The practical criteria by which developmental biologists choose their model systems have evolutionary correlates. The result is a sample that is not merely small, but biased in particular ways, for example towards species with rapid, highly canalized development. These biases influence both data collection and interpretation, and our views of how development works and which aspects of it are important.

Stem cell scientists and ethicists have focused intently on questions relevant to the developmental stage and developmental capacities of stem cells. Comparably less attention has been paid to an equally important set of questions about the nature of stem cells, their common characteristics, their non‐negligible differences and their possible developmental species specificity. Answers to these questions are essential to the project of justly inferring anything about human stem cell biology from studies in non‐human model systems—and so to the (...) possibility of eventually developing human therapies based on stem cell biology. After introducing and discussing these questions, I conclude with a brief discussion of the creation of novel model systems in stem cell biology: human‐to‐animal embryonic chimeras. Such novel model systems may help to overcome obstacles to extrapolation, but they are also scientifically and ethically contentious. BioEssays 26:1005‐1012, 2004. © 2004 Wiley Periodicals, Inc. (shrink)

Neurobiology studies mechanisms of cell signalling. A key question is how cells recognise specific signals. In this context, olfaction has become an important experimental system over the past 25 years. The olfactory system responds to an array of structurally diverse stimuli. The discovery of the olfactory receptors (ORs), recognising these stimuli, established the olfactory pathway as part of a greater group of signalling mechanisms mediated by G-protein-coupled receptors (GPCRs). GPCRs are the largest protein family in the mammalian genome and involved (...) in numerous fundamental physiological processes. The OR family exhibits two characteristics that make them an excellent model system to understand GPCRs: its size and the structural diversity of its members. Research on the OR binding site investigates what amino acid sequences determine the receptor-binding capacity. This promises a better understanding of how the basic genetic makeup of GPCRs relates to their diversification in ligand-binding capacities. (shrink)

The potential of the vertebrate limb as a model system to study developmental mechanisms is particularly well illustrated by the analysis of the Hox gene network. These genes are probably involved in the establishment of patterns encoding positional information. Their functional organisation during both limb and trunk development are very similar and seem to involve the progressive activation in time, along the chromosome, of a battery of genes whose products could differentially instruct those cells where they are expressed. This (...) process may be common to all organisms that develop according to an anterior‐posterior morphogenetic progression. The possible linkage of this system to a particular mechanism of segmentation as well as its phylogenetic implications are discussed. (shrink)

The potential of the vertebrate limb as a model system to study developmental mechanisms is particularly well illustrated by the analysis of the Hox gene network. These genes are probably involved in the establishment of patterns encoding positional information. Their functional organisation during both limb and trunk development are very similar and seem to involve the progressive activation in time, along the chromosome, of a battery of genes whose products could differentially instruct those cells where they are expressed. This (...) process may be common to all organisms that develop according to an anterior‐posterior morphogenetic progression. The possible linkage of this system to a particular mechanism of segmentation as well as its phylogenetic implications are discussed. (shrink)

The multiplicity of deubiquitinating enzymes (DUBs) encoded by vertebrate genomes is partly attributable to whole genome duplication events that occurred early in chordate evolution. By surveying the literature for the largest family of DUBs (the ubiquitin-specific proteases), extensive functional redundancy for duplicated genes has been confirmed as opposed to singletons. Dramatically conflicting results have been reported for loss of function studies conducted through RNA interference as opposed to inactivating mutations, but the contradictory findings can be reconciled by a recently proposed (...) compensatory mechanism involving nonsense-mediated RNA degradation. Duplicated genes are often inactivated to become pseudogenes, and it is proposed that such is the fate of the USP15 gene of zebrafish, a commonly used model system. As it is reviewed here, these observations have implications not only for the interpretation of model system phenotypes but also for therapeutic interventions designed to target DUBs. (shrink)

Physicists regularly invoke universal laws, such as those of motion and electromagnetism, to explain events. Biological and medical scientists have no such laws. How then do they acquire a reliable body of knowledge about biological organisms and human disease? One way is by repeatedly returning to, manipulating, observing, interpreting, and reinterpreting certain subjects—such as flies, mice, worms, or microbes—or, as they are known in biology, “model systems.” Across the natural and social sciences, other disciplinary fields have developed canonical (...) examples that have played a role comparable to that of biology’s model systems, serving not only as points of reference and illustrations of general principles or values but also as sites of continued investigation and reinterpretation. The essays in this collection assess the scope and function of model objects in domains as diverse as biology, geology, and history, attending to differences between fields as well as to epistemological commonalities. Contributors examine the role of the fruit fly Drosophila and nematode worms in biology, troops of baboons in primatology, box and digital simulations of the movement of the earth’s crust in geology, and meteorological models in climatology. They analyze the intensive study of the prisoner’s dilemma in game theory, ritual in anthropology, the individual case in psychoanalytic research, and Athenian democracy in political theory. The contributors illuminate the processes through which particular organisms, cases, materials, or narratives become foundational to their fields, and they examine how these foundational exemplars—from the fruit fly to Freud’s Dora—shape the knowledge produced within their disciplines. Contributors Rachel A. Ankeny Angela N. H. Creager Amy Dahan Dalmedico John Forrester Clifford Geertz Carlo Ginzburg E. Jane Albert Hubbard Elizabeth Lunbeck Mary S. Morgan Josiah Ober Naomi Oreskes Susan Sperling Marcel Weber M. Norton Wise. (shrink)

In the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, the initiation of DNA replication is controlled at a point called START. At this point, the cellular environment is assessed; only if conditions are appropriate do cells traverse START, thus becoming committed to initiate DNA replication and complete the remainder of the cell cycle. The cdc2+ / CDC28+ gene, encoding the protein kinase p34, is a key element in this complex control. The identification of structural and functional homologues of p34 suggests that (...) it has a role in the control of DNA replication in all eukaryotes. The WHI1+, CLN1+ and CLN2+ gene products, identified in S. cerevisiae, are positive regulators that function at START and may interact with p34. Determining how passing the START control point leads to the initiation of DNA replication is a major outstanding challenge in cell cycle studies. (shrink)

This paper argues that the biochemistry of memory consolidation provides valuable model systems for exploring the multiple realization of psychological states.

The system-parametric method developed by A. Uyemov allows creating a model of the contemporary bifurcational reality. There are many terms adopted from other sciences which are often used in postmodern philosophy. Bifurcation is one of such terms adopted from synergetics. In this article emphasis is placed on the contemporary time which is bifurcational in its essence. Using the key thesis of the systems method which states that any object can be presented as a system, we propose to create (...) a model of social ladenness. The mere fact that ladenness exists, makes the system of crisis nature. The social ladenness is defined using system descriptors. This definition contains the concept, the structure, and the substrate of the object and analysis of their elements. Consistence and hierarchical arrangement of the descriptors is the social ladenness model under discussion. The elements identified in the social ladenness model are the economic, political, technical, ecological, religious, creative and bifurcation impact. We identified some markers of human existence in the community system. The coronavirus pandemic is used as an example to demonstrate the way the bifurcation society system model can be built in order to find solutions to overcome the social and individual crises. (shrink)

An abundance of information about lung development in animal models exists; however, comparatively little is known about lung development in humans. Recent advances using primary human lung tissue combined with the use of human in vitro model systems, such as human pluripotent stem cell‐derived tissue, have led to a growing understanding of the mechanisms governing human lung development. They have illuminated key differences between animal models and humans, underscoring the need for continued advancements in modeling human lung development (...) and utilizing human tissue. This review discusses the use of human tissue and the use of human in vitro model systems that have been leveraged to better understand key regulators of human lung development and that have identified uniquely human features of development. This review also examines the implementation and challenges of human model systems and discusses how they can be applied to address knowledge gaps. (shrink)

Spontaneous mutations that perturb myelination occur in a range of species including man, and together with engineered mutations have been used to study disease, normal myelination and axon/glial inter‐relationships. Only a minority of the currently defined mutations have an apparently simple pathogenesis due to lack of a functional protein. Mutations in the myelin basic protein gene lead to a lack of protein, resulting in changes in the structure of myelin, which can be rescued by transgenic complementation. The pathogenesis of autosomal (...) dominant and X‐linked mutations affecting either oligodendrocytes or Schwann cells is more complex. Point mutations may act in a dominant negative manner and gene dosage is clearly linked to phenotypic change. Mutations in regulatory genes, such as those encoding transcription factors, can also disturb myelination by selected cell types. Other less‐well studied and unexpected consequences of myelin mutations, such as seizures in mutations affecting genes expressed in Schwann cells and axonal changes associated with dysmyelination, are also considered. With the major developments in gene mapping and cloning it is now relevant to study mutations in a variety of species with the real prospect of defining their molecular basis. Examples are given of unusual, but potentially useful, uncharacterised mutations in dog and bovine. (shrink)

Fictionalists believe that scientific models are about model systems that are imaginary. Michael Weisberg has claimed that fictionalism is indefensible because many scientific models are about model systems that are unimaginable. According to a certain account of imagination, what Weisberg says is plausible. According to another, more defensible account of imagination, it is not. I discuss these issues within the context of an allegedly unimaginable model system in ecology, but the conclusions I draw are more (...) general. I then describe how fictionalism should be recast in order to deal with Weisberg’s critique. (shrink)

This article by Juri Lotman from the third volume of Trudy po znakovym sistemam (Sign Systems Studies) in 1967, deals with the problem of artistic modelling. The general working questions are whether art displays any characteristic traits that are common for all modelling systems and which could be the specific traits that can distinguish art from other modelling systems. Art is seen as a secondary modelling system, more precisely, as a play-type model, which is characterised simultaneously (...) by practical and conventional behaviour and constant awareness of the possibility of alternate meanings to the one that is currently being perceived. At the same time art has play-like elements but is not the same as play, since play is inherently rule-bound, whereas art is a more flexible model thepurpose of which is truth. Art is a special type of modelling system, since it is on one hand suitable for storing very large amount of complex information, but onthe other hand it can increase the stored information and transform the consumer. (shrink)

Aphids display an abundance of adaptations that are not easily studied in existing model systems. Here we review the biology of a new genomic model system, the pea aphid, Acyrthosiphon pisum. We then discuss several phenomena that are particularly accessible to study in the pea aphid: the developmental genetic basis of polyphenisms, aphid–bacterial symbioses, the genetics of adaptation and mechanisms of virus transmission. The pea aphid can be maintained in the laboratory and natural populations can be studied (...) in the field. These properties allow controlled experiments to be performed on problems of direct relevance to natural aphid populations. Combined with new genomic approaches, the pea aphid is poised to become an important model system for understanding the molecular and developmental basis of many ecologically and evolutionarily relevant problems. BioEssays 28: 747–755, 2006. © 2006 Wiley Periodicals, Inc. (shrink)

This article by Juri Lotman from the third volume of Trudy po znakovym sistemam (Sign Systems Studies) in 1967, deals with the problem of artistic modelling. The general working questions are whether art displays any characteristic traits that are common for all modelling systems and which could be the specific traits that can distinguish art from other modelling systems. Art is seen as a secondary modelling system, more precisely, as a play-type model, which is characterised simultaneously (...) by practical and conventional behaviour and constant awareness of the possibility of alternate meanings to the one that is currently being perceived. At the same time art has play-like elements but is not the same as play, since play is inherently rule-bound, whereas art is a more flexible model thepurpose of which is truth. Art is a special type of modelling system, since it is on one hand suitable for storing very large amount of complex information, but onthe other hand it can increase the stored information and transform the consumer. (shrink)

Cooption and modularity are informative concepts in evolutionary developmental biology. Genes function within complex networks that act as modules in development. These modules can then be coopted in various functional and evolutionary contexts. Hormonal signaling, the main focus of this review, has a modular character. By regulating the activities of genes, proteins and other cellular molecules, a hormonal signal can have major effects on physiological and ontogenetic processes within and across tissues over a wide spatial and temporal scale. Because of (...) this property, we argue that hormones are frequently involved in the coordination of life history transitions (LHTs) and their evolution (LHE). Finally, we promote the usefulness of a comparative, non-model system approach towards understanding how hormones function and guide development and evolution, highlighting thyroid hormone function in echinoids as an example. BioEssays 27:64–75, 2005. © 2004 Wiley Periodicals, Inc. (shrink)

Many lymphokine genes have now been cloned from activated T cells and their products have been expressed in mammalian cells. Use of these recombinant lymphokines has provided the opportunity to evaluate both the spectrum of their biological activities and the mechanisms of their action in promoting proliferation and differentiation of hemopoietic and lymphoid cells. Characterization of the structure of lymphokine genes will provide information about their regulated expression in T‐cell activation.

Embryonic stem cells are derived from the preimplantation embryo and can differentiate into virtually any other cell type, which is governed by lineage specific transcriptions factors binding to cis regulatory elements to mediate changes in gene expression. The reliance on transcriptional regulation to maintain pluripotency makes ESCs a valuable model to study the role of distal CREs such as enhancers in modulating gene expression to affect cell fate decisions. This review will highlight recent advance on transcriptional enhancers, focusing on (...) studies performed in ESCs. In addition, we argue that the Nanog locus, which encodes for an ESC-critical TF, is particularly informative because it contains multiple co-regulated genes and enhancers in close proximity to one another. The unique landscape at Nanog permits the study of ongoing questions including whether multiple enhancers function additively versus synergistically, determinants of gene specificity, and cell-to-cell variability in gene expression. Nanog encodes a transcription factor required to maintain ESC pluripotency. The Nanog locus is an ideal model to study enhancers because it contains multiple highly potent super-enhancers within a small region. Nanog and three super-enhancers are in close physical proximity but only two SEs are required for Nanog expression. (shrink)

The phenomenon of corruption as a type of crime is immanently inherent in social and political reality. Sociality as a trans-societal universal form of human community is the environment in which corruption ties are born and function. The socio-political structure is organized as a collective effort, on the one hand, it overcomes disintegration, and on the other, it generates corrupt behaviour patterns. Corruption models of behaviour have an extremely wide scale of distribution and are characterized by active institutional expansion into (...) various spheres and institutions of modern society, they feed business relations and administrative activities, covering huge masses of the population. In this sense, their study is extremely important and relevant. (shrink)

Cancer is one of the most frequent fatal human diseases. It is a genetic disease, and molecular analysis of the genes involved revealed that they belong to several distinct classes of molecules, one of which is the receptor tyrosine kinases. Neoplastic transformation is regarded as the result of a multistep process and, in most cases, it is hard to evaluate what the initial events in tumor formation are. What makes it difficult to approach this question is the paucity of animal (...) models for tumorigenesis allowing investigation of the mechanisms leading to uncontrolled cell proliferation. Melanoma formation in Xiphophorus is one of these model systems. Here, overexpression and activation of a receptor tyrosine kinase causes neoplastic transformation of pigment cells. Xiphophorus provides all the advantages of a well‐characterised genetic system. In addition, some crucial components of the transformation pathway have been identified at the molecular level. As a vertebrate, Xiphophorus might serve as a model system to aid understanding, in more general terms, of the mechanisms of tumorigenesis in human diseases. (shrink)

Invention is an important source of technology, and, to understand invention, one needs a model system or prototype. A candidate model system is the hand tool. Using the hand tool as an example, the authors present a systematic approach to invention, dealing with description, classification, and joining or integrating simpler forms. Heuristics for when to integrate are presented. Finally, the authors introduce a new way of thinking about hand tools: simple spatial transformations applied to an abstract element make (...) possible the re-creation of a large number of tools. (shrink)

This article by Juri Lotman from the third volume of Trudy po znakovym sistemam (Sign Systems Studies) in 1967, deals with the problem of artistic modelling. The general working questions are whether art displays any characteristic traits that are common for all modelling systems and which could be the specific traits that can distinguish art from other modelling systems. Art is seen as a secondary modelling system, more precisely, as a play-type model, which is characterised simultaneously (...) by practical and conventional behaviour and constant awareness of the possibility of alternate meanings to the one that is currently being perceived. At the same time art has play-like elements but is not the same as play, since play is inherently rule-bound, whereas art is a more flexible model thepurpose of which is truth. Art is a special type of modelling system, since it is on one hand suitable for storing very large amount of complex information, but onthe other hand it can increase the stored information and transform the consumer. (shrink)

The demonstration that pluripotent stem cells could be generated by somatic cell reprogramming led to wonder if these so-called induced pluripotent stem (iPS) cells would extend our investigation capabilities in the cancer research field. The first iPS cells derived from cancer cells have now revealed the benefits and potential pitfalls of this new model. iPS cells appear to be an innovative approach to decipher the steps of cell transformation as well as to screen the activity and toxicity of anticancer (...) drugs. A better understanding of the impact of reprogramming on cancer cell-specific features as well as improvements in culture conditions to integrate the role of the microenvironment in their behavior may strengthen the epistemic interest of iPS cells as model systems in oncology. (shrink)

Genes are gained and lost over the course of evolution. A recent study found that over 1,800 new genes have appeared during primate evolution and that an unexpectedly high proportion of these genes are expressed in the human brain. But what are the molecular functions of newly evolved genes and what is their impact on an organism's fitness? The acquisition of new genes may provide a rich source of genetic diversity that fuels evolutionary innovation. Although gene manipulation experiments are not (...) feasible in humans, studies in model organisms, such as Drosophila melanogaster, have shown that new genes can quickly become integrated into genetic networks and become essential for survival or fertility. Future studies of new genes, especially chimeric genes, and their functions will help determine the role of genetic novelty in the adaptation and diversification of species. (shrink)

The discussion over the roles of genes and environment on the phenotypical specification of organisms has held a central role in science philosophy since the late 19th century and has re‐emerged in today's debate over genetic determinism and developmental plasticity. In fin‐de‐siecle Vienna, this debate coincided with a philosophical debate over empiricism/materialism versus idealism/vitalism. Turn‐of‐the‐century Vienna's highly interdisciplinary environment was also the birthplace for the model system of the un‐opposed molar. The un‐opposed molar system features new tissue formation at (...) the roots of teeth and tooth drift once opposing teeth are lost. The un‐opposed molar model system was revived by a group of Viennese scientists who left Vienna during the Nazi period to address Vienna's questions about evolution and heredity and about genes and environment in Chicago's post‐WWII scientific exile community. Here we are using the colorful history of the un‐opposed molar to investigate the role of culture and method in the scientific evolution of a model system. BioEssays 29:819–830, 2007. © 2007 Wiley Periodicals, Inc. (shrink)

Like other sciences, biosemiotics also has its time-honoured archive, consisting of writings by those who have been invented and revered as ancestors of the discipline. One such example is Jakob von Uexküll. As to the people who ‘invented’ him, they are either, to paraphrase a French cliché, ‘agents du cosmopolitisme sémiotique’ like Thomas Sebeok, or de jure and de facto progenitor like Thure von Uexküll. In the archive is the special issue of Semiotica 42. 1 (1982) edited by the late (...) Sebeok and introduced by Thure von Uexküll. It is in the opening essay that Thure von UexküIl tries to restore Jakob von Uexküll’s role as a precursor of semiotics by negotiating the Elder with Saussure and the linguistics-oriented ‘semiology’ in his wake. However, semiotic mapping, in the strictly ‘disciplinary’ sense, of Jakob von Uexküll is no easy task because he ‘knew neither Peirce nor Saussure and did not use their terminology’ (Thure von Uexküll 1982,2). Because Thure prefers to call the Elder’s science ‘general semiotics’ (Thure von Uexküll 1982), this paper begins by assessing Thure von Uexküll’s semiotic configuration of Jakob, probe into the force and limits of the linguistic analogy, revisit the already time-honoured debate on the primary and secondary modelling systems, which was made famous by the Moscow-Tartu semioticians in the early 1970s, but severely criticized by Sebeok and his followers. The paper engages Sebeok from several fronts, directed first at his relegation of the Saussurian linguistic model, then at his critique of the Primary Modelling System, and finally at his reservation about evolutionism in light of the current debate on gene/meme co-evolution. (shrink)