological
meaning.
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Copying semiosis
In protein synthesis, a sequence of nucleotides is used to produce a sequence of
amino acids according to the rules of the genetic code. In that case, there is no
necessary connections between the components of the two molecules and the
codons of nucleotides are used as conventional organic signs, i.e., as organic
symbols. A sequence of nucleotides, however, can also be used by a copymaker
(a polymerase) to produce a complementary copy of itself, and in that case the
relationship between the two sequences is no longer established by adaptors
but by direct physical interactions between complementary regions. These
interactions, however, occur between very small regions of the molecules, and
that means that the first sequence provides only a limited number of physical
determinants for the second. The first sequence, in other words, does have a
physical relationship with the second, but such relationship is undetermined
and represents therefore only a ‘cue’, i.e., a natural sign, for the second. This
means that the distinction between natural and conventional signs exists
also at the molecular level, and represents in fact a divide between two very
different types of processes. Sequences of nucleotides are used as conventional
signs in coding and as natural signs in copying. Molecular coding, in short, is
a form of coding semiosis whereas molecular copying is a process of copying
semiosis. The translation of genes into proteins, in other words, is based on
coding semiosis whereas the replication and the transcription of genes are
based on copying semiosis.
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Copymakers
(see Molecular machines)
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Cultural Semiosis
(see Popper’s Three Worlds and )
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Cybernetic brain
(see Brain)
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Essential parameters
The notion of essential parameters captures the essence of the capacity of sys-
tems, such as agents, to persist against the natural tendency of things to dis-
solve as a result of disturbances from the environment. It was introduced by
William Ross Ashby in 1954 as follows: “that a subsystem should keep its in-
tegrity, that is not to disintegrate but remain as a subsystem, certain parame-
ters must remain within certain ‘physiological’ limits. What these parameters
are, and what the limits, are fixed when we have named the subsystem we are
working with.” For example, all earthly systems, including the earth itself,
have temperature among their essential parameters, because if the surround-
ing temperature rises above a certain limit no such system will persist. The
notion of essential parameters can be used to explain the Major Transition
in evolution as a result of evolution by natural conventionalization.
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First modelling system
(see Brain’s first modelling system)
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Function
Icons, Indexes and Symbols
Peirce described three major types of signs, and called them icons, indexes
and symbols.
1. A sign is an icon when it is associated with an object because of a
similarity between them. All trees, for example, are different, and yet
they also have something in common and it is this common pattern
that allows us to recognize any new tree that we happen to encounter
for the first time. Icons, in other words, lead to pattern recognition
and are the basic tools of perception.
2. A sign is an index when it is associated with an object because a
physical link is established between them. We learn to recognize a new
cloud from previous clouds, and a new outbreak of rain from previous
outbreaks, but we also learn that there is often a correlation between
clouds and rain, and we end up with the conclusion that a black cloud
is an index of rain. In the same way, the smell of smoke is an index of
fire, footprints are indexes of preceding animals, and so on. Indexes,
in short, are the basic tools of learning, because they allow animals to
infer the existence of something from a few physical traces of it.
3. A sign is a symbol when it is associated with an object because an
arbitrary link is established between them. There is no similarity and
no physical link between a flag and a country, for example, or between
a name and an object, and a relationship between them can exist only
if it is the result of a convention. Symbols allow us to make arbitrary
associations and build mental images of future events (projects), of
abstract things (numbers), and even of non-existing things (unicorns).
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Information
(see Organic information)
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Innenwelt
The model of the internal body built by the brain of an animal. It is a
subjective model, and any animal lives therefore in a body whose feelings
and instincts are manufactured by its own brain.
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Instinctive brain
(see Brain)
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Intermediate brain
(see Brain)
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Interpretant
(see Peirce model of semiosis)
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Interpretation
Memory allows a system to compare a phenomenon with previous records of
similar phenomena, and it is from such comparisons that a system can ‘learn’
from experience. Memory is clearly a prerequisite for learning, but what
does learning achieve? What is the point of storing mental representations
and comparing them? So far, the best answer to this problem is probably
the idea that memories and learning allows animals to interpret the world.
Interpretation, on the other hand, is a form of semiosis—because it is based
on signs—but it is a new form because it also requires memory and learning.
What is interpreted, furthermore, is not the world but representations of the
world, and only multicellular systems can build them. Single cells decode the
signals from the environment but do not have the physical means to build
internal representations of them and therefore cannot interpret them. They
are sensitive to light, but do not ‘see’; they react to sounds but do not ‘hear’;
they detect hormones but do not ‘smell’ and do not ‘taste’ them. It takes
many cells which have undertaken specific processes of differentiation to allow
a system to see, hear, smell and taste, so it is only multicellular creatures
that have these experiences. The evolution from single cells to animals was a
true macroevolution because it created absolute novelties such as feelings and
instincts. Later on, another macroevolution gave to many animals the ability
to interpret the world, and we can actually prove that this ability evolved
in stages. The origin of interpretation provided animals with a new means
of obtaining information about the world—a second modelling system—and
gave origin to a new type of semiosis that can be referred to as interpretive,
or Peircean, semiosis.
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Interpreter
(see Peirce model of semiosis)
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Interpretive semiosis
(see Coding semiosis and Biosemiotics)
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Macroevolution
There is a close association between the great events of macroevolution and
the appearance of organic codes. The origin of the genetic code, for example,
gave origin to biological specificity, the most fundamental of life’s properties.
It was the origin of protein-based life, i.e. of life-as-we-know-it. The data
from molecular biology have revealed that all known cells belong to three pri-
mary kingdoms, or domains, that have been referred to as Archaea, Bacteria
and Eucarya (Woese, 1987, 2000). These cells have three distinct signalling
systems, and this does suggest that each domain arose by the combination of
the universal genetic code with three distinct signal-transduction codes. An-
other great innovation was brought about by the codes of splicing, because
splicing requires a separation in time between transcription and translation
and that was a precondition for their separation in space, i.e. for the ori-
gin of the nucleus. Many other eukaryotic innovations were brought into
existence by organic codes. The cytoskeleton codes, for example, allowed
the cells to build their own scaffoldings, to change their own shapes and to
perform their own movements, including those of mitosis and meiosis. The
histone code provided the rules of chromatin regulation, the adhesion codes
allowed the cells to aggregate in multicellular groups and the codes of pat-
tern made it possible to create systems capable of embryonic development.
The major events in the history of life, in short, went hand in hand with
the appearance of new organic codes, and this suggests a deep link between
codes and macroevolution. More precisely, it suggests that the great events of
macroevolution were made possible by the appearance of new organic codes.
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Meaning
(see organic meaning)
[Back to Contents]
Modelling systems
(see Brain as a modelling system)
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Molecular machines
The simplest molecular machines that could appear spontaneously on the
primitive Earth were bondmakers, molecules that could stick monomers to-
gether at random and produce polymers, such as polypeptides, polynucleotides
and polysaccharides. Some bondmakers, furthermore, acquired the ability to
join monomers together no longer at random, but in the order provided by a
template. Those bondmakers started making copies of other molecules and
became copymakers. The appearance of bondmakers at an advanced stage
of chemical evolution led therefore to a steady increase in the number of
polymers, and eventually to the appearance of the first copymakers, the first
molecular machines that started populating the Earth with copied molecules
and gave origin to genes. The origin of proteins, on the other hand, was
a much more complex affair, because proteins cannot be copied and yet the
information to make them must come from molecules that can be copied, i.e.,
from nucleic acids. The problem is that there is no necessary link between
nucleic acids and amino acids, and only the rules of a code could provide a
bridge between them, which means that the evolution of protein synthesis
had to go hand in hand with the evolution of the genetic code. Proteins arose
therefore from the integration of two different processes, and the final ma-
chine that produced them was a code-and-template-dependent-peptide-maker,
or, more simply, a codemaker. Life, in short, arose by two distinct mecha-
nisms, copying and coding, and each of them was brought into existence
by molecular machines. Copymakers generated genes and codemakers pop-
ulated the Earth with proteins. They were, and still are, the fundamental
‘makers’, the ‘agents’, of life.
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Natural conventionalization
Under certain conditions, individual agents may benefit from coordinating
into a higher level of organization. This is the case whenever there is no
conflict between the essential parameters of the agents and when in addi-
tion there is an overlap between them. In this case, the total (combined)
capacity of the agents to keep essential parameters within physiological lim-
its per essential variable is increased, because the agents each contribute
their full capacity while they each only bring in a fraction of the parameters
that are shared. Since conflicts between the essential parameters of different
agents tend to be eliminated over the course of evolution, for instance due to
natural selection, the probability that these conditions are fulfilled are ben-
eficial tends to increase over time, and will eventually become a certainty.
If agents then are capable of establishing a conventional code through some
process of conventionalization, coordination will effectively occur. This mech-
anism is called evolution by natural conventionalization, and is responsible
for the Major Transitions in macro evolution. That coordination through
a process of conventionalization is responsible for the Major Transitions ex-
plains why these transitions are always characterized by the appearance of
new codes (or new ways of transmitting information as Maynard-Smith an
Szathmary put it), for increased levels of inter-dependency, and why they
give rise to novel, higher level agencies consisting of many (coordinated)
lower level agencies.
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Natural conventions
The discovery of the genetic code has proved that there are two distinct
molecular mechanisms at the basis of life, the copying of genes and the cod-
ing of proteins. The discovery of other organic codes, furthermore, allows us
to generalize this conclusion because it proves that coding is not limited to
protein synthesis. Copying and coding, in other words, are distinct molecular
mechanisms that have operated in all living systems ever since the origin of
life, and this suggests that there are two distinct mechanisms of evolution
because an evolutionary mechanism is but the long term result of a funda-
mental molecular mechanism. More precisely, the fact that coding is not
reducible to copying and the close relationship that exists between organic
codes and macroevolution tell us that coding had indeed a fundamental role
in the history of life. All of which means that there are two distinct types
of evolutionary change: evolution by natural selection, based on copying, and
evolution by natural conventions, based on coding.
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Natural selection
The copying of a gene is the elementary act that leads to heredity. When the
process of copying is repeated indefinitely, however, another phenomenon
comes into being. Copying mistakes become inevitable, and in a world of
limited resources not all changes can be implemented, which means that a
process of selection is bound to take place. Molecular copying, in short, leads
to heredity, and the indefinite repetition of molecular copying leads to natural
selection. That is how natural selection came into existence. Molecular
copying started it and molecular copying has perpetuated it ever since. This
means that natural selection would be the sole mechanism of evolution if
copying were the sole molecular mechanism at the basis of life. (See also
selection).
[Back to Contents]
Natural signs
(see Signs and Peirce model of semiosis)
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Neural code
The inputs to the nervous system come from the sense organs, but these
organs arise from the basic histological tissues of the body, and these tissues
(epithelial, connective, muscular and nervous tissues) are the same in all
animals. All signals that are sent to the brain, in other words, come from
organs produced by few universal tissues, and represent a limited number of
universal inputs. But do we also have a limited number of universal outputs?
The neural correlates of the sense organs (feelings and perceptions) can be
recognized by the actions that they produce, and there is ample evidence that
all animals have the same basic instincts. They all seem to experience hunger
and thirst, fear and aggression, and they are all capable of reacting to stimuli
such as light, sound and smells. The neural entities that correspond to the
basic histological tissues, in other words, are associated with the basic animal
instincts and these appear to be the same in all animals. What we observe,
in conclusion, is a universal set of basic histological tissues on one side, a
universal set of basic animal instincts on the other side, and a set of neural
transformation processes in between. The most parsimonious explanation is
that the neural processes in between are also a universal set of operations
that represent the rules a neural code because there is no necessary link
between tissues and feelings. It is plausible, in short, that there has been a
(nearly) universal neural code at the origin of mind just as there has been as
a (nearly) universal genetic code at the origin of life.
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Neural semiosis
(see Popper’s Three Worlds )
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Nominal entities
Science is always expressed in words and we need to give names to the
objects and the processes that we observe in Nature. Names (or nominal
entities, to use a classical term) in general have nothing to do with the
intrinsic features of the named objects, and are therefore mere labels that we
attach to them. The deep divide that exists between ‘names’ and ‘objects’
has been at the centre of many controversies in the past, in particular of
the celebrated medieval dispute over ‘nominal’ versus ‘real’ entities. The
relationship between names and objects is also a crucial issue in science, but
here it has taken on a new form. Let us start by underlining that all names
are sequences of characters (alphabetic, numerical or alpha-numerical) and
that each sequence is unique. Names, in other words, have specificity. In
general, the specificity of a name has nothing to do with the characteristics
of the named object, and in these cases we can truly say that names are
mere labels. Science, however, has invented a new type of names where the
sequence of characters does represent an order that is objectively present in
the named objects, and in these cases we speak no longer of nominal but of
nominable entities.
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Nominable entities
The chemical formula of a molecule describes an objective sequence of atoms,
and any atom can be described by the objective sequence of its quantum
numbers. These sequences are true observables because they describe fea-
tures that we observe in Nature, and have an important characteristic in
common. When atoms and molecules are formed spontaneously, their final
sequences are completely determined by the interactions between their own
components. In the case of a protein, instead, all its different amino acids
interact by the same peptide bonds and a spontaneous assembly would pro-
duce a completely random order (which is incompatible with life). In this
case, a specific sequence can be obtained only if the amino acids are put to-
gether by a molecular machine according to the order provided by a template
that is external to the protein itself. We need therefore to distinguish be-
tween two different types of observables. The sequence of quantum numbers
in an atom, or the sequence of atoms in inorganic molecules, is determined
from within, by internal factors, whereas the sequence of amino acids in a
protein is determined from without, by external templates. In the first case
the sequence is a physically computable entity, in the sense that it is the re-
sult of physical forces, whereas in the second case it can only be described
by ‘naming’ its components, and is therefore a nominable entity (this term
should not be confused with the classical concept of nominal entity, that ap-
plies to all names). A nominable entity is not a label but an observable, and
more precisely a non-computable observable. All names, in conclusion, are
specific sequences of characters, and in science can be divided into two great
classes: labels and observables. The observables, in turn, can be divided into
computable entities and nominable entities. Physics and chemistry deal ex-
clusively with computable entities (physical quantities), whereas nominable
entities (information and coding rules) exist only in living systems.
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Observables
The observables are entities (such as space, time, mass, force, energy, etc.)
that science, and in particular physics, use to describe the world and the his-
tory of science has been systematically accompanied by the discovery of new
observables. In Newton’s physics, for example, the fundamental observables
were time, space and mass, but then electromagnetism required the addition
of electric charge and thermodynamics required the addition of temperature.
In general, it is assumed that biology does not need new observables, but in
reality the very opposite is true. Life is based on the copying of genes and
on the coding of proteins and these processes require entities, like biological
sequences and the rules of the genetic code, that have all the defining char-
acteristics of new observables. This is because the role of the observables is
to describe the world and we simply cannot describe living systems without
sequences and codes, just as we cannot describe physical systems without
space, time, mass, temperature, etc. The only difference is that sequences
and coding rules are non-computable observables, but there is no doubt that
observables they are (we do observe them in living systems) and that they are
fundamental observables (because we cannot describe living systems without
them and because we cannot reduce them to anything else).
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Organic Codes
Are codes between organic molecules. Any organic code is a set of rules
that establish a correspondence between two independent organic worlds by
means of molecular structures, called adaptors, that perform two independent
recognition processes at each step. In the genetic code, for example, the
adaptors are the transfer-RNAs. The adaptors are required because the two
worlds would no longer be independent if there were a necessary link between
them, and a set of rules is required in order to guarantee the specificity of
the correspondence. The adaptors are the key molecules in all organic codes.
They are the molecular fingerprints of the codes, and their presence in a
biological process is a sure sign that that process is based on a code. In
addition to the genetic code, the existence of many other organic codes has
been reported so far. Among them: the sequence codes (Trifonov, 1987, 1989;
1999), the adhesive code (Redies and Takeichi, 1996; Shapiro and Colman,
1999), the splicing codes (Barbieri, 1998, 2003; Pertea et al., 2007; Barash
et al. 2010; Dihr et al., 2010), the signal transduction codes (Barbieri, 1998,
2003), the sugar code (Gabius, 2000, 2009), the histone code (Strahl and
Allis, 2000; Turner, 2000; 2002), the cytoskeleton codes and the compartment
codes (Barbieri, 2003, 2008), the tubulin code (Verhey and Gertig, 2007), a
nuclear signalling code (Maraldi, 2008), and the ubiquitin code (Komander
and Rape, 2012).
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Organic information
In genes and proteins, biological, or organic, information has been defined as
the specific sequence of their subunits. This definition however is not entirely
satisfactory because it gives the impression that information is something
that molecules have simply because they have a sequence. In reality, there
are countless molecules which have a sequence but only in a few cases this
becomes information. This happens only when a sequence provides a guide-
line to a copymaker in a process of copying. It is only an act of copying, in
other words, that brings information into existence. This tells us that organic
information is not just the specific sequence of a molecule, but the specific se-
quence produced by a copying process. This definition underlines the fact that
organic information is not a thing or a property, but the result of a process.
It is, more precisely, an ‘operative’ definition, because information is defined
by the process that brings it into existence. It must also be underlined that
organic information is neither a quantity (because a specific sequence cannot
be measured), nor a quality (because it is an objective feature of all copied
molecules), and belongs instead to a third class of objects that have been
referred to as nominable entities.
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Organic meaning
The Morse code is a correspondence between the letters of the alphabet
and groups of dots and dashes and in the same way the genetic code is a
correspondence between groups of nucleotides and amino acids. Let us notice
now that establishing a correspondence between, say, object 1 and object 2,
is equivalent to saying that object 2 is the meaning of object 1. In the Morse
code, for example, the rule that ‘dot-dash’ corresponds to the letter ‘A’, is
equivalent to saying that letter ‘A’ is the meaning of ‘dot-dash’. By the same
token, the rule of the genetic code that a group of three nucleotides (a codon)
corresponds to an amino acid is equivalent to saying that that amino acid
is the organic meaning of that codon. Anywhere there is a code, be it in
the mental or in the organic world, there is meaning. We can say, therefore,
that meaning is an entity which is related to another entity by a code or a
convention, and that organic meaning exists whenever an organic code exists.
All we need to keep in mind is that meaning is a mental entity when the code
is between mental objects, but it is an organic entity when the code is between
organic molecules. It must also be underlined that organic meaning—like
organic information—is neither a quantity (because a coding rule cannot be
measured), nor a quality (because the organic codes are objective features o
life), and belongs instead to a third class of objects that have been referred
to as nominable entities.
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Organic semiosis
(see Signs and Biosemiotics)
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Peirce model of semiosis
According to the classical doctrine of semiosis developed by Aristotle, Au-
gustine and Aquinas, signs are divided into two great classes that Augustine
(389ad) called signa data and signa naturalia, a distinction that continues
to these days with the terms conventional signs and natural signs. The con-
ventional signs (or symbols) are those where there is no physical relationship
between signs and objects (between a flag and a country, for example) and a
link between them can only be established by arbitrary rules, i.e. by conven-
tions. In natural signs, by contrast, a physical link is always present. Typical
examples are the symptoms that doctors use to diagnose illnesses (spots on
the skin, a fever, a swollen area, etc.), as well as a variety of cues (smoke as
sign of fire, odours as signs of food, footprints as signs of organisms, etc.).
In all these cases there is a physical relationship between the visible signs
and the invisible entities that they point to, and yet the relationship is un-
derdetermined, so much so that it takes an act of interpretation to establish
it. All this suggests that semiosis is based on interpretation in natural signs
and on codes in conventional signs, as Aristotle, Augustine and Aquinas
had indicated. On this point, however, Peirce broke with tradition, argued
that codes too are interpretive processes and concluded that semiosis always
requires interpretation. According to Peirce, in other words, the agent of
semiosis is necessarily an interpreter, and this is why Thomas Sebeok (2001)
declared that “. . . there can be no semiosis without interpretability”. This
conclusion has become known as ‘the Peirce model of semiosis’, a model that
was expressed in formal terms in the treatise Semiotik/Semiotics edited by
Roland Posner, Klaus Robering and Thomas Sebeok (1997), in the following
way: “The necessary and sufficient condition for something to be a semiosis
is that A interprets B as representing C, where A is the interpretant, B is an
object and C is the meaning that A assigns to B”.
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Peircean semiosis
(see Interpretation and Biosemiotics)
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Physical quantities
(see Sequences)
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Popper’s Three Worlds
In the 1970s, Karl Popper argued that the unity of Nature is realized by the
coexistence of three distinct domains, or ‘Worlds’. The first (World 1) is the
domain of all material objects, physical and biological, i.e., atoms, galaxies
and bodies. The second (World 2) is the domain of the mind, the subjec-
tive world of mental states, feelings, emotions and consciousness. The third
(World 3) is the domain of all human artifacts and cultural products. The
three worlds could hardly be more different, and yet they do have something
in common. At the heart of all of them there are codes. The genetic code
and other organic codes in World 1, neural codes in World 2 and countless
cultural codes in World 3. The three worlds of Popper correspond therefore
to three major types of semiosis that are referred to as organic, neural and
cultural semiosis.
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Quantities, qualities and nominables
According to a long tradition, natural entities are divided into quantities and
qualities. Quantities can be measured and are objective, whereas qualities are
subjective and cannot be measured. In the case of the sequences of genes and
proteins, however, this scheme breaks down. The ‘order’ (or ‘information’)
of a sequence is not a quantity because it cannot be measured. But it is
not a quality either, because the specific order of a sequence is a feature
that we find in all organic molecules, and is therefore an objective feature
of the world, not a subjective one. The same is true for the rule of a code.
This too cannot be measured, so it is not a quantity, but it is not a quality
either because the rules of the genetic code, for example, are the same for all
observers in all living systems. A scheme based on quantities and qualities
alone, in short, is not enough to describe the world. In addition to quantities
(objective and measurable) and qualities (subjective and unmeasurable) we
must recognize the existence in Nature of a third type of entities (objective
but unmeasurable). The information carried by biological sequences (organic
information) and the rules of the organic codes (organic meaning) belong
precisely to this new type of entities, and we can also give them a suitable
name. Since organic information and organic meaning can be described only
by naming their components, we can say that they are nominable entities,
or, more simply, ‘nominables’.
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Representations
(see Interpretation)
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Second modelling system
(see Brain’s second modelling system)
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Selection
According to the theory of natural selection, evolution is the consequence of
differential copying. Copying ensures that what has already evolved contin-
ues to exist, whereas variation through differential copying leads to further
evolution or change. Selection then is the long-term result of copying, because
as more copies come into existence and resources are scarce, some copies are
bound to go extinct. This is the core of the Malthusian principle of selec-
tion, which in turn forms the core of Darwin’s theory of natural selection.
However, Malthusian selection is not the only possible form of selection. As
Eug`ene Marais already remarked just after Darwin published his theory on
The Origin of Species, “the struggle for life is not merely the struggle against
competing fellows [but also] against opposing laws of matter which make for
dissolution and the hindrance of growth”. In other words selection is not so
much the preservation of the fit as it is the destruction of the unfit. More
generally, selection is any process in which that which ‘works’ is kept or per-
sists, and that which doesn’t work is dismissed. The determination of what
‘works’, however, is a qualification process, and thus depends on a measure
of quality. Having increased access to scarce resources compared to fellow
copiers is but one possible measure, but others are possible, such as having
increased ability to persist against the natural tendency of things to dissolve,
or having increased capacity to coordinate.
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Semantics
(see Syntax and semantics)
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Semiosis
Semiosis is the production of signs, and semiotics is usually referred to as
the study of signs (from the Greek semeion=sign) but these definitions are
too restrictive because signs are always associated with other entities. A
sign, to start with, is always linked to a meaning, which implies that sign
and meaning cannot be taken apart because they are the two sides of the
same coin. Semiotics, therefore, is the study of signs and meanings together,
and a system of signs, i.e., a semiotic system, is always made of at least two
distinct worlds: a world of entities that we call signs and a world of entities
that represent their meanings. The link between sign and meaning, in turn,
calls attention to a third entity, i.e., to their relationship. A sign is a sign
only when it stands for something that is other than itself, and this otherness
implies at least some degree of independence. It means that there is no
deterministic relationship between signs and meanings. A semiotic system,
therefore, is not any combination of two distinct worlds. It is a combination
of two worlds between which there is no necessary link, and this implies that
a bridge between the two worlds can be established only by conventional
rules, i.e., by the rules of a code. This is what makes semiosis different
from everything else: semiosis requires a system made of two independent
worlds that are connected by the conventional rules of a code. A semiotic
system, in other words, is necessarily made of at least three distinct entities:
signs, meanings and code. Signs, meanings and code, however, do not come
into existence of their own. There is always an ‘agent’ that produces them,
and that agent can be referred to as a codemaker. In the case of culture,
for example, the codemaker is the human brain; in the case of the cell, the
codemaker is the ribonucleoprotein system that makes proteins according to
the rules of the genetic code. We come in this way to a general conclusion that
can be expressed in this way: a semiotic system consists of signs, meanings
and code that are all produced by the same agent, i.e., by the same codemaker.
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Semiotic dynamics
Semiotic dynamics is the study of the self-organizing and evolutionary dy-
namics that lead to the evolution of conventional meaning and codes, includ-
ing language. The term was first introduced in a 1999 paper by Luc Steels
and Frederic Kaplan [1] which reported on a study of the conventionalization
dynamics leading to the emergence of a shared lexicon in a group of au-
tonomous distributed agents situated and grounded in an open environment.
Other publications along this line of research include [2, 3, 4, 5]. The topic
was later picked up by researchers in statistical physics (see, among others,
[6, 7, 8, 9]) and is related to models of the evolution of cooperation and
conventions in the field of evolutionary game theory, specifically signaling
games and pre-play signaling [10, 11]. Some of the main theoretical results
are that conventionalization is bound to occur in a population of agents if the
agents are predisposed or at least have an incentive to cooperate and there
is amplifying individual learning [3, 10] or if there is learning at the popu-
lation level [11, 12]; and that the dynamics of conventionalization are like
the dynamics of phase transitions [6]. These results are compatible with the
hypothesis that the mechanism of evolution by natural conventionalization
is responsible for the Major Transitions in macro evolution.
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Semiotic system
(see Semiosis)
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Sequences
The sequences of genes and proteins are as essential to the description of life
as the physical quantities, and this means that they have the same scientific
‘status’. This conclusion, however, raises immediately a new problem, be-
cause there are two distinct groups of physical quantities: a small group of
fundamental quantities (space, time, mass, charge and temperature) and a
much larger group of derived quantities. This distinction applies to all objec-
tive entities, so we need to find out whether biological sequences belongs to
the first or to the second group. Luckily, this problem has a straightforward
solution because the sequences of genes and proteins have two very specia
characteristics. One is that a change in a single component of a biological
sequence may produce a sequence which has entirely new properties. This
means that although a biological sequence can be said to have ‘components’,
it is at the same time a single indivisible whole. The second outstanding
feature is that from the knowledge of n elements of a biological sequence we
cannot predict the element (n+1). This is equivalent to saying that a specific
sequence cannot be described by anything simpler than itself, so it cannot be
a derived entity. Which means that biological sequences have the same sci-
entific status as the fundamental quantities of physics, and are therefore a
new type of fundamental observables.
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Signs
Signs have been traditionally defined as “something that stands for something
else”, and in antiquity were divided into two great categories—conventional
signs and natural signs—for two different reasons. One is because they derive
either from nature (signa ex natura) or from culture (signa ex cultura). The
other is because they are either symbols (signa symbolica) or symptoms (signa
symptomatica). If we put together both characteristics, signs are defined in
the following way:
1. the conventional signs are signa symbolica ex cultura, and
2. the natural signs are signa symptomatica ex natura.
The discovery of the genetic code came as a bolt from the blue precisely
because it revealed the existence of a third category of signs that all
thinkers of the past had not predicted: the existence of symbols that
come from nature, not from culture. In addition to the two classical
categories, therefore, we now have a third one:
3. the organic signs are signa symbolica ex natura.
This is the immense novelty of the genetic code. It brought to light a third
type of semiosis that exists in the organic world and for this has been called
organic semiosis.
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Symbols
(see Icons, Indexes and Symbols)
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Syntax and Semantics
In biolinguistics syntax refers to the study of the formal rules and principles
that govern when sentences are well formed, without taking into account
their meaning. In logics syntax refers to the formal rules that determine when
logical statements are well formed without taking into account their meaning
and, by extension, their truth-value. In computer science syntax refers to the
rules that determine when statements in a computer program are well formed
without taking into account (the result of) the actual computations denoted
by the statements. Thus in general syntax is defined as the study of the
properties of well formed statements in a symbol system without taking into
account what the meaning or semantics is of the symbols and statements.
There are some subtleties in this definition however. Firstly, symbols do not
exist in or by themselves but only as the result of being qualified as such
by some system, just as codons only exist within the context of a system
consisting of a ribonucleoprotein and tRNA’s. Secondly, the definition does
not specify what it means to be ‘well formed’. Again, deciding whether a
statement is ‘well formed’ is an act of qualification. Since qualification is a
matter of semantics, these issues indicate that syntax and semantics are in
fact inseparable and intrinsically semiotic notions.
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Third modelling system
(see Brain’s third modelling system)
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Umwelt
The model of the external world built by the brain of an animal. It is a
subjective model, and any animal lives therefore in an environment whose
sounds, images, smells and tastes are manufactured by its own brain.
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World 1, 2 and 3
(see Popper’s Three Worlds)
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Zoosemiotics
It is the study of semiotics processes in animals, a field that Thomas Sebeok
started with a research paper in 1963 and to which he gave its present name
in the book Perspectives in Zoosemiotics (1972).
[Back to Contents]
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