The Cell and Protoplasm as Container,Object, and Substance, 1835–1861

This article revisits the development of the protoplasm concept as it originally arose from critiques of the cell theory, and examines how the term “protoplasm” transformed from a botanical term of art in the 1840s to the so-called “living substance” and “the physical basis of life” two decades later. I show that there were two major shifts in biological materialism that needed to occur before protoplasm theory could be elevated to have equal status with cell theory in the nineteenth century. First, I argue that biologists had to accept that life could inhere in matter alone, regardless of form. Second, I argue that in the 1840s, ideas of what formless, biological matter was capable of dramatically changed: going from a “coagulation paradigm” (Pickstone, 1973) that had existed since Theophrastus, to a more robust conception of matter that was itself capable of movement and self-maintenance. In addition to revisiting Schleiden and Schwann’s original writings on cell theory, this article looks especially closely at Hugo von Mohl’s definition of the protoplasm concept in 1846, how it differed from his primordial utricle theory of cell structure two years earlier. This article draws on Lakoff and Johnson’s theory of “ontological metaphors” to show that the cell, primordial utricle, and protoplasm can be understood as material container, object, and substance, and that these overlapping distinctions help explain the chaotic and confusing early history of cell theory.     

Biostructural theory of the living systems

Eugen Macovschi is among the few scientists who tried, and partly succeeded, to explain the differences between "dead" and "living" in biological sciences. He discovered and characterized the so-called biostructure of the living bodies and worked out a biostructural theory, which is the first supramolecular conception in biology. Nevertheless, complex biological systems are currently considered only from the molecular point of view, although they may be regarded as specific phenomena on highly structured bodies within the four-dimensional Universe. According to Macovschi, the biostructure provides organisms with life properties and controls their life processes and chemical changes. Nevertheless, plant cells or bacterial ones differ much from the animal or human cells. In fact, there are various biostructures which are related with cell properties. Hence, this theory creates confusions and cannot be easily used to explain all the properties of the biosystems. Consequently, it is our goal to highlight the principles, advantages, limitations, and applications of the biostructural theory, which might support new ideas and theories in modern life sciences.     

The Origin of Cellular Life and Biosemiotics

Recent successes of systems biology clarified that biological functionality is multilevel. We point out that this fact makes it necessary to revise popular views about macromolecular functions and distinguish between local, physico-chemical and global, biological functions. Our analysis shows that physico-chemical functions are merely tools of biological functionality. This result sheds new light on the origin of cellular life, indicating that in evolutionary history, assignment of biological functions to cellular ingredients plays a crucial role. In this wider picture, even if aggregation of chance mutations of replicator molecules and spontaneously self-assembled proteins led to the formation of a system identical with a living cell in all physical respects but devoid of biological functions, it would remain an inanimate physical system, a pseudo-cell or a zombie-cell but not a viable cell. In the origin of life scenarios, a fundamental circularity arises, since if cells are the minimal units of life, it is apparent that assignments of cellular functions require the presence of cells and vice versa. Resolution of this dilemma requires distinguishing between physico-chemical and biological symbols as well as between physico-chemical and biological information. Our analysis of the concepts of symbol, rule and code suggests that they all rely implicitly on biological laws or principles. We show that the problem is how to establish physico-chemically arbitrary rules assigning biological functions without the presence of living organisms. We propose a solution to that problem with the help of a generalized action principle and biological harnessing of quantum uncertainties. By our proposal, biology is an autonomous science having its own fundamental principle. The biological principle ought not to be regarded as an emergent phenomenon. It can guide chemical evolution towards the biological one, progressively assigning greater complexity and functionality to macromolecules and systems of macromolecules at all levels of organization. This solution explains some perplexing facts and posits a new context for thinking about the problems of the origin of life and mind.     

The redoubtable cell

The cell theory—the thesis that all life is made up of one or more cells, the fundamental structural and physiological unit—is one of the most celebrated achievements of modern biological science. And yet from its very inception in the nineteenth century it has faced repeated criticism from some biologists. Why do some continue to criticize the cell theory, and how has it managed nevertheless to keep burying its undertakers? The answers to these questions reveal the complex nature of the cell theory and the cell concept on which it is based. Like other scientific ‘laws’, the assertion that all living things are made of cells purchases its universality at the expense of abstraction. If, however, this law is regarded merely as a widely applicable empirical generalization with notable exceptions, it still remains too important to discard. Debate about whether the cell or the organism standpoint provides the more correct account of anatomical, physiological, and developmental facts illustrates the tension between our attempts to express the truth about reality in conceptual terms conducive to a unified human understanding.     

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.     

Abstract mathematical molecular biology

The tremendous complexity of even the simplest living unit makes a correct theoretical guess as to its mechanism very difficult. It is therefore suggested that, following the example of the physical sciences, a number of purely abstract cases in molecular biology be studied mathematically at first. Subsequent comparison of the different conclusions of such an abstract theory with available data would enable us to decide which of the conceivable situations are likely to occur in reality. As a first step toward such a study the problem of the minimal size of a living unit is studied. Usually the minimal size is considered to be determined by information-theoretical requirements. It is shown that the minimal size may have a very different origin. It may be determined by the possibility that too small a system, even though performing all necessary biological functions, may not be viable unless it is a member of a large group of other similar systems. This approach is developed both from a metric and from a relational point of view. Some relational characteristics of systems of reactions which possess the elementary metabolic properties of organisms are studied.     

体外模型的发展及其在鲸豚研究中的应用

体外补充替代模型“细胞系”为生命科学研究提供了新的平台,在一定程度上突破了科学研究中伦理、法律、动物福利和动物保护等的限制,从细胞和分子视角更深层次地揭示复杂生命体的生物效应和 调控机制。尤其对于濒危动物,细胞系的建立与超低温冷冻技术相结合,既可以保存濒危动物具有生物表达活性的遗传种质,又可以提供体外保育研究的新平台（如动物毒理学实验）,对动物保护意义 重大。目前细胞培养体系已作为多功能平台被应用于鲸豚类细胞遗传学、病毒学和毒理学的相关研究中,但从物种和组织来源以及细胞类型来看,能长期稳定传代的鲸豚类细胞系仍较单一。优化细胞培 养条件,运用鲸豚类体外细胞揭示更多的生命机制问题,仍是当前鲸豚类体外细胞模型研究所面临的挑战。本文对动物体外模型及其在鲸豚研究中的应用进行了概述,以期推动该技术在鲸豚保育研究中 的创新和发展。     

Franz Boas: cultural history for the present, or obsolete natural history?

Recently, some neo-Boasian anthropologists have portrayed Boas as an anthropologist with a deep sense of history, of the individual, and of agency. Focusing on Boas's ethnographic practice rather than his theoretical and programmatic statements, I first find an 'atomistic' (opposite of holistic) ethnographer, and a deep convergence between this atomism and Linnaean-type natural history. In Foucault and Jacob's interpretation of natural history, this means studying socio-cultural phenomena through their external manifestations, and removes historicity, and even individual cultures, from Boas's ethnography. Reviewing possible counter-evidence from the holistic Boas (his work on style, meaning, the 'genius of a people,' texts, secondary explanations, and psychology), I retrieve the same natural historian, and the same atomism. All these facets of his practice thus appear as surface manifestations of this underlying épistémè , which provides a single interpretative framework making it possible to integrate most of his ethnographic work. Overall, this worldview leaves little, or no, room for individuals and their agency.     

'Like all that lives': biology,medicine and bacteria in the age of Pasteur and Koch

This essay draws a new picture of the science of bacteria in its 'golden age', circa 1880-1900: the organization of its knowledge and practice, its germ theory of disease, the difference between its two major research traditions, and, above all, its place in life science in this period that bristled with theories and debates over inheritance, variation, selection, evolution and that witnessed the transition from natural history to laboratory biology. Pasteur and Koch's science acquired this biological dimension not despite being outside academic biology, nor despite the limitations of its applied, medical matrix, but rather because of that framework. The very practices of vaccine development constituted, at the same time, a new biological model of bacterial species and variation, which aligned them with other living things. Finally, the new picture reveals unsuspected continuity to later microbiology and molecular biology. In illuminating the self-perceptions of these sciences in relation to the past, it situates and opens a critical perspective on writings by bacteriologists such as Ludwik Fleck, Fran?ois Jacob and René Dubos, which have widely informed how we understand science.     

We age because we grow

Why do we age? Since ageing is a near-universal feature of complex organisms, a convincing theory must provide a robust evolutionary explanation for its ubiquity. This theory should be compatible with the physiological evidence that ageing is largely due to deterioration, which is, in principle, reversible through repair. Moreover, this theory should also explain why natural selection has favoured organisms that first improve with age (mortality rates decrease) and then deteriorate with age (mortality rates rise). We present a candidate for such a theory of life history, applied initially to a species with determinate growth. The model features both the quantity and the quality of somatic capital, where it is optimal to initially build up quantity, but to allow quality to deteriorate. The main theoretical result of the paper is that a life history where mortality decreases early in life and then increases late in life is evolutionarily optimal. In order to apply the model to humans, in particular, we include a budget constraint to allow intergenerational transfers. The resultant theory then accounts for all our basic demographic characteristics, including menopause with extended survival after reproduction has ceased.     

Biology of size and gravity]

Gravity is a force that acts on mass. Biological effects of gravity and their magnitude depend on scale of mass and difference in density. One significant contribution of space biology is confirmation of direct action of gravity even at the cellular level. Since cell is the elementary unit of life, existence of primary effects of gravity on cells leads to establish the firm basis of gravitational biology. However, gravity is not limited to produce its biological effects on molecules and their reaction networks that compose living cells. Biological system has hierarchical structure with layers of organism, group, and ecological system, which emerge from the system one layer down. Influence of gravity is higher at larger mass. In addition to this, actions of gravity in each layer are caused by process and mechanism that is subjected and different in each layer of the hierarchy. Because of this feature, summing up gravitational action on cells does not explain gravity for biological system at upper layers. Gravity at ecological system or organismal level can not reduced to cellular mechanism. Size of cells and organisms is one of fundamental characters of them and a determinant in their design of form and function. Size closely relates to other physical quantities, such as mass, volume, and surface area. Gravity produces weight of mass. Organisms are required to equip components to support weight and to resist against force that arise at movement of body or a part of it. Volume and surface area associate with mass and heat transport process at body. Gravity dominates those processes by inducing natural convection around organisms. This review covers various elements and process, with which gravity make influence on living systems, chosen on the basis of biology of size. Cells and biochemical networks are under the control of organism to integrate a consolidated form. How cells adjust metabolic rate to meet to the size of the composed organism, whether is gravity responsible for this feature, are subject we discuss in this article. Three major topics in gravitational and space biology are; how living systems have been adapted to terrestrial gravity and evolved, how living systems respond to exotic gravitational environment, and whether living systems could respond and adapt to microgravity. Biology of size can contribute to find a way to answer these question, and answer why gravity is important in biology, at explaining why gravity has been a dominant factor through the evolutional history on the earth.     

Synthetic biology of minimal living cells: primitive cell models and semi-synthetic cells

This article summarizes a contribution presented at the ESF 2009 Synthetic Biology focused on the concept of the minimal requirement for life and on the issue of constructive (synthetic) approaches in biological research. The attempts to define minimal life within the framework of autopoietic theory are firstly described, and a short report on the development of autopoietic chemical systems based on fatty acid vesicles, which are relevant as primitive cell models is given. These studies can be used as a starting point for the construction of more complex systems, firstly being inspired by possible origins of life scenarioes (and therefore by considering primitive functions), then by considering an approach based on modern biomacromolecular-encoded functions. At this aim, semi-synthetic minimal cells are defined as those man-made vesicle-based systems that are composed of the minimal number of genes, proteins, biomolecules and which can be defined as living. Recent achievements on minimal sized semi-synthetic cells are then discussed, and the kind of information obtained is recognized as being distinctively derived by a constructive approach. Synthetic biology is therefore a fundamental tool for gaining basic knowledge about biosystems, and it should not be confined at all to the engineering side.     

Graph theoretic topology of the Great but small Barrier Reef world

The transport of larvae between coral reefs is critical to the functioning of Australia’s Great Barrier Reef (GBR) because it determines recruitment rates and genetic exchange. One way of modelling the transport of larvae from one reef to another is to use information about currents. However the connectivity relationships of the entire system have not been fully examined. Graph theory provides a framework for the representation and analysis of connections via larval transport. In the past, the geometric arrangement (topology) of biological systems, such as food webs and neural networks, has revealed a common set of characteristics known as the ‘small world’ property. We use graph theory to examine and describe the topology and connectivity of a species living in 321 reefs in the central section of the GBR over 32 years. This section of the GBR can be described by a directional weighted graph, and we discovered that it exhibits scale-free small-world characteristics. The conclusion that the GBR is a small-world network for biological organisms is robust to variation in both the life history of the species modelled and yearly variation in hydrodynamics. The GBR is the first reported mesoscale biological small-world network.     

Diffusion theory in biology: a relic of mechanistic materialism

Diffusion theory explains in physical terms how materials move through a medium, e.g. water or a biological fluid. There are strong and widely acknowledged grounds for doubting the applicability of this theory in biology, although it continues to be accepted almost uncritically and taught as a basis of both biology and medicine. Our principal aim is to explore how this situation arose and has been allowed to continue seemingly unchallenged for more than 150 years. The main shortcomings of diffusion theory will be briefly reviewed to show that the entrenchment of this theory in the corpus of biological knowledge needs to be explained, especially as there are equally valid historical grounds for presuming that bulk fluid movement powered by the energy of cell metabolism plays a prominent note in the transport of molecules in the living body. First, the theory's evolution, notably from its origins in connection with the mechanistic materialist philosophy of mid nineteenth century physiology, is discussed. Following this, the entrenchment of the theory in twentieth century biology is analyzed in relation to three situations: the mechanism of oxygen transport between air and mammalian tissues; the structure and function of cell membranes; and the nature of the intermediary metabolism, with its implicit presumptions about the intracellular organization and the movement of molecules within it. In our final section, we consider several historically based alternatives to diffusion theory, all of which have their precursors in nineteenth and twentieth century philosophy of science. This revised version was published online in July 2006 with corrections to the Cover Date.     

The Theory of Tensegrity and Spatial Organization of Living Matter

There is still no consensus on the mechanisms regulating the formation and maintenance of morphological structures in the individual development of living organisms. The hypothesis that the mechanical forces are important for biological morphogenesis was put forward more than 100 years ago. In recent decades, studies indicating the regulatory role of mechanical stresses at different levels of organization of life have appeared. The signaling mechanisms that are responsible for the reception of mechanical influences and reprogramming of the properties of cells and tissues are studied. Since the mid-1970s, the principles of selfstressed structures or the tensegrity (tensional integrity) theory have been applied to understand the structure and functions of living structures in statics and dynamics. According to this standpoint, the cell can be represented as a self-stressed structure in which microtubules function as rigid rods and microfilaments serve as elastic threads. Such a system is anchored to extracellular matrix through cellular contacts, since it is adjusted to the external patterns of mechanical stresses. The notion of living systems as self-stressed structures provides a fresh look at the mechanotransduction, developing organism integrity, and biological morphogenesis. Although the application of the ideas of tensegrity to biological systems has not yet received broad support among biologists, the influence of these ideas on the formation of modern mechanobiology and understanding the crucial role of cytoskeletal structures in cellular processes should be mentioned.     

The emergence of life on Earth

Combined top-down and bottom-up research strategies and the principle of biological continuity were employed in an attempt to reconstruct a comprehensive origin of life theory, which is an extension of the coevolution theory (Lahav and Nir, Origins of Life Evol. Biosphere (1997) 27, 377-395). The resulting theory of emergence of templated-information and functionality (ETIF) addresses the emergence of living entities from inanimate matter, and that of the central mechanisms of their further evolution. It proposes the emergence of short organic catalysts (peptides and proto-ribozymes) and feedback-loop systems, plus their template-and-sequence-directed (TSD) reactions, encompassing catalyzed replication and translation of populations of molecules organized as chemical-informational feedback loop entities, in a fluctuating (wetting-drying) environment, functioning as simplified extant molecular-biological systems. The feedback loops with their TSD systems are chemically and functionally continuous with extant living organisms and their emergence in an inanimate environment may be defined as the beginning of life. The ETIF theory considers the emergence of bio-homochirality, a primordial genetic code, information and the incorporation of primordial metabolic cycles and compartmentation into the emerging living entities. This theory helps to establish a novel measure of biological information, which focuses on its physical effects rather than on the structure of the message, and makes it possible to estimate the time needed for the transition from the inanimate state to the closure of the first feedback-loop systems. Moreover, it forms the basis for novel laboratory experiments and computer modeling, encompassing catalytic activity of short peptides and proto-RNAs and the emergence of bio-homochirality and feedback-loop systems.     

History of the membrane (pump) theory of the living cell from its beginning in mid-19th century to its disproof 45 years ago--though still taught worldwide today as established truth

The concept that the basic unit of all life, the cell, is a membrane-enclosed soup of (free) water, (free) K+ (and native) proteins is called the membrane theory. A careful examination of past records shows that this theory has no author in the true sense of the word. Rather, it grew mostly out of some mistaken ideas made by Theodor Schwann in his Cell Theory. (This is not to deny that there is a membrane theory with an authentic author but this authored membrane theory came later and is much more narrowly focussed and accordingly can at best be regarded as an offshoot of the broader and older membrane theory without an author.) However, there is no ambiguity on the demise of the membrane theory, which occurred more than 60 years ago, when a flood of converging evidence showed that the asymmetrical distribution of K+ and Na+ observed in virtually all living cells is not the result of the presence of a membrane barrier that permits some solutes like water and K+ to move in and out of the cell, while barring--absolutely and permanently--the passage of other solutes like Na+. To keep the membrane theory afloat, submicroscopic pumps were installed across the cell membrane to maintain, for example, the level of Na+ in the cell low and the level of K+ high by the ceaseless pumping activities at the expense of metabolic energy. Forty-five year ago this version of the membrane theory was also experimentally disproved. In spite of all these overwhelming evidence against the membrane-pump theory, it still is being taught as verified truth in all high-school and biology textbooks known to us today. Meanwhile, almost unnoticed, a new unifying theory of the living cell, called the association-induction hypothesis came into being some 40 years ago. Also little noticed was the fact that it has received extensive confirmation worldwide and has shown an ability to provide self-consistent interpretations of most if not all known experimental observations that are contradicting the membrane-pump theory as well as other observations that seem to support the membrane pump theory.     

Koffka, Köhler, and the "crisis" in psychology

This paper examines the claims of the Gestalt psychologists that there was a crisis in experimental psychology ca. 1900, which arose because the prevailing sensory atomism excluded meaning from among psychological phenomena. The Gestaltists claim that a primary motivation of their movement was to show, against the speculative psychologists and philosophers and Verstehen historians, that natural scientific psychology can handle meaning. Purportedly, they revealed this motivation in their initial German-language presentations but in English emphasized their scientific accomplishments for an American audience. The paper finds that: there was a recognized crisis in the new experimental psychology ca. 1900 pertaining especially to sensory atomism; that the Gestaltists responded to the crisis with new experimental findings and theoretical concepts (Gestalten) that challenged atomism; in both languages, they raised problems of meaning and discussed the contest with speculative psychology and philosophy only after presenting their scientific case; that they introduced phenomenological observations on meaning and perceptual organization into their psychology but did not develop a theory of meaning or solve philosophical problems; that they argued "philosophically," that is, using abstract, conceptual arguments; and that this aspect of their cognitive style was not received well by some prominent members of their American audience.     

Species concepts and the ontology of evolution

Biologists and philosophers have long recognized the importance of species, yet species concepts serve two masters, evolutionary theory on the one hand and taxonomy on the other. Much of present-day evolutionary and systematic biology has confounded these two roles primarily through use of the biological species concept. Theories require entities that are real, discrete, irreducible, and comparable. Within the neo-Darwinian synthesis, however, biological species have been treated as real or subjectively delimited entities, discrete or nondiscrete, and they are often capable of being decomposed into other, smaller units. Because of this, biological species are generally not comparable across different groups of organisms, which implies that the ontological structure of evolutionary theory requires modification. Some biologists, including proponents of the biological species concept, have argued that no species concept is universally applicable across all organisms. Such a view means, however, that the history of life cannot be embraced by a common theory of ancestry and descent if that theory uses species as its entities.These ontological and biological difficulties can be alleviated if species are defined in terms of evolutionary units. The latter are irreducible clusters of reproductively cohesive organisms that are diagnosably distinct from other such clusters. Unlike biological species, which can include two or more evolutionary units, these phylogenetic species are discrete entities in space and time and capable of being compared from one group to the next.