A comprehensive evolutionary theory deduced from thermodynamics

Studies on evolution have made significant progress in multiple disciplines, but evolutionary theories remain scattered and controversial. Here we deduce that, thermodynamically, many carbon-based entities (CBEs) on the Earth tend to absorb energy from widespread relatively temperate heat streams on the Earth flowing from the solar, geothermal, and other energy sources, to form higher-hierarchy CBEs (HHCBEs). This has been the driving force of evolution leading to accumulation and regeneration of HHCBEs for billions of years. We further deduce three progressive mechanisms of evolution from the driving force. We hence establish the CBE evolutionary theory (CBEET) which suggests that evolution driven hierarchy-wise by thermodynamics favors fitness and diversity. The CBEET provides novel explanations for origin of life (abiogenesis), macroevolution, natural selection, sympatric speciation, and animal group evolution in a comprehensive and comprehensible way. It elucidates that altruism, collaboration, and obeying rules with increasing freedom are important throughout the CBE evolution. It refutes thoroughly the notion that negative entropy leads to order in biology which is distinct from order in thermodynamics. It integrates with research advances in multiple disciplines and links up laws of physics, evolution in biology, and harmonious development of human society.


Introduction
Charles Darwin's evolutionary theory built on natural selection is a breakthrough in science. This theory was updated with the Modern Synthesis last century, which changed the definition of natural selection from "survival of the fittest" to "gradual replacement with those carrying adaptive mutations" [1][2][3]. Thereafter, the Modern Synthesis has met challenges from research advances in molecular biology and epigenetics, and has not integrated with these challenges [1][2][3][4][5][6][7]. Moreover, the Modern Synthesis is unable to interpret the mechanisms for origin of life and macroevolution [1][2][3].
Here we deduced a comprehensive evolutionary theory, which can integrate with research advances in multiple disciplines and interpret the mechanisms for origin of life and macroevolution. This theory relies on extrapolation from microevolution in determining the theory's details, and deduction from thermodynamics in determining the theory's framework. This theory is termed the CBE evolutionary theory (CBEET), where CBE denotes carbon-based entity. CBEs include some small molecules (e.g. methane and ethanol), middle organic molecules (e.g. amino acids and nucleotides), large organic molecules (e.g. proteins and nucleic acids), and organisms (e.g. bacteria, animals, and plants). CBEs have hierarchies, and large organic molecules are higher-hierarchy CBEs (HHCBEs) compared with middle organic molecules, but they are lower-hierarchy CBEs (LHCBEs) compared with organisms. The differences between the CBEET and previous theories are outlined in Figure 1 and listed in Table 1.

Definitions
Autocatalysis: the phenomenon that the product of a reaction has the activity to catalyze the reaction to produce the product itself.
Multiple other concepts including altruism, CBE, HHCBE, LHCBE, the extrapolation logic, the deduction logic, the backstepping logic, microevolution, macroevolution, natural selection, positive selection, negative selection, punctuated equilibrium, chemical evolution, animal group evolution, and cultural evolution are defined at relevant sites in the main text. [17,18] The first law of thermodynamics: increase of internal energy of a closed system is equal to the work the outside gives to the system plus the heat the outside gives to the system. and blue arrows represent the driving force mechanism, the structural mechanism, and the natural selection mechanism, respectively. Table 1. Differences between the evolutionary theory CBEET and previous theories.

Topics Previous theories CBEET views
Logic Extrapolation from microevolution, like using fishes' eyes to reveal the structure of a river Extrapolation from microevolution (like using fishes' eyes to reveal details of a river) and deduction from thermodynamic laws (like using satellites to reveal the panorama of a river) The driving force of evolution Natural selection, genetic drift, mutation, or competition (none of them provide energy) The tendency of carbon-based entities (CBEs) to absorb energy from heat streams on the Earth to form higher-hierarchy CBEs (HHCBEs) The second law of thermodynamics: heat can spontaneously flow from a hotter body to a colder body, and cannot spontaneously flow from a colder body to a hotter body; the entropy of an isolated system never decreases over time.
The third law of thermodynamics: the entropy of a system approaches a constant value as its temperature approaches absolute zero, and the entropies of perfect crystals at absolute zero temperature are zero.
The Clausius inequality of entropy: dS ≥ δQ/T, where dS, δQ, and T denote changes of the entropy of a closed system, heat absorbed by the system from the outside, and absolute temperature, respectively.

Deduction and Validation
Deduction of the CBEET was detailed below. The major views of the CBEET are validated through one or two ways: whether the views can explain some phenomena which have not been well explained; whether the views reflect the reality better.

Deduction of the driving force of evolution
The earth's surface has widespread relatively temperate heat streams flowing from the solar, geothermal, and other energy sources. The earth, as a rare habitable planet in astronomy, is in a suitable orbit and receives temperate sunlight, which leads to temperate heat streams on the Earth for billions of years [14]. Meanwhile, many sites on the Earth, particularly at hydrothermal vents, have emitted geothermal energy for long periods [15,16]. The huge amount of water on the Earth and the atmosphere of the Earth regulate these energy flows through evaporation, diffusion, and rainfall, making them more temperate, last longer, and distributed more widely.
The widespread relatively temperate heat streams on the Earth trigger many changes and movements. According to the second law of thermodynamics (i.e. heat can spontaneously flow from a hotter location to a colder location) [17,18], stones can spontaneously absorb heat from these heat streams and increase their temperatures, and many CBEs can spontaneously absorb heat from these heat streams to form HHCBEs through covalent bonds, partially because carbon atoms are apt to form covalent bonds after absorbing heat [19]. Meanwhile, many CBEs are mobile, they can hence meet and collaborate with other CBEs to form HHCBEs not through covalent bonds. For example, lipid molecules can form bilayer membranes and ants can form ant groups in this way, where energy required for the movement of these CBEs is directly or indirectly from the widespread relatively temperate heat streams on the Earth.
Although all HHCBEs shall degrade sooner or later, many HHCBEs are relatively stable and can be accumulated. HHCBEs have hence been formed, degraded, regenerated, and accumulated at a myriad of places for billions of years, due to the widespread relatively temperate heat streams on the Earth, which constitutes the evolution of CBEs (Figure 1). Therefore, the tendency of CBEs on the Earth to absorb energy to form HHCBEs, is the driving force of evolution.
Initially, the driving force of evolution was from solar energy and geothermal energy. Later, with the increase of organisms on the Earth, biological energy became a source of the driving force of evolution. This is of paramount significance for animals which can actively obtain energy and materials from other organisms. Energy from coal, petrol, water flow, and even nuclear power has been utilized by humans for the development of human society.
The above driving force can explain why non-living organic molecules evolved to lives, why unicellular organisms evolved to multicellular organisms, and why ectotherm animals evolved to warm-blooded animals, because all these three macroevolution events were the processes where CBEs absorbed energy and formed HHCBEs. They cannot be well explained with previous theories including natural selection, because none of the processes added fitness to CBEs [3][4][5]10,20,21].
During the whole history of the Earth, the amount and the diversity of HHCBEs including organisms on the Earth are generally increasing [22]. However, meteorite impacts, huge volcano eruptions, long glacial periods, and other catastrophes can destroy the temperate heat streams on the Earth and structures of many organisms [23][24][25]. Consequently, the amount and the diversity of organisms could decline greatly for these catastrophes, sometimes leading to mass extinctions [23][24][25].

Deduction of the progressive mechanisms of evolution
Three progressive mechanisms of evolution were deduced from the driving force of evolution. The first is termed the driving force mechanism shown with the red arrows in Figure 1, where the driving force of evolution directly raises the amount of HHCBEs and increases the structural complexity and hierarchy of CBEs. The second is termed the structural mechanism shown with the green arrows in Figure 1, where CBEs with increased structural complexity and hierarchy spontaneously obtain some complicated functions, due to collaboration and altruism of the components inside HHCBEs (altruism is the action supporting the existence and production of other entities). For example, when green fluorescence protein is formed by amino acids, it obtains spontaneously the function of emitting green fluorescence, due to collaboration of its amino acid components which all "sacrifice" their freedom to "work" for the protein.
The third mechanism is termed natural selection shown with the blue arrows in Figure  1, which leads to increase of the diversity and the fitness of CBEs, as detailed below.
As shown in Figure 1, the driving force of evolution leads to formation and accumulation of HHCBEs. The formed HHCBEs shall degrade into LHCBEs sooner or later, due to outer factors (e.g. fire burning) or inner factors (e.g. natural aging) [1,2]. Therefore, lots of CBEs on the Earth are in the cycle of formation and degradation of HHCBEs, leading to regeneration of HHCBEs. Regenerated HHCBEs usually carry some changes which influence the overall fitness of HHCBEs. Some regenerated HHCBEs are formed faster and/or degrade more slowly than some other HHCBEs, resulting from the overall fitness of HHCBEs.
Natural selection is defined in the CBEET as survival of fit HHCBEs and elimination of unfit HHCBEs as per their overall fitness. The overall fitness of HHCBEs is determined not only by collaboration and altruism of components of HHCBEs, but also by the environment. For example, great fitness in a hot rainforest can be a terrible burden in a cold desert. Moreover, when the environment is comfortable, the fitness threshold of natural selection is low, which allows survival of HHCBEs carrying various changes [26]. In contrast, the fitness threshold of natural selection increases greatly when a catastrophe occurs, which can lead to mass extinction of organisms including those quite fit previously [23][24][25].
The CBEET definition of natural selection maintains the core feature of the concept of natural selection in Charles Darwin's evolutionary theory and in the Modern Synthesis [3][4][5]: fitness of organisms increases over time because natural elimination of the unfit, making unfit HHCBEs survive less time and/or reproduce fewer progenies.
The CBEET definition of natural selection is also different from previous definitions in multiple aspects. First, the CBEET definition covers non-living CBEs and can be extended to origin of life. Second, as shown in Figure 1, complicated functions, fitness, and order of HHCBEs are all based on collaboration and altruism of components of HHCBEs, and the collaboration and altruism are under natural selection and influenced by changes of HHCBEs. Moreover, all these processes can be deduced from laws of thermodynamics. Therefore, unlike that natural selection in previous theories is supported by itself and hence suspected of tautology [27], natural selection in the CBEET is supported by structures of HHCBEs and laws of thermodynamics. Third, the CBEET definition (survival of fit HHCBEs) is less harsh and more inclusive than "survival of the fittest" in Charles Darwin's theory and "gradual replacement with those carrying advantageous mutations" in the Modern Synthesis [1][2][3][4], and the CBEET definition reflects the reality correctly because research advances in molecular biology suggest that most genomic changes are likely neutral without increase in fitness [3][4][5]10,12,28]. Fourth, the CBEET definition of natural selection highlights the overall fitness because the reality is that the existence of an HHCBE is determined by its overall fitness, although a certain trait may play a leading role in the overall fitness of an HHCBE. Therefore, the CBEET allows an organism to have disadvantageous traits, if its overall fitness is adequate. For example, antelopes are less strong than buffaloes to fight against carnivores, but they run fast and have other advantages, making them have adequate fitness in general. This suggests a novel mechanism of sympatric speciation, because multiple combinations of traits can all have adequate fitness in occupying the same ecological niche in the same area. Previously, only the mechanism for sympatric speciation targeting different ecological niches in the same area through diverging selection pressure has been proposed [3]. Fifth, genetic mutations, epigenetic changes, and uninheritable changes all influence the overall fitness of HHCEBs, and they are thus all under natural selection. For example, vaccination which is uninheritable makes many animals survive viral infections and pass the relevant natural selection. Sixth, previous definitions usually assume that mutations under natural selection occur randomly. Now it has been known that many organisms have the complicated function which makes many mutations occur not randomly, as evidenced in the evolution of microbial genomes and mammalian immunoglobulin genes [9,29].
Organisms accumulated much fitness through long geological periods. Therefore, organisms are under both positive selection (supporting those changes which add fitness) and negative selection (inhibiting those changes which reduce fitness) [30]. Because natural selection "selects" organisms as per their overall fitness which is influenced by all genomic sites and all traits, all genomic sites and all traits are under both positive selection and negative selection [30,31]. Accordingly, natural selection functions extensively in evolution. Moreover, a conserved trait or genomic site without change during a long geological period does not mean that the trait or site is not under natural selection, but likely under strong negative selection [30].
Natural selection in the CBEET targets all hierarchies of CBEs. For example, giraffe groups, giraffe individuals, and cells, large organic molecules including genes in giraffes are all under natural selection along with giraffe groups. If a giraffe group is favored by natural selection, the LHCBEs involved in the formation of the giraffe group, including genes of the giraffe group, are also favored by natural selection.
Natural selection, mutation, genetic drift, and competition were claimed to be the driving force of evolution [3][4][5]20,28,31]. These "driving forces" are not directly related to energy, and they are largely mechanisms or processes of evolution. The role of energy in biological evolution was highlighted previously [32,33], but energy was not associated with the driving force of evolution. Here the driving force of evolution from thermodynamics provides energy for the evolution of CBEs. Moreover, all the three progressive mechanisms of evolution are derived from the driving force of evolution (Figure 1). Therefore, the driving force of evolution plays the first leading role in evolution, although natural selection functions extensively in evolution and remains a leading role in evolution.

Deduction of the process of evolution
The driving force of evolution from thermodynamics leads to formation and accumulation of HHCBEs hierarchy by hierarchy. For example, amino acids, nucleotides and other middle organic molecules could not bypass the intermediate hierarchy of large organic molecules to form unicellular organisms, and large organic molecules could not bypass the intermediate hierarchy of unicellular hierarchy to form multicellular organisms. Accordingly, as per the backstepping logic (i.e. if hierarchy A exists, the hierarchies lower than hierarchy A should have existed in advance), there should be the following seven major steps constituting the whole evolution of CBEs on the Earth (Figure 1).
Step 7, many animal individuals of the same species collaborate with each other and form animal groups, which include groups of bees, ants, humans, and many other animals. Animal groups have novel functions which cannot be fulfilled by animal individuals. For example, some ant groups plant fungi for food, which cannot be fulfilled by ant individuals [34]. Some animal groups are eusocial, where some individuals reduce their own lifetime reproductive potential to raise the offspring of others. Many other animal groups are presocial, where the parents take care of their own progenies [46]. Although presocial species are much more common than eusocial species, eusocial species have disproportionately large populations [35].
Step 6, many cells collaborate with each other and form multicellular organisms, which include fungi, plants, and animals. Multicellular organisms have novel functions which cannot be fulfilled by any cells (e.g. birds can fly faraway which cannot be fulfilled by any cells).
Step 5, many complexes of large organic molecule aggregates collaborate with each other and form the first batch of unicellular organisms, which are the units having the complicated functions of self-replication via catalysis (for efficiently generating HHCBEs) and self-protection (for efficiently maintaining HHCBEs). The first batch of unicellular organisms emerged at a tiny possibility, and this tiny possibility was realized through the effect of vast spaces and vast time.
Step 4, many large organic molecule aggregates collaborate with each other and form complexes of large organic molecule aggregates which, like organelles in the unicellular organisms, have some complicated functions (e.g. synthesis of proteins).
Step 3, many large organic molecules collaborate with each other and form large organic molecule aggregates (e.g. lipid bilayer membranes and channels allowing ions to pass lipid bilayer membranes) [36]. From this step to the seventh step, energy is not always required to form chemical bonds, but is required for the movement of CBEs to meet and collaborate with other CBEs.
Step 2, many middle organic molecules (e.g. amino acids, nucleotides, glucose) collaborate with each other and form proteins, nucleic acids, polysaccharides, and other large organic molecules. Before origin of life, few mechanisms were available to direct the synthesis of large organic molecules according to certain orders, and so proteins, nucleic acids, lipids, polysaccharides were produced with few repetitions, and thus the products were of a myriad of diversity. These highly diversified large organic molecules could provide abundant candidates for forming HHCBEs in Steps 3−7. This was beneficial for complexes of large organic molecule aggregates to form unicellular cells at a tiny possibility.
Step 1, many small molecules (e.g. CO2, CH4, H2O, H2S) collaborate with each other and form middle organic molecules (e.g. amino acids, nucleotides, glucose). This step has also occurred on other planets, and lots of middle organic molecules were sent to the Earth by meteorites [37].
Steps 1−5 constitute chemical evolution which is also termed abiogenesis or origin of life. Steps 5−7 constitute biological evolution excluding abiogenesis.
Step 7 constitutes animal group evolution including the development of human society.
Steps 1−5 suggest that, before origin of lives, there were five successive and overlapping worlds: the world of small molecules, the world of middle organic molecules, the world of large organic molecules, the world of large organic molecule aggregates, and the world of complexes of large organic molecule aggregates. Compared with previous theories which emphasize the special role of RNA and some organic molecules with the function of autocatalysis [38,39], the CBEET highlights collaboration and altruism of various molecules.
Obeying rules is embodied throughout the evolution of CBEs. For example, molecules should obey some rules in cells, and cells should obey some rules in multicellular organisms. Individuals in animal groups should obey some rules, including that lion kings should take their responsibility to fight against invaders, and worker bees should work diligently all days for their groups, and drivers should obey traffic rules. Obeying rules is the basis of collaboration and altruism of inside HHCBEs which, in turn, determine the overall fitness of HHCBEs. Additionally, freedom of components inside HHCBEs increases with the CBE evolution, because as for the seven steps given above, components inside HHCBEs are restricted within molecules (Steps 1 and 2), within molecular aggregates or complexes (Steps 3 and 4), within cells (Step 5), within multicellular organisms (Step 6), or within certain areas (Step 7).

Significance for human society
The CBEET aids the harmonious development of human society. First, previous evolutionary theories stress selfishness, competition, and elimination of those less fit in certain traits [1][2][3][4][5]24]. Particularly, social Darwinism which was established on the wrong view of "survival of the fittest" in the fierce competition [1][2][3][4], has been employed to justify authoritarianism, eugenics, racism, imperialism, fascism, and Nazism [40]. In contrast, the CBEET not only emphasizes selfish (self-reproduction and self-protection), fitness, and competition, but also emphasizes co-existence of many differences and changes if the relevant HHCBEs have adequate fitness. This suggests that we should respect diversity in races, culture, and management systems. Second, previous evolutionary theories stress genetic differences, while the CBEET not only emphasizes genetic differences, but also emphasizes the effects of endeavor to increase fitness, even if the effects are uninheritable. Third, previous evolutionary theories stress advantages of a single trait, while the CBEET emphasizes overall fitness. This is important for humans in making correct decisions. Moreover, the CBEET demonstrates that collaboration, altruism, and obeying rules with increasing freedom are all fundamental throughout the evolution of CBEs including development of human society.

Significance in physics
The CBEET refuted the notion that negative entropy leads to order in biology. Evolution leads to increase of order in biology, which seems contrary to the second law of thermodynamics leading to increase of entropy in isolated systems, because entropy represents chaos in thermodynamics [17,18,41]. Scientists assumed that organisms are systems with low entropy because they have much order, and organisms keep low entropy through absorbing low-entropy matter and discharging high-entropy matter, and hence the controversial notion of "negative entropy" was established [41]. We believe that this notion is wrong as per the definitions of entropy [17,18], and order in biology is distinct from order in thermodynamics. For example, the order in biology of a dog declines, and the order in thermodynamics of the same dog increases, when the dog is dying in the snow with heat being lost from the body, as per the Clausius inequality of entropy [17,18]. Live dogs are warm and moving systems with many microstates, and they have hence high entropy, compared with perfect crystals at absolute zero temperature which have the lowest entropy and the highest order in thermodynamics, as per the Boltzmann formula of entropy and the third law of thermodynamics [17,18]. Moreover, during the period that fertilized eggs grow into mature dogs, the order in biology of these dog change little while their entropies have increased billions of times, as per the additive property of entropy [17,18]. In effect, order in biology is established through billions of years' evolution, rather than a shorttime metabolic effect of negative entropy. Contrary to the notion of negative entropy, Ludwig Boltzmann who created the Boltzmann formula of entropy pointed that animate beings struggle for entropy, which becomes available through the transition of energy from the hot sun to the cold earth [42]. Interestingly, this view was inherited and detailed by the CBEET.