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@article{doi:10.1002/anie.201403708,
title = {Organic Chemistry as a Language and the Implications of Chemical Linguistics for Structural and Retrosynthetic Analyses},
author = {Andrea Cadeddu and Elizabeth K Wylie and Janusz Jurczak and Matthew Wampler-Doty and Bartosz A Grzybowski},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/anie.201403708},
doi = {10.1002/anie.201403708},
year = {2014},
date = {2014-01-01},
journal = {Angewandte Chemie International Edition},
volume = {53},
number = {31},
pages = {8108-8112},
abstract = {Abstract Methods of computational linguistics are used to demonstrate that a natural language such as English and organic chemistry have the same structure in terms of the frequency of, respectively, text fragments and molecular fragments. This quantitative correspondence suggests that it is possible to extend the methods of computational corpus linguistics to the analysis of organic molecules. It is shown that within organic molecules bonds that have highest information content are the ones that 1) define repeat/symmetry subunits and 2) in asymmetric molecules, define the loci of potential retrosynthetic disconnections. Linguistics-based analysis appears well-suited to the analysis of complex structural and reactivity patterns within organic molecules.},
keywords = {Zipf's law for word frequencies},
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},
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{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\textemdashperhaps (arguably) the most “organized” of stellar systems\textemdashas 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{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{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{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{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{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}
}