Selfishness, warfare, and economics; or integration, cooperation, and biology

Abstract

The acceptance of Darwin's theory of evolution by natural selection is not complete and it has been pointed out its limitation to explain the complex processes that constitute the transformation of species. It is necessary to discuss the explaining power of the dominant paradigm. It is common that new discoveries bring about contradictions that are intended to be overcome by adjusting results to the dominant reductionist paradigm using all sorts of gradations and combinations that are admitted for each case. In addition to the discussion on the validity of natural selection, modern findings represent a challenge to the interpretation of the observations with the Darwinian view of competition and struggle for life as theoretical basis. New holistic interpretations are emerging related to the Net of Life, in which the interconnection of ecosystems constitutes a dynamic and self-regulating biosphere: viruses are recognized as a macroorganism with a huge collection of genes, most unknown that constitute the major planet's gene pool. They play a fundamental role in evolution since their sequences are capable of integrating into the genomes in an “infective” way and become an essential part of multicellular organisms. They have content with “biological sense” i.e., they appear as part of normal life processes and have a serious role as carrier elements of complex genetic information. Antibiotics are cell signals with main effects on general metabolism and transcription on bacterial cells and communities. The hologenome theory considers an organism and all of its associated symbiotic microbes (parasites, mutualists, synergists, amensalists) as a result of symbiopoiesis. Microbes, helmints, that are normally understood as parasites are cohabitants and they have cohabited with their host and drive the evolution and existence of the partners. Each organism is the result of integration of complex systems. The eukaryotic organism is the result of combination of bacterial, virus, and eukaryotic DNA and it is the result of the interaction of its own genome with the genome of its microbiota, and their metabolism are intertwined (as a “superorganism”) along evolution. The darwinian paradigm had its origin in the free market theories and concepts of Malthus and Spencer. Then, nature was explained on the basis of market theories moving away from an accurate explanation of natural phenomena. It is necessary to acknowledge the limitations of the dominant dogma. These new interpretations about biological processes, molecules, roles of viruses in nature, and microbial interactions are remarkable points to be considered in order to construct a solid theory adjusted to the facts and with less speculations and tortuous semantic traps.

Diversity-Function Relationships in Natural, Applied, and Engineered Microbial Ecosystems

“…All of these deleterious microorganisms can interact with, perturb and be affected by the commensal microbiota and the host immune system Bancroft, Hayes, & Grencis, 2012;Zaiss & Harris, 2016), and the resistance to colonisation by, and control of, pathogens and pathobionts is an additional major function of the gut microbial community (Buffie & Pamer, 2013;Kamada et al, 2013). Thus, considering the GI tract and, by extension, the entire human body as a "superorganism" composed of the cells, genomes and activities of all its constituent microorganisms, viruses and parasites, interacting via multiple pathways and influencing each other's evolution (Salvucci, 2012), yields our updated, much more detailed but still poorly-understood concept of the holobiont (Zilber- Rosenberg & Rosenberg, 2008).…”

Microbial genomics challenge Darwin

“…It seems appropriate therefore that two articles in the present collection venture outside evolutionary biology and into economic theory and philosophy. Salvucci emphasizes the importance of moving away from simplistic models of market economy, such as those of Smith and Malthus that inspired Darwin to more integrative approaches suitable for analysis of the diverse interactions between different life forms that are central to evolution (Salvucci, 2012). Finally, Baquero and Moya address the problem of intelligibility of complex microbial systems by turning to the ideas of Wittgenstein and advocate the development of complex models that will be commensurate with the complexity of life (Baquero and Moya, 2012).…”

Supra-organismal interactions in the human intestine

“…The term “supraorganism” (which we prefer to the more common but slightly less informative “superorganism”) refers to a collection of individuals which behave as a single unit with enhanced function. It was originally applied to groups of genetically-identical individuals such as social insect colonies (Moritz and Fuchs, 1998 ), but has since been expanded to include systems comprised of taxonomically-diverse species from all domains of life, as well as viruses (Salvucci, 2012 ). The human intestine plays host to up to 10 14 bacteria, which outnumber the host's own cells by around an order of magnitude: microbial concentrations in the colon can reach 10 12 cells per gram.…”