Copyright © by Tienzen (Jeh-Tween) Gong
原文见：https://tienzengong.wordpress.com/2014/10/11/intelligent-evolution/

Darwin’s theory drove off the ‘Divine story’ in the Christian Genesis which is indeed a total nonsense. In recent years, those fundamentalist Christian (FC) used an ‘intelligent design’ story to replace the creationism.

For the modern biologists, they ‘constructed’ modern evolutionary synthesis (MES). Then, all new discoveries (selfish-genes, horizontal gene transfers, genetic assimilation, the Hardy–Weinberg principle, Hox genes, punctuated equilibrium, etc.) are packed into this MES. That is, any word (such as, intelligence) used by FC is a no-no for biologists.

While the ‘intelligent design (advocated by the “Discovery Institute”)’ is totally nonsense, the packing of some major differences and conflicts between the newly discovered biological facts into MES is also powered by the ideology. Thus, this book is examining the science of those newly discovered biological facts and their underlying principles.

The current state of this biological sphere is definitely reached by evolution, not by any divine-design. But, is this evolution solely powered by a ‘blind’ process?

If yes, then what is the mechanism for giving rise to the intelligence?

If no, is the ‘intelligence’ embedded in the laws of nature-physics? If yes, then show me. If the ‘intelligence’ is embedded in the laws of nature-physics, the evolution of biological sphere becomes the ‘expression’ of that embedded intelligence. I should first review the Darwinism proper.

Section one: Darwinism ‘proper’ consists of two parts

Part one: the current state of lives is reached via ‘evolution’, not from any strokes of Divine-creation (or divine-intelligence design).

Part two: the evolution mechanism is ‘Nature Selection’ which encompasses the following attributes and definitions.
a. Fitness: not about the power of an individual in the population or in the ecosystem but is all about how many ‘offspring’ that it can produce. Thus, a King of an Empire will be not ‘fit’ if he has no offspring.

b. Selection: an external force which weeds out the not-fit while perpetuates the fit (having more offspring).

c. Selection unit: individual organism, not group nor species.

d. Selection pressures (challenges): disease, climate change, shift in the available food source or isolation, etc.

e. Phenotype: the complete set of observable traits that make up the structure and behavior of an organism [note: many aspects of an organism’s phenotype are not inherited; organismal phenotypes are not uniquely determined by their genotypes].

f. Phenotype variation: nature selection acts on the phenotype. Without phenotype variations, there will be no nature selection.

g. Blindness: nature selection pressure is a blind challenge, without a teleological intention.

h. Continuity and gradualism: Darwin noted in the margin of his 1844 Essay, “Better begin with this: If species really, after catastrophes, created in showers world over, my theory false.”

i. Adaptation: In Darwinism, the natural selection is ‘claimed’ to be the only known cause of adaptation, for being better ‘fit’, having more offspring. [Note: other definition (not Darwin’s) states that ‘adaptation’ is the process that makes organisms better suited to their habitat.]

j. Speciation: when the nature selection selects enough better ‘fit individuals’, the phenotype of the population could be significantly different from the old population. This new population could become a new species, and this is called speciation by nature selection.

In a nutshell, the Darwin-mechanism (DM) is {nature selection pressure acts on phenotype of ‘individual’ of a population gradually and leads to ‘speciation’}.

Section two: the sources of genetic variations and the effectiveness of mutation

While the Darwinism-proper is hinged completely on the heredity (being having more offspring), Darwin did not know anything about the genetics. When the Gregor Mendel genetics was better understood in 1930s, the relationship between the phenotype and the genotype was understood with the following points.
1. The same gene could produce different phenotypes, such as the ecotype, etc.
2. The same phenotype could be produced by different genes, such as the warm blood of birds and mammals.

Thus, the phenotype of an individual is not directly connected to the inheritance, and the claim that the ‘nature selection’ acts on phenotype and leads to speciation is not true. Darwin was simply ignorant about the inheritance-mechanism, and the DM is simply wrong. But some pioneers in the field of population genetics (such as J.B.S. Haldane, Sewall Wright, and Ronald Fisher) ‘claimed’ that mutation on gene is mainly caused by the nature selection pressure, and thus ‘nature selection’ is still the only cause for adaptation. This ‘claim’ became the ‘modern evolutionary synthesis’. But, the ‘modern evolutionary synthesis’ was formulated at the time that ‘molecular biology’ was not known at all.

In molecular biology, the gene-mutations are mostly caused by the gene-dynamics, not by ‘nature-selection-pressure’, and the following is the list of gene-mutation mechanisms.

A. Spontaneous mutations (molecular decay), random mutations arise spontaneously; stochastic and typically occur randomly across genes.

B. Mutations due to error prone replication by-pass of naturally occurring DNA damage (also called error prone translesion synthesis: errors in DNA replication, duplications, insertions, deletions, inversions, and translocations). But, DNA repair mechanisms are able to mend most changes before they become permanent mutations, and many organisms have mechanisms for eliminating otherwise-permanently mutated somatic cells.

C. Errors introduced during DNA repair, errors in the process of replication, or from the insertion or deletion of segments of DNA by mobile genetic elements.

D. Induced mutations caused by mutagens (typically caused by radiation or chemical mutagens). Scientists may also deliberately introduce mutant sequences through DNA manipulation for the sake of scientific experimentation.

E. Gene recombination can also generate particular types of mutations.

Except the induced mutation which subjects to some external (environmental) factors, all the mutation-mechanisms above are well-defined genetic-dynamics, and they are definitely not the results of the Darwin-mechanism (blind selection).

Furthermore, most induced and spontaneous mutations are neutral and deleterious; that is, it will not lead to a better fitness for the ‘individual’ and will not be ‘selected’ by the DM. Thus, this ‘effectiveness’ of mutation on any organism can be expressed by a ‘Bio-evolution-inertia’ equation:

Bio-evolution- inertia: measured by the complexity of the organism; the more complex, the more inertia. The effectiveness of mutation (EoM) is much less for higher inertia. That is,

EoM = P/I
P, the probability of a mutation having effect on a genome.

I, the inertia. I = 1 for single cell genome. For every additional bio-mechanism above single cell (such as becoming multicellular; with differentiations; with complex organs, etc.), it increase a factor of ‘10’ for every addition complexity. So, for differentiated multicellular organism, I = 10^3. For a multicellular organism which has five internal organs, the I = 10^(3 + 5), etc.

For single cell organism, the EoM = P/1 = P
For higher level organism {with n (complexity) = 8}, EoM = P/I = P/10^8. A mutation for this organism has very little effect.

Then, for the high level organism (such as mammals) which reproduces with Meiosis process, it divides its body into two parts: the soma and the germline. In general, the mutations in the somatic cells will not directly link to the germ cells. That is, the majority of the mutations in this organism is not inheritable. So, the nature-selection-pressure of Darwin-mechanism has very little effect on this organism.

With these genetic dynamics, any claim that the ‘mutations’ can lead to Darwin-mechanism is not science. That is, most of the ‘variations’ (required for selection) are having nothing to do with the Darwin-mechanism. Again, all the known ‘speciation-mechanisms’ are in conflict with the Darwin-mechanism, such as:
One: genetic drift (with Founder effect).

Two: hybrid speciation.

Three: horizontal gene transfers.

Four: allopatric speciation.

Five: mutations.

Six: genetic assimilation.

Section three: the global biological evolutionary forces vs the Darwin-mechanism

Then, most of newly developed evolutionary factors are in conflict with the Darwin-mechanism, such as:

First, the selfish genes (will definitely fight against the nature selection pressure).

Second, the punctuated equilibrium (definitely not gradualism).

Third, genetic assimilation: some novelties are ‘acquired’ by genes, not selected externally.

Fourth, toolbox genes (such as, the Hox genes): the expressions of gene are ‘regulated’ internally, not selected externally.

While Darwin-mechanism can explain some species/sub-species movements, there is not a single evidence to show that Darwin-mechanism is the cause of any taxonomic diverging point (not a single one, either in the fossil records or in the molecular biology). In fact, all (not a single exception) biological evolutionary mechanisms do not depend on the Darwin-mechanism.

First, all organisms survive and evolve as a species, not as an individual.
One, the majority of individuals of social-insects (accounts for the half-biomass of all insects) gives up the right of reproduction. The Darwin-mechanism is simply wrong in this case. One example is the existential introduction (being wrong).

Two, all (not a single exception) sexual organisms give up the right for all ‘individuals’ to reproduce itself. The survival of the organisms is a group effort (with partners). The Darwin-mechanism is wrong again in this case. Two example is the existential generalization (being wrong again).

Three, there is a Large Number Law. For a large number population, a few great individuals will have no power to change the ‘average’ of a population. In fact, any novelty which is shared by less than 14% (1/e^2) of the population might not have a chance to become a trait for the population. The Darwin-mechanism (selection on individual) for a large population is simply a mathematical nonsense.

Second, the entire biosphere evolves with two ‘constructions’.
One, the construction of an ecosystem:
a. Biologization: converting the inorganic compounds into biological substances, mainly done by bacteria or archaeans.
b. Global oxygenation: this started with oxygen-producing bacteria and was accelerated with oxygenic photosynthesis.
c. The fungi rescue of wood crisis: restoring the greenhouse gas (stabilizing the globe temperature) and provided space and food for land animals.

It is this constructed ecosystem providing a platform for all lives to survive and to evolve. And, this construction had nothing to do with the Darwin-mechanism.

Two, the construction of the diverse life-forms.
1. Started from single cell: bacteria or archaeans (rising mechanism is unknown). But, it can form a colony.

2. Multicellular organism (non-differentiated): the ubiquitous challenge for anything (such as a colony) growing in size beyond the scale of diffusion can be eased by movement of medium throughout the biofilm, such as forming a tube, etc. This follows the physics and topology totally and is absolutely nothing to do with the Darwin-mechanism (a blind selection).

3. Multicellular organism (differentiated): again, the ‘individual’ cell gives up the right to survive and to reproduce ‘alone’. It plays the game of ‘group surviving and evolution’. Although all the cells in the differentiated organism are having the identical genome, its genes have a set of dip (dual in-line package) switches, and these dip switches are turned on/off by toolbox genes (such as the Hox genes). Again, this multicellular construction (developing the dip switches and toolbox genes) has absolutely nothing to do with the Darwin-mechanism.

This diversification is done in accordance of laws of physics and topology, having nothing to do with the Darwin mechanism.

Three, the Mass Extinction: it ‘reshapes’ the ecosystem and is very important to the evolution of lives. Again, this major evolutionary force is absolutely nothing to do with the Darwin-mechanism.

I have showed a 4-lock litmus test for physics. We now know that there are 4-locks which lock this universe in ‘shape’.

Lock-one: Cabibbo angle (13.5 degrees), Weinberg angle (28.75 degrees), [(1/Alpha) = 137.0359 …]

Lock-two: Planck data (dark energy = 69.2; dark matter = 25.8; and visible matter = 4.82)

Lock-three: the pegs-lock which can only be opened by the exact pegs when they are inserted into the peg-key-holes. There are 48 peg-key-holes in this physical universe, and every peg is distinguished with a set of ‘name-codes’. The 48 matter particles form this pegs-lock.

Lock-four: {delta P x delta S > ħ} lock.

That is, anything which is not key(s) for these 4-locks cannot be a correct theory for the Nature-physics.

Of course, biology can never produce keys for these 4-locks. But, there are two biologic locks: the intelligence and the consciousness which are empirical facts as biological traits. In fact, the Nature-physics must encompass some mechanisms to give rise to these two bio-locks. Then, the valid bio-evolution also must provide the keys for these two bio-locks.

It will be a very intelligent guess that a ‘blind’ process (such as the Darwin-mechanism) will not and cannot give rise to either intelligence or consciousness. Then, there is a ‘semantic’ issue too. A selection can be made internally or externally. For an external selection, the contestants need not to have any internal choosing power while they must be different (with phenotype variations in the case of Darwin-mechanism) by definition. On the other hand, the internal selection requires an internal choosing power (ICP), and this ICP cannot be blind. So, the surviving after an external selection is not an adaptation as it possesses the required attributes for the selection pressures before the selection. For surviving after an internal adjustment (choices), it has overcome the new challenge by ‘adapting’ it by making some choices. So, the Darwin-language that {nature selection is the only way of adaptation} is semantic wrong, totally nonsense.

Section four: the evolution of complexity vs Darwin mechanism

Again, the semantic meaning of ‘selection’ is that the unselected must be forced out or abandoned (that is, extinction in terms of species). Although there are many extinct species fossil records, most of them went extinct during the mass extinctions. The extinctions of Neanderthals and Denisova hominin could be caused by nature disasters, major wars or assimilated by Homo sapiens. In fact, there is not a single fossil record showing that a species went extinct because of the Darwin-mechanism (the nature-selection-pressure which acted on phenotypes of some ‘individuals’ of a population led to the extinction of a mother or a sister species). While the fossil records might not be a good measurement for this ‘selection’ issue, the unfitted bio-mechanism should be abandoned under the Darwin-mechanism. But, while the bio-mechanisms do progress step by step, none of the old steps is abandoned. The following is a brief outline.

One, single cell species (bacteria or archaeans) replicate via binary fission, the simplest ‘division’ mechanism.

Two, eukaryotes could be arisen through fusion of an archaean and an eubacterium, the simplest ‘fusion’ mechanism. [Note: while eukaryote is an evolution advancement, the prokaryotes (bacteria or archaeans) were not ‘selected out’. In fact, Eukaryotes represent only a tiny minority of all living things.]

Three, simple eukaryote replicates via mitosis (asexual) process. Again, the binary fission is not selected out.

Four, meiosis process could be evolved from mitosis. Yet, mitosis is not only not selected out but is kept in all sexual species.

Furthermore, all these evolutions are having nothing to do with the Darwin-mechanism (the nature-selection-pressure which acted on the phenotypes of some ‘individuals’ of a population). Each one of these processes is the results of physics laws, topology and economics (cost and redundancy).

Binary fission (tearing self-apart) is by all means an entity (self) killer, but it increases the chance of survival of ‘species’. Mitosis doubles itself in biomass before tears itself apart, and this process not only increases the ‘chance’ of species survival but increases the biomass for the species. Meiosis divides its ‘information’ into four parts, that is, the life-information of a species will not be placed in one basket (significantly increase the preservation of its life-information). This is also a great strategy to fend off the hackers and keep its life-information secure. Thus, for facultative sex species, it replicates asexually (with mitosis) in general but turns into sexual reproduction (meiosis) during ‘stressful’ situation.

So, the survival of the species is enhanced with three evolutionary advancement.
1. Increase the ‘number’.
2. Increase the ‘biomass’.
3. Preserve and secure the ‘life-information’.

The evolution of these bio-mechanisms shows the following points:
a. The evolution ‘unit’ is species, not individual.

b. The ‘end objective’ for the evolution is to preserve and to secure the ‘life-information’ of the species.

c. The ‘highest and best’ mechanism for reaching this end is the meiosis process (sex-mechanism). [Note: the sex-mechanism forces every ‘individual’ of the species giving up the right to replicate itself. Every ‘individual’ needs a ‘partner’ from the species in order to produce its offspring.]

Processing ‘information’ is intelligence by definition. Now, all bio-mechanisms (generating variations, regulating the expressions of genes, developing morphological and physiological structures, developing life-information preserving and security mechanisms, etc.) are done with ‘well-defined’ genetic dynamics, not caused by any ‘blind’ external selection. These well-defined mechanisms are ‘adapted’ (chosen) by organisms. The blind external pressures are at best acting as ‘challenges’ to these organisms. That is, the evolution force in biology is ‘intelligence’, not an external blind selection. The detailed discussion on this is available at http://sexevolution.wikia.com/wiki/Sexevolution_Wiki .

Section five: conclusion

One, the genetic variations of a species (required for evolution) are produced by a set well-defined genetic dynamics (genetic drift (with Founder effect); hybrid speciation; horizontal gene transfers; allopatric speciation; mutations; genetic assimilation, the Hardy–Weinberg principle, etc.), not by any external blind selection.

Two, the major global evolution stages (Biologization; Global oxygenation; The fungi rescue of wood crisis; etc.) are done at inter-species levels, not by any external blind selection.

Three, the major developments of morphological structures {single cell; multicellular (un-differentiated); multicellular (differentiated), etc.} are following the laws of physics and topology, not by any external blind selection.

Four, the major life-information preserving strategies {binary fission (increasing the ‘number’); mitosis (increasing both the number and the biomass); meiosis (increasing the number, the biomass and reducing the risk of putting all in one basket by increasing the ‘variations’)} are acts of ‘intelligence’, not by any external blind selection.

Five, all the above are done at species and inter-species level. The selection of any (or some) individuals has no effect on evolution unless the number of those selected individuals goes over a threshold (about 14% [1/e^2] of the population). Yes, this threshold can be reached easier when there is a ‘population bottleneck’. Yet, at this threshold, the genetic drift, founder’s effect and genetic assimilation become the dominant evolution forces, again not by any external blind selection (as the population bottleneck could be reached by happenstance [such as, isolation], not by any selection).

Six, at a giving environmental location, there are zillions different organisms with different phenotypes. That is, all those different phenotypes are adapting the same nature-selecting-pressure, and no phenotype was selected-out by any external blind selection.

Seven, for a high level sexual organism (such as mammal), its morphological body is divided into two parts: the somatic and the germline. The external blind pressure is in general acting on the somatic cells. The mutation of the somatic cells can often become cancerous, but this mutation is in general isolated from the germline cells. That is, the mutation of somatic cells is in general not inheritable. On the other hand, when some novelties are ‘acquired’ by the somatic cells, they could be inheritable by genetic (somatic) assimilation. There is a somatic/germline communication pathway. Yet, this mutation/acquiring distinction is a well-defined internal ‘choice’. The bad and harmful somatic mutations will not be transmitted to the germline.

Eight, while Darwin-mechanism (the nature-selection-pressure which acted on phenotypes of some ‘individuals’ of a population) could lead to a new ecotype (subspecies), there is no single taxonomic diverging point which is caused by the Darwin-mechanism (at least no single evidence [fossil or else] show it being otherwise).

With the above, it is very obvious that the Darwin-mechanism (the nature-selection-pressure which acted on phenotypes of some ‘individuals’ of a population) plays a very minimal (minimal, …, minimal, …) role in the ‘global biological evolution’. It is a wrong mechanism for describing the biological evolution. Claiming that Darwin-mechanism is the ‘major’ evolution force and the ‘only’ mechanism for adaptation is a total nonsense.

The evolutionary ‘adaptations’ are intelligent choices to perpetuate the life of species (by preserving and securing its life-information, the genome). In fact, this evolutionary process leads to the full expression of ‘intelligence’. Excluding the nature events (repeated Mass-Extinctions), the biological evolution is powered by ‘intelligence’ (increasing the number, the biomass, the security via variations, etc.). Of course, this ‘intelligence’ is not the one of Christian-intelligent-design (the teleological argument) but is embedded in the base of nature-physics laws (seehttp://www.prequark.org/Biolife.htm ).

Note, add on April 20, 2016: Darwin’s original work is a mediocre scientific work (being mostly wrong). But, the MES (modern evolutionary synthesis) which tries to elevate Darwinianism (especially the nature selection) to the status of G0d is the worst shamelessness in human history, see https://tienzengong.wordpress.com/2016/04/20/deaths-of-two-gods/ .

Note: Sean Carroll had an article “The Evolution of Evolution: Gradualism, or Punctuated Equilibrium? (http://www.preposterousuniverse.com/blog/2014/10/10/the-evolution-of-evolution-gradualism-or-punctuated-equilibrium/ ) asking “Is it [evolution theory] basically in good shape: simply requiring a natural amount of tweaking and updating over time, or is revolutionary re-thinking called for?”