An Illustrated Introduction to the Basic Biological Principles

Abstract ...................................................................2 Table of Contents....................................................3 List of Figures .........................................................4 I. A Rough Sketch ......................................................5 II. A Universal Constraint on Evolution – the Universal Polarity of Unbiased Configuration Sampling and Vigorous Functional Activity..........13 The molecular view of general evolution: conceptual preparations.........................................13 The universal polarity of unbiased configuration sampling and vigorous functional action is the intrinsic conflict between evolvability and fitness ....................................................................17 The spatial constraint on the en bloc evolution: pattern duplication require a spare spatial dimension ..............................................................20 III. The Molecular Interpretation of Genotype-phenotype Mapping .................................................24 The watershed between life and nonlife ................25 Translation breaks the universal polarity...............26 Translation breaks the spatial barrier to en bloc evolution................................................................29 The rule of translation further reduces biases but keeps the dynamics of evolution ...........................30 The essentials of genotype-phenotype mapping....34 The origin of translation and transcription ............36 The essence and the extension of the central dogma....................................................................39 IV. The Molecular Interpretation of Darwinism...44 The molecular view of Darwinian selection..........46 Why natural selection? - the essence of Darwinism.............................................................47 Nuclear compartmentation and gene regulation: the downward extension of the central dogma ......49 The evolution of organelle genome: enslavement through exclusive coupling ...................................52 V. Canalization/Coarse Graining in Genotype-phenotype Mapping – the Basis of Hierarchization ........................................................54 What is coarse graining/canalization?...................55 The profound role of coarse graining/canalization in evolution.........................61 Coarse-grained/canalized selection: the limit to natural selection ....................................................64 Sex: fine-graining selection at populational level .65 The short-term advantage of sex ...........................68 VI. Hierarchization in Genotype-phenotype Mapping – the Conflict and Cooperation in the Multilevel Hierarchy ...............................................69 What is hierarchization?........................................69 The evolution in the obligate hierarchy: inter-level relations ........................................................72 Dissect sexual selection to different levels............73 Mutationism and selectionism: evolution at different levels of hierarchy ..................................78 Altruism: the initiation from the genotype-phenotype division and the fixation by hierarchical conflict...............................................79 Genetic kinship enhances the evolvability of altruism but kin selection is unreal........................82 The neutral and nearly neutral theories .................85 VII. The Extended Central Dogma in Hierarchy – the Integration of Development and Ecology into the General Theory of Evolution ....................88 The upward extension of the central dogma in the multilevel hierarchy.........................................89 The labor division of cells into pattern generator and functional performer: the germ-soma division explains the difference between plant and animal .............................................................92 The flagellation constraint drives the emergence of multicellularity..................................................96 Germ-soma division: the selected strategy for amoeboid multicellularity .....................................99 References............................................................101