Lingvistická a lexikostatistická analýza ve spolupráci lingvistiky

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Lingvistická a lexikostatistická analýza ve spolupráci lingvistiky, matematiky, biologie a psychologie
reg. č.: CZ.1.07/2.3.00/20.0161
An interdisciplinary workshop
INFORMATIONAL FUNDAMENTALS OF LIFE: GENOMES AND LANGUAGES
BOOK OF ABSTRACTS
Palacký University, Olomouc
(May 27 – May 28, 2014)
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GENOME SEQUENCES AND HUMAN TEXTS - BOTH REPRESENTATIONS OF HOMO SAPIENS AS
BIOLOGICAL SPECIES.
Edward N.Trifonov
University of Haifa, Israel
trifonov@research.haifa.ac.il
While genetic history and make-up of H. sapiens is described in encoded way by its genome
sequences, that is, texts in 4-letter alphabet (20-letter alphabet for proteins), the human
history, culture, scientific and technological progress and achievements are described in
books and other printed materials, in form of texts in 15 to 60-letter alphabets. Both kinds
of texts are products of biological evolution, and subject of continuing evolution. Moreover,
all designs, technology, machines are manifestations of biological activity (of H. sapiens), and
therefore – products and subjects of biological evolution, very much like structures built by
termites and mole-rats.
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NON EST SIGNUM.... THE EMERGENCE OF PRE-GENETIC COMPLEXITY
Ernesto Di Mauro
Università "La Sapienza", Roma, Italy
ernesto.dimauro@uniroma1.it
Life is made of the intimate interaction of metabolism and genetics, both built around the
chemistry of the most common elements of the Universe (hydrogen, oxygen, nitrogen,
carbon). The transmissible interaction of metabolic and genetic cycles results in hypercycles
of organization and de-organization of chemical information, of living and non-living. The
origin-of-life quest has long been split in several attitudes exemplified by the aphorisms
“genetics-first” or “metabolism-first”. Overstepping the opposition between these
approaches by a unitary theoretical and experimental frame and taking into account
energetic, evolutionary, proto-metabolic and ur-environmental aspects, we propose a simple
pathway leading to a complete prebiotic reactive system. Specifically, we have analyzed the
synthetic reactions leading from the one-carbon atom compounds HCN and its hydrolyzed
form NH2COH formamide to prebiotically relevant compounds in the presence of catalysts.
We observe the formation of all the extant biological nucleic bases, of carboxylic acids, of
aminoacids and of condensing agents in the presence of tens of catalysts of terrestrial and
meteorite origin, the formation of cyclic nucleotides and their spontaneous polymerization
to oligonucleotides, their terminal ligation yielding longer polymers, a ribozyme activity
causing the terminal transfer of nucleotides between in vitro abiotically generated
oligomers. In vitro generated oligonucleotides thus automatically increase the chemical
information of the system.
These results entail that the spontaneous generation of proto-metabolic and proto-genetic
systems did not require exceeding complexity. Rather, it was likely to be the result of the
interplay between combinatorial casuality and thermodynamic necessity of the existing most
abundant atoms.
How far down towards the Beginnings can the similitude between chemical alphabets and
languages abutting on logical mental processes be stretched?
Considerations on this matter will be presented, including:
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- the need of an Observer; Casuality vs Necessity; Evolution from randomicity; The
earliest phenotypes.
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ON THE ASYMMETRY OF LANGUAGE AND GENES
L-WORDS AND DNA WORDS
Anna Maria Di Sciullo
Université du Québec à Montréal, Canada
disciullo4@gmail.com
1. The genetic code is considered to be a "language". The DNA alphabet of A, T, C, and G
produce enough DNA "words" to specify each of the 20 known amino acids. DNA words are
three-letter long, and the combinations of the alphabet produce 64 words. The questions I
will address are the following: in what sense linguistic words are related to DNA words?
What makes linguistic words unique?
I consider the properties of linguistic words, hereafter L-words, and their meaning in natural
language messages, comparing them to DNA words and the meaning of genetic messages. I
assume the Biolinguistic framework (2005, 2007 a.o., Di Sciullo et al 2010, a.o.). I further
assume the asymmetry model, henceforth A-model, (Di Sciullo 2005, 2014), which has
consequences for the properties of words in human languages. I show that there are striking
parallels as well as differences between L-words and DNA words.
2. Linguistic expressions relate sound and meaning via a syntactic structure. Words do not
differ from phrases in this respect. According to the A-Model, they are however, built in a
different workspace than phrases, since they have different interface properties, including
stress patterns and semantic
interpretation. In the A-model, words are derived by the combination of three elements, a
head and two dependents, as depicted in the minimal tree T, where the head x projects its
features to the root, x contrary to its dependents, α, β. The asymmetrical structure underlies
the properties of the three basic types of verbs, (1). Morphological merger (M-shift) consists
of the substitution of a minimal tree T1 to the complement of a minimal tree T2. This
operation is binary and recursive, as depicted in (2) for the derivation of productive and
productivity. The merger of two minimal trees is subject agreement between two features of
different value. For example, agentive nominal suffixes may merger with transitive or
inergative roots, but not with unergative roots, e.g. writer, sleeper vs. *departer, *arriver.
Likewise aspectual affixes may affect certain verbs and not other according to the internal
aspectual features, as evidenced in Di Sciullo (1998, 2005) for Romance languages, e.g.
enfermer ‘to close’ endormir ‘to get to sleep’ vs. *enarriver, ‘to enarrive’, *endépartir ‘to
endepart’, as well for Algonquian languages, such as Oji-Cree (Slavin 2014).
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(1)
(2)
The asymmetrical structure of the argument structure types and the feature asymmetry of
r morphological merger in the derivation of L-words, could find its biological basis in the
asymmetrical structure of thenucleotide acid A, G, T and C, in (3), the constituents of the
DNA and the amino acids, the constituents of proteins.
(3)
Adenine
Guanine
Thymine
Cytosine
3. I discuss similarities between L-words and DNA words with respect to their structure, as
well as with respect to the combination of their constituents and the replication of their
parts. I also identify similarities between the local merger of certain morphological
structures to the exclusion of others, as well as the local combination of certain elements of
the DNA alphabet, A-to-T and G-to-C, as well as between the replication of the same
elements in L-words, for example in the case of right edge CVC# reduplication found in the
morphology of different languages, for example in Micronesian languages, to detransitivize
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atransitive verb (5a,b), as well as for category alternation (6a), formation of distributive
words, (6b), and derive post-positional adjectives, (6c), and in genetic scripts indicating a
linkage between the propertiesof the basic elements and the generative procedure giving
rise to DNA-words and to L-words.
(5) a. Emmaan eo e-ar mwijit piik eo.
man DET.SG.N-HUM. 3SG.AGR.-PAST. cut.TR. pig DET.SG.N-HUM.
'The man cut the pig.'
b. Emmaan eo e-ar mwijmwij.
Man DET.SG.N-HUM 3SG.AGR.-PAST cut.INTR.
'The man did some cutting.' (Willson 2008)
(6) a. hat: ‘hat’ hathat: ‘wear a hat’
kal: ‘loincloth’ kalkal: ‘wear a loincloth’
wah: ‘canoe’ wahwah: ‘go by canoe’
b. det: ‘sunshine’ detdet ‘full of sunshine’
bat: ‘hill’ batbat: ‘full of hills’
beq: ‘sand’ beqbeq: ‘full of sand’
c. deyaw: ‘be pretty’ deyawyew: ‘pretty’
mayan: ‘be smart’ mayanyan: ‘smart’
mekaj: ‘be fast’ mekajkej: ‘fast’ (Willson 2002)
3.2. L-words and DNA-words have specific properties. L-words are potentially infinite and
their length is not limited to three letters. The length of a DNA word is fixed to three letters,
and the set of DNA-words is limited to 64 words. I also discuss the properties of DNA
sequence replications as opposed to the recursion observed in L-words, which include
indirect and center-embedded recursion. I argue that indirect recursion, that is recursion
mediated by a functional projection, is a core representational property of L-words.
4. Summarizing. L-words are related to DNA words regarding the form of the basic elements
to which the combinatorial procedure applies, and in particular with respect to the fact that
these elements have an internal structure. L-words are unique in that their length is
potentially infinite, as the recursive computational procedure deriving them may affect the
edge as well as non-edge positions. They are not strings of character as the message they
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pass on to the semantic interface is based on asymmetrical structure. The discovery of
convergences and specificities between genetics and linguistic structures maylead to a
deeper understanding of the biological basis of human language.
5. Selected references. Chomsky, Noam. 2007. Of minds and language. Biolinguistics 1, 9-27.
Chomsky, N. 2005. Three factors in language design. Linguistic Inquiry 36:1-22. Di Sciullo,
A.M. 2014. Minimalism and I-Morphology. In P. Kosta, S. Franks and T. Radeva-Bork (eds.),
Minimalism and Beyond:Radicalizing the interfaces. Amsterdam: John Benjamins. Di Sciullo,
A. M. 2005. Asymmetry in Morphology. Cambridge, Mass.: The MIT Press. 264 pp. Di Sciullo
et al. 2010. The biological nature of human language. Biolinguistics. 4: 4-34. Slavin, T. 2014.
XXXX Willson, H. 2008. Subject position and the Marshallese restructuring configuration.
University of Pennsylvania Working Papers in Linguistics.14: Iss.1, Article 27. Willson, H.
2002. The Marshallese Complementizer Phrase. M.A. Arizona State University.
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INTERFACES, DELAYED MERGE, AND THE THEORY OF FRUSTRATED MIND
Peter Kosta1 and Diego Krivochen2
1
University of Potsdam, Germany
peter.kosta@uni-potsdam.de
2
University of Potsdam, Germany/ Universidad Nacional de la Plata, Argentina
diegokrivochen@hotmail.com
In this paper we will reanalyze the basic structure generation operation in Minimalist Syntax,
namely, Merge. We will present a new approach to generation in a wide sense, focusing on
the Faculty of Language (FLN) and its interfaces: C-I and S-M, building on work by Krivochen
(2011a et. seq.), Kosta & Krivochen (2014), and Krivochen & Kosta (2013). Our main claim is
that there is nothing more to “syntax” than Merge and, going further, that the so-called
“syntactic component” of the Faculty of Language is not the only computational system in
the mind-brain: as a consequence, the term “syntax” has wider scope than generally
recognized. By doing so, we attempt to sustain the claim that Merge is a third-factor,
principled operation (Chomsky, 2005). We will analyze and decompose some current
proposals (Chomsky’s 2005, 2007; Adger’s 2011; Hornstein & Pietroski’s 2009 and Boeckx’s,
2010) and other theoretically possible options to rule out any stipulation and, optimally, get
a Radically Minimalist definition of Merge: a system-neutral non-stipulative definition that
can capture the properties of recursion all throughout the mind-brain (understood as a
complex physical system), while retaining descriptive and explanatory adequacy and going
beyond, towards justification in both biological and computational terms. Furthermore, we
will try to show that:
(1) FLN only comprises External Merge (both monotonic and non-monotonic), and only
humans can make use of finite means provided by sound-meaning interfaces to
weakly generate potentially infinite pairs Exp = (π, λ) with information interpretable
for the performance systems.
(2) FLN displays the major human language-specific property, namely, the linking of
sound to meaning (and vice versa) in an intensional way, via computational
manipulation of symbolic representations. While the latter might be shared with
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non-human species (e.g., superior primates), the latter is hypothesized to be humanspecific, related to the structure of the genome.
(3) Only humans’ computational capacities, dynamically ranging from finite-state
grammars (Markovian processes) to Turing-computability allow full recursion (i.e.,
not only head-tail recursion or so-called true recursion, but also inter-sentential
recursion via referential dependencies and cross-clausal connectives: conjuncts and
disjuncts, Quirk et. al., 1985) is able to account for the whole range of soundmeaning relations and the internal structure of each interface.
In the second part of the paper, some problems of molecular genetics research on language
impairments and speech disorders will be discussed, namely molecular genetics methods
with special reference to Specific Language Impairment (SLI) and verbal dyspraxia caused by
mutations, deletions, insertions or duplications of FOXP1 or FOXP2 genes (Watson, 2002).
The crucial question we try to address is whether the computational system responsible for
the so-called language faculty in the narrow sense (FLN, Hauser, Chomsky & Fitch, 2002) is
language-specific or shares any of its properties with other, independent cognitive modules;
both in terms of computational properties and / or neurological bases. Some new findings in
neurolinguistics seem to point into the direction that at least some types of language
impairments are not grammar specific but rather caused by abnormal development of brain
structures that constitute the procedural memory system, where computations are
performed in real time. Thus, we would expect SLI to limit the computational power of FLN
to simpler grammars (e.g., Markovian, Context-free) and impoverish interface-mapping
operations, thus “getting in the way” of sound-meaning relations.
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THE GRAMMAR OF LANGUAGE EVOLUTION
Christina Behme
University of Potsdam, Germany.
Christina.Behme@dal.ca
Language evolution has been called “the hardest problem of science” (Christiansen & Kirby,
2003), and raises many fascinating philosophical questions. One of the most influential views
in linguistics, Chomsky’s generative grammar, proposes that language is a biological organ,
on par with other biological organs like the visual or digestive system (e.g., Chomsky, 2012).
It is not surprising that much work on language evolution focuses on brain evolution,
language acquisition, and communication systems of other primates. I’ll give a brief
overview of some of this work. Yet, my focus will be on some facts of grammar that are
often neglected in the language evolution debates. I show that within linguistics there
remain unresolved disputes about the ontological status of language and the exact
relationship between language and biology. Finally I discuss two phenomena that have
played an important role in disputes between generativist and non-generativist linguists:
strong crossover and island phenomena. Generativists claim these phenomena suggest that
humans have an innate language organ that determines linguistic structure. By contrast,
non-generativist accounts, which are taking a wide range of corpus, lab psycholinguistic and
introspective evidence into account, provide an alternative to a structural account. I suggest
that resolving these debates will have important implications for language evolution
research.
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FREQUENT WORDS AND GENOME ORIGIN
E.N. Trifonov1, Michaela Zemková2 and Daniel Zahradník3
1
University of Haifa, Izrael,
Charles University in Prague, CZ
misa.zemkova@seznam.cz
3
Czech University of Life Sciences- Prague, CZ
zahradnik@fld.czu.cz
2
Inspection of a full vocabulary of the words (16-mers) of human genome reveals that the
top of the list ranked by word occurrence contains almost exclusively simple repeats, and
words from Alu sequences – most abundant short dispersed elements. These excessive
words can be considered as ‘generators” and suggest a simple model of genome evolution:
everlasting intrusion of the generator sequences in “neutral” regions of the genome, and
gradual mutational changes, causing the increase in the sequence complexity. The way to
detect the generators is to find those of which point mutated forms appear less frequently.
Examples of the generators will be presented.
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WHAT IS THE DIFFERENCE BETWEEN LIVING AND INANIMATE OBJECTS?
(WHAT PINOCCHIO MEANT BY WANTING TO BE A REAL BOY?)
Jan Špaček
Institute of Biophysics and Biochemistry of the AS CR, v.v.i.
j.h.spacek@ibp.cz
Some definitions are based on hypotheses or theories which try to explain natural laws.
These definitions can be considered universally true regardless of the cultural background of
the speaker until someone is able to falsify a hypothesis or theory on which such definitions
are built (for example a definition of organic substances based on vitalism was until it´s
falsification a valid scientific definition).
On the other hand there are definitions which aren’t based on a hypothesis, because there
cannot be formed a viable hypothesis about a defined concept. These definitions are usually
based on cultural and historical background of the author and the given historical
background may be defined differently or not at all. In such category fall definitions of units,
definitions of colors, definition of organic chemistry, and in my opinion also all definition of
life I heard about.
Definition by professor Edward Trifonov, that life is evolving replicators and vice versa
evolving replicators are life, is inspiring and will surely lead to closer cooperation of
biologists with linguists, providing new insights in both fields. On the other hand such
definition is not a scientific one, because it is impossible to be falsified*. Therefore, the only
viable scientific hypothesis about life is hypothesis zero: Living things (regardless of the
definition) does not differ from inanimate objects in any observable quality. Therefore we
can either call all things to be a life or we can declare all things not to be life.
*My talk is based on Popper’s philosophy that science has to be falsifiable. In case that science does not have
to be falsifiable, then let me present my new scientific definition of life: “Life is a set of things touched by
invisible pink unicorn guided by flying spaghetti monster just before someone declared that thing to be live.”
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THE MOST FREQUENT [5R, 5Y] DECAMER IN THE GENOMES OF HIGHER ORGANISMS
Jan Hapala 1,2, Edward N. Trifonov1,2
1
University of Haifa,Izrael
2
Masaryk University, Brno, CZ,
jan@hapala.cz
RRRRRYYYYY decamer has been shown to be a nucleosome positioning motif, universal
across higher organisms (eukaryotes) [1]. This decamer is over-represented in the human
genome [2].
We have analysed the occurrence of this decamer in the genomes of other eukaryotic
species. Besides the simple occurrence of the decamer, we have studied the frequency of
the decamer tandemly repeated.
Our results show that the nucleosome positioning decamer (RRRRRYYYYY) is favored by the
analysed genomes, both by occurrence and by periodicity. This dominance, apparently,
reflects the importance of the nucleosome positioning signal in the eukaryotic genomes.
References
[1] Trifonov, E.N. Cracking the chromatin code: precise rule of nucleosome positioning. Phys.
Life Rev. 8: 39–50, 2011.
[2] Li, W., Sosa, D., Jose, M. V. Human Repetitive Sequence Densities are Mostly Negatively
Correlated with R/Y-based Nucleosome-Positioning Motifs and Positively Correlated with
W/S-based Motifs. Genomics. 101 (2): 125-133, 2012
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BLURRY CONTOURS. SEMIOTIC EFFORT IS REQUIRED FOR PARSING THE WORLD
Anton Markoš
Charles University in Prague, CZ,
anton.markos@natur.cuni.cz
No entity in real world can be considered “digital”, i.e. having clear-cut, sharp boundaries: whenever
we focus our attention, it comes out that their contours are smudged. Only entities dwelling in the
objective world, i.e. our abstractions and models (e.g., characters, numbers, mathematical and
logical terms), can be defined, and delineated sharply, unequivocally. It follows that living beings, in
order to orient themselves in their world (umwelt), face two goals: (1) to parse world continuum into
discrete (never digital) entities and (2) to distinguish such entities reliably (but never unequivocally).
Inability to define, as well as recognize, world entities exactly, i.e. with absolute precision, leads to
erroneous, but also to new interpretation and re-interpretation of phenomena. Here is the very basis
of the semiotic and even hermeneutic qualities of life.
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THE PREHISTORY OF HUMAN SPEECH SOUNDS
Damian E. Blasi
Max Planck Institute for Mathematics in the Sciences,
Max Planck Institute for Evolutionary Anthropology, Max Planck Institute for Psycholinguistics,Evolutionary
Processes in Language and Culture Group.
damianblasi@gmail.com
I will critically review evidence from Anthropology, Human Biology and Linguistic Typology
on the nature of speech sounds in the early stages of humanlanguage. In the first part of the
presentation, the putative dating of modern speech organs, as well as the relevant history of
a few genes that have been linked with the occurrence of certain classes of phones in their
host populations will be discussed.
Then I will take the vantage point of the uniformitarian hypothesis, which states that
processes and pressures currently acting upon languages were likely to be present during
the whole history of human languages - thus establishing causal relations between speech
sounds and other social, environmental and functional factors can be used to infer likely
scenarios for the dawn of language. The question of whether languages' phonological
inventories have constant biases towards complexification or simplification (and how they
depend on factors like social structure) will be treated, in particular in relation to the first
population migrations out of Africa of our species. Studies in animal communication suggest
that sound signals are subject to adaptation processes relating to the properties of the
environment; I will comment on how similar ideas were developed for human language.
Finally, the least-effort principle applied to the relative cost of different human vocalizations
leads to testable predictions about the distribution of human speech sounds.
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EMERGENCE OF LIVING LANGUAGE
(AN APPLIED LINGUISTICS FOR MOTHERS)
Michaela Zemková
Charles University in Prague, CZ
misa.zemkova@seznam.cz
Although the language is something deeply embedded in our nature, the question of its
origin is still not entirely resolved. (Quite analogously as the unresolved question of the
origin of life). Following ontogeny-phylogeny recapitulation- frame-work, we propose_ that
studies of language ontogeny, especially its early stages, can bring a new understanding to
language. As M.S. Kennedy points out (Kennedy, 1990), language is not given as an a priori
condition but it is rather a consequence of development. A child doesn’t only acquire_ or
internalize_ but it grows in the language, because this process is implicit in the human
developmental system. Looking at the development of early children´ s utterances we can
follow, similarly to the recapitulation model of evolution of language: From early
vocalization and gestures through canonical babbling and first words to the adult language
of given community.
To illustrate this developmental approach, we review several studies on babbling and early
words to try to answer following questions: What is actually the contribution of child prespeech utterances and early baby-talks to the adult sound system and their vocabulary? Is
there any universal stage of all languages (analogously to phylotype in developmental
biology)? Is the child language just an imitation of the adult language or is it, at least in some
parts (such as period of canonical babbling), an autonomous and generating process? Is the
ontogeny of speech continuous, or discontinuous?
If the development of language is continuous (hence every stage of development is a preadaptation for a later one) and at the same time autonomous, then the child babbling and
early language can be no longer just the imitation, but it must be also an autonomously
creative process. (Furthermore, if the pre-linguistic behaviour and speech are related, what
about our closest non-human relatives?)
Finally, inspired in broadly accepted theory of origin of genome from simple repetitive
sequences, we would like to point out to the analogy between emergence of language and
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living structures: Information represented by some language as well as genetic information
of living beings comes from simple repetitive sequences whose repertoire is given by natural
(physiological or physical-chemical) constraints. This repertoire later differentiates to more
complex structures. So the language and even living beings are not just passive objects but
active self-creating entities.
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BIRDS WHO DON'T SING, BUT SPEAK: STRUCTURE AND DYNAMICS OF VOCAL
COMMUNICATION IN PARROTS
Jitka Lindová
Charles University in Prague, CZ
jitka.lindova@seznam.cz
Parrots manifest their high cognitive skills mainly in the vocal domain, and some other bird
taxa also demonstrate complex vocal communication, including referential vocal signals,
transmission of vocal dialects or constitution of the repertoire of calls on the basis of group
membership. I will review some influential studies of both natural and artificial
communication in parrots, corvids and occasionally other bird taxa to show possible parallels
with the human language.
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BACTERIAL COMMUNICATION
Jaroslav Čepl
Charles University in Prague, CZ
jaroslavcepl@seznam.cz
Cells are building blocks of entire living realm – even the most imposing of trees, the most
mighty of animals or the most brilliant of minds started they journey on the world as a single
cell. This cell multiplicates and differentiates according to contexts of internal and external
signals.
Analogically bacterial cells, despite apparent differences in their cellular structure, act in
their world as agents by means that they “want” some things and “don´t want” another.
They achieve their goals by communication on both cell-to-cell level and whole population
level and decide their fate according to this communication. This concept doubts the
traditional perception of bacteria as a strictly single-cell organism and shows bacterial
population as a cooperating whole.
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The organization of the workshop has been supported by the grants:
Innovation of General Linguistics and Communication Theory Studies in
Cooperation with Natural Science, reg. no.: CZ.1.07/2.2.00/28.0076 and
Linguistic a lexicostatistic analysis in cooperation with linguistics,
mathematics, biology, psychology, grant no. CZ.1.07/2.3.00/20.0161.
Both of these projects are financed by the European Social Fund and
the national Budget of the Czech Republic.
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