Evolution of living organisms as a multilevel process

There is inherent capacity to increase the degree of aggregation within each of the levels of structural organization of living matter. At the macromolecular level (MML), this is an increase in the gene number in the genomes of evolving organisms; at the cellular level (CL), an increase in cell size; and at the multicellular level (MCL), an increase in the number of cells in the multicellular aggregate. However, the increase in the degree of aggregation causes gene incompatibility in case of genome evolution and instability in case of large cells and multicellular aggregates with simple structure. Gene incompatibility may be neutralized by spacio-temporal disconnection of the products of incompatible genes at the cellular and multicellular levels. The larger cells and multicellular aggregates are stabilized by increased structural complexity which is a consequence of the origin of new genes. There is a feedback between the processes of evolution at different levels MML→CL→ MCL.The processes of evolutionary development at different levels of structural organization are also relatively independent. The coincidence of these processes gives rise to stable organisms of higher complexity, which are then subjected to natural selection and population processes to establish a new step in progressive biological evolution. In all of the normal organisms of newly evolved species there is a correspondence between the different levels of structural organization, i.e. in their degree of aggregation, their complexity and functional organization. The form of correspondence for multicellular organisms is presented.     

The minor transitions in hierarchical evolution and the question of a directional bias

The history of life shows a clear trend in hierarchical organization, revealed by the successive emergence of organisms with ever greater numbers of levels of nestedness and greater development, or ‘individuation’, of the highest level. Various arguments have been offered which suggest that the trend is the result of a directional bias, or tendency, meaning that hierarchical increases are more probable than decreases among lineages, perhaps because hierarchical increases are favoured, on average, by natural selection. Further, what little evidence exists seems to point to a bias: some major increases are known – including the origin of the eukaryotic cell from prokaryotic cells and of animals, fungi and land plants from solitary eukaryotic cells – but no major decreases (except in parasitic and commensal organisms), at least at the cellular and multicellular levels. The fact of a trend, combined with the arguments and evidence, might make a bias seem beyond doubt, but here I argue that its existence is an open empirical question. Further, I show how testing is possible.     

Stem cells as probabilistic self-producing entities

Stem cells have the capacity both to self-renew and to give rise to differentiated progeny, and are vital to the organization of multicellular organisms. Stem cells raise a number of fundamental questions regarding lineage restriction and cellular differentiation, and they hold enormous promise for cell-based therapies. Here I propose a theoretical framework for stem cell biology based on the concepts of autopoiesis (self-production) and complementarity. I argue that stem cells are pivotal in the self-production of the organism and that we need complementary approaches to understand their probabilistic behavior. I discuss how this framework generates testable hypotheses regarding stem-cell functions.     

Evolutionary remnants as widely accessible evidence for evolution: the structure of the argument for application to evolution education

Evolution education, in both schools and informal education, often focuses on natural selection and the fit of organisms through natural selection to their environment and way of life. Examples of evidence that evolution has occurred are therefore often limited to a modest number of classic but exotic cases, with little attention to how one might apply principles to more familiar organisms. Many of these classic examples are examples of adaptation; adaptation to local environments is, however, an outcome that could in principle also be explained by supernatural creation or design. A frequent result is the perception among the public is that examples of evolution are rare, and that the existence of well-adapted organisms may just as easily be explained metaphysically. We argue that among categories of evidence of evolution accessible to non-specialists in any environment, the most compelling evidence of common ancestry consists of remnants of evolutionary history evident in homologous features, particularly when those homologies are related to lack of fit of organisms to their way of life (“vestiges”) or to better fit that involves complicated combinations of parts usually assigned other functions (“contrivances”). Darwin emphasized the critical nature of this argument from imperfections, and it has been part of traditional catalogs of “evidence for evolution” for more than a century. Yet while remnants of history are widely used as a category of evidence for evolution, their utility in education of comparative anatomy to document body parts passed on through descent is underemphasized in evolution education at all levels. We explore the use of evolutionary remnants to document common ancestry and evidence for evolution, for application to evolution education.     

Diversification of the Metazoa: Ediacarans,colonies, and the origin of eumetazoan complexity by nested modularity

The Ediacaran biota is profoundly mysterious. There is a growing realization that these organisms should not be grouped in a single taxon, such as Petalonamae or Vendobionta, but debate continues on what the group as a whole represents. It is argued here that the Ediacarans constitute a broad, megascopic, paraphyletic grade of organization which overlaps the stem groups (and perhaps some crown groups) of the Porifera, Ctenophora, Cnidaria and Bilateria.

The modular organization of many Ediacarans suggests that they were fundamentally colonial organisms. The early disc‐shaped forms may have been solitary individuals, perhaps with a choanoflagellate or simple sponge‐like grade of organization; the modular forms may represent bud colonies of those entities. The more complex fronds, as well as other segmented and bilaterally symmetrical Ediacarans, seem to exhibit a trend toward higher levels of integration and individuation. This trend is comparable to those observed among more recent colonial organisms. Interpretation of modular Ediacarans as colonial organisms leads to a new perspective on the evolution of metazoans. It suggests that the earliest solitary Ediacarans furnished a framework for the development of cell and tissue specialization, including the formation of epithelia and complex connective tissues. Later colonial forms provided a mechanism to increase nested or hierarchical complexity, through duplication, integration, and individuation. Early acquisition of complexity had a profound impact on the subsequent evolution of metazoan body plans.

The Ediacarans seem to have evolved the range of colonial forms required to give rise to the radiation of complex bilaterians in the Cambrian. If this is true, it obviates the need to postulate the existence of the microscopic, acoelomate ancestors of basal metazoan taxa that are required by prevailing hypotheses bearing on the early evolution of the Metazoa.     

Increase of efficiency of adaptations and attenuation of organism protective reactions in the process of biological evolution

The major trend in evolution of living organisms is development of the central nervous system and sense organs, an increase of energy exchange, development of homoiothermy and of increasingly more complex forms of behavior, an increase in energy expenditure in connection with a rise of body activity and with development of adaptation to habitat. Such fundamental processes of evolution were and still have been subjected to numerous investigations and discussions. However, in different animals there exist different species-specific peculiarities of evolution of physiological functions, from which eventually the fundamental evolutionary processes are formed. We studied some of these specific processes by separating them into two categories. The first category is “Rise in efficiency of adaptations” in development of biological evolution. By this term we mean development of the amazingly perfect specific physiological mechanisms of adaptive character. The second category is “Weakening of the protective body reactions” under which we mean disturbances of the protective mechanisms of the body immune system, uncoordinated leukocyte movement in microvessels, lack of effective collateral blood circulation in brain and heart, etc.     

A Virtue Made of Necessity: Is the Increasing Hierarchical Complexity of Sexual Clades an Inevitable Outcome of Their Declining (Macro)evolutionary Potential?

The increasing maximal hierarchical complexity of organisms is one of the best-supported macroevolutionary trends. The nature and causes of this trend, as well as several accompanying macroevolutionary phenomena are, however, still unclear. In this theoretical article, we propose that the cause of this trend could be the increasing pressure of species selection, which results from the gradual decrease of (macro)evolutionary potential (i.e. the probability of producing major evolutionary innovations). As follows from the Theory of Frozen Evolution, this process is an inevitable consequence of the sorting of genes, traits, and their integrated groups (modules) based on their contextually dependent stability. In turn, this causes effectively unchangeable elements of genetic architecture to accumulate during the existence of evolutionary lineages. Although (macro)evolutionary potential can be partially restored by several processes, a profound restoration of (macro)evolutionary potential is probably possible only by means of a transition to a higher level of hierarchical complexity. However, the accumulation of contextually more stable elements continues even on this higher level. This leads to the integration of the modular character of composite organisms and a repeated pressure to increase the level of hierarchical complexity. Our model explains all components of McShea’s “Evolutionary Syndrome,” i.e. the trend of increasing the hierarchical complexity of organisms, the growth of variability among elements on the immediately lower level, and their gradual machinification. This pattern should be characteristic of sexual eukaryotes and especially their complex representatives. Our model also sheds new light on several related macroevolutionary phenomena, such as the gradual acceleration of the trend or the striking difference between pre-Neoproterozoic and Phanerozoic evolution.     

Chirality as a primary switch of hierarchical levels in molecular biological systems

A synergetic law, being of common physicochemical and biological sense, is formulated: any evolving system that possesses an excess of free energy and elements with chiral asymmetry, while being within one hierarchical level, is able to change the type of symmetry in the process of self-organization increasing its complexity but preserving the sign of prevailing chirality (left — L or right — D twist). The same system tends to form spontaneously a sequence of hierarchical levels with alternating chirality signs of de novo formed structures and with an increase of the structures’ relative scales. In living systems, the hierarchy of conjugated levels of macromolecular structures that begins from the “lowest” asymmetric carbon serves as an anti-entropic factor as well as the structural basis of “selected mechanical degrees of freedom” in molecular machines. During transition of DNA to a higher level of structural and functional organization, regular alterations of the chirality sign D-L-D-L and L-D-L-D for DNA and protein structures, respectively, are observed. Sign-alternating chiral hierarchies of DNA and protein structure, in turn, form a complementary conjugated chiral pair that represents an achiral invariant that “consummates” the molecular-biological block of living systems. The ability of a carbon atom to form chiral compounds is an important factor that determined the carbon basis of living systems on the Earth as well as their development though a series of chiral bifurcations. The hierarchy of macromolecular structures demarcated by the chirality sign predetermined the possibility of the “block” character of biological evolution.     

Universal common ancestry,LUCA, and the Tree of Life: three distinct hypotheses about the evolution of life

Common ancestry is a central feature of the theory of evolution, yet it is not clear what “common ancestry” actually means; nor is it clear how it is related to other terms such as “the Tree of Life” and “the last universal common ancestor”. I argue these terms describe three distinct hypotheses ordered in a logical way: that there is a Tree of Life is a claim about the pattern of evolutionary history, that there is a last universal common ancestor is an ontological claim about the existence of an entity of a specific kind, and that there is universal common ancestry is a claim about a causal pattern in the history of life. With these generalizations in mind, I argue that the existence of a Tree of Life entails a last universal common ancestor, which would entail universal common ancestry, but neither of the converse entailments hold. This allows us to make sense of the debates surrounding the Tree, as well as our lack of knowledge about the last universal common ancestor, while still maintaining the uncontroversial truth of universal common ancestry.     

Was heißt “lebendig”?

“Life” means “being alive” of special entities, which we call “organisms”. From a physical point of view, living entities are open systems, which exchange matter as well as energy with their surroundings. Against disruptive influences permanently present, they maintain actively and autonomously a steady state far from the thermodynamic equilibrium. This dynamic state of living beings represents a functional order, an internal “organization”. That means that the involved processes one and all must be correlated in such a way that they in sum prevent the breakdown of the living state. Organization implies functionality, which in turn requires structural relationships, and structures require information for their specification. Information in turn presupposes a source, which is constituted in living systems by the nucleic acids. Organisms are unique in having a capacity to use information, which is stored in the nucleic acid and yields the basis for their specific internal organization in its perpetuation: Living beings, and only they, show a self‐maintained organization.     

Implications of clonality for ageing research

Senescence, an organismal performance decline with age, has historically been considered a universal phenomenon by evolutionary biologists and zoologist. Yet, increasing fertility and survival with age are nothing new to plant ecologists, among whom it is common knowledge that senescence is not universal. Recently, these two realities have come into a confrontation, begging for the rephrasing of the classical question that has led ageing research for decades: “why do we senesce?” to a more practical “what are the mechanisms by which some organisms escape from senescence?” Plants are amenable to examining this question because of their rich repertoire of life history strategies. These include the existence of permanent seed banks, vegetative dormancy and ability to produce clones, among others. Here, I use a large number of high resolution demographic models from 181 species that reflect life history strategies and their trade-offs among herbaceous perennials, succulents and shrubs measured under field conditions worldwide to examine whether senescence rates of ramets from clonal plants differ from those of whole plants reproducing either strictly sexually, or with a combination of sexual and clonal mechanisms. Contrary to the initial expectation from the mutation accumulation theory of senescence, ramets of clonal plants were more likely to exhibit senescence than those species employing sexual reproduction. I discuss why these comparisons between ramets and genets are useful, as well as its implications and future directions for ageing research.     

What is a phenotype? History and new developments of the concept

Even though the word “phenotype”, as well as the expression “genotype–phenotype relationship”, are a part of the everyday language of biologists, they remain abstract notions that are sometimes misunderstood or misused. In this article, I begin with a review of  the genesis of the concept of phenotype and of the meaning of the genotype-phenotype “relationship" from a historical perspective. I then illustrate how the development of new approaches for exploring the living world has enabled us to phenotype organisms at multiple levels, with traits that can either be measures or parameters of functions, leading to a virtually unlimited amount of phenotypic data. Thus, pleiotropy becomes a central issue in the study of the genotype–phenotype relationship. Finally, I provide a few examples showing that important genetic and evolutionary features clearly differ with the phenotypic level considered. The way genotypic variation propagates across the phenotypic levels to shape fitness variation is an essential research program in biology.

     

PHYLOGENETIC TRANSITIONS IN THE CHLOROPLASTS OF THE ANTHOCEROTALES I. THE NUMBER AND ULTRASTRUCTURE OF THE MATURE PLASTIDS

Representatives of three genera of anthooerotes were examined: Phaeoceros, Notothylas, and Megaceros. Species of the first two genera were found to exemplify the typical anthocerote plastid condition. This condition is characterized by the presence in each cell of the gametophyte of only a single large chloroplast containing a “multiple” pyrenoid. The genus Megaceros, however, proved to be quite different. In two species of Megaceros the pyrenoid was observed to be composed of a highly subdivided thylakoid system of even greater complexity than the “multiple” pyrenoids of Phaeoceros. In another species only an indistinct “pyrenoid-like” area was noted while in a fourth species no evidence was found for any internal differentiation. Associated with these changes in plastid structure there are corresponding alterations in the number and the size of the chloroplasts. Together they indicate an evolutionary trend away from a primitive, algal-like condition to a more advanced land plant form.     

Reimagining policy: Power,problems, and public stories

The authors of various practitioner and scholarly documents suggest markedly contrasting understandings about the nature of “policy.” These divergent conceptions raise the question: What is at stake by understanding the nature of policy in one way as opposed to another? The purpose of this philosophical inquiry is to interrogate the nature of “policy” as it relates to music education and to question the values that do and might underlie and propagate through contrasting understandings of “policy.” Subsequently, I examine two aspects of policy, problem identification and meaning-making, that have gone largely unexplored in the arts education literature.

Using Foucault's writings, I argue that power-laden policy texts often have the greatest impact, not when they are mandated, but when they go misrecognized as common sense. I also advocate for the consistent use of the terms “policy texts” and “policy actions,” including as an alternative to the imbalanced designations of “soft policies” and “hard policies.” Drawing on Dewey arts educators might form “publics” around problems having consequences that they deem far-reaching, recurrent, and irreparable. Individual and collective political narratives, including what Ganz explains as “stories of self,” “stories of us,” and “stories of now,” can foster the meaningful connections necessary for forming “publics” who address pressing problems in arts education.     

Discovery of myosin I and Pollard-san

In this short review, I describe a brief history of the discovery of myosin I isolated from Acanthamoeba in 1973 by Tom Pollard and Ed Korn. Today, myosins form a large “family tree” that includes more than 30 types of myosins. I discuss the importance of the relationship among actin, myosin, and other actin-binding proteins, many of which were pioneered by Pollard-san (“-san” is a Japanese honorific suffix showing respect, politeness and friendship). At the first conference devoted to actin, Pollard-san, Korn-san, and I discussed the importance of the nucleotide bound at the two ends of the actin filament. I conclude that life is a dynamic accumulation of molecule-molecule bindings, and although we do not yet know how they coordinate with each other to operate a living cell, many enthusiastic and excellent researchers like Pollard-san will unveil mechanisms that will show us what life really looks like.     

Not deconstructing serial homology,but instead,the a priori assumption that it generally involves ancestral anatomical similarity: An answer to Kuznetsov's paper

I am very thankful to Kuznetsov for his comments on our recent paper about serial structures published in this journal. I hope this is just the beginning of a much wider, and holistic, discussion on the evolution of serial homologous structures, and of so-called “serial structures” in general, whether they are truly serial homologs or the secondary result of homoplasy. Strangely, Kuznetsov seems to have missed the main point of our paper, what is particularly puzzling as this point is clearly made in the very title of our paper. For instance, he states that “Siomava et al. claim that the serial homologues are false because they are ancestrally anisomeric (dissimilar)' and that” Siomava et al., (Siomava et al., Journal of Morphology, 2020, 281, 1110–1132) expected that if serial homology was true, then the serial homologs would be identical at the start and then only diverge. “ However, our paper clearly did not state this. Instead, we stated that (a) serial homology is a real phenomenon, and (b) ancestral dissimilarity is actually likely the norm, and not the exception, within serial homology. In particular, our paper showed that, as clearly stated in its title and abstract, within the evolution of serial homologues these structures “many times display trends toward less similarity while in many others display trends toward more similarity, that is, one cannot say that there is a clear, overall trend to anisomerism.” Serial homology is therefore a genuine and much widespread phenomenon within the evolution of life in this planet. It is clearly one of the most important issues—and paradoxically one of the less understood, precisely because of the a priori acceptance of long-standing assumptions that have never been empirically tested, some of them repeated in Kuznetsov's paper—within macroevolution and comparative anatomy.     

Randomness and multilevel interactions in biology

The dynamic instability of living systems and the “superposition” of different forms of randomness are viewed, in this paper, as components of the contingently changing, or even increasing, organization of life through ontogenesis or evolution. To this purpose, we first survey how classical and quantum physics define randomness differently. We then discuss why this requires, in our view, an enriched understanding of the effects of their concurrent presence in biological systems’ dynamics. Biological randomness is then presented not only as an essential component of the heterogeneous determination and intrinsic unpredictability proper to life phenomena, due to the nesting of, and interaction between many levels of organization, but also as a key component of its structural stability. We will note as well that increasing organization, while increasing “order”, induces growing disorder, not only by energy dispersal effects, but also by increasing variability and differentiation. Finally, we discuss the cooperation between diverse components in biological networks; this cooperation implies the presence of constraints due to the particular nature of bio-entanglement and bio-resonance, two notions to be reviewed and defined in the paper.     

Evolutionarily stable strategies and the evolution of life history strategies: I. Density dependent models

The evolution of life history strategies in density dependent situations is considered in both continuous time and discrete time models. The question of equilibrium and of competitively stable strategies, the “invasion” question, are shown to be completely determined by the number of offspring left at a fixed population size. Evolutionarily stable strategies are shown to maximize population size in a certain sense.     

Nippostrongylus brasiliensis: intestinal goblet-cell response in adoptively immunized rats.

Goblet-cell differentiation was studied in the intestinal epithelium of rats infected with the nematode Nippostrongylus brasiliensis. An increase in the proportion of goblet cells occurred at the time of worm expulsion in rats infected with 1000 or 4000 third stage larvae. Adoptive immunization of infected rats with immune-thoracic duct lymphocytes (TDL) induced extensive goblet-cell differentiation whereas the transfer of immune-TDL into normal rats had no effect. The extent of goblet-cell differentiation in adoptively immunized infected rats was proportional to the number of cells transferred. A goblet-cell response also occurred in adoptively immunized rats harboring implanted “normal” and “damaged” worms but recipients of normal worms which were not given cells were unable either to expel their worm burden or to induce a goblet-cell response. Experiments in which the parasites were expelled with an anthelmintic drug suggested that the goblet-cell increase was not simply a repair process associated with the expulsion of the parasites. In all situations where immune expulsion of the parasites occurred, there was a concomitant rise in the proportion of goblet cells. These experiments suggest that thoracic duct lymphocytes either directly or indirectly regulate the differentiation of intestinal goblet cells.