Hierarchies and the Sloshing Bucket: Toward the Unification of Evolutionary Biology

Evolutionary biology presents a bewildering array of phenomena to scientists and students alike—ranging from molecules to species and ecosystems; and embracing 3.8 billion years of life’s history on earth. Biological systems are arranged hierarchically, with smaller units forming the components of larger systems. The evolutionary hierarchy, based on replication of genetic information and reproduction, is a complex of genes/organisms/demes/species and higher taxa. The ecological hierarchy, based on patterns of matter–energy transfer, is a complex of proteins/organisms/avatars/local ecosystems/regional ecosystems. All organisms are simultaneously parts of both hierarchical systems. Darwin’s original formulation of natural selection maps smoothly onto a diagram where the two hierarchical systems are placed side-by-side. The “sloshing bucket” theory of evolution emerges from empirical cases in biological history mapped onto this dual hierarchy scheme: little phenotypically discernible evolution occurs with minor ecological disturbance; conversely, greatest concentrations of change in evolutionary history follow mass extinctions, themselves based on physical perturbations of global extent. Most evolution occurs in intermediate-level regional “turnovers,” when species extinction leads to rapid evolution of new species. Hierarchy theory provides a way of integrating all fields of evolutionary biology into an easily understood—and taught—rubric.

The cell theory--history, present state and prospects (on the 150th anniversary of the development of the cell theory)

The main stages of history of this most important biological conception are presented and the state of the modern cell theory and its future prospects are considered. Since 1839, when T. Schwann expounded his conception of the cell, a long pathway in cognition of the cell function and organization has been covered. From the original picture of the complex organism as a "cellular state", made up of relatively independent "elementary organisms", i.e. cells the modern biology has come to the idea of the cell as an integral system either being a part of a complex organism, or living free in the nature (protists). The cell represents certain qualitatively peculiar level in a complex evolutionary established hierarchy of biological systems. Some particular tight relations, existing between cytology, as a fundamental biological science and molecular biology, genetics, ecology and other biological disciplines are considered. The importance of the cell conception is ascertained for practical aims, especially in medicine.     

Systematics on the threshold of the XXI century. Traditional principles and fundamentals from today's point of view

Systematics as regarded is a purely theoretical domain of biology, and its product, system, as a specific biological theory, or a topologo-genetic model of the biota. Linnaeus was the first to introduce the idea of system and the systematic approach into the natural history. The advent of evolutionism brought new meaning to the old term "affinity", so Linnaeus' slogan of natural system got new life, and Linnaeus taxonomy assimilated the evolutionary ideology quite naturally and much easier than many other departments of biology. The difference between natural and artificial systems is remaining, and it is in their goals, as formulated by Linnaeus: heuristic of the former and cataloguing of the latter. Linnaeus' clairvoyance discovered the existence of an infrageneric level of genetic integration provable by naturalists' experience. He chose for it the designation of "species" and laid it down as primary, basic unit of his system. This is plainly evident from his own writings; the story about Linnaean species being products of a logical division of genera is a pure fiction. Modern populational model of species, by 3 important criteria, appears to be more akin to the Linneaean one than to the ideas of Lamarckism and early Darwinism. Systematic approach focuses rather on the interrelations among elements and their relative position, then on the properties and qualities of separately treated individual elements. In the development of systematics the aspect of "nexification" (study of connections) has been continuously gaining attention especially regarding the nomenclature where connotation has been totally forced out by denotation.     

Rapid adaptation: a new dimension for evolutionary perspectives in ecology

Although the study of adaptation is central to biology, two types of adaptation are recognized in the biological field: physiological adaptation (accommodation or acclimation; an individual organism’s phenotype is adjusted to its environment) and evolutionary–biological adaptation (adaptation is shaped by natural selection acting on genetic variation). The history of the former concept dates to the late nineteenth and early twentieth centuries, and has more recently been systemized in the twenty-first century. Approaches to the understanding of phenotypic plasticity and learning behavior have only recently been developed, based on cellular–histological and behavioral–neurobiological techniques as well as traditional molecular biology. New developments of the former concepts in phenotypic plasticity are discussed in bacterial persistence, wing di-/polymorphism with transgenerational effects, polyphenism in social insects, and defense traits for predator avoidance, including molecular biology analyses. We also discuss new studies on the concept of genetic accommodation resulting in evolution of phenotypic plasticity through a transgenerational change in the reaction norm based on a threshold model. Learning behavior can also be understood as physiological phenotypic plasticity, associating with the brain–nervous system, and it drives the accelerated evolutionary change in behavioral response (the Baldwin effect) with memory stock. Furthermore, choice behaviors are widely seen in decision-making of animal foragers. Incorporating flexible phenotypic plasticity and learning behavior into modeling can drastically change dynamical behavior of the system. Unification of biological sciences will be facilitated and integrated, such as behavioral ecology and behavioral neurobiology in the area of learning, and evolutionary ecology and molecular developmental biology in the theme of phenotypic plasticity.     

Biological species is the only possible form of existence for higher organisms: the evolutionary meaning of sexual reproduction

   

Consistent holistic view of sexual species as the highest form of biological existence is presented. The Weismann's idea that sex and recombination provide the variation for the natural selection to act upon is dominated in most discussions of the biological meaning of the sexual reproduction. Here, the idea is substantiated that the main advantage of sex is the opposite: the ability to counteract not only extinction but further evolution as well. Living systems live long owing to their ability to reproduce themselves with a high fidelity. Simple organisms (like bacteria) reach the continued existence due to the high fidelity of individual genome replication. In organisms with a large genome and complex development, the achievable fidelity of DNA replication is not enough for the precise reproduction of the genome. Such species must be capable of surviving and must remain unchanged in spite of the continuous changes of their genes. This problem has no solution in the frame of asexual ("homeogenomic") lineages. They would rapidly degrade and become extinct or blurred out in the course of the reckless evolution. The core outcome of the transition to sexual reproduction was the creation of multiorganismic entity - biological species. Individual organisms forfeited their ability to reproduce autonomously. It implies that individual organisms forfeited their ability to substantive evolution. They evolve as a part of the biological species. In case of obligatory sexuality, there is no such a thing as synchronic multi-level selection. Natural selection cannot select anything that is not a unit of reproduction. Hierarchy in biology implies the functional predestination of the parts for the sake of the whole. A crucial feature of the sexual reproduction is the formation of genomes of individual organisms by random picking them over from the continuously shuffled gene pool instead of the direct replication of the ancestor's genome. A clear anti-evolutionary consequence of the sexuality is evident from the fact that the genotypes of the individuals with an enhanced competitiveness are not transmitted to the next generation. Instead, after mating with "ordinary" individuals, these genotypes scatter and rearrange in new gene combinations, thus preventing the winner from exploiting the success.     

Kingdom animalia: The zoological malaise from a microbial perspective

Pain and cognitive dissonance abounds amongst biologists: theplant-animal, botany-zoology wound has nearly healed and thenew gash—revealed by department and budget reorganizations—is"molecular" vs. "organismic" biology. Here I contend that resolutionof these tensions within zoology requires that an autopoietic-gaianview replace a mechanical-neodarwinian perspective; in the interestof brevity and since many points have been discussed elsewhere,rather than develop detailed arguments I must make staccatostatements and refer to a burgeoning literature. The first centralconcept is that animals, all organisms developing from blastularembryos, evolved from single protist cells that were unableto reproduce their undulipodia. The second points to the usefulnessof recognizing the analogy between cyclically established symbiosesand meiotic sexuality     

Reviving the superorganism

Individuals become functionally organized to survive and reproduce in their environments by the process of natural selection. The question of whether larger units such as groups and communities can possess similar properties of functional organization, and therefore be regarded as "superorganisms", has a long history in biological thought. Modern evolutionary biology has rejected the concept of superorganisms, explaining virtually all adaptations at the individual or gene level. We criticize the modern literature on three counts. First, individual selection in its strong form is founded on a logical contradiction, in which genes-in-individuals are treated differently than individuals-in-groups or species-in-communities. Imposing consistency clearly shows that groups and communities can be organisms in the same sense that individuals are. Furthermore, superorganisms are more than just a theoretical possibility and actually exist in nature. Second, the view that genes are the "ultimate" unit of selection is irrelevant to the question of functional organization. Third, modern evolutionary biology includes numerous conceptual frameworks for analyzing evolution in structured populations. These frameworks should be regarded as different ways of analyzing a common process which, to be correct, must converge on the same conclusions. Unfortunately, evolutionists frequently regard them as competing theories that invoke different mechanisms, such that if one is "right" the others must be "wrong". The problem of multiple frameworks is aggravated by the fact that major terms, such as "units of selection", are defined differently within each framework, yet many evolutionists who use one framework to argue against another assume shared meanings. We suggest that focusing on the concept of organism will help dispell this fog of semantic confusion, allowing all frameworks to converge on the same conclusions regarding units of functional organization.     

A pervasive denigration of natural history misconstrues how biodiversity inventories and taxonomy underpin scientific knowledge

Embracing comparative biology, natural history encompasses those sciences that discover, decipher and classify unique (idiographic) details of landscapes, and extinct and extant biodiversity. Intrinsic to these multifarious roles in expanding and consolidating research and knowledge, natural history endows keystone support to the veracity of law-like (nomothetic) generalizations in science. What science knows about the natural world is governed by an inherent function of idiographic discovery; characteristic of natural history, this relationship is exemplified wherever an idiographic discovery overturns established wisdom. This nature of natural history explicates why inventories are of such epistemological importance. Unfortunately, a Denigration of Natural History weakens contemporary science from within. It expresses in the prevalent, pervasive failure to appreciate this pivotal role of idiographic research: a widespread disrespect for how natural history undergirds scientific knowledge. Symptoms of this Denigration of Natural History present in negative impacts on scientific research and knowledge. One symptom is the failure to appreciate and support the inventory and monitoring of biodiversity. Another resides in failures of scientiometrics to quantify how taxonomic publications sustain and improve knowledge. Their relevance in contemporary science characteristically persists and grows; so the temporal eminence of these idiographic publications extends over decades. This is because they propagate a succession of derived scientific statements, findings and/or conclusions - inherently shorter-lived, nomothetic publications. Widespread neglect of natural science collections is equally pernicious, allied with disregard for epistemological functions of specimens, whose preservation maintains the veracity of knowledge. Last, but not least, the decline in taxonomic expertise weakens research capacity; there are insufficient skills to study organismal diversity in all of its intricacies. Beyond weakening research capacities and outputs across comparative biology, this Denigration of Natural History impacts on the integrity of knowledge itself, undermining progress and pedagogy throughout science. Unprecedented advances in knowledge are set to follow on consummate inventories of biodiversity, including the protists. These opportunities challenge us to survey biodiversity representatively—detailing the natural history of species. Research strategies cannot continue to ignore arguments for such an unprecedented investment in idiographic natural history. Idiographic shortcuts to general (nomothetic) insights simply do not exist. The biodiversity sciences face a stark choice. No matter how charismatic its portrayed species, an incomplete ‘Brochure of Life’ cannot match the scientific integrity of the ‘Encyclopedia of Life’.     

Gravitational biology within the German Space Program: goals, achievements, and perspectives

Summary. Gravity plays an important role for the evolution, orientation and development of organisms. Most of us, however, tend to overlook its importance because – due to its constant presence from the beginning of evolution some 4 billion years ago – this environmental parameter is almost hardwired into our interpretation of reality. This negligence of gravity is the more surprising as we all have our strong fights with this factor, especially during the very early and again during the late phases of our lives. On the other hand, scientists have been fascinated to observe the effects of gravity especially on plants and microorganisms for more than a hundred years, since Darwin and Sachs demonstrated the role of the root cap for downward growing plants. Different experimental approaches are nowadays available in order to change the influence of gravity and to study the corresponding influences on the physiology of biological systems. With the advent of spaceflight, a long-term nearly nullification of gravity is possible. Utilisation of this so-called “microgravity” condition for research in life sciences thus became an important asset in the space programs of various space agencies around the world. The German Space Life Sciences Program is managed – like all other space programs and activities in Germany – by the German Aerospace Center (DLR) in its role as space agency for Germany. Within the current space program, approved by the German government in May 2001, the overall goal for its life sciences part was defined as to gain scientific knowledge and to disclose new application potential by research under space conditions, especially by utilising the microgravity environment of the International Space Station. Three main scientific fields have been identified in collaboration with the scientific community: integrative human physiology, biotechnological applications of the microgravity environment, and fundamental biology of gravity and radiation responses (i.e., gravitational and radiation biology). In the present contribution, specific goals as well as achievements and perspectives of research in gravitational biology are given. In addition, some information is provided on spaceflight opportunities available. Correspondence and reprints: German Aerospace Center (DLR), Space Agency, P.O. Box 300364, 53183 Bonn, Federal Republic of Germany.     

A No-Holds-Barred Evolution Curriculum for Elementary and Junior High School Students

Understanding the basic mechanism of evolution by natural selection together with examples of how it works in nature is crucial for explaining and teaching the workings of biology and ecology to young students. Dobzhansky said it best in his advice to educators of biology: “Nothing in biology makes sense except in the light of evolution.” This premise is true at all levels of biology but especially so in the elementary years where foundations of science knowledge are laid. Elementary students are capable of learning cohesive and connected stories of biological principles and learning them within a no-holds-barred arena wherein concepts and processes usually reserved for high school years are taught with special care, appropriate exercises, and patient explanations. This story must include solid introductions to the fundamental principles of evolution by natural selection that are threaded within and alongside those of basic biology and ecology. This paper attempts to make the case for the inclusion of connected stories of biology in the earliest years of education and to include within that education the unifying theme of all biology and ecology studies—evolution.     

Organisms as natural purposes: the contemporary evolutionary perspective

Kant's conception of organisms as natural purposes raises a challenge to the adequacy of mechanistic explanation in biology. Certain features of organisms appear to be inexplicable by appeal to mechanical law alone. Some biological phenomena, it seems, can only be accounted for teleologically. Contemporary evolutionary biology has by and large ignored this challenge. It is widely held that Darwin's theory of natural selection gives us an adequate, wholly mechanical account of the nature of organisms. In contemporary biology, the category of the organism plays virtually no explanatory role. Contemporary evolutionary biology is a science of sub-organismal entities-replicators. I argue that recent advances in developmental biology demonstrate the inadequacy of sub-organismal mechanism. The category of the organism, construed as a 'natural purpose' should play an ineliminable role in explaining ontogenetic development and adaptive evolution. According to Kant the natural purposiveness of organisms cannot be demonstrated to be an objective principle in nature, nor can purposiveness figure in genuine explain. I attempt to argue, by appeal to recent work on self-organization, that the purposiveness of organisms is a natural phenomenon, and, by appeal to the apparatus of invariance explanation, that biological purposiveness provides genuine, ineliminable biological explanations.     

Natural history of model organisms: The secret (group) life of Drosophila melanogaster larvae and why it matters to developmental ecology

1. Model organisms such as Drosophila melanogaster have been key tools for advancing our fundamental and applied knowledge in biological and biomedical sciences. However, model organisms have become intertwined with the idea of controlled and stable laboratory environments, and their natural history has been overlooked.
2. In holometabolous insects, lack of natural history information on larval ecology has precluded major advances in the field of developmental ecology, especially in terms of manipulations of population density early in life (i.e., larval density). This is because of relativistic and to some extent, arbitrary methodologies employed to manipulate larval densities in laboratory studies. As a result, these methodologies render comparisons between species impossible, precluding our understanding of macroevolutionary responses to population densities during development that can be derived from comparative studies.
3. We recently proposed a new conceptual framework to address this issue, and here, we provide the first natural history investigation of Drosophila melanogaster larval density under such framework. First, we characterized the distribution of larval densities in a wild population of D. melanogaster using rotting apples as breeding substrate in a suburban area in Sweden.
4. Next, we compiled the commonly used methodologies for manipulating larval densities in laboratory studies from the literature and found that the majority of laboratory studies identified did not manipulate larval densities below or above the densities observed in nature, suggesting that we have yet to study true life history and physiological responses to low and high population densities during D. melanogaster development.
5. This is, to our knowledge, the first direct natural history account of larval density in nature for this model organism. Our study paves the way for a more integrated view of organismal biology which re‐incorporates natural history of model organisms into hypothesis‐driven research in developmental ecology.

     

Ins and Outs of Systems Biology vis-à-vis Molecular Biology: Continuation or Clear Cut?

The comprehension of living organisms in all their complexity poses a major challenge to the biological sciences. Recently, systems biology has been proposed as a new candidate in the development of such a comprehension. The main objective of this paper is to address what systems biology is and how it is practised. To this end, the basic tools of a systems biological approach are explored and illustrated. In addition, it is questioned whether systems biology ‘revolutionizes’ molecular biology and ‘transcends’ its assumed reductionism. The strength of this claim appears to depend on how molecular and systems biology are characterised and on how reductionism is interpreted. Doing credit to molecular biology and to methodological reductionism, it is argued that the distinction between molecular and systems biology is gradual rather than sharp. As such, the classical challenge in biology to manage, interpret and integrate biological data into functional wholes is further intensified by systems biology’s use of modelling and bioinformatics, and by its scale enlargement.     

Homology and the hierarchy of biological systems

Homology is the similarity between organisms due to common ancestry. Introduced by Richard Owen in 1843 in a paper entitled "Lectures on comparative anatomy and physiology of the invertebrate animals", the concept of homology predates Darwin's "Origin of Species" and has been very influential throughout the history of evolutionary biology. Although homology is the central concept of all comparative biology and provides a logical basis for it, the definition of the term and the criteria of its application remain controversial. Here, I will discuss homology in the context of the hierarchy of biological organization. I will provide insights gained from an exemplary case study in evolutionary developmental biology that indicates the uncoupling of homology at different levels of biological organization. I argue that continuity and hierarchy are separate but equally important issues of homology.     

Biology and philosophy in Yellowstone

Yellowstone National Park poses critical issues in biology and philosophy. Among these are (1) how to value nature, especially at the ecosystem level, and whether to let nature take its course or employ hands-on scientific management; (2) the meaning of natural as this operates in park policy; (3) establishing biological claims on th scale of regional systems; (4) the interplay of natural and cultural history, involving both native and European Americans; (5) and sociopolitical forces as determinants in biological discovery. Alston Chase's strident Playing God in Yellowstone is critized and used as a test of David Hull's naturalistic philosophy of biology. Biology and philosophy in Yellowstone ought to combine for an appropriate environmental ethic.The author thanks Donald A. Crosby, Jann Benson, Tom Wolf, William W. Dunmire, Norman A. Bishop, and Paul Schullery for critical help.     

Coral Reef Communities as Prime Resources for Analysis of Evolution and Physiology of Behavior

The abundance and great diversity of life on coral reef ecosystemsprovides many good opportunities for studying the evolutionand specializations of neurophysiological systems and behavior.Crucial stages in the evolution of nervous systems appear tohave occurred in the Precambrian, as revealed in Ediacaran fossilsand their closest living relatives. By the Ordovician, whenChazy "reefs’ exemplify some of the earliest complex animalcommunities fixed in one place, more elaborate neurologicalmechanisms for orientation, predation, and escape reactionsare indicated. With the evolution offish, the behavioral richnessof reef communities became further enhanced. Elaborate specializationsof feeding, defensive, aggressive, signaling, schooling, andreproductive behaviors are common in fish. Several examplesof behavioral studies on reef organisms are used to illustrateresearch methodologies and the types of conclusions which maybe drawn. These examples include: (1) analysis of symbioticbehavior of an invertebrate and a vertebrate—sea anemoneand clownfish; (2) signaling behavior of a fish—the sailfishblenny; and (3) a combined electrophysiological and behavioralanalysis of orientation and feeding/attack behavior—sharks.An almost endless number of possibilities for similar analysismakes the organisms of coral reefs especially useful, and challenging,for teaching purposes as well as further research.     

Diet of the snake Philodryas nattereri (Steindachner, 1870) suggests a high plasticity of foraging in north-eastern Brazil

The knowledge about interactions between predators and prey is essential for understanding the natural history of animals, especially snakes, which are cryptic organisms that are difficult to visualize in the wild. This article reports on the predation of lizards, frogs, bats and venomous snakes by the snake Philodryas nattereri, evidencing its generalist feeding habits.     

Chlamydomonas: Fast tracking from genomics

Elucidating biological processes has relied on the establishment of model organisms, many of which offer advantageous features such as rapid axenic growth, extensive knowledge of their physiological features and gene content, and the ease with which they can be genetically manipulated. The unicellular green alga Chlamydomonas reinhardtii has been an exemplary model that has enabled many scientific breakthroughs over the decades, especially in the fields of photosynthesis, cilia function and biogenesis, and the acclimation of photosynthetic organisms to their environment. Here, we discuss recent molecular/technological advances that have been applied to C. reinhardtii and how they have further fostered its development as a “flagship” algal system. We also explore the future promise of this alga in leveraging advances in the fields of genomics, proteomics, imaging, and synthetic biology for addressing critical future biological issues.