Abstract
In previous chapters, a differing point of initiation for evolutionary development has been introduced through concepts of information management and cell–cell communication. It has been emphasized that evolution proceeds quite differently than it had been supposed. Instead of random genetic variations based on intermittent replication errors, evolution can now be understood as a continuous self-referential process of self-modification in response to environmental stresses through natural cellular engineering and niche construction. Yet, to further comprehend how the modern synthesis must be altered, an accurate perception of the endpoint of all evolutionary processes must be explained. It is now known that all multicellular macro-organisms are holobionts. Taking ourselves as an example, it is currently estimated that there are many trillions of microbes—bacteria, viruses, fungi, and others—that are in us and on us (Sender et al. 2016). They outnumber our eukaryotic cells by a factor estimated by some to be up to 10 to 1 or more (Turnbaugh et al. 2007). When the total genetic complement of this microbial fraction is considered, the full genetic cohort of the associated microbiome outnumbers our innate genetic complement by perhaps as much as 100 to 1 (Bäckhed et al. 2005).
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References
Aagaard K, Ma J, Antony KM, Ganu R, Petrosino J, Versalovic J (2014) The placenta harbors a unique microbiome. Sci Transl Med 6:237ra65
Alfano M, Ferrarese R, Locatelli I, Ventimiglia E, Ippolito S, Gallina P, Cesana D, Canducci F, Pagliardini L, Viganò P, Clementi M (2018) Testicular microbiome in azoospermic men—first evidence of the impact of an altered microenvironment. Hum Reprod 2018 33(7):1212–7
Bäckhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI (2005) Host-bacterial mutualism in the human intestine. Science 307:1915–1920
Baluška F, Miller WB Jr (2018) Senomic view of the cell: senome versus genome. Commun Integr Biol 11(3):1–9
Bohm DJ, Hiley BJ (1975) On the intuitive understanding of nonlocality as implied by quantum theory. Found Phys 5:93–109
Chang JY, Antonopoulos DA, Kalra A, Tonelli A, Khalife WT, Schmidt TM, Young VB (2008) Decreased diversity of the fecal microbiome in recurrent Clostridium difficile—associated diarrhea. J Infect Dis 197:435–438
Chiu L, Gilbert SF (2015) The birth of the holobiont: multi-species birthing through mutual scaffolding and niche construction. Exp Cell Res 8:191–210
Cho I, Blaser MJ (2012) The human microbiome: at the interface of health and disease. Nat Rev Genet 13:260–270
Christakis NA, Fowler JH (2013) Social contagion theory: examining dynamic social networks and human behavior. Stat Med 32:556–577
Cryan JF, Dinan TG (2012) Mind-altering microorganisms: the impact of the gut microbiota on brain and behaviour. Nat Rev Neurosci 13:701–712
Dennis AR, Valacich JS (1999) Rethinking media richness: towards a theory of media synchronicity. In: Proceedings of the 32nd annual Hawaii international conference on systems sciences. IEEE Systems Sciences, Los Alamitos
Fouhy F, Ross RP, Fitzgerald GF, Stanton C, Cotter PD (2012) Composition of the early intestinal microbiota: knowledge, knowledge gaps and the use of high-throughput sequencing to address these gaps. Gut Microbes 3:203–220
Fukuda S, Toh H, Hase K, Oshima K, Nakanishi Y, Yoshimura K, Tobe T, Clarke JM, Topping DL, Suzuki T, Taylor TD, Itoh K, Kikuchi J, Morita H, Hattori M, Ohno H (2011) Bifidobacteria can protect from enteropathogenic infection through production of acetate. Nature 469:543–547
Funkhouser LJ, Bordenstein SR (2013) Mom knows best: the universality of maternal microbial transmission. PLoS Biol 11:e1001631
Gevers D, Knight R, Petrosino JF, Huang K, McGuire AL, Birren BW, Nelson KE, White O, Methé BA, Huttenhower C (2015) The human microbiome project: a community resource for the healthy human microbiome. PLoS Biol 10:e1001377
Gilbert SF (2014) Symbiosis as the way of eukaryotic life: the dependent co-origination of the body. J Biosci 39:201–209
Gilbert SF, McDonald E, Boyle N, Buttino N, Gyi L, Mai M, Prakash N, Robinson J (2010) Symbiosis as a source of selectable epigenetic variation: taking the heat for the big guy. Philos Trans R Soc Lond Ser B Biol Sci 365:671–678
Gilbert SF, Sapp J, Tauber AI (2012) A symbiotic view of life: we have never been individuals. Q Rev Biol 87:325–341
Gordon J, Knowlton N, Relman DA, Rohwer F, Youle M (2013) Superorganisms and holobionts. Microbe 8:152–153
Gunji YP, Sonoda K, Basios V (2016) Quantum cognition based on an ambiguous representation derived from a rough set approximation. Biosystems 141:55–66
Hall WP (2005) Biological nature of knowledge in the learning organisation. Learn Organ: Intern J 12:169–188
Heijtz RD, Wang S, Anuar F, Qian Y, Björkholm B, Samuelsson A, Hibberd ML, Forssberg H, Petterson S (2011) Normal gut microbiota modulates brain development and behavior. Proc Natl Acad Sci 108:3047–3052
Hoffmann AR, Proctor LM, Surette MG, Suchodolski JS (2015) The microbiome the trillions of microorganisms that maintain health and cause disease in humans and companion animals. Vet Path 53:10–21
Hooper LV, Littman DR, Macpherson AJ (2012) Interactions between the microbiota and the immune system. Science 336:1268–1273
Jiménez E, Marín ML, Martín R, Odriozola JM, Olivares M, Xaus J, Rodríguez JM (2008) Is meconium from healthy newborns actually sterile? Res Microbiol 159:187–193
Keller M, Mazuch J, Abraham U, Eom GD, Herzog ED, Volk HD, Kramer A, Maier B (2009) A circadian clock in macrophages controls inflammatory immune responses. Proc Natl Acad Sci 106:21407–21412
Kiessling S, Dubeau-Laramée G, Ohm H, Labrecque N, Olivier M, Cermakian N (2017) The circadian clock in immune cells controls the magnitude of Leishmania parasite infection. Sci Rep 7:10892
Koenig JE, Spor A, Scalfone N, Fricker AD, Stombaugh J, Knight R, Angenent LT, Ley RE (2011) Succession of microbial consortia in the developing infant gut microbiome. Proc Natl Acad Sci U S A 108:4578–4585
Koleva PT, Kim JS, Scott JA, Kozyrskyj AL (2015) Microbial programming of health and disease starts during fetal life. Birth Defects Res C Embryo Today 105:265–277
Lee YK, Mazmanian SK (2010) Has the microbiota played a critical role in the evolution of the adaptive immune system? Science 330:1768–1773
Ling Z, Kong J, Jia P, Wei C, Wang Y, Pan Z, Huang W, Li L, Chen H, Xiang C (2010) Analysis of oral microbiota in children with dental caries by PCR-DGGE and barcoded pyrosequencing. Microb Ecol 60:677–690
Łukasik P, van Asch M, Guo H, Ferrari J, Godfray CJ (2013) Unrelated facultative endosymbionts protect aphids against a fungal pathogen. Ecol Lett 16:214–218
McFall-Ngai M, Hadfield MG, Bosch TC, Carey HV, Domazet-Lošo T, Douglas AE, Dubilier N, Eberl G, Fukami T, Gilbert SF, Hentschel U (2013) Animals in a bacterial world, a new imperative for the life sciences. Proc Natl Acad Sci 110:3229–3236
Miller WB (2013) The microcosm within: evolution and extinction in the hologenome. Universal Publishers, Boca Raton
Miller WB (2016a) Cognition, information fields and hologenomic entanglement: evolution in light and shadow. Biology (Basel) 5(2):21
Miller WB (2016b) The eukaryotic microbiome: origins and implications for fetal and neonatal life. Front Pediatr 4:96
Miller WB (2017) Biological information systems: evolution as cognition-based information management. Prog Biophys Mol Biol 134:1–36
Miller WB Jr, Torday JS (2018) Four domains: the fundamental unicell and Post-Darwinian cognition-based evolution. Prog Biophys Mol Biol 140:49–73
Miller WB, Torday JS, Baluska F (2018) Biological evolution as the defense of self. Prog Biophys Mol Biol 142:54–74
Moeller AH, Li Y, Ngole EM, Ahuka-Mundeke S, Lonsdorf EV, Pusey AE, Peeters M, Hahn BH, Ochman H (2014) Rapid changes in the gut microbiome during human evolution. Proc Natl Acad Sci U S A 111:16431–16435
Moon C, Baldridge MT, Wallace MA, Burnham C-AD, Virgin HW, Stappenbeck TS (2015) Vertically transmissible fecal IgA levels distinguish extra-chromosomal phenotypic variation. Nature 521:90–93
Moya A, Peretó J, Gil R, Latorre A (2008) Learning how to live together: genomic insights into prokaryote—animal symbioses. Nat Rev Genet 9:218–222
Nguyen LD, Viscogliosi E, Delhaes L (2015) The lung mycobiome: an emerging field of the human respiratory microbiome. Front Microbiol 6:89
Nicholson DJ (2014a) The machine conception of the organism in development and evolution: a critical analysis. Stud Hist Phil Biol Biomed Sci 48:162–174
Nicholson DJ (2014b) The return of the organism as a fundamental explanatory concept in biology. Philos Compass 9:347–359
Noble D (2015) Evolution beyond Darwinism: a new conceptual framework. J Exp Biol 218:7–13
O’Hara AM, Shanahan F (2006) The gut flora as a forgotten organ. EMBO Rep 7:688–693
Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO (2007) Development of the human infant intestinal microbiota. PLoS Biol 5:e177
Round JL, Mazmanian SK (2009) The gut microbiota shapes intestinal immune responses during health and disease. Nat Rev Immunol 9:313–323
Saetzler K, Sonnenschein C, Soto AM (2011) Systems biology beyond networks: generating order from disorder through self-organization. Semin Cancer Biol 21:165–174
Saey TH (2014) Beyond the microbiome: the vast virome: scientists are just beginning to get a handle on the many roles of viruses in the human ecosystem. Sci News 185:18–21
Satokari R, Grönroos T, Laitinen K, Salminen S, Isolauri E (2009) Bifidobacterium and Lactobacillus DNA in the human placenta. Lett Appl Microbiol 48:8–12
Sender R, Fuchs S, Milo R (2016) Revised estimates for the number of human and bacteria cells in the body. PLoS Biol 14:e1002533
Tilg H, Kaser A (2011) Gut microbiome, obesity, and metabolic dysfunction. J Clin Invest 121:2126–2132
Tito RY, Macmil S, Wiley G, Najar F, Cleeland L, Qu C, Wang P, Romagne F, Leonard S, Ruiz AJ, Reinhard K, Roe BA, Lewis CM Jr (2008) Phylotyping and functional analysis of two ancient human microbiomes. PLoS One 3:e3703
Tognini P, Murakami M, Sassone-Corsi P (2018) Interplay between microbes and the circadian clock. Cold Spring Harb Perspect Biol 10:a028365
Torday JS, Miller WB Jr (2016b) Biologic relativity: who is the observer and what is observed? Prog Biophys Mol Biol 121:29–34
Torday JS, Miller WB Jr (2016c) Life is determined by its environment. Int J Astrobiol 15:345–350
Turnbaugh PJ, Ley RE, Hamady M, Fraser-liggett C, Knight R, Gordon JI (2007) The human microbiome project: exploring the microbial part of ourselves in a changing world. Nature 449:804–810
Ulanowicz RE (2017) Preface: towards a global understanding of development and evolution. Prog Biophys Mol Biol 131:12–14
Virgin HW (2014) The virome in mammalian physiology and disease. Cell 157:142–150
Wang T, Zeng J, Lowe CB, Sellers RG, Salama SR, Yang M, Burgess SM, Brachmann RK, Haussler D (2007) Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein. Proc Natl Acad Sci 104:18613–18618
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Torday, J., Miller Jr., W. (2020). Holobionts. In: Cellular-Molecular Mechanisms in Epigenetic Evolutionary Biology. Springer, Cham. https://doi.org/10.1007/978-3-030-38133-2_12
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