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Prinz R, Bucher P, Kun Á, Paredes O, Aragno A, Shelby C, Gumbel M, Fimmel E, Strüngmann L. Codes across (life)sciences. Biosystems 2025:105515. [PMID: 40490067 DOI: 10.1016/j.biosystems.2025.105515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2025] [Revised: 06/05/2025] [Accepted: 06/06/2025] [Indexed: 06/11/2025]
Abstract
The concept of "code" connotes different meanings, intentions, and formalizations. From mathematics and computer sciences to psychology and culture, the term becomes less formal, more diverse, and sometimes appears ambiguous. In biology a growing number of codes ignite a debate about their role in evolution, biocomplexity, and agency, to name just a few. Here, a transdisciplinary group of code scientists attempts to capture the big picture of code research across their fields of interest. In this cross-sectional overview commonalities emerge that may pave the way towards a unified theory of life-based-on-codes. Codes underly cellular processes, perception, cognition, and communication. From ecosystems to human language, codes influence how individuals behave in groups, memorize, learn, and take part in cultural practices. Emotions like aggression, fear, anger, frustration, are important motivators of behaviour modulating mutual communication and sculpting individual experience. The inheritance of experience in form of innate release mechanisms, stereotyped behaviour, or archetypes may have phylogenetic and ontogenetic roots that rely on codes and impact our conscious decision making. Unconsciously, even our dreams draw on codes. In the future, conflation of different coding systems, e.g., from synthetic biology and generative artificial intelligence, will merge biological codes with machine logic and computer language to promote next-level transhumanism. Codes emerge as a currency converter between systems of life and between different scientific disciplines.
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Affiliation(s)
| | - Philipp Bucher
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Ádám Kun
- Department of Plant Systematics, Ecology and Theoretical Biology, Eötvös University, Budapest, Hungary; Parmenides Center for the Conceptual Foundations of Science, Parmenides Foundation, Pöcking, Germany
| | - Omar Paredes
- Biodigital Innovation Laboratory, Department of Translational Bioengineering, CUCEI, Universidad of Guadalajara, Mexico
| | - Anna Aragno
- National Association for the Advancement of Psychoanalysis (NAAP), New York, USA
| | | | - Markus Gumbel
- Center for Algorithmic and Mathematical Methods in Medicine, Biology, and Biotechnology, Technical University of Applied Sciences Mannheim, Germany
| | - Elena Fimmel
- Center for Algorithmic and Mathematical Methods in Medicine, Biology, and Biotechnology, Technical University of Applied Sciences Mannheim, Germany
| | - Lutz Strüngmann
- Center for Algorithmic and Mathematical Methods in Medicine, Biology, and Biotechnology, Technical University of Applied Sciences Mannheim, Germany
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2
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Makioka H, Lewis RN, Soma M. The use of artificial songs to assess song recognition in imprinted female songbirds: a concept proposal. Front Psychol 2024; 15:1384794. [PMID: 39295766 PMCID: PMC11408183 DOI: 10.3389/fpsyg.2024.1384794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Accepted: 08/14/2024] [Indexed: 09/21/2024] Open
Abstract
We propose an experimental paradigm to examine acoustic features responsible for song preference and recognition in songbirds. Song preference in female songbirds is often influenced by early song experience. That is why several Estrildid species, including our subject species, the Java sparrow (Padda oryzivora), are known to show an imprinted preference for their father's songs. After confirming that Java sparrow females preferred their father's song compared to non-imprinted through song playbacks (first step), we repeated the playback tests in the same subjects using synthesized stimuli (second step). To create synthesized stimuli, we removed all the complex frequency modulations and subharmonics from song notes that we used for the first step playback tests to see the effect of spectrometric features on song recognition. The results indicated that females showed higher rate of calling towards synthesized father song stimuli, suggesting that the macroscopic patterns would play more important roles in song recognition than the microscopic acoustic features. Although we looked at spectrometric features and father-imprinted song preference in this study, similar testing can be applied in many ways to test preference for local dialects or subspecies-specific songs.
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Affiliation(s)
- Hiroharu Makioka
- Biosystems Science Course, The Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Rebecca N Lewis
- JSPS International Research Fellow, Department of Biology, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Masayo Soma
- Department of Biology, Faculty of Science, Hokkaido University, Sapporo, Japan
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Morita M, Nishikawa Y, Tokumasu Y. Human musical capacity and products should have been induced by the hominin-specific combination of several biosocial features: A three-phase scheme on socio-ecological, cognitive, and cultural evolution. Evol Anthropol 2024; 33:e22031. [PMID: 38757853 DOI: 10.1002/evan.22031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 04/14/2024] [Accepted: 04/26/2024] [Indexed: 05/18/2024]
Abstract
Various selection pressures have shaped human uniqueness, for instance, music. When and why did musical universality and diversity emerge? Our hypothesis is that "music" initially originated from manipulative calls with limited musical elements. Thereafter, vocalizations became more complex and flexible along with a greater degree of social learning. Finally, constructed musical instruments and the language faculty resulted in diverse and context-specific music. Music precursors correspond to vocal communication among nonhuman primates, songbirds, and cetaceans. To place this scenario in hominin history, a three-phase scheme for music evolution is presented herein. We emphasize (1) the evolution of sociality and life history in australopithecines, (2) the evolution of cognitive and learning abilities in early/middle Homo, and (3) cultural evolution, primarily in Homo sapiens. Human musical capacity and products should be due to the hominin-specific combination of several biosocial features, including bipedalism, stable pair bonding, alloparenting, expanded brain size, and sexual selection.
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Affiliation(s)
- Masahito Morita
- Evolutionary Anthropology Lab, Department of Biological Sciences, The University of Tokyo, Tokyo, Japan
- Department of Health Sciences of Mind and Body, University of Human Arts and Sciences, Saitama, Japan
| | - Yuri Nishikawa
- Evolutionary Anthropology Lab, Department of Biological Sciences, The University of Tokyo, Tokyo, Japan
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan
| | - Yudai Tokumasu
- Evolutionary Anthropology Lab, Department of Biological Sciences, The University of Tokyo, Tokyo, Japan
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Romagosa M, Nieukirk S, Cascão I, Marques TA, Dziak R, Royer JY, O'Brien J, Mellinger DK, Pereira A, Ugalde A, Papale E, Aniceto S, Buscaino G, Rasmussen M, Matias L, Prieto R, Silva MA. Fin whale song evolution in the North Atlantic. eLife 2024; 13:e83750. [PMID: 38192202 PMCID: PMC10776088 DOI: 10.7554/elife.83750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/01/2023] [Indexed: 01/10/2024] Open
Abstract
Animal songs can change within and between populations as the result of different evolutionary processes. When these processes include cultural transmission, the social learning of information or behaviours from conspecifics, songs can undergo rapid evolutions because cultural novelties can emerge more frequently than genetic mutations. Understanding these song variations over large temporal and spatial scales can provide insights into the patterns, drivers and limits of song evolution that can ultimately inform on the species' capacity to adapt to rapidly changing acoustic environments. Here, we analysed changes in fin whale (Balaenoptera physalus) songs recorded over two decades across the central and eastern North Atlantic Ocean. We document a rapid replacement of song INIs (inter-note intervals) over just four singing seasons, that co-occurred with hybrid songs (with both INIs), and a clear geographic gradient in the occurrence of different song INIs during the transition period. We also found gradual changes in INIs and note frequencies over more than a decade with fin whales adopting song changes. These results provide evidence of vocal learning in fin whales and reveal patterns of song evolution that raise questions on the limits of song variation in this species.
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Affiliation(s)
- Miriam Romagosa
- Institute of Marine Sciences - OKEANOS & Institute of Marine Research - IMAR, University of the AzoresHortaPortugal
| | - Sharon Nieukirk
- Cooperative Institute for Marine Ecosystem and Resources Studies, Oregon State UniversityCorvallisUnited States
| | - Irma Cascão
- Institute of Marine Sciences - OKEANOS & Institute of Marine Research - IMAR, University of the AzoresHortaPortugal
| | - Tiago A Marques
- Centre for Research into Ecological and Environmental Modelling, University of St AndrewsSt AndrewsUnited Kingdom
- Centro de Estatística e Aplicações, Departamento de Biologia, Faculdade de Ciências, Universidade de LisboaLisboaPortugal
| | - Robert Dziak
- NOAA Pacific Marine Environmental Laboratory, Hatfield Marine Science CenterCorvallisUnited States
| | - Jean-Yves Royer
- CNRS - UBO - UBS - Ifremer, IUEM - Lab. Geo-OceanPlouzaneFrance
| | - Joanne O'Brien
- Marine and Freshwater Research Centre (MFRC), Atlantic Technological UniversityGalwayIreland
| | - David K Mellinger
- Cooperative Institute for Marine Ecosystem and Resources Studies, Oregon State UniversityCorvallisUnited States
| | - Andreia Pereira
- Instituto Dom Luiz (IDL), Universidade de LisboaLisboaPortugal
| | | | - Elena Papale
- Institute for the Study of Anthropic Impacts and Sustainability in the Marine Environment of the National Research Council of Italy (CNR-IAS)Torretta GranitolaItaly
| | | | - Giuseppa Buscaino
- Institute for the Study of Anthropic Impacts and Sustainability in the Marine Environment of the National Research Council of Italy (CNR-IAS)Torretta GranitolaItaly
| | | | - Luis Matias
- Instituto Dom Luiz (IDL), Universidade de LisboaLisboaPortugal
| | - Rui Prieto
- Institute of Marine Sciences - OKEANOS & Institute of Marine Research - IMAR, University of the AzoresHortaPortugal
| | - Mónica A Silva
- Institute of Marine Sciences - OKEANOS & Institute of Marine Research - IMAR, University of the AzoresHortaPortugal
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Farina A, Villa AEP. On the semantics of ecoacoustic codes. Biosystems 2023; 232:105002. [PMID: 37625513 DOI: 10.1016/j.biosystems.2023.105002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/15/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023]
Abstract
Ecological codes have been defined as every biological code integrated by factors originated by the environmental context that participates in the codepoiesis process. Ecological codes create a strict relationship between the inner world of organsims and the external relational world, and represent the mechanism with which the vivo-scape is realized. Acoustic codes are used in nature to decode acoustic signals between individuals of the same or different species and belong to the category of biological codes. Ecoacoustic codes are the outcome of the evolution of acoustic codes, and results as the interplay between acoustic codes and environmental factors. Soundtope codes represent the results of emerging properties of the acoustic communities.
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Affiliation(s)
- Almo Farina
- Department of Pure and Applied Sciences, The University of Urbino, Campus Scientifico "Enrico Mattei", 61029, Urbino, Italy.
| | - Alessandro E P Villa
- Neuroheuristic Research Group, Faculty of Business and Economics HEC, University of Lausanne, CH, 1015, Lausanne, Switzerland
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Four decades later: The highly conserved repertoire of song types in chaffinch (Fringilla coelebs). Behav Processes 2023; 205:104821. [PMID: 36649903 DOI: 10.1016/j.beproc.2023.104821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 12/16/2022] [Accepted: 01/13/2023] [Indexed: 01/15/2023]
Abstract
The long-term stability of culturally transmitted traits like bird song has attracted much attention from researchers; however, it remains insufficiently studied up to the present time. This study investigates, by using spectrographic analysis, whether the repertoire of song types recorded at the same locality is persistent at short terms (of four years) and at long terms (of 38 years) in a migratory European continental population of chaffinches. The population song type repertoires recorded in 1978 and 1982 were only slightly different, thus indicating the high repertoire persistence within a few years. There were more differences between repertoires recorded in 1982 and 2020. In total, eight of the 29 song types (28 %) identified in 1982 were not found in 2020, and 5 of the 26 song types (19 %) discovered in 2020 were completely new compared to 1982. All the other song types recorded in 2020 were similar to those recorded in 1982. The frequency of use of these song types in 1982 and 2020 was also similar. By 2020, mainly those song types had disappeared from the population repertoire, which in 1982 were performed by a limited number of males. These data suggest a high long-term persistence of repertoire of song types in male song of a migratory continental population. This long-term stability of the population repertoire was maintained despite significant changes in the habitat structure caused by a massive expansion of bark beetles in 2010-2014.
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Microgeographical variation in birdsong: Savannah sparrows exhibit microdialects in an island population. Anim Behav 2022. [DOI: 10.1016/j.anbehav.2022.04.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Williams H, Lachlan RF. Evidence for cumulative cultural evolution in bird song. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200322. [PMID: 34894731 PMCID: PMC8666912 DOI: 10.1098/rstb.2020.0322] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 10/05/2021] [Indexed: 12/11/2022] Open
Abstract
In studies of cumulative cultural evolution in non-human animals, the focus is most often on incremental changes that increase the efficacy of an existing form of socially learned behaviour, such as the refinement of migratory pathways. In this paper, we compare the songs of different species to describe patterns of evolution in the acoustic structure of bird songs, and explore the question of what building blocks might underlie cumulative cultural evolution of bird song using a comparative approach. We suggest that three steps occurred: first, imitation of independent sounds, or notes, via social learning; second, the formation of categories of note types; and third, assembling note types into sequences with defined structures. Simple sequences can then be repeated to form simple songs or concatenated with other sequences to form segmented songs, increasing complexity. Variant forms of both the notes and the sequencing rules may then arise due to copy errors and innovation. Some variants may become established in the population because of learning biases or selection, increasing signal efficiency, or because of cultural drift. Cumulative cultural evolution of bird songs thus arises from cognitive processes such as vocal imitation, categorization during memorization and learning biases applied to basic acoustic building blocks. This article is part of a discussion meeting issue 'The emergence of collective knowledge and cumulative culture in animals, humans and machines'.
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Affiliation(s)
- Heather Williams
- Biology Department, Williams College, Williamstown, MA 01267, USA
| | - Robert F. Lachlan
- Department of Psychology, Royal Holloway University of London, London TW20 0EX, UK
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