The Four Basic Mechanisms of Fitness and Complexity ...

[Pages:47]Yong Fu

Basic Mechanisms of Complexity Increase

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The Four Basic Mechanisms of Fitness and Complexity Increase in Evolution:

From the Central Dogma to Consciousness

Yong Fu* Program in Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA

Abstract

The generation, selection, and preservation of the patterns are the essence of evolution. Complete probing of the entire configuration space is critical for the fitness and complexity increase in evolution. The bias in pattern generation is unfavourable for configuration space probing. Therefore, the pattern generation underlying evolution should be as diverse as possible to achieve complete probing. One of the missions of evolution is to minimize the bias in pattern generation. Natural selection is to couple the fate of pattern with the survival of its output, i.e. its host evolutionary entity. This responsibility is the driving force of fitness and complexity increase. Therefore, another mission of evolution is to enhance the efficiency and resolving power of natural selection. During evolution, the selected patterns are inevitably subjected to various deleterious influences, which may compromise the benefit resulting from selection, or even destroy the selected patterns. The third mission of evolution is to preserve the generated and selected patterns from various influences except the coupled selection to the host evolutionary entity. Nonbiotic evolution cannot fulfil these missions because of the primitive mode of nonbiotic evolution. Special mechanisms emerge during the origin of life to perform these missions and thus account for the fitness and complexity of life.

As the vehicle of the terrestrial life, proteins are disadvantaged in pattern generation but advantaged in functional activities: the patterns of protein are restricted in the lowlands of the rugged evolutionary landscape because proteins are active. In contrast, relatively inert DNA/RNA has flat landscape. Therefore, the patterns of DNA/RNA are more diverse than those of proteins. Moreover, one-dimensional DNA/RNA patterns can be separated in 3-dimensional space, while 3dimensional protein patterns cannot be separated without destroying the patterns, because there is no spare dimension for the separation of 3-dimensional protein patterns. Translation, as a biological heterodomain mapping, generates proteins in the configuration converted from DNA patterns through genetic code. Because of the diversity of DNA patterns and the effect of genetic code, the configuration of the proteins generated by translation is not restricted by its landscape. In this way, heterodomain mapping synthesizes the advantages of both protein and DNA: functional activity and pattern diversity. As a responsibility system, the pattern in the source domain has to couple to its translational output in natural selection in

* Correspondence: yongfu@usc.edu; your comments and questions are welcome.

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order to promote the complexity and fitness of host. For instance, the central dogma reflects that genetic information in DNA/RNA couples to the host cell rather than proteins in order to increase the complexity of cell. Specifically, the unidirectionality of translation protects DNA/RNA patterns from the harmful feedbacks of proteins through retrotranslation. Similarly, nuclear membrane and nucleosome control the physicochemical and proteinaceous reactions that may modulate DNA patterns, and reinforce the coupling of the DNA patterns with the host organism. Heterodomain mapping and the coupled selection of its source and target domains are the essence of life.

Although heteromapping is the unique characteristic of life, nonbiotic mechanisms, coarse graining and hierarchization, contribute to the complexity of life. Evolutionary entities can form various new compound entities that have the property and landscape different from individual components. These compound entities are selected as an indivisible unit according to their fitness. In this novel unit of evolution, individual components are masked but still contribute to the evolution of the whole, and that causes the subordination of masked components to the new units, which can further form novel compound entities. In this way, the patterns of component entities are transformed to the patterns of novel units. The pattern transformation through such component masking is called coarse graining. For instance, selection of organisms is a type of coarse graining because selection only concerns the fitness of organism as an indivisible whole and does not discriminate constitutive genes and proteins. Coarse graining transforms one form of evolution to the elementary unit of another form of evolution with a different landscape, and that breaks the limit to complexity increase set by the form of evolution. The consequent subordination of masked components to the whole results in hierarchy, such as the cells in multicellular lives. In the hierarchical life, the evolution of one level enslaves the lower level and provides patterns for the higher level. Because one level of the hierarchy can only get patterns from the adjacent lower level, the patterns at the bottom are transformed by coarse graining and passed upward one level by one level. There are conflicts between hierarchical levels because the evolutionary landscapes of every level are different. Both mutationism and selectionism are the selection at different levels of hierarchy. When the pattern of source domain couples to a level of hierarchy, the complexity of that level will increase in evolution at the cost of other levels. The early-specified germline embodies the principle of coupled selection in hierarchical multicellular organisms: coupling genetic information to multicellular organism rather than individual cells, germline accounts for not only the much greater complexity of animals than that of plants, but also the differences between them in motility, cell fate, development, and oncogenesis. The basic mechanisms of evolution, heteromapping, coupled selection, coarse graining, and hierarchization, explains the origin and evolution of life from protocell to consciousness.

Table of Contents

Abstract..........................................................................1 Table of Contents ..........................................................2

I. Introduction: a start from the central dogma .............3 II. The essence of life ? heterodomain mapping from DNA to protein ..................................................................5

Biological evolution is a special form of general evolution. .......................................................................5 The mechanistic limit to complexity increase................5 The prerequisite to replication: the spare spatial dimension. ...................................................................... 7

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The essence of life: heterodomain mapping. ..................9 Translation: breaking the mechanistic limit using heteromapping. ...............................................................9 Translation: breaking the barrier to replication using the source domain of lower dimensionality than the space. ......................................................................................10 The rule of heterodomain mapping produces further advantage......................................................................11 The essence/cause/foundation of central dogma. .........12 Gene and metabolism: which is the first in biogenesis? ......................................................................................13 The origin of translation. ..............................................13 Genotype, phenotype, and epigenetics. ........................15 General heterodomain mapping. ..................................16 III. The evolution of information ? coupled selection of heteromapping.................................................................16 What is information? ....................................................16 The essence of Darwinian selection: coupled selection of the source and target domains of heteromapping. ........18 The essence of central dogma.......................................19 IV. Coarse graining: the essence of hierarchization.....21 What is coarse graining? ..............................................21 What is hierarchization? ...............................................23 V. Coarse graining vs. fine graining ? the origin and evolution of sex ................................................................24 Coarse-grained selection: the limit to natural selection. ......................................................................................24 Fine-grained selection: recombination and sex. ...........26 The short-term advantage of sex. .................................26 VI. The evolution in hierarchy ? the origin of altruism ..........................................................................................27

The evolution in hierarchy: an integration of mutationism and selectionism. .....................................27 Neutral and nearly neutral theories. .............................29 The conflicts in hierarchy: the origin of altruism.........29 VII. The natural selection in hierarchy ? integration of development into the general theory of evolution ........30 Extension of central dogma to the hierarchy................31 Coupling information to hierarchy: the germline explains the difference between plant and animal........32 The flagellation constraint drives the emergence of multicellularity and germline. ......................................34 VIII. Neural system ? a revolution in the mode of evolution........................................................................... 37 Prelude: enhanced heteromapping and natural selection in adaptive immunity. ..................................................37 Innate neural system.....................................................38 Neural screen and image. .............................................38 The evolution of neural image. ....................................39 The emergence of self image in neural screen. ............40 IX. Consciousness ? a biased neural embodiment of natural selection ..............................................................41 What is consciousness? ................................................41 Consciousness, subconsciousness, and unconsciousness. ..................................................................................... 42 The essence of consciousness: subjectivity..................42 The problem of quale: quality of subjectivity. .............43 The development of consciousness. .............................44 References.................................................................... 45

I. Introduction: a start from the central dogma

The central dogma of molecular biology (Fig. 1) was proposed in 1958(1) and restated in 1970(2) by Francis Crick. It states that "once information has got into a protein it can't get out again(1)" or "information cannot be transferred from protein to either protein or nucleic acid(2)". In addition to this explicit meaning, the central dogma implies that the transfers from RNA to DNA, from RNA to RNA, and from DNA to protein are special cases while only the transfer from DNA to RNA to protein is general(2)(Fig. 1). In advanced organisms, only unidirectional flow of genetic information from DNA to RNA to protein exists, while the special transfers from RNA to DNA, from RNA to RNA, and from DNA to protein are only seen in lower life forms or in the in vitro cell-free system. The

direction of informational flow is not a frozen accident. In stead, it reflects the consequentially different mechanisms of pattern generation, selection, and preservation between life and nonlife. In order to find out the underlying cause of the central dogma, we need to understand the characteristics of general evolution.

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Fig. 1. Why is the informational flow out of protein prohibited? The general transfer of genetic information from DNA to RNA to protein is the only informational flow in most life forms. The special transfer from RNA to DNA or RNA only occurs in the primitive forms of life, such as retroviruses. The mainstream of informational flow is unidirectionally from DNA to RNA to protein. The transfer of information out of protein is undetected despite extensive investigations. The absence of the information flow out of protein is a necessity rather than a frozen accident of biological evolution. Drawn according to Crick F. (1970): Central Dogma of Molecular Biology. Nature 227, 561.

The persistence or elimination of an evolutionary entity in an environment is the selection in general sense, whether the evolutionary entity is biotic or nonbiotic. The so-called natural selection of life is only a specific form of general selection. Given that natural selection is universal, selection alone cannot explain why only a specific type of evolutionary entities, i.e. life, has extraordinary complexity. The answer of this question is the internal mechanisms of pattern generation and preservation of life, which explain why and how life acquires extraordinary complexity.

The innovation of mutations has been raised before the dominance of neo-Darwinism(3) and is reemphasized recently(4-6). The role of mutation is only a special case of the innovation of internal evolution of life. Internal evolution is not only the passive gene frequency changes caused by natural selection. Instead, it is the active and innovative pattern

generation to ensure the complete probing of configuration space, and the effective preservation of selected patterns inside the life. Both the innovation of internal evolution and the selection of external environment are required by evolution, but they play different role in evolution. Evolution is the cycles of the generation of patterns, the natural selection of generated patterns, and the preservation of selected patterns. Both the divergent pattern generation and convergent pattern selection are essential to the fitness and complexity increase of life. The fitness and complexity increase in evolution is determined by the diversity of generated patterns, the efficiency of selection, and the effectiveness of preservation.

In general evolution, there are some polarities that are unfavorable for the increase of fitness and complexity. Special mechanisms are required to solve these polarities. Functional activity and unbiased pattern generation are one polarity of evolution. For instance, proteins are advantaged in functional activities but disadvantaged in pattern generation: the patterns of protein are restricted in the lowlands of the rugged evolutionary landscape because proteins are active. In contrast, relatively inert DNA/RNA has flat landscape. Therefore, the patterns of DNA/RNA are more diverse than those of proteins. That is why genetic information only flows from DNA/RNA to proteins. Moreover, one-dimensional DNA patterns can be separated in 3-dimensional space, while 3-dimensional protein patterns cannot be separated without destroying the pattern, because there is no spare dimension for the separation of 3dimensional protein patterns. That is why genetic information cannot transfer from protein to protein. As a type of heterodomain mapping, translation transforms the patterns of DNA evolution to the patterns of protein evolution through genetic coding, and significantly improves the generation, selection, and preservation of patterns. The source domain, DNA, has advantage in the generation and preservation of patterns, while target domain, proteins, has advantage in action and function. Heteromapping combines the advantages of both domains, and thus breaks the mechanistic limit to the fitness and complexity increase of one domain.

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Heteromapping is a mechanism essential to life and accounts for both the extraordinary complexity of life and the central dogma of genetic information. In addition to heteromapping, other mechanisms contribute to the evolution of life: coupled selection, coarse graining, and hierarchization. The interaction between these basic internal mechanisms systematically and parsimoniously explains all important events and characters of life in addition to the central dogma.

II. The essence of life ? heterodomain mapping

from DNA to protein

Biological evolution is a special form of general evolution. An evolutionary entity can be an elementary particle, a group of stars, a hypercycle of Eigen's type(7), a human, or a political idea. Change from one state to another is the evolution in a general sense. Existence can change its form but never be destroyed: evolution is the state change of perpetual existence. The state is the form of existence. Existence without state change is stasis. The state change of an entity is determined by the property of the entity per se and all other interacting entities, which are collectively referred to as the environment. Under a certain environment, the ability of an entity to remain static is stability. Birth and death of a life is the assembly and disassembly of a complex entity, and that is still a state change rather than the beginning and end of existence. In terms of this generalization, biological evolution is only a special type of formal change. The so-called natural selection is also a subset of the selection of the form of evolutionary entities by the environment. Fitness of life is a special type of stability: the persistence of genetic information during the alternation of generations. Biological evolution is a special type of general evolution.

The mechanistic limit to complexity increase. Evolution is the temporal extension of the form of existence. Therefore, it is neither purposeful nor directional. Complexity does not necessarily increase in evolution. However, why and how

some specific types of evolutionary entities have acquired more complexity than others is the concern of scientists.

The property of an evolutionary system is the manifestation of its composition and configuration. Evolution of a compound system is the configurational change of that system. To a specific evolutionary entity, its evolution is the motion in its configuration space under the constraint of environment. For convenience of understanding, let's use the concept of evolutionary landscape of biological evolution to study general evolution: low altitude stands for high stability and close-to-equilibrium, while high altitude stands for low stability and far-from-equilibrium (Fig.). The physical trend of evolution is from high altitude to low altitude, like the water flow. Because complexity is the deviation from equilibrium, the direction of complexity increase goes against the physical trend. A stable complex entity, such as life, must be in disequilibrium, and that is represented as a high-altitude local minimum on the landscape, as the crater of volcanoes (Fig. 2). The fitness of life is determined by the local stability of life, namely the depth of the local minimum.

As a concept of the group rather than the individual, fitness is a measurement of the ability of a group or a species of organisms to persist in the environment. On the evolutionary landscape, the ability of an evolutionary entity to persist is determined by the height of surrounding local maximum, or the depth of the local minimum where the entity resides. The number and survival rate of offspring are only one of factors that contribute to fitness. Complexity is the deviation from equilibrium and not necessarily correlates with fitness. For instance, although the panda is much more complex than E. coli, E. coli has higher fitness. Because evolution starts from the equilibrium, fitness niches of low complexity are occupied first in evolution. Therefore, new forms of fitness are generally more complex than the old ones. That is the reason why evolution results in complexity increase, although complexity stasis and decrease occur at the same time.

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Every evolutionary entity has its own landscape. The roughness of landscape represents the activity of the entity. It is difficult for a highly active entity to escape from a valley, i.e. a local minimum, or climb over a mountain, i.e. a local maximum, on its landscape. For example, highly active sodium can readily form stable complex with oxygen, and that arrests the further evolution of sodium. Accordingly, the evolution of highly active entities is the ineffective thermallike motion restricted in local minimums. The configuration space of the entity has high peaks that are complex and farfrom-equilibrium, but it is very difficult for the entity to reach the high peaks (Fig. 2). In other words, probing the configuration space by active entities is very biased and restricted in the local minimums of low altitude. If the activity of the constitutive entities is low, the landscape will be relatively smooth and the switch between different configurations will be easy. The patterns generated by relatively inert entities are less biased and more diverse than

the patterns generated by active entities, which are restricted in the valleys of low altitude on their rugged landscape. However, such entity is evolutionarily and functionally inert: it cannot have any useful function due to its inertness. In other words, the whole configuration space is close to equilibrium, the entity cannot acquire significant complexity or useful function (Fig. 2). In short, evolution has polarity: active entities have potential complexity but their pattern generation is biased and configuration space probing is restricted, while functionally inert entities have diverse pattern generation and full probing of configuration space. This polarity can be described in an intuitional way: a rugged landscape has peaks and valleys but the motion is entrapped in the valleys of low altitude, while the motion on a flat landscape is not restricted but has no evolutionary altitude (Fig. 2). The fundamental cause of this polarity is that the physical trend of regression to equilibrium in evolution, i.e. the increase of entropy, is adverse to the increase of complexity and organization.

Fig. 2. Evolutionary landscape and heterodomain mapping. A. The lower smooth landscape represents the evolution of source domain; the upper rugged landscape represents the evolution of target domain. Low altitude stands for low complexity, high stability,

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and close-to-equilibrium, while high altitude stands for high complexity, low stability, and far-from-equilibrium. A complex and stable entity is a high-altitude local minimum on the landscape, like the crater of volcanoes. Red arrows on landscape represent the evolution of corresponding domain. Blue arrows represent heteromapping from the source domain to the target domain. A spontaneous upward evolution from a low-altitude local minimum to a high-altitude local minimum is rare on the target domain, but it can be achieved through heteromapping from a smooth evolution on the source domain. B. The protein has advantage in functional activity, but has rugged landscape. The configuration of the protein is restricted in the valleys of low altitude (blue area). It is difficult for protein evolution to reach valleys of high altitude, which represents complex configurations including the terrestrial life. DNA is inert in functional activity compared to the protein. However, due to this inertness, DNA has flat evolutionary landscape and thus the patterns generated in DNA evolution are more diverse. C. Translation, as a biological heteromapping, generates proteins in the configuration specified by DNA patterns. Because of the diversity of DNA patterns, the configuration of the proteins generated by translation is not restricted by its landscape anymore: it combines both DNA patterns and spontaneous protein patterns. In this way, heteromapping synthesizes the advantages of both protein and DNA: functional activity and pattern diversity.

Energy dissipation can help the evolutionary entity to climb peaks on the landscape. However, complexity gained in this way is still very unstable. Energy is a double-edged sword: it equally accelerates the disintegration of complex structures. Moreover, energy is an intrinsic part of evolution. The diversity of the patterns generated in energy flow is still limited by the form and nature of specific type of evolution.

The prerequisite to replication: the spare spatial dimension. Natural selection would be meaningless without variation(8). However, branching of evolution is as important as variation in promoting evolution. Variation without branching is only serial fluctuation rather than parallel diversification that is the basis of natural selection. Parallel diversity plus natural selection improves fitness and

complexity step by step: every branching is a small step of improvement. Despite the complexity increase in every step may be very small, the branched evolution will acquire significant fitness and complexity given sufficient time. Although biological branching, namely reproduction, is very complicated, the key of branching is the replication of the patterns of life. However, there is a general spatial barrier to replication of patterns, and that imposes a limit to complexity increase. Such limit to complexity increase is a special and important type of mechanistic limit to complexity increase. Breaking through the barrier to replication is an important progression logically following the emergence of protein translation, although both are the different sides of heterodomain mapping.

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Fig. 3. Replication requires spare spatial dimensions. A. Separation of patterns, an essential step in all types of replication, requires at least one spare spatial dimension, i.e. one spare degree of freedom. As illustrated, separating concentric circles without breaking the circles requires one spare dimension. In a 2-D plane with 2-D concentric circles, the interior circle cannot be separated from the exterior circle without breaking the exterior circle. In a 3-D space, the interior circle can be separated from the exterior circle through the third dimension. B. Although DNA is 3-D, the DNA patterns that are used in life are 1-D. Therefore, the DNA patterns are not changed during replication and separation in 3-D space. Even when DNA is severed by topoisomerase, the pattern can be maintained by proteins through other two dimensions. C. The patterns of the cell are 3-D, including organelles and folded proteins. Cells cannot be replicated and separated without destroying these patterns. In cell division, most organelles, such as nuclear envelop, are destructed to prepare for the separation of two 3-D daughter cells. The information for restoring the organelles is mainly stored in DNA as 1-D patterns, which are intact during division. Actually, the pattern of lower dimensionality than the space is the only escape from the destruction during cell division.

In 3-D space, it is impossible to separate intertwined 3D patterns without changing these patterns. The reason is that all spatial degrees of freedom are used in construction of patterns, and thus no spare degree is available for uninjurious separation. As illustrated in Fig. 2, in a 2-dimensional (2-D) plane with 2-D concentric circles, the interior circle cannot be separated from the exterior circle without breaking the exterior circle; however, in the 3-D space, the interior circle can be separated from the exterior circle through the third dimension (Fig. 3). Similarly, separating intertwined 3-D patterns in 3-D

space must destroy the patterns, as undoing a knot in 3-D space needs to cut the knot. If the dimensionality of intertwined patterns is lower than the dimensionality of space, the separation can be fulfilled without changing the patterns, same as undoing a knot in 4-dimensional space(9). The functionally active protein can catalyze the replication of DNA and RNA. Why the protein cannot be replicated by other enzymatic proteins? The profound reason is the unavailability of spare degree of freedom for the 3-D protein.

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