The Other Edge of Ockham’s Razor: The A-PR Hypothesis and the Origin of Mind

Charles Darwin’s theory of evolution characterized all life as engaged in a “struggle for existence”. To struggle requires internal data processing to detect and interpret patterns to guide behavior, a mechanism to struggle for existence. The cognitive bootstrapping A-PR cycle (Autonomy | Pattern Recognition) couples the origin of life and mind, enabling their symbiotic co-evolution. Life processes energy to create order. Mind processes data to create meaning. Life and mind co-evolve toward increased functional effectiveness, using A-PR feedback cycles that reflect the two Laws deduced from Ockham’s Razor. The Law of Parsimony is only one of two laws that have emerged from debate about Ockham’s Razor. Less well known is the “other edge of Ockham’s Razor”, the Law of Succinctness which, when viewed through the lens of Charles Darwin’s theory of evolution, enables the A-PR Hypothesis to fulfill the criteria of Ockham’s Razor.     

The genetic code and the origin of life

The problem of the origin of life understandably counts as one of the most exciting questions in the natural sciences, but in spite of almost endless speculation on this subject, it is still far from its final solution. The complexity of the functional correlation between recent nucleic acids and proteins can e.g. give rise to the assumption that the genetic code (and life) could not originate on the Earth. It was Portelli (1975) who published the hypothesis that the genetic code could not originate during the history of the Earth. In his opinion the recent genetic code represents the informational message transmitted by living systems of the previous cycle of the Universe. Here however, we defend the existence of a certain strategy in the syntheses of the genetic code during the history of the Earth. The strategy of correlation between amino acid and nucleotide polymers made an increasing velocity of the chemical evolution possible, that is, it increased the velocity of formation of the genetic code. Thus, life with the recent genetic code could originate on the Earth within the present cycle of the Universe.Present address: Institute for Pharmacy and Biochemistry, 533 51 Pardubice, Czechoslovakia.     

The evolution of anisogamy: a game-theoretic approach

A popular theory has proposed that anisogamy originated through disruptive selection acting on an ancestral isogamous population, though recent work has emphasized the importance of other factors in its evolution. We re-examine the disruptive selection theory, starting from an isogamous population with two mating types and taking into account the functional relationship, g(m), between the fitness of a gamete and its size, m, as well as the relationship, f(S), between the fitness of a zygote and its size, S. Evolutionary game theory is used to determine the existence and continuous stability of isogamous and anisogamous strategies for the two mating types under various models for the two functions g(m) and f(S). In the ancestral unicellular state, these two functions are likely to have been similar; this leads to isogamy whether they are sigmoidal or concave, though in the latter case allowance must be made for a minimal gamete size. The development of multicellularity may leave g(m) relatively unchanged while f(S) moves to the right, leading to the evolution of anisogamy. Thus, the disruptive selection theory provides a powerful explanation of the origin of anisogamy, though other selective forces may have been involved in the subsequent specialization of micro- and macrogametes.     

The neutral theory of molecular evolution: a review of recent evidence

In sharp contrast to the Darwinian theory of evolution by natural selection, the neutral theory claims that the overwhelming majority of evolutionary changes at the molecular level are caused by random fixation (due to random sampling drift in finite populations) of selectively neutral (i.e., selectively equivalent) mutants under continued inputs of mutations. The theory also asserts that most of the genetic variability within species at the molecular level (such as protein and DNA polymorphism) are selectively neutral or very nearly neutral and that they are maintained in the species by the balance between mutational input and random extinction. The neutral theory is based on simple assumptions, enabling us to develop mathematical theories based on population genetics to treat molecular evolution and variation in quantitative terms. The theory can be tested against actual observations. Neo-Darwinians continue to criticize the neutral theory, but evidence for it has accumulated over the last two decades. The recent outpouring of DNA sequence data has greatly strengthened the theory. In this paper, I review some recent observations that strongly support the neutral theory. They include such topics as pseudoglobin genes of the mouse, alpha A-crystallin genes of the blind mole rat, genes of influenza A virus and nuclear vs. mitochondrial genes of fruit flies. I also discuss such topics as the evolution of deviant coding systems in Mycoplasma, the origin of life and the unified understanding of molecular and phenotypic evolution. I conclude that since the origin of life on Earth, neutral evolutionary changes have predominated over Darwinian evolutionary changes, at least in number.     

The rise and falls of introns

There has been a lively debate over the evolution of eukaryote introns: at what point in the tree of life did they appear and from where, and what has been their subsequent pattern of loss and gain? A diverse range of recent research papers is relevant to this debate, and it is timely to bring them together. The absence of introns that are not self-splicing in prokaryotes and several other lines of evidence suggest an ancient eukaryotic origin for these introns, and the subsequent gain and loss of introns appears to be an ongoing process in many organisms. Some introns are now functionally important and there have been suggestions that invoke natural selection for the ancient and recent gain of introns, but it is also possible that fixation and loss of introns can occur in the absence of positive selection.     

The Theory of Evolution is Not an Explanation for the Origin of Life

The propagation of misconceptions about the theory of biological evolution must be addressed whenever and wherever they are encountered. The recent article by Paz-y-Mino and Espinoza in this journal contained several such misconceptions, including: that biological evolution explains the origin of life, confusion between biological and cosmological evolution, and the use of the term “Darwinism,” all of which we address here. We argue that science educators, and biology educators particularly, must be aware of these (and other) misconceptions and work to remove them from their classrooms.     

The Big Bang, Superstring Theory and the origin of life on the Earth

This article examines the origin of life on Earth and its connection to the Superstring Theory, that attempts to explain all phenomena in the universe (Theory of Everything) and unify the four known forces and relativity and quantum theory. The four forces of gravity, electro-magnetism, strong and weak nuclear were all present and necessary for the origin of life on the Earth. It was the separation of the unified force into four singular forces that allowed the origin of life.     

History of Human Impact on Natural Environments

Anthropology, in the sense of the Natural History of Humanity, not only satisfies our curiosity about the past but is also essential in understanding our place in the natural world, confronting the environment and facing future adversities. Sociality and intelligence are the two basic interacting features that marked human evolution, which mutually enhanced control over the environment. Interactions between humans and the environment also gave rise to technological developments leading to agriculture and animal domestication, innovations that made possible the accumulation of energy-food surpluses and removed the most important restraint on demographic increase in hunter–gatherer communities. In the last two centuries, increase in life expectancy at birth, exploitation of resources and control of humans over the environment have contributed to a dramatic demographic increase. It is necessary to ask what is the number of people that can be supported by the planet and hypothesize some possible scenarios for the future. Three different scenarios are presented and discussed. A balance between the human population and the natural environment must be preserved for the very survival of our species. A new political and ethical approach is needed. Bioethics is an anthropological and naturalistic science, which attempts to form a pact between humans and nature in order to ensure the possibility of our continued life on this Planet.     

Emergence and subsequent functional specialization of kindlins during evolution of cell adhesiveness

Kindlins are integrin-interacting proteins essential for integrin-mediated cell adhesiveness. In this study, we focused on the evolutionary origin and functional specialization of kindlins as a part of the evolutionary adaptation of cell adhesive machinery. Database searches revealed that many members of the integrin machinery (including talin and integrins) existed before kindlin emergence in evolution. Among the analyzed species, all metazoan lineages—but none of the premetazoans—had at least one kindlin-encoding gene, whereas talin was present in several premetazoan lineages. Kindlin appears to originate from a duplication of the sequence encoding the N-terminal fragment of talin (the talin head domain) with a subsequent insertion of the PH domain of separate origin. Sequence analysis identified a member of the actin filament–associated protein 1 (AFAP1) superfamily as the most likely origin of the kindlin PH domain. The functional divergence between kindlin paralogues was assessed using the sequence swap (chimera) approach. Comparison of kindlin 2 (K2)/kindlin 3 (K3) chimeras revealed that the F2 subdomain, in particular its C-terminal part, is crucial for the differential functional properties of K2 and K3. The presence of this segment enables K2 but not K3 to localize to focal adhesions. Sequence analysis of the C-terminal part of the F2 subdomain of K3 suggests that insertion of a variable glycine-rich sequence in vertebrates contributed to the loss of constitutive K3 targeting to focal adhesions. Thus emergence and subsequent functional specialization of kindlins allowed multicellular organisms to develop additional tissue-specific adaptations of cell adhesiveness.     

From prebiotic chemistry to cellular metabolism--the chemical evolution of metabolism before Darwinian natural selection

It is generally assumed that the complex map of metabolism is a result of natural selection working at the molecular level. However, natural selection can only work on entities that have three basic features: information, metabolism and membrane. Metabolism must include the capability of producing all cellular structures, as well as energy (ATP), from external sources; information must be established on a material that allows its perpetuity, in order to safeguard the goals achieved; and membranes must be able to preserve the internal material, determining a selective exchange with external material in order to ensure that both metabolism and information can be individualized. It is not difficult to understand that protocellular entities that boast these three qualities can evolve through natural selection. The problem is rather to explain the origin of such features under conditions where natural selection could not work. In the present work we propose that these protocells could be built by chemical evolution, starting from the prebiotic primordial soup, by means of chemical selection. This consists of selective increases of the rates of certain specific reactions because of the kinetic or thermodynamic features of the process, such as stoichiometric catalysis or autocatalysis, cooperativity and others, thereby promoting their prevalence among the whole set of chemical possibilities. Our results show that all chemical processes necessary for yielding the basic materials that natural selection needs to work may be achieved through chemical selection, thus suggesting a way for life to begin.     

Lethal mutants and truncated selection together solve a paradox of the origin of life

Background

Many attempts have been made to describe the origin of life, one of which is Eigen''s cycle of autocatalytic reactions [Eigen M (1971) Naturwissenschaften 58, 465–523], in which primordial life molecules are replicated with limited accuracy through autocatalytic reactions. For successful evolution, the information carrier (either RNA or DNA or their precursor) must be transmitted to the next generation with a minimal number of misprints. In Eigen''s theory, the maximum chain length that could be maintained is restricted to nucleotides, while for the most primitive genome the length is around . This is the famous error catastrophe paradox. How to solve this puzzle is an interesting and important problem in the theory of the origin of life.

Methodology/Principal Findings

We use methods of statistical physics to solve this paradox by carefully analyzing the implications of neutral and lethal mutants, and truncated selection (i.e., when fitness is zero after a certain Hamming distance from the master sequence) for the critical chain length. While neutral mutants play an important role in evolution, they do not provide a solution to the paradox. We have found that lethal mutants and truncated selection together can solve the error catastrophe paradox. There is a principal difference between prebiotic molecule self-replication and proto-cell self-replication stages in the origin of life.

Conclusions/Significance

We have applied methods of statistical physics to make an important breakthrough in the molecular theory of the origin of life. Our results will inspire further studies on the molecular theory of the origin of life and biological evolution.     

The organic codes. The basic mechanism of macroevolution.

The origin of the genetic code coincided with the origin of life, while the human codes of cultural evolution emerged almost four billion years later. Modern biology does not recognize any other organic code in nature, and is bound therefore to conclude that the whole of cellular evolution consisted of informational changes. Semantic transformations, natural conventions and biological meaning are things that officially do not exist in the organic world, and play no part in our reconstruction of development and evolution. And yet the properties of organic codes are beginning to emerge in various biological processes. Here it is shown that splicing, signal transduction and pattern formation can be accounted for precisely by the existence of organic codes. It is also shown that those processes were instrumental in bringing about major changes in the history of life, and it is concluded that every main step of macroevolution corresponded to the origin of a new organic code.     

Symbiogenesis: the hidden face of Constantin Merezhkowsky

Constantin Merezhkowsky is celebrated today for his theory of symbiogenesis, postulated in the early decades of the twentieth century, particularly that chloroplasts were symbiotic cyanophytes (cyanobacteria). While biologists point singularly to what they see as his heroic achievement, its neglect and subsequent rediscovery, we introduce a broader and much more complex perspective on his science, his troubled life and career. We present a view of Merezhkowsky as zoologist, anthropologist, botanist, philosopher, and novelist. We explain the genesis of his theory of the origin of chloroplasts and of nucleus and cytoplasm as symbionts, as well as his depiction of the geo-chemical context of the origins and early evolution of life on earth. We also disclose his sordid social and political activities, his eugenics and racist writings, his paedophilia, and his metaphysics. Finally, we describe the context of his elaborate suicide in 1921.     

遗传伦理问题起源的研究与对策

遗传伦理问题是生命科学领域最具争议并最难以妥善解决的问题之一。近年来, 此类问题的研究主要是围绕遗传伦理问题的种类及解决方法进行的。但关于遗传伦理问题起源的系统研究尚不多见, 这也使相应对策的提出显得缺乏理论支撑。文章从人类生物进化与文化进化的双重角度深入探讨了遗传伦理问题发生的进化根源和演化规律。人类是生物进化与文化进化的双重产物, 是地球上唯一既具有生物属性又具有文化属性的物种。通过对人类生物进化与文化进化及其生物属性与文化属性特点的比较研究, 文章提出了任何伦理问题都可以从人类的生物进化与文化进化之间相互作用所产生的冲突中找到其发生根源的观点, 其目的是为研究遗传伦理问题及其对策的提出寻求理论和实践上的依据。同时, 提出了一系列关于遗传伦理问题的对应策略。文章的最终目的并非仅仅为某种观点能被接受, 而是希望通过对遗传伦理问题及其起源的了解和认识, 使遗传学领域的决策者和研究者更具使命感与责任感, 使一般公众对遗传学研究及其应用少一些误解, 多一些理性, 从而使遗传学事业能健康、持续发展, 造福人类。     

Historic and functional biology: the inadequacy of a system theory of evolution

In the first half of the 20th century neo-Kantianism in a broad sense proved itself the main conceptual and methodological background of the central European biology. As such it contributed much to the victory on the typological, idealistic-morphological and psycho-vitalistic interpretations of life. On the other hand it could not give tools to the biologists for working out a strictly darwinian evolution theory. Kant's theory of organism was conceived without evolution as a theory of the internal functionality of the organism. There was only some 'play' with the evolutionary differentiation of the species. Since then the disputes around the work of August Weismann, a synthetical evolution theory which is now behind time, arose. This theory developed from coinciding claims, elaborated by geneticists, mathematicians, and by biologists studying development, natural history and systematics. This was done under a strong influence of marxist ideas. Through the interweaving of such different approaches it was possible for this evolutionary synthesis to influence successfully the development of evolution research during more than 40 years. Philosophically speaking modern evolution theory means therefore an aversion, even a positive abolition of Kantian positions. A number of biologists however--as L. von Bertalanffy--refused to adhere to a misinterpreted Kantian methodology and oriented themselves to an approach via system theory, which obtained a place in evolution research. In fact this is a Kantian approach as well. They only repeated the Kantian dilemma of the evolution which can also be found in Lamarck and Hegel. The system theory of the functionality of the organism never reaches to the level of the evolving species, but remains always on the level of epigenetic thinking, because of its philosophical origin. This paper points out the consequences of this still current dilemma. At the same time an all-enclosing reflection on the methodological, epistemological and the important historical questions of evolutionary biology in its scientific context is recommended.     

Possible mechanism for origin of chiral specificity during origins of life

We have earlier (Origins of Life 10 (1980), 15-30) proposed a conformational theory for the origin of nucleic acid-directed adaptor-mediated ordered and proliferative synthesis of proteins and hence origin of life. Conjunction of L-amino acids and beta-D-ribonucleotides emerges as a natural consequence of a template fitting interaction in this theory of the origin of the genetic decoding apparatus. Here we propose an interesting new concept for the origin of chiral specificity, by showing that two autonomously developing systems of protein-synthesizing machinery, one manufacturing L-peptides (L-system) and the other, D-peptides (D-system) could have arisen and during early stages of evolution L-system could have developed a killer enzyme to destroy the D-system, causing the presently existing chiral specificity in all the evolved organisms on Earth. It would be interesting to look for such 'killer enzymes' in the present-day organisms. Of course, the existence of D-amino acid-containing antibiotics gives some credence to this theory.     

The influence of UV radiation on protistan evolution

Ultraviolet radiation has provided an evolutionary challenge to life on Earth. Recent increases in surficial ultraviolet B fluxes have focused attention on the role of UV radiation in protistan ecology, cancer, and DNA damage. Exploiting this new wealth of data, I examine the possibility that ultraviolet radiation may have played a significant role in the evolution of the first eukaryotes, that is, protists. Protists probably arose well before the formation of a significant ozone shield, and thus were probably subjected to substantial ultraviolet A, ultraviolet B, and ultraviolet C fluxes early in their evolution. Evolution consists of the generation of heritable variations and the subsequent selection of these variants. Ultraviolet radiation has played a role both as a mutagen and as a selective agent. In its role as a mutagen, it may have been crucial in the origin of sex and as a driver of molecular evolution. As a selective agent, its influence has been broad. Discussed in this paper are the influence of ultraviolet radiation on biogeography, photosynthesis, and desiccation resistance.     

Too early? on the apparent conflict of astrobiology and cosmology

An interesting consequence of the modern cosmological paradigm is the spatial infinity of the universe. When coupled with naturalistic understanding of the origin of life and intelligence, which follows the basic tenets of astrobiology, and with some fairly incontroversial assumptions in the theory of observation selection effects, this infinity leads, as Ken Olum has recently shown, to a paradoxical conclusion. Olum's paradox is related, to the famous Fermi's paradox in astrobiology and “SETI” studies. We, hereby, present an evolutionary argument countering the apparent inconsistency, and show how, in the framework of a simplified model, deeper picture of the coupling between histories of intelligent/technological civilizations and astrophysical evolution of the Galaxy, can be achieved. This strategy has consequences of importance for both astrobiological studies and philosophy.     

The early role of nitric oxide in evolution

Nitric oxide (NO), which today serves many different purposes in regulating complex cellular functions, must have played a crucial role in the early stages of the evolution of life. The formation of NO may have been a critical defence mechanism for primitive microorganisms at a time when life faced the problem of rising atmospheric levels of ozone (03) formed upon photolysis of oxygen (Oz), which occurred shortly after the development of respiration in cyanobacteria. The production of NO by organisms would have allowed neutralization of toxic 03 by chemical reaction outside the cell, thus acting as a protective mechanism against oxidative destruction, allowing evolutionary advantage. Later, NO production might have allowed the control of reactive OZ species within cells before the development of specific electron-accepting enzymes. The pathway of NO formation was then consequently developed further to serve other useful functions. Although mammalian cells produce NO from L-arginine, the origin of this ability might have arisen from the essential process of either nitrification or denitrification in prokaryotic cells.     

Temperature-related sex allocation shifts in a recovering keystone species,Pinus palustris

Summary

In the light of all that has been discovered about the mechanism of evolution it has become tempting to follow Darwin's lead and to “see no limit to this power“. Yet a careful examination of situations in which evolution is known to be occurring in some species, shows complete absence of evolution in others. This not because these species have not had the opportunity; in many situations there may even be uncolonised bare space.

The explanation must lie in the supply of appropriate variation. A tacit assumption of evolution by natural selection is that the necessary variation is always available. Yet there is no a priori justification for this. Evidence from populations in nature, particularly of species which are potential colonists of old metal mine workings and similar metal contaminated habitats, shows that the species that successfully colonise these habitats, by the evolution of metal tolerant populations, possess within their normal populations the necessary variation. But those species which fail to colonise these habitats, despite the opportunity, do not possess this variation. This applies also at the level of the population, in the replicated evolutionary situations occurring under electricity pylons.

Such evidence, together with arguments from theory, suggests that the failures of evolution have been as important as its successes in moulding the living world as we see it today, and that the reasons for failure must be sought at the molecular level in limitations to the origin of new variation.