**5. Genotype-Phenotype-Entanglement and Genome Ecology**

The most important implication from the findings described above is most likely the multilistic entanglement between genotype and phenotype being the natural outcome of Darwinian natural selection and Lamarkian self-referenced manipulation in a genome ecology framework, which is connected directly to the origin of genomes and life itself: While entropy grows like an inexorable river, local disturbances lead to ever more ordered self-organizing and self-sustaining resistors, more complex structures, and finally life. In the 1970s Manfred Eigen [5, 6] showed how from the primordial soup autocatalytic chemical reaction-networks emerged and how they form ever more complex cooperatively organized networks and systems of so called hypercycles. With environmental separation by the emergence of units as cells and specialization of subunits, then genomes have developed as specialized keepers of the blueprint needed to maintain, regulate, and develop this syntropic machinery. Since genetic information is physically stored in molecular structures with dedicated architecture and dynamics, it is thus also obvious that the material carrier for the storage, usage, and replication of genetic information co-evolved inseparably. Yet another inevitable consequence of our results leading to the consistent statistical systems genome mechanic framework is indeed our proof [26, 27] that architecture, dynamics, and DNA sequence are co-evolutionary unseparably entangled (in a quantum mechanical sense): All architecture/dynamics levels have not only left a footprint on the DNA sequence level but beyond also all levels have left a footprint on all other levels with an astonishing degree of detail (see Section 2.4). Consequently, the co-evolution of all levels has also co-evolved not only to a higher degree than previously thought, but also indeed as an entire system where all levels are (equally ?) determinant (**Figure 5**).

In evolutionary terminology the genotype (i.e. the double helix) creates a phenotype (the nucleosome) and this phenotype recursively conditions the genotype (i.e. again the double helix). The nucleosome is also a genotype conditioning the quasi-fibre phenotype, recursively conditioning the nucleosome and DNA, etc. Since this is happening with all levels simultaneously this inseparable dualism extends in the present genome organisation to a multilism, shaping evolutionary development in hierarchical terms from bottom to top by Darwinian natural selection as well as from top to bottom by Lamarkian self-referenced manipulation. Thus, our finding that indeed all genome architecture/dynamic levels are tightly entangled with each other also immediately resolves the falsely assumed paradoxes between Darwinian and Lamarckian evolution by uniting them at least on the genome level. This is remarkable not only in historic terms considering the even politically and religiously extremely hot debates/fights about "man evolving from apes" as well as the "intentionally planed long neck of giraffes", but also heuristically, since the in principle relatively simple final completion of the 3D genome architecture/dynamics at the limit of the resolution leads not only to a consistent 3D genome organization and statistical systems genome mechanics, but beyond reveals in one go some and perhaps the most important fundamentals of life (**Figure 5**).

A Consistent Systems Mechanics Model of the 3D Architecture and Dynamics of Genomes

http://dx.doi.org/10.5772/intechopen.89836

85

Beyond, this strong entanglement over several orders of magnitude (**Figures 1**, **2**) within the genome, the described genotype-phenotype-entanglement can be driven conceptually even further considering the influence of both the a) hierarchically constituting elements giving rise to the system, i.e. chemical molecular base, atomic, and subatomic units, which will be called here i(!)nvironment, and b) the hierarchical higher levels, i.e. tissues, organs, animal etc., which are the environment. Although this may seem far fetched, but influences from both "directions" are well known (see e.g. Section 3), although due to their complexity this is often hard to track down in a reductionistic manner, thus hence their degree of influence is just emerging. In this respect the found entanglements bridging so many multi-scale levels and orders of magnitude in space and time, are on the one hand already astonishing in terms of the obviously wrong assumption that such influences would die-off very fast, while on the other hand this has general implications for all hierarchic systems showing that complex inter-, cross-, and even multi-cross-level influences are much more frequent and far reaching. Actually, the here shown multilistic genotype-phenotype entanglement shows a highly interwoven, networked, and recursive structure: instead of more or less separate hierarchic layers where only first or at the most secondary neighbour layers are connected, there are also influential connections to more distant layers at least locally if not in every part of the layer space. Thus, the genotype-phenotype entanglement embedded within an i(!)n- and environment actually results in a genome ecology in direct analogy to e.g. human ecology, autopoieses of social systems, or just any kind of systems theoretic entity [77–82].

Nature has created ever more complex forms of life by creating structural and dynamical islands of systems with specialized organelles such as genomes being responsible for storage, access, and replication of the information for their persistence and development. Despite the epic quest to determine the details and origin of inheritance, only recently we were finally able to fill the debated gaps of the central part of genome architecture and dynamics - despite the pioneering

**6. Conclusion**

**Figure 5.** Genome ecology emerging from the system mechanics of genomes in relation to the genotype-phenotype entanglement and its embedding in- and environment: Genomes are interwoven holistic multi-scale hierarchic systems entities in which all organizational levels are also manifest, i.e. fingerprinting, on all other levels. Thus, immediately each level is a phenotype of its underlying genotype immediately conditioning back on it recursively. Thus, both genotype and phenotype are entangled inseparably in a (due to the involvement and entanglement of all levels) multilistic manner. In consequence this not only unites Darwinian and Lamarckian evolutionary paradigms, but also embeds and relates genomes with their in- and environment, and thus giving rise to a general genome ecology.

In evolutionary terminology the genotype (i.e. the double helix) creates a phenotype (the nucleosome) and this phenotype recursively conditions the genotype (i.e. again the double helix). The nucleosome is also a genotype conditioning the quasi-fibre phenotype, recursively conditioning the nucleosome and DNA, etc. Since this is happening with all levels simultaneously this inseparable dualism extends in the present genome organisation to a multilism, shaping evolutionary development in hierarchical terms from bottom to top by Darwinian natural selection as well as from top to bottom by Lamarkian self-referenced manipulation. Thus, our finding that indeed all genome architecture/dynamic levels are tightly entangled with each other also immediately resolves the falsely assumed paradoxes between Darwinian and Lamarckian evolution by uniting them at least on the genome level. This is remarkable not only in historic terms considering the even politically and religiously extremely hot debates/fights about "man evolving from apes" as well as the "intentionally planed long neck of giraffes", but also heuristically, since the in principle relatively simple final completion of the 3D genome architecture/dynamics at the limit of the resolution leads not only to a consistent 3D genome organization and statistical systems genome mechanics, but beyond reveals in one go some and perhaps the most important fundamentals of life (**Figure 5**).

Beyond, this strong entanglement over several orders of magnitude (**Figures 1**, **2**) within the genome, the described genotype-phenotype-entanglement can be driven conceptually even further considering the influence of both the a) hierarchically constituting elements giving rise to the system, i.e. chemical molecular base, atomic, and subatomic units, which will be called here i(!)nvironment, and b) the hierarchical higher levels, i.e. tissues, organs, animal etc., which are the environment. Although this may seem far fetched, but influences from both "directions" are well known (see e.g. Section 3), although due to their complexity this is often hard to track down in a reductionistic manner, thus hence their degree of influence is just emerging. In this respect the found entanglements bridging so many multi-scale levels and orders of magnitude in space and time, are on the one hand already astonishing in terms of the obviously wrong assumption that such influences would die-off very fast, while on the other hand this has general implications for all hierarchic systems showing that complex inter-, cross-, and even multi-cross-level influences are much more frequent and far reaching. Actually, the here shown multilistic genotype-phenotype entanglement shows a highly interwoven, networked, and recursive structure: instead of more or less separate hierarchic layers where only first or at the most secondary neighbour layers are connected, there are also influential connections to more distant layers at least locally if not in every part of the layer space. Thus, the genotype-phenotype entanglement embedded within an i(!)n- and environment actually results in a genome ecology in direct analogy to e.g. human ecology, autopoieses of social systems, or just any kind of systems theoretic entity [77–82].
