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Advances in biodiversity: metagenomics and the unveiling of biological dark matter

机译：生物多样性方面的进展：宏基因组学和生物暗物质的发现

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Background Efforts to harmonize genomic data standards used by the biodiversity and metagenomic research communities have shown that prokaryotic data cannot be understood or represented in a traditional, classical biological context for conceptual reasons, not technical ones. Results Biology, like physics, has a fundamental duality—the classical macroscale eukaryotic realm vs. the quantum microscale microbial realm—with the two realms differing profoundly, and counter-intuitively, from one another. Just as classical physics is emergent from and cannot explain the microscale realm of quantum physics, so classical biology is emergent from and cannot explain the microscale realm of prokaryotic life. Classical biology describes the familiar, macroscale realm of multi-cellular eukaryotic organisms, which constitute a highly derived and constrained evolutionary subset of the biosphere, unrepresentative of the vast, mostly unseen, microbial world of prokaryotic life that comprises at least half of the planet’s biomass and most of its genetic diversity. The two realms occupy fundamentally different mega-niches: eukaryotes interact primarily mechanically with the environment, prokaryotes primarily physiologically. Further, many foundational tenets of classical biology simply do not apply to prokaryotic biology. Conclusions Classical genetics one held that genes, arranged on chromosomes like beads on a string, were the fundamental units of mutation, recombination, and heredity. Then, molecular analysis showed that there were no fundamental units, no beads, no string. Similarly, classical biology asserts that individual organisms and species are fundamental units of ecology, evolution, and biodiversity, composing an evolutionary history of objectively real, lineage-defined groups in a single-rooted tree of life. Now, metagenomic tools are forcing a recognition that there are no completely objective individuals, no unique lineages, and no one true tree. The newly revealed biosphere of microbial dark matter cannot be understood merely by extending the concepts and methods of eukaryotic macrobiology. The unveiling of biological dark matter is allowing us to see, for the first time, the diversity of the entire biosphere and, to paraphrase Darwin, is providing a new view of life. Advancing and understanding that view will require major revisions to some of the most fundamental concepts and theories in biology.
机译：背景技术协调生物多样性和宏基因组研究界使用的基因组数据标准的努力表明，由于概念上的原因，而不是技术上的原因，无法在传统的经典生物学环境中理解或表示原核生物数据。结果生物学与物理学一样，具有基本的对偶性-经典的宏观真核生物领域与量子微尺度微生物领域-这两个领域彼此之间有着截然不同的直觉差异。就像古典物理学是从量子物理学的出现而不能解释量子物理学的微观领域一样，古典生物学也无法从原生物学的微观领域出现并且不能解释量子物理学的微观领域。古典生物学描述了多细胞真核生物熟悉的宏观领域，它们构成了生物圈的高度衍生且受限制的进化子集，无法代表包括地球生物量至少一半的原核生物的广阔且大多未被看见的微生物世界。及其大部分遗传多样性。这两个领域占据着根本不同的巨型生态位：真核生物主要与环境机械相互作用，原核生物主要在生理上相互作用。此外，许多经典生物学的基本原理根本不适用于原核生物学。结论经典遗传学认为，排列在染色体上的基因像一串串珠子一样，是突变，重组和遗传的基本单位。然后，分子分析表明没有基本单位，没有珠子，没有线。同样，经典生物学认为个体生物和物种是生态，进化和生物多样性的基本单位，构成了单根生命树中客观真实，由谱系定义的群体的进化历史。现在，宏基因组学工具正迫使人们认识到，没有完全客观的个体，没有独特的血统，也没有一棵真正的树。仅仅通过扩展真核宏观生物学的概念和方法就不能理解新发现的微生物暗物质生物圈。生物暗物质的揭开使我们第一次看到了整个生物圈的多样性，用达尔文来解释，这提供了一种新的生命观。推进和理解这种观点将需要对生物学中一些最基本的概念和理论进行重大修改。

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