1
A NATURAL HISTORY OF LIFE: INTRODUCTION
The natural history of life in the 19th and 20th
century was recounted in the framework of Neodarwinism, with its core paradigms
(a) “chance mutations” in the genetic text lead to the origin of new species,
genera and organismic kingdoms, and (b) “natural selection” in the struggle for
life which leads to “survival of the fittest” of the newly created organisms.
Although “natural selection” agrees well with the empirical data of adaptation,
the core paradigm of “chance mutations” explains the evolution of new organisms
only dogmatically. More recently, the Serial Endosymbiotic Theory of Lynn
Margulis contradicts this paradigm. Serial Endosymbiotic Theory (SET) proves
that the evolution of eukaryotic cells is the result of merging processes of
different bacterial ancestors. Accordingly, the natural history of life becomes
a story involving the merger of different organisms with different abilities
and capabilities into more complex organisms. Building on Margulis schema, I
will propose that the study of interactions between microorganisms clearly
shows that the underlying processes are not primarily mechanistic, but rather
are complex communication processes in which chemical molecules serve as signs
in rule-governed sign-mediated interactions (rsi’s). These signs have a
relation to (a) each other, (b) the sign user/interpreter, (c) designated
something (i.e. have a meaning function), so that we may identify them in
obeying semiotic rules. I will argue that interorganismic communication
processes between members of a species are almost always embedded in parallel
intraorganismic (intracellular) and metaorganismic (transpecific) communication
processes.
I will also propose that the correct approach to
these communication processes is to begin with human processes of
understanding, because a language and communication concept coherent with our
self-understanding cannot be founded through a pure observer perspective. To be
coherent with our self-understanding the approach has to incorporate the basics
of a pragmatic turn, i.e. the results of analyzing human rule governed sign
mediated interactions or “how to do things with words”. Ultimately, however, we
have no choice but to achieve understanding among ourselves using language and
communication.
2
AN EXCLUSIVE BACTERIAL WORLD UNTIL HALF TIME
Lynn Margulis theory is well supported by numerous genetic
analyses: the higher development of species, genera and organismic kingdoms on
our planet developed beyond the bacteria stage through the merging of different
bacteria with different capabilities (Margulis 1996, 1999, 2004; Margulis et
al., 2000; Margulis and Sagan, 2002; Cavalier-Smith, 2002; Stechmann and
Cavalier-Smith, 2003). The SET proposes that the differentiation of bacteria
groups with very different capabilities during the first two billion years of
our planet’s natural history of life gave rise to a global bacterial gene pool
of astounding diversity. Today we know that the first half of biological
natural history was not characterized by biological monads, but rather by
highly complex social life-worlds of the bacteria groups, which entered into
symbiotic and parasitic relationships with one another.
Later I will argue that even on the level of
bacteria, symbiotic associations require numerous rule-governed sign-mediated
interactions (rsi’s); without them coordinated behaviour cannot
function. The bacterial world is a social and communicative one (Kaiser and
Losick 1993, Fuqua et al., 1996; Losick and Kaiser, 1997; Zook, 1998; Bassler,
1999; Crespi , 2001; Schauder and Bassler, 2001; Schauder et al., 2001; Federle
and Bassler, 2003). The production and the exchange of messenger molecules
enable unicellular organisms to coordinate their behaviour like a
multicellular organism (Shapiro, 1998; Schauder and Bassler, 2001; Ben
Jacob, 2004). The rsi’s in bacteria communities are not restricted to
species-specific levels but represent a clear metaorganismic, multilevel
communication that enables hundreds of different bacteria groups to co-occupy
one and the same ecological niche (Walker, 2003; Bais, 2004). It has been
proven that bacteria groups use quorum sensing (QS) to determine their strength
and to react by coordinating their behaviour (Montana State University 1999; Sharma
et al., 2003). “Studies of quorum sensing systems demonstrate that bacteria
have evolved multiple languages for communicating within and between species.
Intra- and interspecies cell-cell communication allows bacteria to coordinate
various biological activities in order to behave like multicellular organisms”
(Schauder and Bassler, 2001: 1476). Bacteria use a form of “bacterial
esperanto” to communicate with other bacteria groups (Schauder and Bassler ,2001).
3
SYMBIOGENESIS: FROM RAMIFICATION TO UNIFICATION
Natural scientists have described ten thousand different
species of bacteria. The capabilities of the individual subgroups often differ
considerably, i.e. anaerobic and aerobic, photo- and chemosynthetically active,
acido-, thermoacidophilic, halophilic, methane- and oxygen-producing, osmotic
and lipophilic. Natural scientists have recently become aware that in early
evolution bacteria exchanged gene components, even entire gene blocks, with one
another. Such gene blocks suddenly enriched the genome of another bacterium
that had previously not had the respective competence, i.e. the genome
enrichment often had a direct phenotypic effect. Horizontal Gene Transfer (HGT)
enables the bacteria kingdom to merge different basic competences (Wagner et
al., 1999; Wolf, 1999, 2000; Jain et al., 1999, 2003; Xie et al., 2004; Timmis
et al., 2004).
What were these mergings like? They represent
nothing less than the substantial change of protein individuals with
particular, immutable basic characteristics into protein individuals that
differ substantially from their predecessors. It involves a true creation from
simple to more complex organisms. If symbiogenesis, via symbiosis, creates a
new species and therefore extinguishes the formerly independent individuals,
then this involves generative DNA text processing in which genetically
different gene pools are combined into one DNA text. Rather than involving a
physical change in aggregate status, this is one of the most revolutionary
phenomena in biology. It requires a recombination that makes the foreign data
set into one’s own, the “non-self” to a “self”, an object of external
perception to a subject of internal proprioception.
The eukaryotic revolution marked the beginning
of a development in which bacteria groups conquered space and time: organisms
in the eukaryotic kingdoms such as animals, fungi and plants are themselves
inhabited up to 90 % by bacteria groups (Blech, 2000), which thereby vanquish
limitations of space (vertical, horizontal) and time (movement, mobility). The
symbiotic (metaorganismic) communication with this bacterial world is vital for
all eukaryotic organisms.
The SET underlines that the origin of new
tissues, organs, organisms and species lie in the long-term and continuous
symbioses that they enter into. Symbiogenesis, in the next step, enables
life-forms to incorporate entire organisms along with their genetic makeup.
Thus bacteria became permanently incorporated into plant and animal cells as
plastids and mitochondria. The novel aspect of symbiogenesis is that the
natural history of life is no longer one of chance mutations and their
selection: symbiogenesis unites individuals into larger individuals composed of
many separate elements.
The fact that genetic subunits (e.g.
organelles) in eukaryotic cells are present within the cell structures, but
outside the nucleus, is remarkable. Margulis draws attention to the fact that
some genetic factors in plants and animals are distributed throughout the cell
and therefore, whatever the role of ‘genetic determination’, are not only
determined by the genes in the nucleus. She points to experiments that prove
without doubt that plastids and mitochondria clearly influence heredity. These
extra-nuclear parts of the cell, with their peculiar hereditary history, are
remnants of formerly free-living bacteria. Margulis proposes that a
double-tracked hereditary system – with (formerly independent) cells inside
other cells – is involved (Margulis 1999).
The SET also proposes serial evolution, which
indicates that the sequence of merging is important. The initial merger
involved (1) a thermoacidophilic bacterium (sulphur reduction/fermentation)
with (2) one that could swim (Spirochaeta) in the nucleocytoplasm. These were
still anaerobes. This was followed by a merger with (3) an aerobic form, a-proteobacteria (aerobic respiration).
The resulting organism was able to survive the increasing oxygen
concentrations. The final step was the merger with (4) a photosynthetic
bacterium (Synechococcus cyanobacteria).
With this approach, Margulis contradicts
traditional theories of evolution, all of which firmly held that evolutionary
directions lay in ramification rather than merging. SET, on the other
hand, states one integrated genome was sufficient in the initial merger
of the archae- and eubacterium; in the Proctista, two integrated genomes were
necessary; in the fungi three; in animals at least four; and in
the plant kingdom (400 million years ago) at least five, perhaps even
seven (Margulis 1996, 1999). Thus, one of the symbiogenetically most
complex merging processes, which gave rise to the plant kingdom, is the
youngest symbiogenesis of a new organismic kingdom in the natural history of
life. The enormous group comprising the flowering plants is only half as old
(150 million years) as the chronological origin of the plant kingdom. The
corresponding development of seeds and fruits ultimately created an environment
that was crucial for the survival of higher animals (Margulis and Schwartz,
1988).
Another example is that of cilia, the rods in
the retina, the tail of sperm cells, sensory hairs and many similar appendages
of nucleated cells which arose during the original merger of archaebacteria and
a swimming bacterium. The bodies they contain (so-called “centriole-kinetosomes”)
arose through this archaic merger. There is also a genetic relationship between
cilia and the mitotic spindles responsible for chromosome movement during cell
division. According to Margulis, the Spirochaeta are the modern, free-living
relatives of these symbiogenetically merged centriole-kinetosomes (Margulis,
1999: 65).
The SET supports this assumption with the fact
that most of the DNA found in the cytoplasm of protoctists, animals, fungi and
plants stems from the genes of bacteria that became organelles, and does not
occur via genetic drift or mutations. Hereditary factors that control metabolic
processes are similar to those of archaebacteria. Eukaryotic genes that
participate in information-processing (e.g. translation, transcription), on the
other hand, show a close relationship to eubacteria. This higher development
after the eukaryotic revolution was also promoted by the ability of bacteria to
exchange genes and DNA components very simply and quickly, even between
different species, through conjugation or via plasmids. The genetic material of
bacteria is much better suited for these processes than eukaryotic material.
Evolution therefore progressed, in its most dynamic phases, at a speed
reflecting the ability of bacteria for gene-flux.
This demonstrates that complex genomic
make-ups could be passed on directly and that the step-by-step development via
chance mutations is an outdated conception. Whereas Darwin’s natural selection
has been documented in numerous studies, the higher development of species or
even the origin of new organismic kingdoms could never be satisfactorily
explained by chance mutations. In fact, most observed mutations are lethal
rather than promoting higher or further development.
Margulis does not explain how the simplest
archaebacteria or the RNA-world originated. Early RNA-world is plausible
because RNA can reproduce itself autocatalytically, which DNA cannot. Moreover,
RNA controls the assemblage of amino acids into protein sequences. Some RNAs
are as competent as proteins: it can splice itself, i.e. rearrange its own
molecular shape anew – it rearranges and reorganizes genetic material.
Something like these capabilities of ribozymes had to have been
components of the first cells. The metabolism of the first cells functioned
without feeding. Photoautotrophic and chemoautotrophic organisms do not need to
feed: they obtain their energy from sunlight or from hydrogen-rich compounds.
The first eukaryotic microorganisms developed
an incredible diversity, but even today remain poorly studied and
insufficiently described. Their role in the natural history of life was deemed
too insignificant, even though they were positioned at the base of the
eukaryotic superkingdom. Only few of the 250 000 protoctist species (eukaryotic
microorganisms) have actually been named (Margulis, 1999: 84).
There is a standard assumption in the history
of natural science, namely, plants and animals were the outstanding products of
evolution. This now appears in an entirely different light. In fact, animals
and plants are more similar to one another than to all other organismic
kingdoms, both plants and animals go through an embryonic stage and thereby
document their particularly close kinship, compared with other life-forms. The
major differences lie elsewhere: the greatest divide lies between the pro- and
eukaryotes.
A natural history of the development of a
global symbiotic interdependence of all life-forms prompts the “holistic
reflex”: “Gaia”, in the form of a global superorganism coating the earth, the
sum of all parts, the whole created by the many separate individuals and its
metabolism. Such a holism proposed by James Lovelock (Margulis, 1999: 141) is a
classical metaphysical construction. It dissolves each organism’s factual
individuality into a hypothetical whole, reflecting the cognitive simulation of
a quasi-extraterrestrial observer. Margulis therefore rejects this “holistic
Gaia,” that is to say, a concept of Gaia as superorganism, but accepts Gaia as
a useful model to represent the sum of interacting ecosystems. In other
words, Gaia models the sum of growing, interacting and dying populations, a
sheath of many species covering our planet, consisting of countless, highly
different individual organisms.
4
SYMBIOGENESIS BY RULE GOVERNED SIGN MEDIATED INTERACTIONS
4.1
“MERGING”, “FUSION”, “INCORPORATION”
The major defect of SET from my perspective is that it
describes the highly complex interactions of a symbiosis and, subsequently, of
symbiogenesis, in the classical mechanistic language of natural science:
“merging”, “fusion”, and “incorporation”. I will argue that we are dealing less
with a “merging” than with communication processes which are multi-leveled,
regulative, constitutive and generative and whose success depends on whether
the required sign processes proceed in a rule-based manner, or fail.
Communication processes between cells and cell components, do not “incorporate”,
rather they integrate genetic data sets into available genomes and therefore
lead to the development of a new individual.
Biosemiotics has taught us that life functions
are always connected to sign processes, or, more precisely, that sign processes
regulate and constitute life functions (Noeth, 2000: 254; Kull, 2005).
Defective sign processes restrict or terminate life processes. These sign
processes regulate life processes on several levels simultaneously:
intracellularly, within the cell (DNA, RNA activities, messenger substances,
etc.), and intercellularly in the form of cell-cell communication.
4.2
MICROBIAL AND PLANT MULTILEVEL COMMUNICATION
“Communication is the key element in successful
organization” (Kolenbrander et al., 2002: 486). The coordinated community, for
example of oral bacteria in humans, relies on intra- and interspecies
communication. This community encompasses ca. 500 different species, some of
which cooperate, others which compete (Kolenbrander et al., 2002). The
complexity of potential interactions in the oral cavity and the number of
possibilities reach unimaginable proportions if we assume that each of the 500
bacteria species can regulate its genes in response to host-produced molecules
and interacts with all the other bacteria species (Kolenbrander et al., 2002).
Highly complex interspecies communication
enables bacteria species to communicate even in special sites of hosts such as
the gastrointestinal tract, where they can gauge their population sizes by
exchanging molecules despite the incredible number of similar molecules
surrounding them. Even in such critical situations, the species can reliably
differentiate between population-specific (interorganismic) signals, foreign
signals and “noise” (Federle and Bassler, 2003).
The microbiological community is exposed to a
broad range of chemical substances in which an incredible variety of chemical
messenger substances is embedded, from which they must be able to take up and
interpret the correct ones in order to survive. It is very difficult to imagine
how bacteria can differentiate between sense and nonsense in their chemical
environment, in which they are constantly bombarded from all sides by small
molecules (Dunn and Handelsman, 2002).
The
discovery of species-specific and trans-specific signal molecules reveals an
unexpectedly highly developed communication. In nature, where bacteria
typically live together with numerous other species, signal molecules allow
them to determine how large their populations are, how many other communities
are present and their sizes, and to respond appropriately to this information
by adapting their gene expression (Federle and Bassler, 2003).
This discovery has led to the suggestion that
under real-life conditions, microorganisms must simultaneously be able
to conduct many molecular conversations with different types of organisms and
even organismic kingdoms (Dunn and Handelsman, 2002). “Using these advanced
linguistic capabilities, bacteria can lead rich social lives for the group
benefit. They can develop collective memory, use and generate common knowledge,
develop group identity, recognize the identity of other colonies, learn from
experience to improve themselves, and engage in group decision-making, an
additional surprising social conduct that amounts to what should most
appropriately be dubbed as social intelligence” (Ben Jacob et al., 2004).
The communicative abilities of bacteria are
also present in symbiogenetically derived higher eukaryotes such as plants. The
rhizosphere of plants is a realm of overlapping communicative interactions
(Yoder, 1999; Walker et al., 2003; Bais et al., 2004; Baluska et al., 2005).
The rhizosphere is a dynamic environment featuring dense microbiological life,
high growth rates and metabolic activities, as well as rapidly changing
physical conditions (Dessaux, 2004). Most of the decisions that plants make
regarding their growth and development involve communication processes between
all parts of the plant and works as neuronal communication (Dustin et al., 2001;
Roshchina, 2001; Trewavas, 2003; Davies, 2004; Baluska et al., 2005). Learning
and memory are two characteristic features for neuronal networks that require a
large number of nerve cells to communicate with one another. Interestingly,
nerve cells and plant cells use very similar sequences of signal molecules so
that we speak today of neuronal communication in plant neurobiology, not any
longer of the dominant role of action potentials in plant physiology (Trewavas,
2003; Baluska, 2004; Davies. 2004; Baluska et al., 2005).
The communication processes between tissues
and cells in plants is incredibly complex and encompasses nucleic acids,
oligonucleotides, proteins and peptides, minerals, oxidative signals, gases,
mechanical signals, electrical signals, fatty acids, and oligosaccharides,
growth factors, several amino acids, various secondary products and simple
sugars (Trewavas, 2003).
Communication, i.e. rule governed sign
mediated interactions, is indispensable for the normal development of cells,
tissues, organs and bodies (Witzany, 2005). They (rsi) control movement
and coordinated behaviour, developmental stages in time, symbiotic interactions
as well as defence strategies. Associated cells require a precise coordination
in sending and receiving signals. Disturbance of rule-governed sign-mediated
interactions lead to pathological situations ranging from abnormal cell proliferation
to cell death (Perbal, 2003).
As in every biosemiotic process of real
lifeworld (pragmatic) situations, context determines semantic meaning of
signals. Auxin, for example, is an ancient signalling molecule in plants. Since
it functions in different hormonal, morphogen and transmitter signalling
pathways, it is very difficult to decipher the actual semantics of Auxin which
depends on whether it is used as hormonal or morphogen or transmitter signal
(Baluska et al., 2005: 108). Because the same signal can take on different
meanings and trigger different effects, depending on whether it reaches the
whole plant, a tissue or a cell, the respective developmental status of the
organism serves as a memory for each individual plant. The individual plant is
a complex multicellular and multi-tissue organism in which development is a permanent
process and in which communication is the driving force (Trewavas, 2003):
“Biologists suggest
that intelligence encompasses the characteristics of detailed sensory perception,
information processing, learning, memory, choice, efficient optimisation of
resource sequestration with minimal outlay, self-recognition, and foresight by
predictive modelling. There is good evidence that individual plant species
exhibit all of these intelligent behavioural capabilities” (Trewavas, 2005).
I will now
give further illustrations of how sign processes regulate and constitute life
functions.
5
THE geMetaCode: CODINGS OF “NON-CODING” DNA
If symbiogenesis, via symbiosis, creates a new species and
therefore extinguishes the formerly independent individuals, then this involves
generative DNA text processing in which genetically different gene pools are
combined into one DNA text. This is one of the most revolutionary phenomena in
biology. Recombination makes a foreign data set into one’s own, the “non-self”
to a “self”, an object of external perception to a subject of internal
proprioception.
Over the past 20 years, the field of molecular
biology has yielded tens of thousands of articles describing in great detail
the processes of recombinant DNA, splicing, RNA editing, coding, copying, major
and minor repairs, transcription, translation, RNA processing, insertion, the
importance of introns and exons for the reading processes, the complementary role
of DNAs and RNAs. In the last decade even the significance and indispensable
structural function of non-coding RNA becomes more and more interesting
(Cavalier-Smith and Beaton, 1999; Sternberg, 2002; Baluska et al., 2004;
Shapiro and Sternberg, 2005; Schmitt and Paro, 2004).
In every case, enzyme proteins competent in
text processing carry out these highly differentiated tasks on protein-coding
DNA regions with great precision.
“No technical production system, regardless
how perfect, even approaches the low error rate achieved in the DNA
reproduction process in living organisms. This degree of precision is vital for
humans as well: even a single mistake in the transmission of hereditary
information can have lethal consequences, as for example in sickle cell anaemia
or cancer. In the course of developing from a fertilized egg to an adult human
being, the three billion letter pairs of the human genome are reproduced nearly
a quadrillion times. These orders of magnitude underscore the monumental scale
of the task involved in correct transmission. An error rate as low as one in a
million would still mean ca. 3000 mistakes per transmission: normal development
would be impossible. Three enzymatically controlled processes are responsible
for suppressing errors during the reproduction of the genetic text. Polymerases
are responsible for selecting the correct letters, i.e., the nucleotide
building blocks for the new DNA strands, while exonucleases are responsible for
rejecting damaged letters. After these two steps, the error rate is reduced to
one in ten million. The third and decisive step – correcting mistakes in the
overall manuscript – is far more complex. Several proteins work hand in hand in
this process. They recognize and excise sites in which the letters of one
strand do not fit with those of the complementary strand. The missing piece is
completed by polymerases. After this final quality control step, the error rate
is reduced to a mere one in ten billion” (Spektrum der Wissenschaft,
1988: 119).
But this text processing on protein-coding DNA
is overruled by the genome processing abilities of repetitive DNA of introns
coding not for proteins but a lot of RNAs among them active micro-RNAs. Typically,
any mistakes in protein-coding and non-protein coding text processing have
grave if not lethal consequences for the organism.
Until recently, only the protein-coding
regions of DNA was thought to be crucial to coding. While this may well be the
case in the prokaryotes, in higher eukaryotes this region is marginal (3%), for
97% of the eukaryotic genome consists of non-coding DNA. Long termed “junk” DNA
because no important functions could be attributed, it was thought to represent
ancient remnants of evolutionary history. Accordingly, research concentrated on
the 3% that coded. Such one-sided approach, however, left many questions
unanswered: Why are the protein-coding genes of humans and mice 99% identical?
What actually happens with the 97% RNA remnants during post-transcriptional
processing? Why is there no correlation between the complexity of organisms and
the number of protein-coding genes, yet a correlation between complexity and
the proportion of non-coding DNA?
My thesis here is the existence of an
innovation code (text-generating code, evolution code) hidden in the non-coding
DNA (Witzany, 1993 b; 1997; 2000: 200), a thesis which I developed in the early
90s and which I further developed (Witzany, 2000: 200-212) in the discussion of
the contributions to The Concept of the Gene in Development
and Evolution (Beurton et al., 2000). My assumption that this innovation
code codes for enzyme proteins competent in text-processing, proteins that
generate the new genetic texts for new organisms may prove to be present in the
early DNA-world of simple organisms. But it is not proteins that create
the genome ratio of new eukaryotic texts, but rather a MetaCode1
(Witzany, 2000: 202) which encodes numerous RNAs, among them
active micro-RNAs, and is able to generate new genetic datasets. It enables the
conduction of structural changes as basic prerequisite of the evolution of
diversity in the eukaryotic superkingdom.
5.1
“NON-CODING” DNA IS CODING FOR MICRO-RNAs
What was formerly described as “junk” DNA has genetic
functions that are not controlled by enzyme proteins, but rather by repetitive
elements in the introns of DNA which encode for the manifold forms of
micro-RNAs. They originate during the transcriptional process, when the actual
text building blocks are put together for a protein and when most of the
non-protein-coding RNA is cut out and appears to be left over. This involves an
incredible 97% of the genome’s transcriptional output. Comparative genetics has
demonstrated that introns are strongly conserved over long evolutionary
distances, often in large blocks, i.e. they are functionally related. This
conservation is much more conservative than that of the protein-coding DNA
(Shapiro and Sternberg, 2005).
5.2
MULTI-TASKS OF MICRO-RNAs:
Active micro-RNAs control and integrate large-scale
structures of the chromosome. The number of different micro-RNAs is estimated
to exceed several 10,000 (Mattick and Gagen, 2001). Some of the discovered
tasks of these micro-RNAs are co-suppression, suppression of transposition,
position effect variegation, start-stop signals, RNA interference, imprinting,
chromosomal methylation, transvection, transcriptional and post-transcriptional
gene silencing along with numerous other RNA-DNA, RNA-RNA (trans-acting RNAs),
RNA-protein interactions. These active RNAs are as competent as proteins in catalysing,
signalling and switching (riboswitch) (Mattick and Gagen, 2001).
5.3
PHENOTYPIC VARIATION
“Cellular differentiation and phenotypic variation
result primarily from variations in this high order regulation, not in the
proteins themselves” (Mattick and Gagen, 2001: 1612). The phenotypic variation
in complex organisms is the result of a different use of a set of
protein-coding core components (Mattick and Gagen, 2001). The higher order
regulation in non-protein-coding genome architecture is able to manage a larger
genetic data set in its phenotypic range. As far as evolutionary processes are
concerned, it is naturally much simpler to change or expand a number of very
small control sequences than to duplicate an entire network of protein-coding
genes (Mattick and Gagen, 2001: 1623). Variations of this higher order
regulation can create an enormous spectrum of different protein expression
profiles and we can understand at last why one and the same gene can be used
for “multiple protein meanings” (Ast, 2005).
5.4
TERMINOLOGY: SYSTEMS BIOLOGICAL/COMPUTATIONAL VS. BIOSEMIOTIC
Currently, the abilities of the non-protein- yet
micro-RNAs-coding regions still receive different scientific designations. The
terms are “endogenous network control molecules” or “higher-order regulatory
system”, “controlled multitasked Gene Networks”, “major architectonic role of
repetitive components” (Mattick, 2001; Mattick and Gagen, 2001; Mattick, 2003;
Mattick, 2005; Shapiro and Sternberg, 2005).
In the perspective of biosemiotics undoubtedly
a semiotic code is involved. I recommend that we refer to a genome editing (ge)
MetaCode, because this obeys different semiotic rules than does the protein
code.2 There are good reasons for assuming that the semiotic rules
of the geMetaCode determine the pragmatic rules and therefore the
semantics of the protein code.
5.5
EVOLUTION BY VARIATIONS IN THE geMetaCode
When the protein-coding regions in the genome of higher
eukaryotes do not differ significantly from one another and represent a set
of core components, then phenotypic differences are understandably
determined by the different geMetaCode. It organizes, i.e. variously
structures, the largely uniform protein-coding dataset of higher
eukaryotes, thereby generating different organisms. Biosemiotically we can
speak of a rule constituting and rule changing competence (“rule changing
creativity” Witzany, 2000: 193) hidden in the geMetaCode.
In the light of the SET these
non-protein-coding sequences (for example, the repetition elements of introns)
arose after the innovation of eukaryotic cells, although also
archaebacteria genomes may have some introns. The innovation of eukaryotic
cells could be an effect of new symbolic functions,3 constituted by
more complex intracellular communication after the separation of
transcription and translation conferring “(…) an advantage by facilitating the
modular shuffling of eukaryotic protein domains in evolutionary time and in
real time via alternative splicing (…)” (Mattick, 2001: 987). The
absence of these regulation functions of the geMetaCode in the
eubacterial genome (with rare exceptions of viral introns) shows that a pure
protein code had only very limited evolutionary possibilities. Simple organisms
are using proteins both for functions and control systems that had reached the
limit of analog communicative possibilities. These possibilities became
dramatically expanded by the innovative intronic functions, forming the basis
for the evolution of the eukaryotic superkingdom (Mattick, 2001).
5.6
PROTEIN CODE OBEYS SEMIOTIC RULES OF THE geMetaCode
The unification of several bacteria species into the early
form of the eukaryotic cell represented highly complex text processing rather
than a merger. The biosemiotic complexity increases many-fold through the overlying
regulative and constitutive role of the geMetaCode and its
grammatical, semantic and pragmatic rules. “Major evolutionary events can
initiate within the repetitive sector of the genome and do not have to follow
changes in the coding sector” (Shapiro and Sternberg, 2005:16). This enables
abrupt evolutionary developments as proposed in Gould’s theory of a “punctuated
equilibrium” or as revolutionary-evolutive phases such as in the
Cambrian explosion (Witzany, 1993 b: 226). Namely, the geMetaCode can
integrate larger genetic data sets into the phenotypic range:
“Different genome system architecture can
have distinct transmission and expression properties even with the same coding
sequences. Meaningful evolutionary change can take place in the repetitive
component of the genome without altering coding sequences” (Shapiro and
Sternberg, 2005:17).
The geMetaCode has also regulatory
functions in chromsomal methylation which decide about different signalling
pathways of the same genetic setups through different rules of gene silencing
and special starts and stops via alternative splicing. With this chromosomal
methylation, organisms are able to handle multiple protein meanings of
the same genetic dataset. As shown through some authors of epigenetics these (geMetaCode-)
functions are influenced and altered through environmental and other reasons
which are (reversibly) hereditable but do not involve or depend on mutations of
the DNA itself. (Turner, 2000; Jenuwein and Allis,
2001; Turner, 2002; Spotswood and Turner, 2002; Jaenisch and Bird, 2003; True
et al., 2004; Wang et al., 2004; Waterland and Jirtle, 2004).4
The geMetaCode contains the
regulating-, constituting- and innovating rules with which existing protein
codes are structured. This is possible because, I maintain, the genome is
linguistically structured and communicatively organized. It also confirms a
thesis of the pragmatic philosophy of biology about central features of language
and communication in principle, that “using a finite number of signs and finite
number of grammatic, semantic and pragmatic rules, existing rules of sign use
can be indefinitely expanded, altered and/or newly combined to yield a new
genetic text, new species, genera, organismic kingdoms, new forms of behavior,
and new norms of (human) actions” (Witzany, 1993 b: 229).
6
HISTORY OF INTERACTION - HISTORY OF EVOLUTION
If we deal with linguistically structured
(analog/symbolic) genome ratio and communicative organization (rule governed
sign mediated) of living organisms we have to ask whether we should use
traditional terms and concepts for a description of "Life”: autopoiesis,
emergence, information system or constructivism, game theory,
statistic-quantifying models, etc. After mainstream philosophy gave up
explanations of Life and transferred these to natural science we find only partially
holistic or sometimes hermeneutic approaches to “Life”. Most natural science
approaches are founded through three common argumentations: (a) We speak about
the world of objects in a language of the exact natural sciences, which draws
its claim to validity from the laws governing the physical world. Or (b) we
assume that the observed objects have a direct empirical significance that need
not be further questioned because the laws of physics are reflected 1:1 in the
material foundations of the brains of humans which construct utterances
(universal syntax). Or (c) some simulate the radical monological perspective of
a quasi-extraterrestrial observer and assume that there is an overriding “system“
in which human populations are a subsystem that communicates about itself and
about its co-systems on an information-theoretical basis (Witzany, 2002 a).
To get things straight we have to remind
ourselves of the discussion between 1920 and 1980 in the history of theory of
science and the transition of metaphysics to “the linguistic turn” and
afterwards, to the foundation and justification of scientific languages in “the
pragmatic turn”. In various contributions I have reconstructed this discourse
in great detail and connected it with the realm of biosemiotics (Witzany, 1993
a, b; 1995; 1998; 2000; 2002; 2003; 2005) which I will briefly summarize here:
a) The linguistic turn was the result of an
attempt to delimit the logic of science from philosophy and other “unscientific“
cognitive methods. With good reasons the linguistic turn states that we do not
understand per se objects, relations, structures, intelligence, mind,
consciousness, cognition, construction, matter, energy, information, system,
natural law, etc. but linguistic sentences in utterances. Only protocol
propositions of observations that are reproducible in experimental setups are
capable of depicting reality on a 1:1 basis. This is also valid for
propositions of a language of theory that would have to be brought into
agreement with these protocol propositions. What is required is a language that
can be formalized, as in logical calculations, algorithms. This language would
represent a universal syntax that would be universally valid (a) in the
things of the external world, (b) in the physicalistic laws and (c) in the
material reality of the brain of humans speaking in formalizable propositions
(Witzany, 1995; 2005 a). But after several trials Logical Empiricism had to
abandon its effort to achieve the ultimate validity claim of a physicalistic
universal language. The logical and linguistical 1:1 depiction of physical
reality is not possible in principle.
b) The pragmatic turn refers to the
communicative everyday interactions of historically evolved linguistic communities
which are the basis for learning and training linguistic and communicative
competences. Historically grown communicative practice of linguistic
communities is the prerequiste for organization and coordination of social
interactions and later on linguistic abstractions like poetry, fine arts and
scientific languages. The pragmatic turn enables the reconstruction of the a
priori of linguistic communities being decisive for constituting a
linguistically mediated and communicatively shared human self-understanding.
The pragmatic turn founded and justified the intersubjective-communicative
character of thought, experience and research and was therefore able to avoid
the omnipresent subject-object dichotomy and its unavoidable consequences,
solipsism and objectivism (Witzany 2005).
As we are speaking together we interact. Everyday
language analysis shows the actional character of speech acts, or
"how to do things with words" (Austin, 1962; Searle, 1974). As we are
subjects and objects of our utterances we are in a privileged position
to take in account, at the same time, our historically evolved everyday
language. We need not describe this from outside like the solus ipse
pure observer who has no alternative possibility to describe communicative
actions as classifications of equal behavioral features. To the contrary, we
understand utterances as participants of communicative, representative,
constitutive and expressive speech acts. This enables us to understand central
marks of speech acts as there are, for example:
· The simultaneous understanding of identical meanings in two
interacting partners, as expressed in successfully coordinated activity
· The differentiation between deep and superficial grammar of a
statement along with differentiation between locutionary, illocutionary and
perlocutionary speech acts with which the statements are made
· The differentiation between communication-oriented action and
strategic manipulation of the communicating partners
· The critical judgment of the validity being claimed when making a
particular statement
An understanding of these marks is not possible for monological
solus ipse concepts of linguistic turn and its non-participating yet
pure observer perspective. Also the monological sender-receiver model together
with its “decoding” of meanings by analyzing the cognitive conctructional
features of brain functions brings less chances for adequate explanation of
understanding than the concept of "empathy", a term long used for a
metaphysical-psychological approach to explain "understanding" by
trying to feel “mentally” within the receiving person.
The pragmatic turn replaces all solus ipse
subjects of knowledge by the a prori of linguistic community. This is the end
for the former approach, a methodological ideal which lasted nearly 2000 years
and which maintained as a principle that one subject alone could get
knowledge. Its the end of monological Descartes/Kant conceptions of scientific
knowledge and its unsoluble metaphysical apparent problems or how Thomas
McCarthy said: “The monological approach preordained certain ways of posing the
basic problems of thought and action: subject versus object, reason versus
sense, reason versus desire, mind versus body, self versus other, and so on” (McCarthy,
1984: ix).
The pragmatic turn emphazises interactional
features of communication. Its decisive aspects are not only its regulative
but also its constitutive features. Not the sign, symbol or word is the
elementary unit of communication, but rather the production of signs, symbols
or words in the framework of linguistic actions. It is important to stress the constitutive
character of linguistic rules because linguistic behavior can never be
explained by regulative rules alone: there is no a priori activity of speaking
a language that could be regulated by rules. The possibility to speak a
language depends on constitutive rules.
Languages (human and non human, bee languages) have
a finite number of signs (Witzany, 2000: 45-52). They stand in relation to each
other in an orderly manner which we term syntactic or grammatic rules. (1)
These must be followed in a correct way or they fail. Then (2) there are rules
of interacting which decide whether communication processes are successful
or not, i.e. validity claims which are connected with our utterances, and which
may be accepted or refuted by the linguistic community. Thus obeying or failing,
pragmatic rules (2) decide about functioning communication – they are the
prerequisite for successful social coordination and organization. Concrete
interactional context decides about (3) meaning of utterances. One and the same
sentence (sequence of signs) may take completely different meanings in different
contexts. The meaning of "The shooting of the hunters" in training
programs of professional hunters for learning rules about when to shoot in a
coordinated action during hunting has a completely different meaning to a
criminal inquiry of an unexplored, violent crime, on several hunters.
These analyses of some aspects of communicative
rationality show its dependency on everyday language features with which we
organize and coordinate interactions in the real lifeworld and therefore the
historicity of its genesis and its development. It also shows that we are able
to constitute indefinite possibilities of combinations with a finite set of
signs and a finite set of rules. These features of linguistic capabilities
constitute, in principle, history as indefinite process. Human knowledge
is according to Peirce always a provisional result and in the end - as result
of all possible and real speech acts – would be the "ultimate
opinion" of the "indefinite community of investigators".
Modern biological research documents very clearly,
that interactions in and between living organisms are sign mediated and rule
governed. We can try to describe these interactions as communication processes
and the genome ratio as linguistically structured because of its
analog/symbolic features. We do not participate in plant-plant communication,
but we may accept that we as humans are participants in a global community of
interdependent symbiotic lifeworlds. As eukaryotic organisms we are able to
survive because we are involved in irreplacable interactional levels with, for example,
microorganisms. If we would measure the cells of our body, we would find only
10% being originally human, 90% being endo- and ektosymbiotic microorganisms,
without them we could not live (Blech, 2000).
If, at the onset, we specifically discuss the terms
“language” and “communication” to achieve a linguistically and communicatively
fixed understanding of these terms (Witzany 1993 a/b; 1995; 1998; 2000; 2002
b), then we ourselves are in the best position to gain an understanding
of human language and communication because the theoretical description of
these terms must be coherent with, and not in contrast to, our
self-understanding, our communicative experience. Moreover, I would argue that
the investigator is not the observer in the third person -pure observer-
perspective but is a performative participant of the communicating scientific
community which is (a) part of the investigation itself, (b) part of the
planetary symbiotic interdependence of the communicating living nature.
It therefore makes little sense to refer to sign use
in the communication processes of plant or bacterial lifeworlds, all the while
presupposing an objectivististic language and communication concepts, and using
an empirical methodological ideal to explain the evolution of communicative
interactions from the amoeba to humans. This would lead to the dead-end of the
solipsistic subject of knowledge and hopeless entanglement in the
subject-object dichotomy of objectivism/ physicalism/ naturalism.
The reverse pathway is correct, beginning with
humans, and human self-understanding, which must be coherent with the used
concept of “language” and “communication”. The alternative is to use
pre-pragmatic solus ipse conceptions with their entanglement in
metaphysical foundations. As I have argued before:
Referring back to the rules of
communicative rationality provides an opportunity to answer questions of
evolutionary logic and dynamics as questions of interaction logic and dynamics.
Evolutionary history could then be understood as a developmental history of interaction
semiosis. If we could further establish that the
rules governing evolution are equivalent to the communication rules behind the
history of interaction, then we could justify the view that rule-governed
sign-mediated behavior is a factor not only in humans, but especially in
non-human living nature (Witzany, 1993, 2000: 13).
So if we use the term of communicative rationality developed
in this article for rsi's of non human organisms we may use the same rsi
features as being equally involved in human and non human communication
processes. In addition, a three leveled sign relation which does not eliminate
all the various features of rsi's in different species,
genera, organismic kingdoms is already available.
7
THREE-LEVELED SEMIOTICS AND REDUCTION EFFECTS
The semiotics of C. S. Peirce may be helpful here. It can
provide immutable conditions for adequately analysing language use, linguistic
communication, and even sign use via a three-leveled semiotics. Peirce decisive
change - as opposed to Descartes and Kant’s solus-ipse subject of knowledge –
is his emphasis on the community of interpretation in the “indefinite community
of investigators”. Scientific knowledge is only possible for members of a community
of interpreters, not for a solipsistic subject of knowledge. This approach
allows Peirce, to underline the intersubjective-communicative character of
thought, experience and research – or as the post-Tractatus Wittgenstein meant,
no isolated individual can follow one rule.5 Intersubjective
validity of scientific knowledge requires a linguistic communication about
sense and consensus-building about statements.
Those who overlook or feel they can negate
linguistic communication-a priori (which itself requires a historically
evolved and reconstructible linguistic community) will commit one of these
forms of reductive fallacy. That person will shift the highest point of
knowledge (a) in the unity of a self-consciousness like Kant or transfer this
point (b) into the reality of a higher system logic that represents a
principally unrecognizable yet proximate objective world (objectivism and
realism). That person will no longer be in a position to derive the
sign-mediated knowledge in the sign-sense interpretation and
truth-consensus-building of an indefinite interpretation community of
researchers.
According to Peirce, a (1) sign denotes (2)
something for an (3) interpreter. Semiotics is an irreducable three-leveled
relation of syntactic (1), semantic (2) and pragmatic (3) rules. Each of the
three levels of the sign function already assumes, for its function, the other
two. According to Peirce, those who, in an unreflective manner, fail to
consider, incompletely consider or reduce this principally irreducible relation
to two levels (syntactic/semantic) or one level (universal grammar), commit an
abstractive/reductive fallacy (Apel, 1974). There are quite a number of these:
1. Signs
(1) without the signified (some)thing (2) and without sign interpreter (3):
yields
abstraction from the a priori of the linguistic community which reflects
on the world and produces propositions with validity claims. Examples are
linguistic Platonism, model-Platonism of the logic of science in the linguistic
turn: in which the linguistic expressions or the explanatory model are
the real (some)thing.
2. The sign
interpreter (3) without signs (1) and without the signified (some)thing (2):
yields idealism of consciousness: abstraction from the a priori of the
linguistic community (Descartes, Kant, Fichte, Hegel, Husserl): that is to say
subjective/objective reason is the real (some)thing. Language is only a
secondary means of explanation; the external world exists only through
reason/rationality.
3. Sign
interpreter (3) and sign (1) without the signified (some)thing (2): this yields
semiotic idealism: sign and sign interpreters are the signified (some)thing.
Everything is a sign: Pansemiotics/metaphysical semioticism.
4. The
signified (some)thing (2) without signs (1) and without sign interpreter (3):
This yields realism and materialism, pre-Kantian ontology/metaphysics: Being is
a physical- chemical law of the material world. We are part of this particular
material and can at best recognize approximately, with our sense organs,
partial perspectives of this material being. Sign use and sign interpretation
are pre-scientific constructions that lack a correspondence in the material
world (illusion).
5. The
signified (some)thing (2) and the sign interpreter (3) without signs (1):
yields psychologism or affection-realism; Leibniz, Locke, Berkeley, Hume, positivism
of the sensory data, Popper: the observational language and theoretical language
of the logic of science can be brought into agreement. The material function of
the sensory organs adheres to a “universal syntax” that is identical to the
laws of physics and chemistry.
6. The
signified (some)thing (2) and the sign (1) without the sign interpreter (3):
yields ontosemantic realism, constructivism, systems theory, information
theory. Abstraction from the a priori of the linguistic community yields
subjectless, syntactic-semantic phase of a modern science of logic in Carnap,
Russell, Frege, (Tractatus-)Wittgenstein, Tarski, Popper; solipsism and
realism: each speaker/listener is equipped with the same syntax (depicting
material reality), alleviating any need for communication about the structure of
language or the structure of the world. Abstraction by the cognizant subject
produces scientifically exact statements which depict, in agreement with the
laws of physics and chemistry, material reality on a 1:1 basis. Subjects of
knowledge only disturb this naturalism and muddy the exact cognitive process.
In contrast, a pragmatic philosophy of biology
integrates the irreducible three-leveled semiotics into its justification, just
as it does the formal-pragmatic preconditions for the possibility of successful
rule-governed sign-mediated interactions in agreement with the post-Tractatus
Wittgenstein (Philosophical Investigations), Austin, Searle, Apel and
Habermas. It therefore avoids the reductive/abstractive fallacy and enables a
non-solipsistic and non-objectivistic understanding of the linguistically
structured and communicatively organized living nature.
8
CONCLUSIONS
Planets without living organisms have no unstable
mixing conditions of gases and temperatures. The gas composition and the
temperatures can be determined solely based on physical factors. A planet with
living organisms deviates considerably from this scheme. The gas composition
and temperature will vary in a manner that cannot be predicted exclusively by
the laws of physics and chemistry. Planets with life will have an atmosphere
whose temperature and gas-molecular composition is regulated by the totality of
biological individuals and not by solar energy and the laws of physics and
chemistry alone.
The relation between organisms and matter is one of
organisms structuring their non-biological environment according to biological
principles. The relationship to other organisms is a communicative one: their mutual
behavior underlies changeable rules (within the frame of natural laws), more
precisely (semiotic) rules of sign use with which the biological individuals
interact, i.e. coordinate and organize. The relationship of sign users and sign
interpreters to the rules of sign use is not strict and immutable, but rather
is changeable, alterable and renewable, although it can ensure relative
stability.
The organization of life depends on
successful intra-, inter- and metaorganismic communication processes.
Interestingly, rule governed sign mediated interactions are not only the basis
for human communication and coordination but a true principle of life itself.
As demonstrated, it is the main principle also in and between microbial as in
higher eukaryotic organisms as well as between organisms of different
organismic kingdoms.
The structure of the genome itself is a
linguistic one, more analog in eubacteria, more symbolic in archaebacteria and
(higher) eukaryotes. It obeys syntactic, semantic and pragmatic rules.
Interestingly the neodarwinistic paradigm of chance mutations and selection is
refuted nowadays through research results which identify a higher order
regulation code in the non-protein coding regions of genome architecture. This
higher order regulation code is subject/object to environmental influences
which become hereditable, with the effect that a different use of
protein coding core components leads to different genetic organization.
A non-solipsistic and non-reductionistic
understanding of the linguistically structured and communicatively organized
living nature can thus provide the methodological basis for a biology as an
understanding social science, one whose descriptions are based not on a third person
pure observer perspective but rather on the perspective of performative
participants of the planetary communicating community of living nature (Witzany
2005).
REFERENCES
Apel, K.O. 1974. Zur Idee einer
transzendentalen Sprachpragmatik. Die Dreistelligkeit der Zeichenrelation und
die “abstractive fallacy” in den Grundlagen der klassischen
Transzendentalphilosophie und der sprachanalytischen Wissenschaftslogik.
In J. Simon. Ed. Aspekte und Probleme der Sprachphilosophie.
Freiburg/München: Karl Alber, pp. 283-326.
Ast, G. 2005. The Alternative Genome. Scientific
American, 4.
Austin, J.L. 1962. How to Do Things
with Words. Oxford: Oxford University Press.
Bais, H.P. et al. 2004. How plants
communicate using the underground information superhighway. Trends in Plant
Science, 9(1): 26-32.
Baluska F. et al. 2004. Eukaryotic
Cells and their Cell Bodies: Cell Theory Revised. Annals of Botany,
94: 9-32.
Baluska, F. et al. 2005. Plant
synapses: actin-based domains for cell-to-cell communication. Trends in Plant Science, 10(3): 106-111.
Bassler, B.L. 1999. How bacteria talk
to each other: Regulation of gene expression by quorum sensing. Current
Opinion in Microbiology, 2: 582-587.
Ben Jacob, E. et al. 2004. Bacterial
linguistic communication and social intelligence. Trends
in Microbiology, 12(8): 366-372.
Beurton, P. et al. 2000. The Concept of
the Gene in Development and Evolution. Cambridge University Press.
Blech, J. 2000. Leben auf dem Menschen.
Die Geschichte unserer Besiedler. Hamburg: Rowohlt Taschenbuch Verlag.
Caporale, L.H.
1998. Genomic Strategies for Evolutionary Adaptation: The rate, location and
extent of genetic variation is not monotonous. InterJournal Genetics,
178.
Caporale, L.H.
2003. Natural selection and the Emergence of a Mutation Phenotype: An Update of
the Evolutionary Synthesis Considering Mechanisms that Affect Genome Variation.
Annual Review of Microbiology, 57: 467-485.
Caporale, L.H. 2004. Genomes don’t play
dice. New Scientist,
March 2004, 42-51.
Cavalier-Smith, T. and M. J. Beaton.
1999. The skeletal function of non-coding DNA: new evidence from ancient cell
chimeras. Genetics, 106: 3-13.
Cavalier-Smith, T. 2002. Chloroplast
evolution: secondary symbiogenesis and multiple losses. Current Biology,
12: 62-64.
Crespi, B.J. 2001. The evolution of
social behavior in microorganisms. Trends in Ecology & Evolution,
16: 178-183.
Cvrcková, F. and Markos, A. 2005.
Beyond bioinformatics: can similarity be measured in the digital world? Journal of Biosemiotics, 1: 87-105.
Davies. E. 2004. New functions for
electrical signals in plants. New Phytology, 161: 607-610.
Dessaux Y. 2004. Biological
Communications and Interactions in the Rhizosphere. (unpublished). Presented at
“Rhizosphere 2004” Congress, 12.-17 September, Munich, Germany.
Dunn, A.K. and J. Handelsman. 2002.
Toward an understanding of microbial communities through analysis of
communication networks. Antonie van Leeuwenhoek, 81: 565–574.
Dustin, M.L. et al. 2001.
Identification of self through two-dimensional chemistry and synapses. Annual
Review of Cell Developmental Biology, 17: 133-157.
Emmeche, C. and Hoffmeyer, J. 2005.
Code-Duality and the Semiotics of Nature. Journal of Biosemiotics, 1: 48
Federle, M. J. and Bassler, B. L. 2003.
Interspecies communication in bacteria.
The Journal of Clinical
Investigation, 112(9): 1291–1299.
Fuqua, C. et al. 1996. Census and
Consensus in bacterial ecosystems: The LuxR-LuxI family of quorum
sensing transcriptional regulators. Annuals Review
of Microbiology, 50: 727-751.
Habermas, J. 1994. Actions, speech
acts, linguistically mediated interactions and the lifeworld. In G.
Floistad Ed. Philosophical problems today, 1: 45-74.
Hoffmeyer, J. 1998. Digital codes do
nothing. In T.A. Sebeok and J.U. Sebeok Eds. Semiotica 120(3/4), pp.
475.
Jaenisch, R. and A. Bird. 2003.
Epigenetic regulation of gene expression: how the genome integrates intrinsic
and environmental signals. Nature genetics supplement, 33: 245-254.
Jain, R. et al. 1999. Horizontal gene
transfer among genomes: the complexity hypothesis. Proceedings of the
National Academy of Sciences of the USA, 96: 3801-3806.
Jain, R. et al. 2003. Horizontal Gene
Transfer Accelerates Genome Innovation and Evolution; Molecular Biology and
Evolution, 20(10): 1598–1602.
Jenuwein, T. and C.D. Allis. 2001.
Translating the histone code. Science, 293: 1074-1080.
Kaiser, D. and R. Losick. 1993. How and
why Bacteria Talk to Each Other. Cell, 73(5): 873-85.
Kolenbrander, P.E. et al. 2002.
Communication among Oral Bacteria. Microbiology and Molecular Biology
Reviews, 66(3): 486–505.
Kull, K. 2005. A brief history of
Biosemiotics. Journal of Biosemiotics, 1: 1-34.
Losick, R. and D. Kaiser. 1997. Why and
how Bacteria Communicate. Scientific American, 2: 52-58.
Mantegna, R.N. et al. 1994. Linguistic
Features of Noncoding DNA Sequences. Physical Review Letters, 73(23):
3169-3172.
Margulis, L. 1996. Archaeal-eubacterial
mergers in the origin of Eukarya: Phylogenetic classification of life. Proceedings
of the National Academy of Sciences of the USA, 93: 1071-1076.
Margulis, L. 1999. Die andere Evolution.
Heidelberg: Spektrum Akademischer Verlag.
Margulis, L., et al. 2000. The chimeric
eukaryote: origin of the nucleus from the karyomastigont in an amitochondriate
protists. Proceedings of the National Academy of Sciences of the USA,
97: 6954-6959.
Margulis, L. 2004. Serial endosymbiotic
theory (SET) and composite individuality.
Transition from bacterial to eukaryotic
genomes. Microbiology Today, 31: 173-174.
Margulis, L. and D. Sagan. 2002. Acquiring
Genomes. A Theory of the Origin of Species. New York: Basic Books.
Margulis, L. and K.V.
Schwartz. 1988. Five Kingdoms. New York: W.H. Freeman.
Mattick, J.S. 2001. Non-coding RNAs:
the architects of eukaryotic complexity. EMBO Reports, 2(11): 986-991.
Mattick, J.S. 2003. Challenging the
dogma: the hidden layer of noncoding RNAs in complex organisms. BioEssays, 25(10): 930.
Mattick, J.S. 2005. Das verkannte
Genom-Programm. Spektrum der Wissenschaft, 3: 62-69.
Mattick, J.S. and M. J. Gagen. 2001.
The Evolution of Controlled Multitasked Gene Networks: The Role of Introns and
Other Noncoding RNAs in the Development of Complex Organisms. Molecular
Biology and Evolution, 18(9): 1611-1630.
Montana State University. 1999. Cell-Cell
Communication Collection. Center of Biofilm Engineering, online paper:
http://www.erc.montana.edu/Res-Lib99-SW/Image_Library/Cell-Cell_Communication/default.htm.
McCarthy, T. 1984.
Translator’s Introduction. In J. Habermas. The Theory of Communicative
Action. Vol.1. Boston: Beacon Press. P. ix.
Noeth, W. 2000. Handbuch der Semiotik.
Stuttgart: Metzler.
Perbal, B. 2003. Communication is the key. Cell Communication and Signaling, 1:
3.
Roshchina, V.V. 2001. Neurotransmitters
in Plant Life. Science Publishers.
Schauder, S. and B.L. Bassler. 2001.
The languages of bacteria. Genes & Development, 15: 1468-1480.
Schauder, S. et al. 2001. The LuxS-family
of bacterial autoinducers: Biosynthesis of a novel quorum sensing signal
molecule. Molecular Microbiology, 41(2): 463-76.
Searle, J.R. 1976. Speech Acts. An
Essay in the Philosophy of Language. Cambridge: Cambridge University Press.
Schmitt, S. and R. Paro. 2004. A reason
for reading nonsense. Nature, 429: 510-511.
Shapiro, J.A. 1998. Thinking about
bacterial populations as multicellular organisms. Annual Review of
Microbiology, 52: 779-806.
Shapiro, J.A. and R.v. Sternberg. 2005.
Why repetitive DNA is essential to genome function. Biological Review,
80: 1-24.
Sharma, A. et al. 2003. Microbial
communication in the rhizosphere: Operation of quorum sensing. Current Science, 85(8): 1164-1172.
Spektrum der Wissenschaft. 1988(9). Heidelberg.
Spotswood, H.T. and B.M. Turner. 2002. An increasingly complex code. The Journal of Clinical
Investigation, 110 (5): 577-582.
Stechmann, A. and T. Cavalier-Smith.
2003. The root of the eukaryote tree pinpointed. Current
Biology, 13(17): 665-666.
Sternberg, R.v. 2002. On the Roles of
Repetitive DNA Elements in the Context of a Unified Genomic-Epigenetic System. Annals
of the New York Academy of Sciences, 981: 154-188.
Timmis, J. N. et al. 2004.
Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nature
Reviews Genetics, 5: 123-135.
Trewavas, A. 2003. Aspects of Plant
Intelligence. Annals of Botany, 92: 1-20.
Trewavas, A. 2005. Green Plants as
Intelligent Organisms. Presented at the “1st Meeting on Plant
Neurobiology”, May 17-20, Florence, Italy.
True, H. et al. 2004. Epigenetic
regulation of translation reveals hidden genetic variation to produce complex
traits. Nature, 431: 184-187.
Turner, B.M. 2000. Histone acetylation
and an epigenetic code. Bioessays, 22: 836-845.
Turner, B. M. 2002. Cellular Memory and
the Histone Code. Cell, 111: 285-291.
Vollmert, B. 1985. Das Molekül und das
Leben. Reinbek: Rowohlt.
Wagner, E. et al. 1999. From Symbiosis to Eukaryotism. ENDOCYTOBIOLOGY VII
Proceedings of the International Congress
on Endocytobiology, Symbiosis and Biomedicine, University of Freiburg,
University of Geneva.
Walker, T. S. 2003. Root exudation and
Rhizosphere Biology. Plant Physiology, 132: 44-51.
Wang, Y. et al.
2004. Beyond the Double Helix: Writing and Reading the Histone Code. In
G. Bock and J. Goode. Eds. Reversible Protein Acetylation. Novartis
Foundation, 2004.
Waterland, R.A. and R.L. Jirtle. 2004. Early Nutrition, Epigenetic Changes at Transposons and Imprinted
Genes, and Enhanced Susceptibility to Adult Chronic Diseases. Nutrition, 20(1):
63-68.
Watson, J.D. et al. 21992. Recombinant
DNA. Scientific American Books.
Witzany, G. 1993 a. Zeichenprozesse als
Bedingungen der Möglichkeit von Leben und Evolution. Zeitschrift für
Semiotik, 15(1/2): 107-125.
Witzany, G. 1993 b. Natur der Sprache –
Sprache der Natur. Sprachpragmatische Philosophie der Biologie. Würzburg :
Königshausen and Neumann.
Witzany, G. 1995. From the “logic of
the molecular syntax” to molecular pragmatism. Evolution and Cognition,
1(2): 148-168.
Witzany, G. 1997. Semiosis and
Evolution. In I. Rauch. Ed. Semiotics around the World: Synthesis in
Diversity. Berlin: Mouton de Gruyter, pp 977-980.
Witzany, G. 1998. Explaining
and Understanding LIFE. Semiotica, 120(3/4): 421-438.
Witzany, G. 2000. Life: The
Communicative Structure. A New Philosophy of Biology. Norderstedt: Libri
Books on Demand,
Witzany, G. 2002 a. Reduction of
biological phenomena? Deficits of systems theory and the alternatives. In
W. Schmitz. Ed. Processes in Complex Systems. Berlin/New York:Mouton de
Gruyter, pp 303-307.
Witzany, G. 2002 b. Sprache und
Kommunikation als zentrale Struktur- und Organisationsprinzipien belebter
Natur. In Albers, L. and O. Leiss. Eds. Körper-Sprache-Weltbild. Integration
biologischer und kultureller Interpretationen in der Medizin. Stuttgart/New
York: Schattauer, pp 87-96.
Witzany, G. 2003. Metaphysics in
Physics and Biology. Presented at the meeting of the International Society
for the History, Philosophy and Social Studies of Biology, Vienna 2003.
Witzany, G. 2005. From biosphere to
semiosphere to social lifeworlds. Biology as an understanding social science. Journal
of Biosemiotics, 2 (forthcoming).
Wittgenstein, L. 1968. Philosophical
Investigations. Basil & Blackwell, Oxford.
Wolf, Y.I. 1999. Evolution of
Aminoacyl-tRNA Synthetases—Analysis of Unique Domain Architectures and
Phylogenetic Trees Reveals a Complex History of Horizontal Gene Transfer
Events. Genome Research, 9: 689-710.
Wolf, Y.I. 2000. Genome Alignment,
Evolution of Prokaryotic Genome Organization, and Prediction of Gene Function
Using Genomic Context. Genome Research, 11: 356-372.
Xie G. et al. 2004. Inter-genomic
displacement via lateral gene transfer of bacterial trp operons in an
overall context of vertical genealogy. BioMedCentral Biology, 2: 15.
Yoder, J.I. 1999. Parasitic plant
responses to host plant signals: a model for subterranean plant-plant
interactions. Current Opinion in Plant Biology, 2: 65-70.
Zook, D. 1998. A New Symbiosis Language.
ISS Symbiosis News, 1(3): 1-3
ENDNOTES
1 In her
excellent articles Lynn Caporale (Caporale, 1998; 2003; 2004) demonstrates that
the genome finds ways and means to use blind chance for its own purposes. The
hereditary material itself decides at which site mutations occur and where they
are blocked. The genome contains information with which it can describe
itself. This agrees with the research results of Mattick und Shapiro, who
were able to document the higher-order regulation functions of active
micro-RNAs that are coded in the non-protein-coding DNA, for example in the
repetitive elements of introns. In a certain sense, this contradicts an
assumption of Hoffmeyer (“Digital codes do nothing”, Hoffmeyer 1998:
475).
2 With regard to the geMetaCode, Watson
postulated in 1992 that he expected to find “information bearing molecules” in
the chromosomes (Watson, 1992:6). Mantegna et al. drew the correct conclusions
in 1994 based on statistical-linguistic studies: “These
results are consistent with the possible existence of one (or more than one)
structured biological language(s) present in non-coding DNA sequences”
(Mantegna et al., 1994: 3172).
3 The
growth of complexity from analogous languages to symbolic ones is not limited
to genetic codes but a typical characteristic of linguistically structured nature
in general. For example, symbolic communication between bees of the northern
hemisphere is much more complex than analogous communication between bees of
the southern hemisphere. Thus northern hemisphere bees conducted much more
complex and indeed new ways of coordinated behaviour. Why the terminology analogous/symbolic
should be preferred to analogous/digital in describing this semiotic relation
has been explained convincingly by Cvrcková and Markos (Cvrcková and Markos
2005).
4 This contradicts the conviction, that acquired
characters are not inherited: “The rejection of so called ‘lamarckism’,
precisely amounts to the claim, that no events in the life of an individual
will change the content of the genetic information carried by that individual.
Acquired characters are not inherited” (Emmeche and Hoffmeyer, 2005: 48).
5 “Is
what we call “obeying a rule” something that it would be possible for only one
man to do, and to do only once in his life? (…) It is not possible that there
should have been only one occasion on which someone obeyed a rule. It is not
possible that there should have been only one occasion on which a report was
made, an order given or understood, and so on – To obey a rule, to make a
report, to give an order, to play a game of chess, are customs (uses,
institutions)” (Wittgenstein 1968: 80).
One sign alone is not a sign! A sign is a sign only as part of a
context of signs. An interpreter is an interpreter only as a co-subject. In his
analysis of the concept “to obey a rule”, Wittgenstein provides proof that the
identity of meanings logically depends on the ability to obey intersubjectively
valid rules together with at least one further subject.
