The cuticle of the nematode Caenorhabditis elegans forms the barrier between the animal and its environment. In addition to being a protective layer, it is an exoskeleton which is important in maintaining and defining the normal shape of the nematode. The cuticle is an extracellular matrix consisting predominantly of small collagen‐like proteins that are extensively crosslinked. Although it also contains other protein and non‐protein compounds that undoubtedly play a significant part in its function, the specific role of collagen (...) in cuticle structure and morphology is considered here. The C. elegans genome contains between 50 and 150 collagen genes, most of which are believed to encode cuticular collagens. Mutations that result in cuticular defects and grossly altered body form have been identified in more than 40 genes. Six of these genes are now known to encode cuticular collagens, a finding that confirms the importance of this group of structural proteins to the formation of the cuticle and the role of the cuticle as an exoskeleton in shaping the worm. It is likely that many more of the genes identified by mutations giving altered body form, will be collagen genes. Mutations in the cuticular collagen genes provide a powerful tool for investigating the mechanisms by which this group of proteins interact to form the nematode cuticle. (shrink)

Comparisons between related species often allow the detailed genetic analysis of evolutionary processes. Here we advocate the use of the nematode Caenorhabditis elegans (and several other rhabditid species) as model systems for microevolutionary studies. Compared to Drosophila species, which have been a mainstay of such studies, C. elegans has a self‐fertilizing mode of reproduction, a shorter life cycle and a convenient cell‐level analysis of phenotypic variation. Data concerning its population genetics and ecology are still scarce, however. We review molecular, (...) behavioral and developmental intraspecific polymorphisms for populations of C. elegans, Oscheius sp. 1 and Pristionchus pacificus. Focusing on vulval development, which has been well characterized in several species, we discuss relationships between patterns of variations: (1) for a given genotype (developmental variants), (2) after mutagenesis (mutability), (3) in different populations of the same species (polymorphisms) and (4) between closely related species. These studies have revealed that evolutionary variations between sister species affect those characters that show phenotypic developmental variants, that are mutable and that are polymorphic within species. BioEssays 23:807–819, 2001. © 2001 John Wiley & Sons, Inc. (shrink)

Nematodes pervade Earth's biosphere and occupy innumerable ecological niches. The role of Caenorhabditis elegans as a model for developmental processes has encouraged us to cultivate a second nematode, Pristionchus pacificus, as a comparative counterpoint to address questions in development, behavior and ecology in nematode evolution. We hope that this endeavor, now more than a decade underway, will allow us to project findings onto other comparative models for biological processes. To this end, our laboratory has made an extensive genetic (...) map and mutant screens to understand changes in developmental programs. Recently, we have been capitalizing on the whole genome sequence of P. pacificus to describe more thoroughly the molecular basis for these changes, as well as to better integrate our molecular knowledge with the biodiversity of Pristionchus species. BioEssays 28: 651–659, 2006. © 2006 Wiley Periodicals, Inc. (shrink)

This study focuses on the concept of a 'model organism' in the biomedical sciences through an historical and philosophical examination of research with the nematode Caenorhabditis elegans. I explore the choice of C. elegans in the mid-1960s, showing a rich context existed within which the organism was selected as the focus for a molecular biological research program, including an experimental life prior to Sydney Brenner's work. I argue that this choice can be seen as an obvious outcome of what (...) was a complex search procedure, and that the success of the 'worm project' depended not only on organismal choice but also on the conceptual and institutional framework at the Laboratory of Molecular Biology in Cambridge within which it was pursued. Examination of C. elegans work in the late 1960s through the early 1980s illuminates several additional theses. Although development and behavior were the general areas of interest for the project, the original goals and proposed methodology were extremely vague. As the project evolved, which investigations proved to be tractable using the worm depended not only on which methodologies were fruitful but also on the interests and skills of early workers. Much of the power of C. elegans as a model organism can be traced historically to the investment of resources which resulted in an unprecedented, complete description of the organism, and represented a return to a more naturalistic biological tradition. In light of the historical study, I develop a philosophical analysis of C. elegans as a model organism through exploration of the three kinds of modeling with the worm: modeling of structures, processes, and information. I expand the notion of a descriptive model, arguing that C. elegans is best understood as a prototype of the metazoa, and that C. elegans as a model organism has been not only heuristically valuable, but also essential to this research project particularly in its pre-explanatory stages. I conclude by suggesting that more investigation of descriptive prototypes such as those in the worm project must be done to capture important aspects of the biomedical sciences that will be neglected if explanatory models are the sole focus in the philosophy of science. (shrink)

The process of chromatin diminution in Parascaris and Ascaris is a developmentally controlled genome rearrangement, which results in quantitative and qualitative differences in DNA content between germ line and somatic cells. Chromatin diminution involves chromosomal breakage, new telomere formation and DNA degradation. The programmed elimination of chromatin in presomatic cells might serve as an alternative way of gene regulation. We put forward a new hypothesis of how an ancient partial genome duplication and chromatin diminution may have served to maintain the (...) genetic balance in somatic cells and simultaneously endowed the germ line cells with a selective advantage. (shrink)

Comparative analysis of nematode development has revealed considerable variations in how the fates of embryonic cells are specified. Such early variations seem enigmatic as they do not influence the resultant structure or performance of the emerging animal. Three different nematode species are used to consider why alternative ways to reach the same goal may have been established during evolution and why early steps of embryogenesis are particularly variable. A scenario is sketched with a shift from late to early (...) cell specification, along with an increase in maternal contribution and developmental tempo and a decrease in regulative potential expressing different developmental strategies. Future studies of larger numbers of species are needed to assess the extent of such variations and to understand more fully the under lying mechanisms, rules and driving forces. BioEssays 23:841–847, 2001. © 2001 John Wiley & Sons, Inc. (shrink)

Signal transduction pathways are largely conserved throughout the animal kingdom. The repertoire of pathways is limited and each pathway is used in different intercellular signaling events during the development of a given animal. For example, Wnt signaling is recruited, sometimes redundantly with other molecular pathways, in four cell specification events during Caenorhabditis elegans vulva development, including the activation of vulval differentiation. Strikingly,a recent study finds that Wnts act to repress vulval differentiation in the nematode Pristionchus pacificus,1 demonstrating evolutionary flexibility (...) in the use of intercellular signaling pathways. BioEssays 27:765–769, 2005. © 2005 Wiley Periodicals, Inc. (shrink)

This essay considers biotrophic cyst and root‐knot nematodes in relation to their biology, host–parasite interactions and molecular genetics. These nematodes have to face the biological consequences of the physical constraints imposed by the soil environment in which they live while their hosts inhabit both above and below ground environments. The two groups of nematodes appear to have adopted radically different solutions to these problems with the result that one group is a host specialist and reproduces sexually while the other has (...) an enormous host range and reproduces by mitotic parthenogenesis. We consider what is known about the modes of parasitism used by these nematodes and how it relates to their host range, including the surprising finding that parasitism genes in both nematode groups have been recruited from bacteria. The nuclear and mitochondrial genomes of these two nematode groups are very different and we consider how these findings relate to the biology of the organisms. BioEssays 30:249–259, 2008. © 2008 Wiley Periodicals, Inc. (shrink)

The endomesoderm gene regulatory network (GRN) of C. elegans is a rich resource for studying the properties of cell‐fate‐specification pathways. This GRN contains both cell‐autonomous and cell non‐autonomous mechanisms, includes network motifs found in other GRNs, and ties maternal factors to terminal differentiation genes through a regulatory cascade. In most cases, upstream regulators and their direct downstream targets are known. With the availability of resources to study close and distant relatives of C. elegans, the molecular evolution of this network can (...) now be examined. Within Caenorhabditis, components of the endomesoderm GRN are well conserved. A cursory examination of the preliminary genome sequences of two parasitic nematodes, Haemonchus contortus and Brugia malayi, suggests that evolution in this GRN is occurring most rapidly for the zygotic genes that specify blastomere identity. BioEssays 28: 1010–1022, 2006. © 2006 Wiley Periodicals, Inc. (shrink)

During May-October 2007, soil and root samples from 539 fields were collected from 11 monsoon rice varieties in 12 regions in Myanmar. All regions surveyed and 90% of fields sampled were infested with the rice root nematode Hirschmanniella oryzae. The average H. oryzae population was 10/100 mL soil and 419/20 g roots respectively. In 6.9% of the fields sampled 50 H. oryzae/g root were found. The average root population densities were the highest (640/20 g roots) in Taungpyan variety and (...) the lowest (155/20 g roots) in Immayebaw variety. The lowest soil and the second-lowest root populations of H. oryzae were observed in Shwethweyin which may indicate that this rice variety is less susceptible to H. oryzae. Among three cropping sequences, the highest frequency of occurrence (94%) was found in the rice-rice cropping sequence. Based on the prominence value (a combination of the frequency of occurrence and abundance) of H. oryzae, Hlaingtharyar was the most infested region where susceptible rice varieties are grown and rice-rice cropping sequence is practiced. The rice production in this region may be the most at risk of suffering important yield losses due to H. oryzae. (shrink)

To understand how morphological characters change during evolution, we need insight into the evolution of developmental processes. Comparative developmental approaches that make use of our fundamental understanding of development in certain model organisms have been initiated for different animal systems and flowering plants. Nematodes provide a useful experimental system with which to investigate the genetic and molecular alterations underlying evolutionary changes of cell fate specification in development, by comparing different species to the genetic model system Caenorhabditis elegans. In this review, (...) I will first discuss the different types of evolutionary alterations seen at the cellular level by focusing mainly on the analysis of vulva development in different species. The observed alterations involve changes in cell lineage, cell migration and cell death, as well as induction and cell competence. I then describe a genetic approach in the nematode Pristionchus pacificus that might identify those genetic and molecular processes that cause evolutionary changes of cell fate specification. (shrink)

The pathway that controls sexual fate in the nematode Caenorhabditis elegans has been well characterized at the molecular level. By identifying differences between the sex‐determination mechanisms in C. elegans and other nematode species, it should be possible to understand how complex sex‐determining pathways evolve. Towards this goal, orthologues of many of the C. elegans sex regulators have been isolated from other members of the genus Caenorhabditis. Rapid sequence evolution is observed in every case, but several of the orthologues (...) appear to have conserved sex‐determining roles. Thus extensive sequence divergence does not necessarily coincide with changes in pathway structure, although the same forces may contribute to both. This review summarizes recent findings and, with reference to results from other animals, offers explanations for why sex‐determining genes and pathways appear to be evolving rapidly. Experimental strategies that hold promise for illuminating pathway differences between nematodes are also discussed. BioEssays 25: 221–231, 2003. © 2003 Wiley Periodicals, Inc. (shrink)

Nicotinic acetylcholine receptors (nAChRs) are ligand‐gated ion channels that bring about a diversity of fast synaptic actions. Analysis of the Caenorhabditis elegans genome has revealed one of the most‐extensive and diverse nAChR gene families known, consisting of at least 27 subunits. Striking variation with possible functional implications has been observed in normally conserved motifs at the acetylcholine‐binding site and in the channel‐lining region. Some nAChR subunits are particular to neurons whilst others are present in both neurons and muscles. The localization (...) of subunits in non‐synaptic regions suggests novel roles for nAChRs. Genetic and heterologous expression studies have identified a subset of nAChR subunits that are important drug targets while the study of mutants has identified genes functionally‐linked to nAChRs. Future studies using C. elegans offer the prospect of increasing our understanding of the functional diversity of a complex nAChR gene family as well as addressing the role of nAChRs and associated proteins in human disorders. BioEssays 26:39–49, 2004.© 2003 Wiley Periodicals, Inc. (shrink)

Chemotaxis and thermotaxis in Caenorhabditis elegans are based on the chemical senses (smell and taste) and the thermal sense, respectively, which are important for the life of the animal. Laser ablation experiments have allowed identification of sensory neurons and some interneurons required for these senses. Many mutants that exhibit various abnormalies have been isolated and analyzed. These studies have predicted novel signaling pathways whose components include a putative odorant specific transmembrane receptor (ODR‐10) and a cyclic nucleotide‐gated channel (TAX‐4/TAX‐2) functioning in (...) taste and thermosensation as well as in smell. The emerging picture of the mechanisms of sensory transduction in C. elegans seems to be basically similar to what is known of visual and olfactory sensory transduction in vertebrates. Thus, molecular and cellular analyses of chemotaxis and thermotaxis in C. elegans have proved useful and will continue to provide significant implications for the molecular basis of sensory systems in higher animals. (shrink)

Radopholus Similis (R. Similis) or burrowing nematode, is one of the most damaging and widespread nematodes attacking bananas, causing toppling or blackhead disease. A mathematical model for the population dynamics of R. Similis is considered, with the aim of investigating the impact of climatic factors on the growth of R. Similis. In this paper, based on the life cycle of R. Similis, we first propose a mathematical model to study and control the population dynamics of this banana pest. We (...) show also how control terms based on biological and chemical controls can be integrated to reduce the population of R. Similis within banana-plantain roots. Sensitivity analysis was performed to show the most important parameters of the model. We present the theoretical analysis of the model. More precisely, we derive a threshold parameter N0\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\mathcal{N}}_0$$\end{document}, called the basic offspring number and show that the trivial equilibrium is globally asymptotically stable whenever N0≤1\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\mathcal{N}}_0\le 1$$\end{document}, while when N0>1\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\mathcal{N}}_0> 1$$\end{document}, the non trivial equilibrium is globally asymptotically stable. After, we extend the proposed model by taking account climatic factors that influence the growth of this pest. Biological and chemical controls are now introduced through impulsive equations. Threshold and equilibria are obtained and global stabilities have been studied. The theoretical results are supported by numerical simulations. Numerical results of model with biological and chemical controls reveal that biological methods are more effective than chemical methods. We also found that the month February is the best time to apply these controls. (shrink)

In the last few years, annexins have been discovered in several nematodes and other parasites, and distinct differences between the parasite annexins and those of the hosts make them potentially attractive targets for anti‐parasite therapeutics. Annexins are ubiquitous proteins found in almost all organisms across all kingdoms. Here, we present an overview of novel annexins from parasitic organisms, and summarize their phylogenetic and biochemical properties, with a view to using them as drug or vaccine targets. Building on structural and biological (...) information that has been accumulated for mammalian and plant annexins, we describe a predicted additional secondary structure element found in many parasite annexins that may confer unique functional properties, and present a specific antigenic epitope for use as a vaccine. (shrink)

The nematode C. elegans exhibits a variety of reponses to touch. When specific sets of mechanosensory neurons are killed with a laser, specific touch responses are abolished. Many mutations that result in defective mechanosensation have been identified. Some of the mutations define genes that specify the fate of a set of mechanoreceptors called the touch cells, which mediate response to light touch to the body of the worm. Genes specifying touch cell fate appear to regulate genes that encode touch‐cell (...) differentiation proteins, including apparent subunits of a touch‐cell‐specific ion channel, rare mutant forms of which lead to swelling and lysis of the touch cells. Molecular attachments of the ion channel, both to extracellular matrix components and, intracellularly, to a special large‐diameter microtubule, may be required for mechanical gating of the channel. A mechanoreceptor‐interneuron‐motorneuron reflex circuit for response to light touch has been proposed. (shrink)

Nematodes are important parasites of humans and other animals. Nematode parasitism is thought to have evolved by free‐living, facultatively developing, arrested larvae becoming associated with animals, ultimately becoming parasites. The formation of free‐living arrested larvae of the nematode Caenorhabditis elegans is controlled by the environment, and involves dafachronic acid (DA) and transforming growth factor (TGF)‐β signalling. Recent data have shown that DA acid signalling plays a conserved role in controlling larval development in both free‐living and parasitic species. In (...) contrast, TGF‐β signalling does not seem to be conserved; this difference perhaps points to how nematode parasitism did evolve. (shrink)

Studies plant-parasitic nematodes and their impact on agriculture and ecosystems.

The parasitic nematode Ascaris lives in the low‐oxygen intestinal folds of over one billion people world‐wwide. The worm has an octameric hemoglobin that binds oxygen four orders of magnitude more tightly than does human hemogobin. Our studies have focused on elucidating the molecular mechanism of oxygen avidity, the basis of multimerization and the function of this remarkable molecule. We now believe that we understand a fair amount about the molecular interactions that result in enhanced avidity, have some preliminary ideas (...) on octamer formation, and have some hypotheses about possible function. Along the way we have stumbled into the disciplines of intron evolution, sterol biosynthesis and oxygen‐regulated gene expression. (shrink)

Development of the nematode Caenorhabditis elegans has been described completely on a cell‐by‐cell basis. In an invariant pattern five somatic founder cells and the primordial germ cell are generated within the first hour after the onset of cleavage. Using a laser microbeam for manipulation of individual blastomers several aspects of early embryogenesis have been investigated, including the expression of cellular polarity, the localization of lineage‐specific cleavage potential, the necessity for early cell–cell interaction, and the control of differential cell‐cycle timing. (...) The experiments demonstrate the central importance of a correct partitioning of cytoplasmic components during early embryogenesis and suggest a stepwise, binary segregation mechanism associated with the unequal cleavages in the germline. (shrink)

Motivational trade-off behaviours, where an organism behaves as if flexibly weighing up an opportunity for reward against a risk of injury, are often regarded as evidence that the organism has valenced experiences like pain. This type of evidence has been influential in shifting opinion regarding crabs and insects. Critics note that (i) the precise links between trade-offs and consciousness are not fully known; (ii) simple trade-offs are evinced by the nematode worm Caenorhabditis elegans, mediated by a mechanism plausibly too (...) simple to support conscious experience; (iii) pain can sometimes interfere with rather than support making trade-offs rationally. However, rather than undermining trade-off evidence in general, such cases show that the nature of the trade-off, and its underlying neural substrate, matter. We investigate precisely how. (shrink)

The question of the influence of genes on behavior raises difficult philosophical and social issues. In this paper I delineate what I call the Developmentalist Challenge (DC) to assertions of genetic influence on behavior, and then examine the DC through an indepth analysis of the behavioral genetics of the nematode, C. elegans, with some briefer references to work on Drosophila. I argue that eight "rules" relating genes and behavior through environmentally-influenced and tangled neural nets capture the results of developmental (...) and behavioral studies on the nematode. Some elements of the DC are found to be sound and others are criticized. The essay concludes by examining the relations of this study to Kitcher's antireductionist arguments and Bechtel and Richardson's decomposition and localization heuristics. Some implications for human behavioral genetics are also briefly considered. (shrink)

The biological sciences have become increasingly reliant on so-called 'model organisms'. I argue that in this domain, the concept of a descriptive model is essential for understanding scientific practice. Using a case study, I show how such a model was formulated in a preexplanatory context for subsequent use as a prototype from which explanations ultimately may be generated both within the immediate domain of the original model and in additional, related domains. To develop this concept of a descriptive model, I (...) focus on use of the nematode worm Caenorhabditis elegans and the wiring diagrams that were developed as models of its neural structure. In addition, implications of the concept of a descriptive model, particularly its relevance for the data-phenomena distinction as well as its relation to long-standing debates on realism, are briefly examined. (shrink)

Motivational trade-off behaviours, where an organism behaves as if flexibly weighing up an opportunity for reward against a risk of injury, are often regarded as evidence that the organism has valenced experiences like pain. This type of evidence has been influential in shifting opinion regarding crabs and insects. Critics note that (i) the precise links between trade-offs and consciousness are not fully known; (ii) simple trade-offs are evinced by the nematode worm Caenorhabditis elegans, mediated by a mechanism plausibly too (...) simple to support conscious experience; (iii) pain can sometimes interfere with rather than support making trade-offs rationally. However, rather than undermining trade-off evidence in general, such cases show that the nature of the trade-off, and its underlying neural substrate, matter. We investigate precisely how. (shrink)

Right after Philo’s about-face in Part 12 of the Dialogues, he gives an argument that the dispute between the theist and the atheist is merely verbal. Since everything is at least a little like everything else, the atheist must concede that the source of order is at least remotely like a human intellect, even if this source is something like a rotting turnip. This passage provides a major argument for dismissing Hume’s apparent avowals of theism in the Dialogues and elsewhere, (...) since Philo’s assertions are so loose as to let in a rotting turnip. The right reading of the passage is more interesting. The paragraph was written in 1776, right before Hume’s death. It’s thus one of the few philosophical texts written late enough to reflect his encounter with the French philosophes in the 1760s. We have good biographical evidence that Hume was criticized for being too much of a theist in France. The turnip is rotting not in order to make fun of the argument from design, but in order to make fun of d’Holbach's and Diderot's account of the origin of life, accounts that generalized dramatically from John Needham’s observations of nematodes in rotting wheat. In the rotting turnip paragraph, Hume is attempting to establish that the dispute between the theist and the atheist isn’t empirically tractable, that atheists will never outflank the apophatic theologian on the question of whether human minds are unlike God, and that if atheists are consistent with their analogical methods, they ought to be more open to the argument from design. (shrink)

The Bermuda Principles for DNA sequence data sharing are an enduring legacy of the Human Genome Project. They were adopted by the HGP at a strategy meeting in Bermuda in February of 1996 and implemented in formal policies by early 1998, mandating daily release of HGP-funded DNA sequences into the public domain. The idea of daily sharing, we argue, emanated directly from strategies for large, goal-directed molecular biology projects first tested within the “community” of C. elegans researchers, and were introduced (...) and defended for the HGP by the nematode biologists John Sulston and Robert Waterston. In the C. elegans community, and subsequently in the HGP, daily sharing served the pragmatic goals of quality control and project coordination. Yet in the HGP human genome, we also argue, the Bermuda Principles addressed concerns about gene patents impeding scientific advancement, and were aspirational and flexible in implementation and justification. They endured as an archetype for how rapid data sharing could be realized and rationalized, and permitted adaptation to the needs of various scientific communities. Yet in addition to the support of Sulston and Waterston, their adoption also depended on the clout of administrators at the US National Institutes of Health and the UK nonprofit charity the Wellcome Trust, which together funded 90% of the HGP human sequencing effort. The other nations wishing to remain in the HGP consortium had to accommodate to the Bermuda Principles, requiring exceptions from incompatible existing or pending data access policies for publicly funded research in Germany, Japan, and France. We begin this story in 1963, with the biologist Sydney Brenner’s proposal for a nematode research program at the Laboratory of Molecular Biology at the University of Cambridge. We continue through 2003, with the completion of the HGP human reference genome, and conclude with observations about policy and the historiography of molecular biology. (shrink)

In recent years, immune systems have sparked considerable interest within the philosophy of science. One issue that has received increased attention is whether other phyla besides vertebrates display an adaptive immune system. Particularly the discovery of CRISPR-Cas9-based systems has triggered a discussion about how to classify adaptive immune systems. One question that has not been addressed yet is the transgenerational aspect of the CRISPR-Cas9-based response. If immunity is acquired and inherited, how to distinguish evolutionary from immunological adaptation? To shed light (...) on this issue and obtain conceptual clarity, I will investigate the inheritance of small RNA responses to pathogens in the nematode C. elegans as a further potential instantiation of a transgenerational adaptive immune system. I will explore how to make sense of systems that lie at the crossroads between genetic, immunological, and evolutionary spheres and explore the consequences of a transgenerational perspective on immune systems for immunology and its philosophy. (shrink)

The rapid development of autonomous systems, some of which emulate animal abilities, raises a question about how to understand and compare their complexity. Taking an “agent” to be any system that can be well-explained by attributing goals and intentional states to it, in what sense should we understand some agents as more “complex” than others? There is a sizable literature about complexity in biology, notably in comparative psychology, where an animal’s complexity informs predictions about its abilities and guides experimental design. (...) In engineering and artificial intelligence, complexity is often assumed to be a sign of progress – we want to build more complex, capable machines. While the goals of researchers in these fields are different, they plausibly overlap in common conceptions of what a “more complex agent” entails. Existing work on “environmental complexity” and its relationship to “complex cognition” inquires into the origins of complexity, but not what it means to be a complex agent. Recognizing that complex behavior comes not just from complex cognition but from the interplay of body, environment, and cognition, we articulate an account of agent complexity in terms of Gibson’s (The Ecological Approach to Visual Perception (Classic), Houghton Mifflin, Boston, 1979) notion of affordances. We distinguish between cognitive and behavioral dimensions of affordances, and offer a framework for comparing agents based on the range of affordances they can exploit. Our approach ecologically grounds the sense in which some agents are more complex than others, while also clarifying why the answer to “which agent is more complex?” is sometimes indeterminate. It enables systematic comparison across diverse agent types, as we demonstrate through a detailed analysis of the nematode C. elegans and the hexapod robot RHex. We hope our account can advance discourse around the complexity of animals and guide the development of complex, agential machines. (shrink)

A hypothesis on the evolutionary origin of the genetic pathway of sex determination in the nematode Caenorhabditis elegans is presented here. It is suggested that the pathway arose in steps, driven by frequency‐dependent selection for the minority sex at each step, and involving the sequential acquisition of dominant negative, neomorphic genetic switches, each one reversing the action of the previous one. A central implication is that the genetic pathway evolved in reverse order from the final step in the hierarchy (...) up to the first. The possible applicability of the model to the other well‐characterized sex determination pathway, that of Drosophila melanogaster, and to sex determination in mammals, is discussed, along with some potential implications for pathway evolution in general. Finally, the specific molecular and population genetic questions that the model raises are described and some tests are proposed. (shrink)

In this review, we introduce the concept of “dual thermosensing mechanisms,” highlighting the functional collaboration between G protein‐coupled receptors (GPCRs) and transient receptor potential (TRP) channels that enable sophisticated cellular thermal responsiveness. GPCRs have been implicated in thermosensory processes, with recent findings identifying several candidates across species, including mammals, fruit flies, and nematodes. In many cases, these GPCRs work in conjunction with another class of thermosensors, TRP channels, offering insights into the complex mechanisms underlying thermosensory signaling. We examine how GPCRs (...) function as thermosensors and how their signaling regulates cellular thermosensation, illustrating the complexity of thermosensory systems. Understanding these dual thermosensory mechanisms would advance our comprehension of cellular thermosensation and its regulatory pathways. (shrink)

The Cuban government has undertaken the task of transforming insect pest and weed management from conventional to organic and more sustainable approaches on a nationwide basis. This paper addresses past programs and current major areas of research and implementation as well as provides examples of programs in insect and weed management. Topics covered include the newly constructed network of Centers for the Reproduction of Entomophages and Entomopathogens (CREEs), which provide the infrastructure for the implementation of biological control on state, cooperative, (...) and private farm operations. CREE programs include the mass rearing and release of Trichogramma spp. to manage insect pests of cassava, tobacco, sugarcane, and improved pasture. The entomopathogens, Bacillus thuringiensis, Beauveria bassiana, Metarhizium anisopliae, and Verticillium lecanii, are being mass produced in the CREEs and applied to control a number of key insect pests. A traditional method employed by peasant farmers of using the predatory ant Pheidole megacephala (Fabricius) in the biological control of sweetpotato and banana insect pests has been further developed and implemented. Efforts are underway to rear nematode species that attack insect pests and identify plant extracts with insecticidal qualities as potential management tools. Weed management has moved away from dependence on herbicides and toward alternative techniques that include weed suppression based on rotation schemes, limited use of selective herbicides, and new tillage equipment and practices. (shrink)

It has been claimed that the intentional stance is necessary to individuate behavioral traits. This thesis, while clearly false, points to two interesting sets of problems concerning biological explanations of behavior: The first is a general in the philosophy of science: the theory-ladenness of observation. The second problem concerns the principles of trait individuation, which is a general problem in philosophy of biology. After discussing some alternatives, I show that one way of individuating the behavioral traits of an organism is (...) by a special use of the concept of biological function, as understood in an enriched causal role (not selected effect) sense. On this view, a behavioral trait is essentially a special kind of regularity, namely a regularity that is produced by some regulatory mechanism. Regulatory mechanisms always require goal states, which can only be provided by functional considerations. As an example from actual (as opposed to folk) science, I examine the case of social behavior in nematodes. I show that the attempt to explain this phenomenon actually transformed it. This supports the view that scientific explanation does not explain an explanandum phenomenon that is given prior to the explanation; rather, the explanandum is changed by the explanation. This means that there could be a plurality of stances that have some heuristic value initially, but which will be abandoned in favor of a functional characterization eventually. (shrink)

It is necessary to complement next‐generation sequencing data on the soil resistome with theoretical knowledge provided by ecological studies regarding the spread of antibiotic resistant bacteria (ARB) in the abiotic and, especially, biotic fraction of the soil ecosystem. Particularly, when ARB enter agricultural soils as a consequence of the application of animal manure as fertilizer, from a microbial ecology perspective, it is important to know their fate along the soil food web, that is, throughout that complex network of feeding interactions (...) among members of the soil biota that has crucial effects on species richness and ecosystem productivity and stability. It is critical to study how the ARB that enter the soil through the application of manure can reach other taxonomical groups (e.g., fungi, protists, nematodes, arthropods, earthworms), paying special attention to their presence in the gut microbiomes of mesofauna‐macrofauna and to the possibilities for horizontal gene transfer of antibiotic resistant genes. (shrink)

Although the type‐I interferon (IFN‐I) response is considered vertebrate‐specific, recent findings about the Intracellular Pathogen Response (IPR) in nematode Caenorhabditis elegans indicate that there are similarities between these two transcriptional immunological programs. The IPR is induced during infection with natural intracellular fungal and viral pathogens of the intestine and promotes resistance against these pathogens. Similarly, the IFN‐I response is induced by viruses and other intracellular pathogens and promotes resistance against infection. Whether the IPR and the IFN‐I response evolved in (...) a divergent or convergent manner is an unanswered and exciting question, which could be addressed by further studies of immunity against intracellular pathogens in C. elegans and other simple host organisms. Here we highlight similar roles played by RIG‐I‐like receptors, purine metabolism enzymes, proteotoxic stressors, and transcription factors to induce the IPR and IFN‐I response, as well as the similar consequences of these defense programs on organismal development. (shrink)

Cell communication is crucial for many aspects of growth and differentiation during the development of the nematode Caenorhabditis elegans. Two genes, glp‐1 and lin‐12, mediate a number of known cell–cell interactions. Genetic and molecular analyses of these two genes lead to the conclusion that they are structurally and functionally related. We summarize these studies as well as those involving the identification of other genes that interact with glp‐1 and / or lin‐12.

Different animal groups exhibit a surprisingly diversity of sex determination systems. Moreover, even systems that are superficially similar may utilize different underlying mechanisms. This diversity is illustrated by a comparison of sex determination in three well‐studied model organisms: the fruitfly Drosophila melanogaster, the nematode Caenorhabditis elegans, and the mouse. All three animals exhibit male heterogamety, extensive sexual dimorphism and sex chromosome dosage compensation, yet the molecular and cellular processes involved are now known to be quite unrelated. The similarities must (...) have arisen by convergent evolution. Studies of sex determination demonstrate that evolution can produce a variety of solutions to the same basic problems in development. (shrink)

Wnt glycoproteins are signaling molecules that control a wide range of developmental processes in organisms ranging from the simple metazoan Hydra to vertebrates. Wnt signaling also plays a key role in the development of the nematode C. elegans, and is involved in cell fate specification and determination of cell polarity and cell migration. Surprisingly, the first genetic studies of Wnt signaling in C. elegans revealed major differences with the established (canonical) Wnt signaling pathways of Drosophila and vertebrates. Thus, the (...) Wnt-dependent induction of endoderm in the early embryo and the specification of several asymmetric cell divisions during larval development are mediated by as yet novel Wnt signaling pathways that repress, rather than activate the TCF/LEF-1 transcription factor POP-1. Recently, however, it has been shown that, in addition to these divergent Wnt pathways, C. elegans also has a canonical Wnt pathway that converts POP-1 into an activator and controls the expression of several homeobox genes. Interestingly, these different Wnt pathways use distinct beta-catenins to control POP-1 function: the endoderm induction pathway requires the beta-catenin WRM-1 and parallel input from a mitogen-activated kinase (MAPK) pathway to downregulate POP-1, whereas the canonical Wnt pathway employs the beta-catenin BAR-1 to activate Wnt target gene expression. (shrink)

Sex determination in most organisms involves a simple binary fate choice between male or female development; the outcome of this decision has profound effects on organismal biology, biochemistry and behaviour. In the nematode C. elegans, there is also a binary choice, either male or hermaphrodite. In C. elegans, distinct genetic pathways control somatic and germline sexual cell fate. Both pathways share a common set of globally acting regulatory genes; however, germline-specific regulatory genes also participate in the decision to make (...) male or female gametes. The determination of sexual fate in the germline of the facultative hermaphrodite poses a special problem, because first sperm then oocytes are produced. It has emerged that additional layers of post-transcriptional regulation have been imposed to modulate the activities of the global sex-determining genes, tra-2 and fem-3; the balance between these activities is crucial in controlling sexual cell fate in the hermaphrodite germline. BioEssays 23:596–604, 2001. © 2001 John Wiley & Sons, Inc. (shrink)

New C. elegans studies imply that lipases and lipid desaturases can mediate signaling effects on aging. But why might fat homeostasis be critical to aging? Could problems with fat handling compromise health in nematodes as they do in mammals? The study of signaling pathways that control longevity could provide the key to one of the great unsolved mysteries of biology: the mechanism of aging. But as our view of the regulatory pathways that control aging grows ever clearer, the nature of (...) aging itself has, if anything, grown more obscure. In particular, focused investigations of the oxidative damage theory have raised questions about an old assumption: that a fundamental cause of aging is accumulation of molecular damage. Could fat dyshomeostasis instead be critical? (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)

The sex chromosomes of many species differ in dosage but the total gene expression output is similar, a phenomenon referred to as dosage compensation. Previously, diverse mechanisms were postulated to account for compensation in distantly related taxa. However, two recent papers present evidence that dosage compensation in Drosophila, mammals and nematodes share the property that there is an approximately two‐fold upregulation of the single active X chromosome in each case.1,2 The results suggest that a common mechanism might operate in these (...) different cases. BioEssays 28: 565–568, 2006. © 2006 Wiley Periodicals, Inc. (shrink)