An Illustrated Introduction to the Basic Biological Principles

Evolution is the sampling of configuration space * Incomplete sampling can be due to the insufficient number of individuals (parallel sampler) for sampling all possible configurations at every step. In this case, giving sufficient time, evolution can still locate extremely small regions of the vast configuration space of life (repeated sampling). In other by physical entities under environmental constraint.

Evolution as a whole is not biased to fitness or complexity increase. However, why and how some specific types of evolutionary entities have become more complex than others is the focus of evolutionary biology. As an evolutionary entity with extraordinary complexity and fitness, terrestrial life occupies only extremely small regions in the enormous configuration space 1 . The major theme of evolution is how blind evolution finds its way to these small regions under environmental constraint. Although the blindness of evolution has been widely accepted as a rebuttal to creationism and intelligent design [4][5][6][7][8][9] , the profound influence of blindness on evolution is not fully appreciated. The key to understand the role of blindness is to recognize that because evolution is blind and purposeless, incomplete sampling of the possible configurations of the next step is unfavorable to the increase of fitness and complexity. Due to its blindness and purposelessness, evolution does not “know” in advance which path will lead to the increase of fitness or complexity or how fluctuating environment will change. Therefore, retrospectively, the best “strategy” to increase complexity and fitness is to take every possible path at every next step. As a result, no complex or fit configurations will be missed. In contrast, if the evolutionary entity only takes a part of paths at the current location, only configurations downstream of these paths can be reached: all other configurations will be missed.

From the angle of blind evolution rather than intelligent humans, the greater the incompleteness in configuration sampling, the smaller the probability for blind evolution to increase complexity or fitness is. Even when intelligent humans (re)design enzymes, blind random mutagenesis followed by screening is more successful than “rational” approaches using computational predictions based on chemical principles 10 . There is no better “strategy” for blind evolution, especially during the origin and early evolution of life. It must be emphasized there is no purposeful pursue for the “strategy”: some branches blindly acquired the mechanisms of such a “strategy” and consequently had high evolvability and complexity. Dec. 13, 09 words, if the missed configurations are distributed randomly, namely unbiased, the incompleteness of sampling can be remedied by parallel or repeated sampling. However, if the incompleteness is biased to certain configurations, parallel or repeated sampling cannot remedy it. The bias in configuration sampling is harmful for blind evolution to increase fitness and complexity, because the bias prevents complete configuration sampling. The conventional concept of diversity is actually the degree of the unbiasedness in configuration sampling. The blindness of evolution answers why diversity, a property without involving net fitness gain, is beneficial to life. The degree of the unbiasedness in configuration space sampling is one of the two essentials of evolvability; the other one is the resolution and efficiency of natural selection (chapter V).

It has already been noticed that evolutionary biases, such as mutational robustness and thermostability, constrain evolution, as the ridges on the landscape blocks evolutionary exploration [11][12][13][14][15][16] .

However, those findings are not linked to the blindness of evolution to explicitly conclude that bias is harmful to the increase of the fitness and complexity of evolution. As a result, the understanding of evolutionary bias is unclear. In the conventional view, a process of evolution is not clearly distinguished from the associated bias. For example, mutational bias is often confused with mutation per se and hence is consider introducing novelty for evolution 17 . Mutation generates novelty/diversity, but mutational bias only makes the available paths less than the possible paths and thus reduces the novelty/diversity.

It is understandable that completely unbiased sampling is only an unattainable ideal in real condition. Can evolutionary sampling approach unbiasedness close enough that sampling bias is reduced to a harmless level? The answer is no, because there is an intrinsic and universal conflict between the unbiased sampling and the functional activity required by terrestrial life.

The existing configurations of macromolecules and their organization are not random samples of the configuration space. Sampling configuration space by an evolutionary entity is performed by its internal physicochemical processes under environme

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