Welcome

@article{FERRERICANCHO2013216,

title = {Erratum to “Random models of Menzerath\textendashAltmann law in genomes” (BioSystems 107(3) (2012) 167\textendash173)},

author = {Ramon Ferrer-i-Cancho and Jaume Baixeries and Antoni Hern\'{a}ndez-Fern\'{a}ndez},

url = {http://www.sciencedirect.com/science/article/pii/S0303264713000191},

doi = {https://doi.org/10.1016/j.biosystems.2013.01.004},

issn = {0303-2647},

year  = {2013},

date = {2013-01-01},

journal = {Biosystems},

volume = {111},

number = {3},

pages = {216 - 217},

abstract = {Here we improve the mathematical arguments of Baixeries et al (BioSystems 107(3) (2012) 167\textendash173). The corrections do not alter the conclusion that the random breakage model yields an insufficient fit to the scaling of mean chromosome length as a function of chromosome number in real genomes.},

keywords = {Menzerath-Altmann law},

pubstate = {published},

tppubtype = {article}

}

@article{doi:10.1080/09296174.2013.773141,

title = {The Parameters of the Menzerath-Altmann Law in Genomes},

author = {Jaume Baixeries and Antoni Hern\'{a}ndez-Fern\'{a}ndez and N\'{u}ria Forns and Ramon Ferrer-i-Cancho},

url = {https://doi.org/10.1080/09296174.2013.773141},

doi = {10.1080/09296174.2013.773141},

year  = {2013},

date = {2013-01-01},

journal = {Journal of Quantitative Linguistics},

volume = {20},

number = {2},

pages = {94-104},

publisher = {Routledge},

abstract = {Abstract The relationship between the size of the whole and the size of the parts in language and music is known to follow the Menzerath-Altmann law at many levels of description (morphemes, words, sentences, …). Qualitatively, the law states that the larger the whole, the smaller its parts, e.g. the longer a word (in syllables) the shorter its syllables (in letters or phonemes). This patterning has also been found in genomes: the longer a genome (in chromosomes), the shorter its chromosomes (in base pairs). However, it has been argued recently that mean chromosome length is trivially a pure power function of chromosome number with an exponent of −1. The functional dependency between mean chromosome size and chromosome number in groups of organisms from three different kingdoms is studied. The fit of a pure power function yields exponents between −1.6 and 0.1. It is shown that an exponent of −1 is unlikely for fungi, gymnosperm plants, insects, reptiles, ray-finned fishes and amphibians. Even when the exponent is very close to −1, adding an exponential component is able to yield a better fit with regard to a pure power-law in plants, mammals, ray-finned fishes and amphibians. The parameters of the Menzerath-Altmann law in genomes deviate significantly from a power law with a −1 exponent with the exception of birds and cartilaginous fishes.},

keywords = {Menzerath-Altmann law},

pubstate = {published},

tppubtype = {article}

}

@article{doi:10.1002/cplx.21429,

title = {The challenges of statistical patterns of language: The case of Menzerath's law in genomes},

author = {Ramon Ferrer-I-Cancho and N\'{u}ria Forns and Antoni Hern\'{a}ndez-Fern\'{a}ndez and Gemma Bel-enguix and Jaume Baixeries},

url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/cplx.21429},

doi = {10.1002/cplx.21429},

year  = {2013},

date = {2013-01-01},

journal = {Complexity},

volume = {18},

number = {3},

pages = {11-17},

abstract = {Abstract The importance of statistical patterns of language has been debated over decades. Although Zipf's law is perhaps the most popular case, recently, Menzerath's law has begun to be involved. Menzerath's law manifests in language, music and genomes as a tendency of the mean size of the parts to decrease as the number of parts increases in many situations. This statistical regularity emerges also in the context of genomes, for instance, as a tendency of species with more chromosomes to have a smaller mean chromosome size. It has been argued that the instantiation of this law in genomes is not indicative of any parallel between language and genomes because (a) the law is inevitable and (b) noncoding DNA dominates genomes. Here mathematical, statistical, and conceptual challenges of these criticisms are discussed. Two major conclusions are drawn: the law is not inevitable and languages also have a correlate of noncoding DNA. However, the wide range of manifestations of the law in and outside genomes suggests that the striking similarities between noncoding DNA and certain linguistics units could be anecdotal for understanding the recurrence of that statistical law.},

keywords = {Menzerath-Altmann law},

pubstate = {published},

tppubtype = {article}

}

@article{Ferrer_i_Cancho_2012,

title = {The span of correlations in dolphin whistle sequences},

author = {Ramon Ferrer-i-Cancho and Brenda McCowan},

url = {https://doi.org/10.1088%2F1742-5468%2F2012%2F06%2Fp06002},

doi = {10.1088/1742-5468/2012/06/p06002},

year  = {2012},

date = {2012-06-01},

journal = {Journal of Statistical Mechanics: Theory and Experiment},

volume = {2012},

number = {06},

pages = {P06002},

publisher = {IOP Publishing},

abstract = {Long-range correlations are found in symbolic sequences from human language, music and 

DNA. Determining the span of correlations in dolphin whistle sequences is crucial for shedding 

light on their communicative complexity. Dolphin whistles share various statistical properties 

with human words, i.e. Zipf’s law for word frequencies (namely that the probability of the 

ith most frequent word of a text is about i−α) and a parallel of the tendency of more frequent words to have more meanings. The finding 

of Zipf’s law for word frequencies in dolphin whistles has been the topic of an intense 

debate on its implications. One of the major arguments against the relevance of Zipf’s law 

in dolphin whistles is that it is not possible to distinguish the outcome of a die-rolling 

experiment from that of a linguistic or communicative source producing Zipf’s law for word 

frequencies. Here we show that statistically significant whistle\textendashwhistle correlations extend 

back to the second previous whistle in the sequence, using a global randomization test, and 

to the fourth previous whistle, using a local randomization test. None of these correlations 

are expected by a die-rolling experiment and other simple explanations of Zipf’s law for 

word frequencies, such as Simon’s model, that produce sequences of unpredictable 

elements.},

keywords = {Zipf\'s law for word frequencies},

pubstate = {published},

tppubtype = {article}

}

@article{Freeberg2012a,

title = {Information theoretical approaches to chick-a-dee calls of Carolina chickadees (Poecile carolinensis)},

author = {T. M. Freeberg and J. R. Lucas},

doi = {10.1037/a0024906},

year  = {2012},

date = {2012-01-01},

journal = {Journal of Comparative Psychology},

volume = {126},

issue = {1},

pages = {68\textendash81},

abstract = {One aim of this study was to apply information theoretical analyses to understanding the structural complexity of chick-a-dee calls of Carolina chickadees, Poecile carolinensis. A second aim of this study was to compare this structural complexity to that of the calls of black-capped chickadees, P. atricapillus, described in an earlier published report (Hailman, Ficken, \& Ficken, 1985). Chick-a-dee calls were recorded from Carolina chickadees in a naturalistic observation study in eastern Tennessee. Calls were analyzed using approaches from information theory, including transition probability matrices, Zipf's rules, entropies, and information coding capacities of calls and notes of calls. As described for black-capped chickadees, calls of Carolina chickadees exhibited considerable structural complexity. Most results suggested that the call of Carolina chickadees is more structurally complex than that of black-capped chickadees. These findings add support to the growing literature on the complexity of this call system in Paridae species. Furthermore, these results point to the feasibility of detailed cross-species comparative analyses that may allow strong testing of hypotheses regarding signal evolution.},

keywords = {Zipf\'s law for word frequencies},

pubstate = {published},

tppubtype = {article}

}

@article{BAIXERIES2012167,

title = {Random models of Menzerath\textendashAltmann law in genomes},

author = {Jaume Baixeries and Antoni Hern\'{a}ndez-Fern\'{a}ndez and Ramon Ferrer-i-Cancho},

url = {http://www.sciencedirect.com/science/article/pii/S0303264711001924},

doi = {https://doi.org/10.1016/j.biosystems.2011.11.010},

issn = {0303-2647},

year  = {2012},

date = {2012-01-01},

journal = {Biosystems},

volume = {107},

number = {3},

pages = {167 - 173},

abstract = {Recently, a random breakage model has been proposed to explain the negative correlation between mean chromosome length and chromosome number that is found in many groups of species and is consistent with Menzerath\textendashAltmann law, a statistical law that defines the dependency between the mean size of the whole and the number of parts in quantitative linguistics. Here, the central assumption of the model, namely that genome size is independent from chromosome number is reviewed. This assumption is shown to be unrealistic from the perspective of chromosome structure and the statistical analysis of real genomes. A general class of random models, including that random breakage model, is analyzed. For any model within this class, a power law with an exponent of −1 is predicted for the expectation of the mean chromosome size as a function of chromosome length, a functional dependency that is not supported by real genomes. The random breakage and variants keeping genome size and chromosome number independent raise no serious objection to the relevance of correlations consistent with Menzerath\textendashAltmann law across taxonomic groups and the possibility of a connection between human language and genomes through that law.},

keywords = {Menzerath-Altmann law},

pubstate = {published},

tppubtype = {article}

}

@article{doi:10.1002/cplx.20398,

title = {Menzerath's law at the gene-exon level in the human genome},

author = {Wentian Li},

url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/cplx.20398},

doi = {10.1002/cplx.20398},

year  = {2012},

date = {2012-01-01},

journal = {Complexity},

volume = {17},

number = {4},

pages = {49-53},

abstract = {Abstract A previous discussion of a linguistic law called Menzerath's law (the longer a word, the shorter the syllables) in the genomic context was focused on the genome-chromosome-base level (the more number of chromosomes in a genome, the smaller the chromosome size). We apply this linguistic metaphor to more appropriate levels of gene, exon, and base. Using the human gene data, we found that the Menzerath's law at these levels holds true: the more number of exons in a gene, the shorted the averaged exon size. Since this negative correlation can be a trivial consequence of the constant size of the messenger RNA coded by the gene, we also exclude this possibility by showing that messenger RNA size increases with the number of exons. This increase of messenger RNA size is however not fast enough for genes with large number of exons to maintain a constant exon size.},

keywords = {Menzerath-Altmann law},

pubstate = {published},

tppubtype = {article}

}

@article{DOYLE2011406,

title = {Information theory, animal communication, and the search for extraterrestrial intelligence},

author = {Laurance R. Doyle and Brenda McCowan and Simon Johnston and Sean F. Hanser},

url = {http://www.sciencedirect.com/science/article/pii/S0094576509005682},

doi = {https://doi.org/10.1016/j.actaastro.2009.11.018},

issn = {0094-5765},

year  = {2011},

date = {2011-01-01},

journal = {Acta Astronautica},

volume = {68},

number = {3},

pages = {406 - 417},

abstract = {We present ongoing research in the application of information theory to animal communication systems with the goal of developing additional detectors and estimators for possible extraterrestrial intelligent signals. Regardless of the species, for intelligence (i.e., complex knowledge) to be transmitted certain rules of information theory must still be obeyed. We demonstrate some preliminary results of applying information theory to socially complex marine mammal species (bottlenose dolphins and humpback whales) as well as arboreal squirrel monkeys, because they almost exclusively rely on vocal signals for their communications, producing signals which can be readily characterized by signal analysis. Metrics such as Zipf's Law and higher-order information-entropic structure are emerging as indicators of the communicative complexity characteristic of an “intelligent message” content within these animals’ signals, perhaps not surprising given these species’ social complexity. In addition to human languages, for comparison we also apply these metrics to pulsar signals-perhaps (arguably) the most “organized” of stellar systems-as an example of astrophysical systems that would have to be distinguished from an extraterrestrial intelligence message by such information theoretic filters. We also look at a message transmitted from Earth (Arecibo Observatory) that contains a lot of meaning but little information in the mathematical sense we define it here. We conclude that the study of non-human communication systems on our own planet can make a valuable contribution to the detection of extraterrestrial intelligence by providing quantitative general measures of communicative complexity. Studying the complex communication systems of other intelligent species on our own planet may also be one of the best ways to deprovincialize our thinking about extraterrestrial communication systems in general.},

note = {SETI Special Edition},

keywords = {Zipf\'s law for word frequencies},

pubstate = {published},

tppubtype = {article}

}

@article{doi:10.1098/rsbl.2010.0455,

title = {Brevity is not always a virtue in primate communication},

author = {Bruna M. Bezerra and Antonio S. Souto and Andrew N. Radford and Gareth Jones},

url = {https://royalsocietypublishing.org/doi/abs/10.1098/rsbl.2010.0455},

doi = {10.1098/rsbl.2010.0455},

year  = {2011},

date = {2011-01-01},

journal = {Biology Letters},

volume = {7},

number = {1},

pages = {23-25},

abstract = {Semple et al. (Semple et al. in press, Biol. Lett. (doi:10.1098/rsbl.2009.1062)) argued that the ‘law of brevity’ (an inverse relationship between word length and frequency of use) applies not only to human language but also to vocal signalling in non-human primates, because coding efficiency is paramount in both situations. We analysed the frequency of use of signals of different duration in the vocal repertoires of two Neotropical primate species studied in the wild-the common marmoset (Callithrix jacchus) and the golden-backed uakari (Cacajao melanocephalus). The key prediction of the law of brevity was not supported in either species: although the most frequently emitted calls were relatively brief, they were not the shortest signals in the repertoire. The costs and benefits associated with signals of different duration must be appreciated to understand properly their frequency of use. Although relatively brief vocal signals may be favoured by natural selection in order to minimize energetic costs, the very briefest signals may be ambiguous, contain reduced information or be difficult to detect or locate, and may therefore be selected against. Analogies between human language and vocal communication in animals can be misleading as a basis for understanding frequency of use, because coding efficiency is not the only factor of importance in animal communication, and the costs and benefits associated with different signal durations will vary in a species-specific manner.},

keywords = {Zipf\'s law of abbreviation},

pubstate = {published},

tppubtype = {article}

}

@article{e13081465,

title = {Size of the Whole versus Number of Parts in Genomes},

author = {Antoni Hern\'{a}ndez-Fern\'{a}ndez and Jaume Baixeries and N\'{u}ria Forns and Ramon Ferrer-i-Cancho},

url = {https://www.mdpi.com/1099-4300/13/8/1465},

doi = {10.3390/e13081465},

issn = {1099-4300},

year  = {2011},

date = {2011-01-01},

journal = {Entropy},

volume = {13},

number = {8},

pages = {1465\textendash1480},

abstract = {It is known that chromosome number tends to decrease as genome size increases in angiosperm plants. Here the relationship between number of parts (the chromosomes) and size of the whole (the genome) is studied for other groups of organisms from different kingdoms. Two major results are obtained. First, the finding of relationships of the kind “the more parts the smaller the whole” as in angiosperms, but also relationships of the kind “the more parts the larger the whole”. Second, these dependencies are not linear in general. The implications of the dependencies between genome size and chromosome number are two-fold. First, they indicate that arguments against the relevance of the finding of negative correlations consistent with Menzerath-Altmann law (a linguistic law that relates the size of the parts with the size of the whole) in genomes are seriously flawed. Second, they unravel the weakness of a recent model of chromosome lengths based upon random breakage that assumes that chromosome number and genome size are independent.},

keywords = {Menzerath-Altmann law},

pubstate = {published},

tppubtype = {article}

}

@article{Genty2010,

title = {Why do gorillas make sequences of gestures?},

author = {Emilie Genty and Richard W. Byrne},

url = {https://doi.org/10.1007/s10071-009-0266-4},

doi = {10.1007/s10071-009-0266-4},

issn = {1435-9456},

year  = {2010},

date = {2010-01-01},

journal = {Animal Cognition},

volume = {13},

number = {2},

pages = {287-301},

abstract = {Great ape gestures have attracted considerable research interest in recent years, prompted by their flexible and intentional pattern of use; but almost all studies have focused on single gestures. Here, we report the first quantitative analysis of sequential gesture use in western gorillas (Gorilla gorilla gorilla), using data from three captive groups and one African study site. We found no evidence that gesture sequences were given for reasons of increased communicative efficiency over single gestures. Longer sequences of repeated gestures did not increase the likelihood of response, and using a sequence was seldom in reaction to communicative failure. Sequential combination of two gestures with similar meanings did not generally increase effectiveness, and sometimes reduced it. Gesture sequences were closely associated with play contexts. Markov transition analysis showed two networks of frequently co-occurring gestures, both consisting of gestures used to regulate play. One network comprised only tactile gestures, the other a mix of silent, audible and tactile gestures; apparently, these clusters resulted from gesture use in play with proximal or distal contact, respectively. No evidence was found for syntactic effects of sequential combination: meanings changed little or not at all. Semantically, many gestures overlapped massively with others in their core information (i.e. message), and gesture messages spanned relatively few functions. We suggest that the underlying semantics of gorilla gestures is highly simplified compared to that of human words. Gesture sequences allow continual adjustment of the tempo and nature of social interactions, rather than generally conveying semantically referential information or syntactic structures.},

keywords = {Zipf\'s law for word frequencies},

pubstate = {published},

tppubtype = {article}

}

@article{doi:10.1002/cplx.20326,

title = {Genome size, self-organization and DNA's dark matter},

author = {Ricard V. Sol\'{e}},

url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/cplx.20326},

doi = {10.1002/cplx.20326},

year  = {2010},

date = {2010-01-01},

journal = {Complexity},

volume = {16},

number = {1},

pages = {20-23},

abstract = {Abstract Chromosomes exhibit several features indicating that its spatiotemporal dynamics is self-organized. It has been recently suggested that a negative correlation between genome size and mean chromosome number would also be a fingerprint of selforganization, related to how human language is organized at the level of words and syllables. However, the vast dominance of non-coding DNA in eukaryotic genomes should prevent an interpretation of genome/chromosome size based on functional trade-offs related to information storage and transmission. Moreover, the reported negative correlation is shown to be an inevitable consequence of the definitions of chromosome and genome length and it is thus unrelated to any type of special generative process.},

keywords = {Menzerath-Altmann law},

pubstate = {published},

tppubtype = {article}

}

@article{doi:10.1002/cplx.20296,

title = {The self-organization of genomes},

author = {Ramon Ferrer-i-Cancho and N\'{u}ria Forns},

url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/cplx.20296},

doi = {10.1002/cplx.20296},

year  = {2010},

date = {2010-01-01},

journal = {Complexity},

volume = {15},

number = {5},

pages = {34-36},

abstract = {Abstract Menzerath-Altmann law is a general law of human language stating, for instance, that the longer a word, the shorter its syllables. With the metaphor that genomes are words and chromosomes are syllables, we examine if genomes also obey the law. We find that longer genomes tend to be made of smaller chromosomes in organisms from three different kingdoms: fungi, plants, and animals. Our findings suggest that genomes self-organize under principles similar to those of human language},

keywords = {Menzerath-Altmann law},

pubstate = {published},

tppubtype = {article}

}

@article{doi:10.1098/rsbl.2009.1062,

title = {Efficiency of coding in macaque vocal communication},

author = {Stuart Semple and Minna J. Hsu and Govindasamy Agoramoorthy},

url = {https://royalsocietypublishing.org/doi/abs/10.1098/rsbl.2009.1062},

doi = {10.1098/rsbl.2009.1062},

year  = {2010},

date = {2010-01-01},

journal = {Biology Letters},

volume = {6},

number = {4},

pages = {469-471},

abstract = {A key characteristic of human language efficiency is that more frequently used words tend to be shorter in length-the ‘law of brevity’. To date, no test of this relationship between frequency of use and length has been carried out on non-human animal vocal communication. We show here that the vocal repertoire of the Formosan macaque (Macaca cyclopis) conforms to the pattern predicted by the law of brevity, with an inverse relationship found between call duration and rate of utterance. This finding provides evidence for coding efficiency in the vocal communication system of this species, and indicates commonality in the basic structure of the coding system between human language and vocal communication in this non-human primate.},

keywords = {Zipf\'s law of abbreviation},

pubstate = {published},

tppubtype = {article}

}

@article{doi:10.1002/cplx.20266,

title = {Efficient coding in dolphin surface behavioral patterns},

author = {Ramon Ferrer-i-Cancho and David Lusseau},

url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/cplx.20266},

doi = {10.1002/cplx.20266},

year  = {2009},

date = {2009-01-01},

journal = {Complexity},

volume = {14},

number = {5},

pages = {23-25},

abstract = {Abstract We show that the law of brevity, i.e. the tendency of words to shorten as their frequency increases, is also found in dolphin surface behavioral patterns. As far as we know, this is the first evidence of the law in another species, suggesting that coding efficiency is not unique to humans.},

keywords = {Zipf\'s law of abbreviation},

pubstate = {published},

tppubtype = {article}

}

@article{e11040688,

title = {A Law of Word Meaning in Dolphin Whistle Types},

author = {Ramon Ferrer-i-Cancho and Brenda McCowan},

url = {https://www.mdpi.com/1099-4300/11/4/688},

doi = {10.3390/e11040688},

issn = {1099-4300},

year  = {2009},

date = {2009-01-01},

journal = {Entropy},

volume = {11},

number = {4},

pages = {688\textendash701},

abstract = {We show that dolphin whistle types tend to be used in specific behavioral contexts, which is consistent with the hypothesis that dolphin whistle have some sort of . Besides, in some cases, it can be shown that the behavioral context in which a whistle tends to occur or not occur is shared by different individuals, which is consistent with the hypothesis that dolphins are communicating through whistles. Furthermore, we show that the number of behavioral contexts significantly associated with a certain whistle type tends to grow with the frequency of the whistle type, a pattern that is reminiscent of a law of word meanings stating, as a tendency, that the higher the frequency of a word, the higher its number of meanings. Our findings indicate that the presence of Zipf's law in dolphin whistle types cannot be explained with enough detail by a simplistic die rolling experiment.},

keywords = {Law of meaning distribution, Meaning-frequency law},

pubstate = {published},

tppubtype = {article}

}

@article{SUZUKI2005F9,

title = {The use of Zipf's law in animal communication analysis},

author = {Ryuji Suzuki and John R. Buck and Peter L. Tyack},

url = {http://www.sciencedirect.com/science/article/pii/S0003347204003471},

doi = {https://doi.org/10.1016/j.anbehav.2004.08.004},

issn = {0003-3472},

year  = {2005},

date = {2005-01-01},

journal = {Animal Behaviour},

volume = {69},

number = {1},

pages = {F9 - F17},

keywords = {Zipf\'s law for word frequencies},

pubstate = {published},

tppubtype = {article}

}

@article{MCCOWAN2005F1,

title = {The appropriate use of Zipf's law in animal communication studies},

author = {B. McCowan and L. R. Doyle and J. M. Jenkins and S. F. Hanser},

url = {http://www.sciencedirect.com/science/article/pii/S000334720400346X},

doi = {https://doi.org/10.1016/j.anbehav.2004.09.002},

issn = {0003-3472},

year  = {2005},

date = {2005-01-01},

journal = {Animal Behaviour},

volume = {69},

number = {1},

pages = {F1 - F7},

keywords = {Zipf\'s law for word frequencies},

pubstate = {published},

tppubtype = {article}

}

@article{Furusawa2003,

title = {Zipf's law in gene expression},

author = {Chikara Furusawa and Kunihiko Kaneko},

doi = {10.1103/PhysRevLett.90.088102},

year  = {2003},

date = {2003-01-01},

journal = {Physical Review Letters},

volume = {90},

pages = {088102},

abstract = {Using data from gene expression databases on various organisms and tissues, including yeast, nematodes, human normal and cancer tissues, and embryonic stem cells, we found that the abundances of expressed genes exhibit a power-law distribution with an exponent close to -1; i.e., they obey Zipf's law. Furthermore, by simulations of a simple model with an intracellular reaction network, we found that Zipf's law of chemical abundance is a universal feature of cells where such a network optimizes the efficiency and faithfulness of self-reproduction. These findings provide novel insights into the nature of the organization of reaction dynamics in living cells.},

keywords = {Zipf\'s law for word frequencies},

pubstate = {published},

tppubtype = {article}

}

@article{McCowan2002,

title = {Using information theory to assess the diversity, complexity and development of communicative repertoires},

author = {B. McCowan and L. R. Doyle and S. F. Hanser},

doi = {10.1037/0735-7036.116.2.166},

year  = {2002},

date = {2002-01-01},

journal = {Journal of Comparative Psychology},

volume = {116},

pages = {166-172},

abstract = {The application of quantitative and comparative measures from information theory on animal communication can provide novel insights into the ecological, environmental, social, and contextual properties that shape the structure, organization, and function of signal repertoires. Using 2 phylogenetically different mammalian species that share similar ecological and social constraints as examples, the authors quantitatively examined the internal structure and development of a subsystem of these species' vocal repertoires in comparison with that of human language and illustrated that these species exhibit convergent developmental processes. The authors also discussed how predictions on the structure and organization of animal communication systems can be made from this new application of information theoretic measures with respect to behavioral ecology.},

keywords = {Zipf\'s law for word frequencies},

pubstate = {published},

tppubtype = {article}

}

@article{Searls2002,

title = {The language of genes},

author = {David B. Searls},

url = {https://doi.org/10.1038/nature01255},

doi = {10.1038/nature01255},

issn = {1476-4687},

year  = {2002},

date = {2002-01-01},

journal = {Nature},

volume = {420},

number = {6912},

pages = {211-217},

abstract = {Linguistic metaphors have been woven into the fabric of molecular biology since its inception. The determination of the human genome sequence has brought these metaphors to the forefront of the popular imagination, with the natural extension of the notion of DNA as language to that of the genome as the 'book of life'. But do these analogies go deeper and, if so, can the methods developed for analysing languages be applied to molecular biology? In fact, many techniques used in bioinformatics, even if developed independently, may be seen to be grounded in linguistics. Further interweaving of these fields will be instrumental in extending our understanding of the language of life.},

keywords = {Zipf\'s law for word frequencies},

pubstate = {published},

tppubtype = {article}

}

@article{MCCOWAN1999409,

title = {Quantitative tools for comparing animal communication systems: information theory applied to bottlenose dolphin whistle repertoires},

author = {Brenda McCowan and Sean F. Hanser and Laurance R. Doyle},

url = {http://www.sciencedirect.com/science/article/pii/S0003347298910004},

doi = {https://doi.org/10.1006/anbe.1998.1000},

issn = {0003-3472},

year  = {1999},

date = {1999-01-01},

journal = {Animal Behaviour},

volume = {57},

number = {2},

pages = {409 - 419},

abstract = {Comparative analysis of nonhuman animal communication systems and their complexity, particularly in comparison to human language, has been generally hampered by both a lack of sufficiently extensive data sets and appropriate analytic tools. Information theory measures provide an important quantitative tool for examining and comparing communication systems across species. In this paper we use the original application of information theory, that of statistical examination of a communication system’s structure and organization. As an example of the utility of information theory to the analysis of animal communication systems, we applied a series of information theory statistics to a statistically categorized set of bottlenose dolphinTursiops truncatus, whistle vocalizations. First, we use the first-order entropic relation in a Zipf-type diagram (Zipf 1949Human Behavior and the Principle of Least Effort) to illustrate the application of temporal statistics as comparative indicators of repertoire complexity, and as possible predictive indicators of acquisition/learning in animal vocal repertoires. Second, we illustrate the need for more extensive temporal data sets when examining the higher entropic orders, indicative of higher levels of internal informational structure, of such vocalizations, which could begin to allow the statistical reconstruction of repertoire organization. Third, we propose using ‘communication capacity’ as a measure of the degree of temporal structure and complexity of statistical correlation, represented by the values of entropic order, as an objective tool for interspecies comparison of communication complexity. In doing so, we introduce a new comparative measure, the slope of Shannon entropies, and illustrate how it potentially can be used to compare the organizational complexity of vocal repertoires across a diversity of species. Finally, we illustrate the nature and predictive application of these higher-order entropies using a preliminary sample of dolphin whistle vocalizations. The purpose of this preliminary report is to re-examine the original application of information theory to the field of animal communication, illustrate its potential utility as a comparative tool for examining the internal informational structure of animal vocal repertoires and their development, and discuss its relationship to behavioural ecology and evolutionary theory.},

keywords = {Zipf\'s law for word frequencies},

pubstate = {published},

tppubtype = {article}

}

@article{BURGOS1996227,

title = {Zipf-scaling behavior in the immune system},

author = {Javier D. Burgos and Pedro Moreno-Tovar},

url = {http://www.sciencedirect.com/science/article/pii/0303264796016188},

doi = {https://doi.org/10.1016/0303-2647(96)01618-8},

issn = {0303-2647},

year  = {1996},

date = {1996-01-01},

journal = {Biosystems},

volume = {39},

number = {3},

pages = {227 - 232},

abstract = {The Zipf law, an approach to analyzing linguistic texts, was applied to study the Cytotoxic T Lymphocytes (CTL) repertoire, one of the major components of the immune system. A Zipf-scaling behavior was observed in those CTL repertoires obtained in normal or conventional mice. In contrast, CTL repertoires from irradiated chimeric animals, showed a non-scaling statistical behavior when tested by the Zipf analysis,suggesting that normal repertoires work like a structured biological language. The fractal dimension (D) was derived from the Zipf plots, and correlates well with the nature of the repertoires: high, D \> 0.8, in conventional mice. Non-fractal, D \> 1, in chimeric animals, and low, D \< 0.3, in athymic mice. Then, D seems to be an useful tool to characterize the current status of the immune system.},

keywords = {Zipf\'s law for word frequencies},

pubstate = {published},

tppubtype = {article}

}

@article{BURGOS199619,

title = {Fractal representation of the immune B cell repertoire},

author = {Javier D. Burgos},

url = {http://www.sciencedirect.com/science/article/pii/0303264795015744},

doi = {10.1016/0303-2647(95)01574-4},

issn = {0303-2647},

year  = {1996},

date = {1996-01-01},

journal = {Biosystems},

volume = {39},

number = {1},

pages = {19\textendash24},

abstract = {The immune repertoire is characterized by a complex and dynamic organization. Here I suggest, based on the presence of well-defined immune reactivity patterns (RP) analyzed using a linguistic analogy, that the B cell repertoires could possess a fractal structure. A simple estimation method of the fractal dimension (D) for a given immune B repertoire was developed, and D demonstrated to be an useful tool to define what complexity is regarding the immune repertoire, and to evaluate the complexity level of the immune B repertoire among age-structured groups of mice sensitized with the hemagglutinin (HA) molecule of influenza virus. Also, since a fractal-linguistic point of view, considerations are made about the ontogeny, connectivity, chaotic regimes, and size of the immune repertoire. Fractal analysis indicates that the immune repertoire shows a Zipf-like scaling behavior, a statistical property of natural languages. This result suggests that immune repertoire is structured like a powerful language.},

keywords = {Zipf\'s law for word frequencies},

pubstate = {published},

tppubtype = {article}

}

@article{Ficken1994,

title = {The chick-a-dee call system of the Mexican chickadee},

author = {M. S. Ficken and E. D. Hailman and J. P. Hailman},

doi = {10.2307/1369065},

year  = {1994},

date = {1994-01-01},

journal = {Condor},

volume = {96},

pages = {70-82},

abstract = {Chick-a-dee calls of the Mexican Chickadee (Parus sclateri) are composed of combinations of three common note types (A, C and D) and one very rare type (B). Calls have the invariant sequence of notes A-B-C-D, where any note type may be omitted, given once or repeated a variable number of times before transiting to the next type. The B and C notes are phonologically similar to the B and C notes of chick-a-dee calls of the Black-capped Chickadee (P. atricapillus), but the A note is markedly different and the D note somewhat different from equivalent notes of the congener. A total of 2,071 calls recorded yielded 60 different call types, and Zipf-Mandelbrot plots show that the call system is "open"; as the sample size is increased new call types will be found without demonstrable bound. In relatively undisturbed contexts (with mate on territory, in fall flocks, alone in fall) birds gave mainly [A][D] calls with lesser numbers of [A] and [C] calls, where brackets indicate variable repetition of note types. In disturbed contexts (mobbing plastic Great Horned Owl, mobbing speaker playing calls of the Northern Pygmy-Owl, observer sitting under the nest cavity) the birds gave more [C] calls with [A][C] as well. In the longest mobbing session to owl calls, birds gave mainly [A] calls when approaching, switched to [C] calls while flying about the speaker, and then resumed [A] calls and moved off when the playback was stopped. Outside of human language, this is the second truly combinatorial system of vocal communication found in animals, the first being chick-a-dee calls of the Black-capped Chickadee. This study provides the first data substantiating quantitative differences in calls from different contexts, an important step toward understanding what kinds of information combinatorial chick-a-dee calls encode.},

keywords = {Zipf\'s law for word frequencies},

pubstate = {published},

tppubtype = {article}

}

@article{Hailman1994,

title = {Constrained permutation in 'chick-a-dee' like calls of a black-lored tit em Parus em Xanthogenys},

author = {J. P. Hailman},

doi = {10.1080/09524622.1994.9753270},

year  = {1994},

date = {1994-01-01},

journal = {Bioacoustics},

volume = {6},

pages = {33-50},

abstract = {Examined the vocalizations of 2 wild-caught black-lored tits. It was found that the Ss gave chick-a-dee-like calls in response to a stuffed owl. The tit used combinations of 4 note types to create 65 different call types. The repertoire of call types had the language-like property of openness to formation of new call types without limit. Calling under constant stimulus conditions changed unidirectionally during the course of mobbing, with the 4 note types replacing each other in calls, as time progressed. Thus, the tit had a constrained type of permuted order of note types, which enlarged the potential for call variety and closely resembled properties of language.},

keywords = {Zipf\'s law for word frequencies},

pubstate = {published},

tppubtype = {article}

}

@article{Hailman1987a,

title = {Constraints on the structure of combinatorial "chick-a-dee" calls},

author = {J. P. Hailman and M. S. Ficken and R. Ficken},

doi = {10.1111/j.1439-0310.1987.tb00642.x},

year  = {1987},

date = {1987-01-01},

journal = {Ethology},

volume = {75},

pages = {62-80},

abstract = {Chickadee calls include 4 note types (A, B, C, and D) that occur in fixed sequence. Quantitative analyses determining the nature of departures from 1st-order transitional probabilities between successive notes in calls of the blackcapped chickadee found that (1) some constraint limited the length of calls (i.e., shortening of repetition strings, omitting of note types) and (2) there was an opposing tendency to include at least 1 D-note at the end of a call. The 2nd feature suggests semantic properties of D-notes. A chicakadee call is thought to resemble a natural sentence of spoken human language.},

keywords = {Zipf\'s law of abbreviation},

pubstate = {published},

tppubtype = {article}

}

@article{10.2307/2742889,

title = {The genetic code and Zipf's Law},

author = {M. L. Bender and Pritmohinder Gill},

url = {http://www.jstor.org/stable/2742889},

issn = {00113204, 15375382},

year  = {1986},

date = {1986-01-01},

journal = {Current Anthropology},

volume = {27},

number = {3},

pages = {280\textendash283},

publisher = {University of Chicago Press, Wenner-Gren Foundation for Anthropological Research},

keywords = {Zipf\'s law for word frequencies},

pubstate = {published},

tppubtype = {article}

}

@article{Hailman1985,

title = {The 'chick-a-dee' calls of em Parus em atricapillus: a recombinant system of animal communication compared with written English},

author = {J. P. Hailman and M. S. Ficken and R. W. Ficken},

doi = {10.1515/semi.1985.56.3-4.191},

year  = {1985},

date = {1985-01-01},

journal = {Semiotica},

volume = {56},

pages = {121-224},

keywords = {Zipf\'s law of abbreviation},

pubstate = {published},

tppubtype = {article}

}

@article{FICKEN1978630,

title = {A model of repetitive behaviour illustrated by chickadee calling},

author = {Millicent S. Ficken and Jack P. Hailman and Robert W. Ficken},

url = {http://www.sciencedirect.com/science/article/pii/0003347278900751},

doi = {10.1016/0003-3472(78)90075-1},

issn = {0003-3472},

year  = {1978},

date = {1978-01-01},

journal = {Animal Behaviour},

volume = {26},

pages = {630 - 631},

abstract = {If the probability of an animal's continuing (or repeating) a given behavioral pattern is independent of the elapsed time (or number of previous acts), the data conform to the exponential distribution generated by a Poisson process. The number of chickadee calls/bout was recorded for 1,524 bouts. Results show a negative linear relation between the number of calls/bout and the cumulative frequency of bouts when plotted on logarithmic axes.},

keywords = {Zipf\'s law of abbreviation},

pubstate = {published},

tppubtype = {article}

}

@article{10.1121/1.1908584,

title = {Linguistic considerations of porpoise sounds},

author = {John J. Dreher},

doi = {10.1121/1.1908584},

year  = {1961},

date = {1961-01-01},

journal = {The Journal of the Acoustical Society of America},

volume = {33},

number = {12},

pages = {1799-1800},

abstract = {A brief comparison of intonation and tone languages is given, with criteria of the latter applied to observed whistle contours appearing in underwater recordings of Tursiops truncatus and Langenorhynchus obliquidens.},

note = {The author actually reports evidence of an exponential-like distribution, rather than the power-law like distribution of Zipf's law for word frequencies.},

keywords = {Zipf\'s law for word frequencies},

pubstate = {published},

tppubtype = {article}

}