Abstract
Although the knowledge about biological systems has advanced exponentially in recent decades, it is surprising to realize that the very definition of Life keeps presenting theoretical challenges. Even if several lines of reasoning seek to identify the essence of life phenomenon, most of these thoughts contain fundamental problem in their basic conceptual structure. Most concepts fail to identify either necessary or sufficient features to define life. Here, we analyzed the main conceptual frameworks regarding theoretical aspects that have been supporting the most accepted concepts of life, such as (i) the physical, (ii) the cellular and (iii) the molecular approaches. Based on an ontological analysis, we propose that Life should not be positioned under the ontological category of Matter. Yet, life should be better understood under the top-level ontology of “Process”. Exercising an epistemological approach, we propose that the essential characteristic that pervades each and every living being is the presence of organic codes. Therefore, we explore theories in biosemiotics and code biology in order to propose a clear concept of life as a macrocode composed by multiple inter-related coding layers. This way, as life is a sort of metaphysical process of encoding, the living beings became the molecular materialization of that process. From the proposed concept, we show that the evolutionary process is a fundamental characteristic for life’s maintenance but it is not necessary to define life, as many organisms are clearly alive but they do not participate in the evolutionary process (such as infertile hybrids). The current proposition opens a fertile field of debate in astrobiology, epistemology, biosemiotics, code biology and robotics.
Similar content being viewed by others
References
Barbieri M (2012) Code biology—a new science of life. Biosemiotics 5:411–437
Barbieri M (2013) The paradigms of biology. Biosemiotics 6:33–59
Barbieri M (2014a) Introduction to code biology. Biosemiotics 7:167–179
Barbieri M (2014b) From biosemiotics to code biology. Biol Theory. 9:239–249
Barbieri M (2016) From the common ancestor to the first cells: the code theory. Biol Theory 11:102–112
Bedau MA (1998) Four puzzles about life. Artif life 4:125–140
Boltzmann L (1877) Über die Beziehung zwischen dem zweiten Hauptsatze der mechanischen Wärmetheorie und der Wahrscheinlichkeitsrechnung respective den Sätzen über das Wärmegleichgewicht. Wien Ber 76(1877):373–435
Brauckmann S (2006) The organism and the open system: Ervin Bauer and Ludwig von Bertalanffy. Ann NY Acad Sci 901(1):291–300. https://doi.org/10.1111/j.1749-6632.2000.tb06288.x
Capurro R, Hjørland B (2003) The Concept of Information. Annu Rev Inform Sci Technol 37:343–411
Chi MTH, Roscoe RD (2002) The processes and challenges of conceptual change. In: Limón M, Mason L (eds) Reconsidering conceptual change. Issues in theory and practice. Springer, Dordrecht, pp 3–27
Chi MTH, Slotta JD, Leeuw N (1994) From things to process: a A theory of conceptual change for learning science concepts. Learn instr 4:27–43
Chuong EB (2018) The placenta goes viral: retroviruses control gene expression in pregnancy. PLoS Biol 16(10):e3000028
Cleland CE, Chyba CF (2002) Defining ‘life.’ Orig Life Evol Biosph 32(4):387–393
Cronin L, Walker SI (2016) Beyond prebiotic chemistry. Science 352(6290):1174–1175. https://doi.org/10.1126/science.aaf6310
Darwin C (1859) On the origin of species by means of natural selection, or, the preservation of favoured races in the struggle for life. J. Murray, London
Dieguez A (2008) Es la vida un género natural? Dificultades para lograr una definición del concepto de vida. ArtefaCTos 1:81–100
Dieguez A (2013) Life as a homeostatic property cluster. Biol Theory 7:180–186
Drack M, Apfalter W, Pouvreau D (2007) On the making of a system theory of life: Paul A Weiss and Ludwig von Bertalanffy’s conceptual connection. Q Rev Biol 82(4):349–373. https://doi.org/10.1086/522810
Dupré J (2012) The constituents of life 2: organisms and systems. Processes of life essays in the philosophy of biology. Oxford University Press, New York, pp 85–100
Dupré J, Guttinger S (2016) Viruses as living processes. Stud Hist Philos Sci C 59:109–116
Dupré J, Nicholson D (2018) A manisfesto for a processual pilosophy of biology. Everything flows: towards a processual philosophy of biology. Oxford University Press, Oxford, pp 3–45
Dworkin JP, Lazcano A, Miller SL (2003) The roads to and from the RNA world. J Theor Biol 7:222
Emmeche C (1998) Defining life as a semiotic phenomenon. Cybern Hum Knowing 5(1):3–17
Farias ST, Jheeta S, Prosdocimi F (2019) Viruses as a survival strategy in the armory of life. Hist Philos Life Sci 41:45. https://doi.org/10.1007/s40656-019-0287-5
Gilbert W (1986) Origin of life: the RNA world. Nature 319(6055):618–618
Guerrier-Takada C, Gardiner K, Marsh T, Pace N, Altman S (1983) The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 35(3 Pt 2):849–857
Hoffmeyer JS, Emmeche C (1991) Code-duality and the semiotics of nature. In: Anderson M, Merrell F (eds) On semiotic modeling. Mouton de Gryter, Berlin, New York, pp 117–166
Hofmeyr JS (2018) The first Special Issue on code biology—a bird’s-eye view. Biosystems 164:11–15. https://doi.org/10.1016/j.biosystems.2017.12.007
Jeffares DC, Poole AM, Penny D (1998) Relics from the RNA world. J Mol Evol 46:18–36
Joyce GF (1994) The RNA world: life before DNA and protein. In: Zuckerman B, Hart M (eds) Extraterrestrials–where are they? II. Cambridge University Press, Cambridge
Keller MA, Turchyn AV, Ralser M (2014) Non-enzymatic glycolysis and pentose phosphate pathway-like reactions in a plausible Archean ocean. Mol Syst Biol 10(4):725. https://doi.org/10.1002/msb.20145228
Keller MA, Zylstra A, Castro C, Turchyn AV, Griffin JL, Ralser M (2016) Conditional iron and pH-dependent activity of a non-enzymatic glycolysis and pentose phosphate pathway. Sci Adv 2(1):e1501235. https://doi.org/10.1126/sciadv.1501235
Kruger K, Grabowski PJ, Zaug AJ, Sands J, Gottschling DE, Cech TR (1982) Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena. Cell 31(1):147–157
Lang AS, Rise ML, Culley AI, Steward GF (2009) RNA viruses in the sea. FEMS Microbiol Rev 33(2):295–323
Lanier KA, Petrov AS, Williams LD (2017) The central symbiosis of molecular biology: molecules in mutualism. J Mol Evol 85(1–2):8–13. https://doi.org/10.1007/s00239-017-9804-x
Lazcano A (2012) The biochemical roots of the RNA world: from zymonucleic acid to ribozymes. Hist Philos Life Sci 34:407–423
Mayr E (2004) What makes biology unique?: Considerations on the autonomy of a scientific discipline. Cambridge University Press, Cambridge
Neveu M, Kim HJ, Benner SA (2013) The “strong” RNA world hypothesis: fifty years old. Astrobiology 13:391–403. https://doi.org/10.1089/ast.2012.0868
O’Malley MA (2016) The ecological virus. Stud Hist Philos Sci C 59:71–79
Poole AM, Jeffares DC, Penny D (1998) The path from the RNA world. J Mol Evol 46:1–17
Prigogine I (1980) From being to becoming. W. H. Freeman, SanFrancisco
Prosdocimi F, Farias ST (2021) Vírus: reinterpretando a história natural e sua importância ecológica. Rev Helius 3(2, fasc. 3):1791–1811
Ralser M (2018) An appeal to magic? The discovery of a non-enzymatic metabolism and its role in the origins of life. Biochem J 475(16):2577–2592. https://doi.org/10.1042/BCJ20160866
Reyes-Prieto F, Hernández-Morales R, Jácome R, Becerra A, Lazcano A (2012) Coenzymes, viruses and the RNA world. Biochimie l 94:1467–1473. https://doi.org/10.1016/j.biochi.2012.01.004
Ruiz-Mirazo K, Peretó J, Moreno A (2004) A universal definition of life: autonomy and open-ended evolution. Orig Life Evol Biosph 34(3):323–346
Schrödinger E (1944) What is life? The physical aspect of the living cell. Cambridge University Press, Cambridge
Sebeok TA (1988) Communication, language and speech: evolutionary considerations. In: Herzfeld M, Melazzo L (eds) Semiotic theory and practice: proceedings of the third international congress of the IASS Palermo, 1984, vol II. Mouton de Gruyter, Berlin, pp 1083–1091
Simons P (2018) Process and precipitates. In: Nicholson DJ, Dupré J (eds) Everything flows: towards a processual philosophy of biology. Oxford University Press, Oxford, pp 49–60
Sosa D, Miramontes P, Li W, Mireles V, Bobadilla JR, José MV (2013) Periodic distribution of a putative nucleosome positioning motif in human, nonhuman primates, and archaea: mutual information analysis. Int J Genom 2013:963956
Suttle CA (2007) Marine viruses—major players in the global ecosystem. Nat Rev Microbiol 5:801–812
Vega F (2018) A critique of Barbieri’s code biology through Rosen’s relational biology: reconciling Barbieri’s biosemiotics with Peircean biosemiotics. Biol Theory. https://doi.org/10.1007/s13752-018-0302-1
Vitas M, Dobovišek A (2018) In the beginning was a Mutualism—on the origin of translation. Orig Life Evol Biosph 48(2):223–243. https://doi.org/10.1007/s11084-018-9557-6
Zhang YZ, Shi M, Holmes EC (2018) Using metagenomics to characterize an expanding virosphere. Cell 172(6):1168–1172
Acknowledgements
STF was supported for Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPQ) and the Program of Pos-graduation in Philosophy at the Universidade Federal de Santa Catarina, Brazil. FP was supported by Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ, CNE E-26/202.780/2018) and by the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq, PDE 205072/2018-6).
Funding
STF was supported for Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPQ) and the Program of Pos-graduation in Philosophy at the Universidade Federal de Santa Catarina, Brazil. FP was supported by Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ, CNE E-26/202.780/2018) and by the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq, PDE 205072/2018-6).
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that they have no conflict of interest to disclose.
Consent to participate
All authors consented.
Consent for publication
All author consented.
Additional information
Publisher’s Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
About this article
Cite this article
de Farias, S.T., Prosdocimi, F. & Caponi, G. Organic Codes: A Unifying Concept for Life. Acta Biotheor 69, 769–782 (2021). https://doi.org/10.1007/s10441-021-09422-2
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10441-021-09422-2