Compositionality in Plant Fixed Expressions Shelley Ching-yu Hsieh, Chinfa Lien, Sebastian Meier Abstract This paper examines fixed expressions that contain plant names in Mandarin Chinese and German corpora. It aims to reveal the compositionality of the concepts of the vehicle flower by means of frame semantics, and then popular vehicles (plant names) and underlying conceits (the associations between vehicles and meanings) of plant fixed expressions in these two languages will be (...) explored. The linguistic frames of flowers show that German focuses on function by adopting usability and edibility of plants in their expressions, whereas Mandarin Chinese perceives outer appearance of plants and compile “visualized” Chinese expressions. People observe and perceive plants from different standpoints and thus compose different concepts in their minds and languages. Chinese vehicles fall mainly into the categories of trees and flowers, while German vehicles are fruits and divisions of plants such as seeds and roots. This confirms the functional and visual perspective of the respective languages and further suggests the individualism of the Germans as well as the holism of the Mandarin Chinese speakers. (shrink)

Truth-theoretic deflationism holds that truth is simple, and yet that it can fulfil many useful logico-linguistic roles. Deflationism focuses on axioms for truth: there is no reduction of the notion of truth to more fundamental ones such as sets or higher-order quantifiers. In this paper I argue that the fundamental properties of reasonable, primitive truth predicates are at odds with the core tenets of classical truth-theoretic deflationism that I call fix, express, and quantify. Truth may be regarded as a broadly (...) logical, sui generis notion. However, this has little to do with the original aims of the deflationary theory of truth. (shrink)

This article examines the issues raised by religious adherents’ wish to express their beliefs in the public domain through, for example, their modes of dress, their performance of public roles, and their response to homosexuality. It considers on what grounds religion might merit special treatment and how special that treatment should be. A common approach to these issues is through the notion of religious identity, but both the idea of religious identity and its use to ground claims against others prove (...) deeply problematic. An alternative and more productive approach is through the notion of harm. People should enjoy the freedom to express their religious convictions subject to the harm principle, but harm should include the undermining of people’s status as free and equal citizens. The article concludes by considering the grounds upon which this alternative approach might recognize religion as special and might justify giving an overriding status to civic equality. (shrink)

Light effects on the activity of several genes have recently been exploited in studies of plant gene expression. We discuss here some examples involving nuclear genes of higher plants, with emphasis on responses mediated by the phytochrome system. Recent work has revealed considerable diversity in the responses of different genes, indicating that several different regulatory programs are probably involved. A start has been made in studies of nuclear events associated with the changes in expression. Transcriptional regulation almost certainly occurs, (...) although many details remain to be studied and effects on mRNA processing and turnover have not been ruled out. Recent in vitro mutagenesis and gene transfer experiments with the gene for the small subunit of RuBP carboxylase indicate that sequences involved in regulating the level of expression in the light are located 5′ to the gene within about 1 kb of the start of transcription. (shrink)

Despite the fact that they play a prominent role in everyday speech, the representation and processing of fixed expressions during language production is poorly understood. Here, we report a study investigating the processes underlying fixed expression production. “Tip-of-the-tongue” (TOT) states were elicited for well-known idioms (e.g., hit the nail on the head) and participants were asked to report any information they could regarding the content of the phrase. Participants were able to correctly report individual words for idioms (...) that they could not produce. In addition, participants produced both figurative (e.g., pretty for easy on the eye) and literal errors (e.g., hammer for hit the nail on the head) when in a TOT state, suggesting that both figurative and literal meanings are active during production. There was no effect of semantic decomposability on overall TOT incidence; however, participants recalled a greater proportion of words for decomposable rather than non-decomposable idioms. This finding suggests there may be differences in how decomposable and non-decomposable idioms are retrieved during production. (shrink)

The formulae "perhaps" and "perhaps not," [] we adopt in place of "perhaps it is and perhaps it is not" []. But here again we do not fight about phrases [] these expressions are indicative of non-assertion. Sextus Empiricus, Outlines of Pyrrhonism One could spend years on [] the perhaps [] whose modality will render fictional and fragile everything that follows []. One does not testify in court and before the law with "perhaps." Jacques Derrida, Demeure: Fiction and Testimony.

L’expression « vivre-ensemble » est devenue omniprésente dans le discours social et politique. Exigence de notre époque, clé de voûte de l’éducation pour le XXIe siècle, le vivre-ensemble est devenu un leitmotiv qu’il semble commode de ne pas définir ‒ chacun pouvant dès lors lui donner sa propre acception, voire l’utiliser à toutes les sauces. Nous avons donc entrepris d’en éclairer le sens par l’analyse d’écrits dans le champ de l’éducation, où le terme « vivre-ensemble » figure dans le libellé (...) du titre. Le lecteur ou la lectrice qui s’intéresse à la question du vivre-ensemble trouvera dans cet ouvrage une définition et ses déclinaisons de cette expression pouvant servir de pistes pour situer sa propre perspective, ou encore pour établir ce que peuvent sous-entendre ceux et celles qui utilisent ce terme, d’apparence consensuelle, dans l’espace public. (shrink)

In the idealistic movement of the late nineteenth and early twentieth centuries, British philosophy under Hegelian influence endeavoured to demonstrate the rationality of the universe as based on logical construction. The keynote of the Hegelian dialectic, as interpreted by both F. H. Bradley and J. E. McTaggart is that the mind is there from the first. In the advance from the bare abstraction of Being to the fully concrete whole—“Before the mind there is a single conception, but the whole mind (...) itself which does not appear, engages in the process, operates on the datum, and produces the result.” The idea expressed by poetry in Tennyson's “Flower in the crannied wall,” which as the mind is fixed upon it reveals in an expansion to the universe the nature of God and Man, illustrates in a simple way the central philosophic conception of the British metaphysical idealists. Poetry could overlook the hard struggle of the little plant to keep its foothold against crowding competitors. Philosophy was perhaps too oblivious of this in its compelling postulate of the all pervading unity in which every difference and seeming contradiction would be reconciled. (shrink)

We study the expressive power in the finite of the logic Fixed-Point+Counting, the extension of first-order logic which is obtained through adding both the fixed-point constructor and the ability to count. To this end an isomorphism preserving (`generic') model of computation is introduced whose PTime restriction exactly corresponds to this level of expressive power, while its PSpace restriction corresponds to While+Counting. From this model we obtain a normal form which shows a rather clear separation of the relational vs. (...) the arithmetical side of the algorithms involved. In parallel, we study the relations of Fixed-Point+Counting with the infinitary logics L r ∞ω (∃ ≥ m ) m∈ω and the corresponding pebble games. The main result, however, involves the concept of an arithmetical invariant. By this we mean a functor taking every finite relational structure to an expansion of (an initial segment of) the standard arithmetical structure. In particular its values are linearly ordered structures. We establish the existence of a family of arithmetical invariants (J r ) r≥ 1 with the following properties: $\bullet$ The invariants themselves can be evaluated in polynomial time. $\bullet$ A class of finite relational structures is definable in Fixed-Point+Counting if and only if membership can be decided in polynomial time on the basis of the values of one of the invariants. $\bullet$ The invariant J r classifies all finite relational structures exactly up to equivalence with respect to the logic L r ∞ω (∃ ≥ m ) m∈ω . We also give a characterization of Fixed-Point+Counting in terms of sequences of formulae in the L r ωω (∃ ≥ m ) m∈ω : It corresponds exactly to the polynomial time computable families (φ n ) n∈ω in these logics. Towards a positive assessment of the expressive power of Fixed-Point+Counting, it is shown that the natural extension of fixed-point logic by Lindström quantifiers, which capture all the PTime computable properties of cardinalities of definable predicates, is strictly weaker than what we get here. This implies in particular that every extension of fixed-point logic by means of monadic Lindstrom quantifiers, which stays within PTime, must be strictly contained in Fixed-Point+Counting. (shrink)

We study the relationship between least and inflationary fixed-point logic. In 1986, Gurevich and Shelah proved that in the restriction to finite structures, the two logics have the same expressive power. On infinite structures however, the question whether there is a formula in IFP not equivalent to any LFP-formula was left open.In this paper, we answer the question negatively, i.e. we show that the two logics are equally expressive on arbitrary structures. We give a syntactic translation of IFP-formulae to (...) LFP-formulae such that the two formulae are equivalent on all structures.As a consequence of the proof we establish a close correspondence between the LFP-alternation hierarchy and the IFP-nesting depth hierarchy. We also show that the alternation hierarchy for IFP collapses to the first level, i.e. the complement of any inflationary fixed point is itself an inflationary fixed point. (shrink)

This review provides a current perspective on the insertion of genes into plants. Some of the knowledge on the structure and control of plant genes gained recently from genetic engineering approaches is described, together with developments that can be expected to emerge from further exploitation of gene transfer techniques.

In response to the liar’s paradox, Kripke developed the fixed-point semantics for languages expressing their own truth concepts. Kripke’s work suggests a number of related fixed-point theories of truth for such languages. Gupta and Belnap develop their revision theory of truth in contrast to the fixed-point theories. The current paper considers three natural ways to compare the various resulting theories of truth, and establishes the resulting relationships among these theories. The point is to get a sense of (...) the lay of the land amid a variety of options. Our results will also provide technical fodder for the methodological remarks of the companion paper to this one. (shrink)

The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development stages for (...) all plants, particularly the land plants (bryophytes through angiosperms). As a case study to illustrate the general approach, we examine variation in gene expression across embryo development stages in Arabidopsis and maize, demonstrating how the PO can be used to compare patterns of expression across stages and in developmentally different species. Although many genes appear to be active throughout embryo development, we identified a small set of uniquely expressed genes for each stage of embryo development and also between the two species. Evaluating the different sets of genes expressed during embryo development in Arabidopsis or maize may inform future studies of the divergent developmental pathways observed in monocotyledonous versus dicotyledonous species. The PO and its annotation databasemake plant data for any species more discoverable and accessible through common formats, thus providing support for applications in plant pathology, image analysis, and comparative development and evolution. (shrink)

Plant cells are caged within a distended polymeric network (the cell wall), which enlarges by a process of stress relaxation and slippage (creep) of the polysaccharides that make up the load‐bearing network of the wall. Protein mediators of wall creep have recently been isolated and characterized. These proteins, called expansins, appear to disrupt the noncovalent adhesion of matrix polysaccharides to cellulose microfibrils, thereby permitting turgor‐driven wall enlargement. Expansin activity is specifically expressed in the growing tissues of dicotyledons and monocotyledons. (...) Sequence analysis of cDNAs indicates that expansins are novel proteins, without previously known functional motifs. Comparison of expansin cDNAs from cucumber, pea, Arabidopsis and rice shows that the proteins are highly conserved in size and amino acid sequence. Phylogenetic analysis of expansin sequences suggests that this multigene family diverged before the evolution of angiosperms. Speculation is presented about the role of this gene family in plant development and evolution. (shrink)

Michael Kremer defines fixed-point logics of truth based on Saul Kripke’s fixed point semantics for languages expressing their own truth concepts. Kremer axiomatizes the strong Kleene fixed-point logic of truth and the weak Kleene fixed-point logic of truth, but leaves the axiomatizability question open for the supervaluation fixed-point logic of truth and its variants. We show that the principal supervaluation fixed point logic of truth, when thought of as consequence relation, is highly complex: it (...) is not even analytic. We also consider variants, engendered by a stronger notion of ‘fixed point’, and by variant supervaluation schemes. A ‘logic’ is often thought of, not as a consequence relation, but as a set of sentences – the sentences true on each interpretation. We axiomatize the supervaluation fixed-point logics so conceived. (shrink)

Imogen Dickie develops an account of aboutness-fixing for thoughts about ordinary objects, and of reference-fixing for the singular terms we use to express them. Extant discussions of this topic tread a weary path through descriptivist proposals, causalist alternatives, and attempts to combine the most attractive elements of each. The account developed here is a new beginning. It starts with two basic principles, the first of which connects aboutness and truth, and the second of which connects truth and justification. These principles (...) combine to yield a third principle connecting aboutness and justification. Dickie uses the principle to explain how the relations to objects that enable us to think about them--perceptual attention; understanding of proper names; grasp of descriptions--do their aboutness-fixing and thought-enabling work. The book includes discussions of the nature of singular thought and the relation between thought and consciousness. (shrink)

In this paper I argue that it’s impossible for there to be a single universal theory of meaning for a language. First, I will consider some minimal expressiveness requirements a language must meet to be able to express semantic claims. Then I will argue that in order to have a single unified theory of meaning, these expressiveness requirements must be satisfied by a language which the semantic theory itself applies to. That is, we would need a language which can express (...) its own meaning. It has been well-known since Tarski that theories of meaning whose central notion is truth can’t be expressed in a language which they apply to. Here, I develop Quine’s formulation of the Liar Paradox in grammatical terms and use this to extend Tarski’s result to all theories of meaning. This general version of the paradox can be formalised as a special case of the Lawvere Fixed-Point Theorem applied to a categorial grammar. Taken together with the initial arguments, I infer that a universal theory of meaning is impossible and conclude the paper with a brief discussion on what alternatives are available. (shrink)

‘Now that all parts and members of the mortal creature had been fashioned into one, seeing that it must be the creature's lot for reasons of necessity to spend its life in the domain of fire and air and that it was like to waste away being continually melted and emptied by their onslaught, the gods contrived reinforcement for it. Blending a being kindred to man's being but with different shapes and senses, they brought it into life, a second kind (...) of living creature. Trees, plants, and seeds are these, and those among them which are cultivated types to-day have arrived at their mild benevolence to man only because they have been civilized by his husbandry; formerly only the wild kinds existed, for these are older than the cultivated. Now everything that is alive, whatever it be, may perfectly correctly and of right be termed ‘a living creature’. The creature now in question has at any rate the third kind of soul which our discourse told us is situated between the midriff and the navel. This kind of soul has nothing of opining or of reasoning mind, but it has sensation of pleasant and painful with attendant desires. For continually it is subject to every impression. Its manner of birth has not granted it the power to revolve by itself in itself upon itself rejecting outside motion and asserting its own and thus by beholding all things by native endowment of soull to reason out aught of its own concerns. So it has life and is not some second being other than a living creature, but it stays fixed, rooted, motionless, for it has never been granted movement of its own initiation.’. (shrink)

The Plant Ontology (PO; http://www.plantontology.org/) is a publicly-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of (...) the PO has been expanded to include all green plants. The PO was the first multi-species anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. There are about 2.2 million annotations linking PO terms to over 110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and Quantitative Traits Loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users, and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs. (shrink)

Silicon Valley and its innovation center counterparts have come upon food and agriculture as the next frontier for their unique style of innovation and impact. But what exactly can the tech sector, with expertise in information and communication technologies, bring to a domain in which the biophysical materiality of soil, plants, animals and human bodies have most challenged farmers and food companies? Based on a detailed analysis of all of the companies that have pitched their products at events sponsored by (...) the Silicon Valley-based convener, Foodbytes!, we show that a large proportion of tech-driven solutions are digital technologies transferred from other domains. These technologies at best inform decision-making on the ecological processes of food and farming, but do not provide tools to treat them, and otherwise provide business solutions not even aimed at major challenges in food and farming. Drawing on a small set of interview data, we additionally suggest that tech entrepreneurs migrate to food and agriculture because it seems purposeful, exciting, or lucrative, but sometimes lack a clear understanding of the problems they might solve with their digital technologies. In making our case about the mismatch of problem and solution, we bring into conversation recent critiques of digital solutionism with abiding concerns in agrarian political economy and critical food studies regarding the role of the biological in both challenging food production and spurring technological intervention. (shrink)

In addition to obviating the use of synthetic agrochemicals and emphasizing farming in accordance with agro-ecological guidelines, organic farming acknowledges the integrity of plants as an essential element of its natural approaches to crop production. For cultivated plants, integrity refers to their inherent nature, wholeness, completeness, species-specific characteristics, and their being in balance with their (organically farmed) environment, while accomplishing their “natural aim.” We argue that this integrity of plants has ethical value, distinguishing integrity of life, plant-typic integrity, genotypic (...) integrity, and phenotypic integrity. We have developed qualitative criteria to ethically evaluate existing practices and have applied these criteria to assess whether current plant breeding and propagation techniques violate the integrity of crop plants. This process has resulted in a design of a holistic, scientific approach of organic plant breeding and seed production. Our evaluation has met considerable criticism from mainstream (crop) scientists. We respond to the following questions: (1). Can ethics be incorporated into objective crop sciences? (2). What is the nature of the intrinsic value of plants in organic farming? We argue that criteria to take integrity into account can only be assessed from a holistic perspective and we show that a holistic approach is needed to design such ethical notions in a consistent way. The ethical notions have been further elaborated by formulating human responsibility and respect towards crop plants. Responsibility and respect can only be shown by providing crop plants the right to be nurtured and to express natural behavior at all levels of integrity. (shrink)

It is increasingly clear that chromatin is not just a device for packing DNA within the nucleus but also a dynamic material that changes as cellular environments alter. The precise control of chromatin modification in response to developmental and environmental cues determines the correct spatial and temporal expression of genes. Here, we review exciting discoveries that reveal chromatin participation in many facets of plant development. These include: chromatin modification from embryonic and meristematic development to flowering and seed formation, the (...) involvement of DNA methylation and chromatin in controlling invasive DNA and in maintenance of epigenetic states, and the function of chromatin modifying and remodeling complexes such as SWI/SNF and histone acetylases and deacetylases in gene control. Given the role chromatin structure plays in every facet of plant development, chromatin research will undoubtedly be integral in both basic and applied plant biology. BioEssays 24:234–243, 2002. © 2002 Wiley Periodicals, Inc.; DOI 10.1002/bies.10055. (shrink)

We consider fixed point logics, i.e., extensions of first order predicate logic with operators defining fixed points. A number of such operators, generalizing inductive definitions, have been studied in the context of finite model theory, including nondeterministic and alternating operators. We review results established in finite model theory, and also consider the expressive power of the resulting logics on infinite structures. In particular, we establish the relationship between inflationary and nondeterministic fixed point logics and second order logic, (...) and we consider questions related to the determinacy of games associated with alternating fixed points. (shrink)

MicroRNAs are non‐coding regulators of gene expression and key factors in development, disease, and targets for bioengineering. Consequently, microRNAs have become essential elements of already burgeoning draft plant genome descriptions where their annotation is often particularly poor, contributing unduly to the corruption of public databases. Using the Citrus sinensis as an example, we highlight and review common failings of miRNAome annotations. Understanding and exploiting the role of miRNAs in plant biology will be stymied unless the research community acts (...) decisively to improve the accuracy of miRNAome annotations. We encourage genome annotation teams to do it right or not at all. (shrink)

Light mediates plant development partly by orchestrating changes in gene expression, a process which involves a complex combination of positive and negative signaling cascades. Genetic investigations using the small crucifer Arabidopsis thaliana have demonstrated a fundamental role for the down‐regulation of light‐inducible genes in response to darkness, thus offering a suitable model system for investigating how plants repress gene expression in a developmental context. Rapid progress in eukaryotic gene repression mechanisms in general, and light control of plant gene (...) expression in particular, sheds new light on how a class of ten pleiotropic COP/DET/FUS genes might function to down‐regulate light‐inducible genes in plants. (shrink)

Philosophers and scientists propose the idea that plants are cognitive, which has been met with criticisms. These criticisms focus on the fact that plants do not possess the properties traditionally associated with cognition. By contrast, several proponents introduce novel ways to conceptualize cognition. How should we make sense of this debate? In this paper, I argue that the plant cognition debate is not about whether plants meet a set of well-delineated and agreed-upon criteria according to which they count as (...) cognitive. Rather, many proponents are hypothesizing about cognition. They construe COGNITION not as an expression of what cognition is, but rather as a conjecture about what cognition might be. These conjectures orient research that can uncover novel similarities amongst the phenomena to which these concepts extend. In defending this view, I argue that investigating plant cognition is valuable, even if the results of these investigations lead us to reject the claim that plants are cognitive. (shrink)

This article analyzes Italian research and experimentation on the economic potential of certain plant species in the late eighteenth and early nineteenth centuries, also providing insight into beekeeping and honey production. It focuses on continuity of method and progress across regimes and on the invisibility of many of the actors involved in the development of agricultural science and food research. Specifically, “continuity” refers to the continuation of certain threads of Old-Regime experimentation by the scientific apparatus put in place during (...) the Napoleonic era. These threads were reworked and strengthened with the new means available to Frenchified Europe. The concept of “invisibility” derives from an expression by Steven Shapin and refers to actors who contributed to the development of agricultural science while remaining in the shadows. These include various types of technicians and members of rural society who supported the scientific work of scholars without receiving overt recognition. Continuity and invisibility were therefore two fundamental components both in the epistemological development of agricultural science and in the improvement of food research. The article analyzes case studies mainly from northern Italy – or rather, the various geopolitical entities existing in this geographical region – during the late Old Regime and the Napoleonic era, comparing them with examples from all over Europe. (shrink)

I defend the hypothesis that the semantic paradoxes, the paradoxes about collections, and the sorites paradoxes, are all paradoxes of reference fixing: they show that certain conventionally adopted and otherwise functional reference-fixing principles cannot provide consistent assignments of reference to certain relevant expressions in paradoxical cases. I note that the hypothesis has interesting implications concerning the idea of a unified account of the semantic, collection and sorites paradoxes, as well as about the explanation of their “recalcitrance”. I also note (...) that it does not necessarily imply that one should not expect the sometimes hoped for “unique” solution to a paradox of these kinds. (shrink)

The most efficient known method for solving certain computational problems is to construct an iterated map whose fixed points are by design the problem's solution. Although the origins of this idea go back at least to Newton, the clearest expression of its logical basis is an example due to Mermin. A contemporary application in image recovery demonstrates the power of the method.

Every year, unfavorable environmental factors significantly affect crop productivity and threaten food security. Plants are sessile; they cannot move to escape unfavorable environmental conditions, and therefore, they activate a variety of defense pathways. Among them are processes regulated by stress‐associated proteins (SAPs). SAPs have a specific zinc finger domain (A20) at the N‐terminus and either AN1 or C2H2 at the C‐terminus. SAP proteins are involved in many biological processes and in response to various abiotic or biotic constraints. Most SAPs play (...) a role in conferring transgenic stress resistance and are stress‐inducible. The emerging field of SAPs in abiotic or biotic stress response regulation has attracted the attention of researchers. Although SAPs interact with various proteins to perform their functions, the exact mechanisms of these interactions remain incompletely understood. This review aims to provide a comprehensive understanding of SAPs, covering their diversity, structure, expression, and subcellular localization. SAPs play a pivotal role in enabling crosstalk between abiotic and biotic stress signaling pathways, making them essential for developing stress‐tolerant crops without yield penalties. Collectively, understanding the complex regulation of SAPs in stress responses can contribute to enhancing tolerance against various environmental stresses through several techniques such as transgenesis, classical breeding, or gene editing. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:"Everything is Breath":Critical Plant Studies' Metaphysics of MixtureElisabeth Weber (bio)In her book Braiding Sweetgrass: Indigenous Wisdom, Scientific Knowledge, and the Teachings of Plants, Robin W. Kimmerer contrasts two creation stories that are thoroughly incompatible. One starts with an all-powerful male creator calling the world and its vegetation and animals into existence through words, and forming the first human beings from clay; the other starts with Skywoman tumbling through (...) the air with seeds in her fist from the Tree of Life growing in Skyworld. One ends with the condemnation of woman to give birth in "very severe" pains, with the cursing of the ground ordered to "produce thorns and thistles" as punishment for man who will eat his food only after "painful toil," and the expulsion from the garden; the other ends in gratitude for the collective caring of the animals, with the creation of "a garden for the well-being of all." One includes an original fall from grace whose burden will be passed down from generation to generation; the other acknowledges suffering without a trace of the burden of unearned guilt. One predicts death as a return to the dust from whence mankind was created; the other imagines death as becoming plant and fruit, as becoming gift, a rejoining the spirits of all ancestors, human and others, who surround the living in everything that is. The threat of one is the inexorability of a trajectory "from dust to dust" and the latter's association, with Plato, of something so diffuse that it doesn't merit a concept or idea; the promise of the other is an abiding relationship with all that is, the reciprocity of giving and gratitude, and the gladly assumed responsibility for the "inspirited" land.Kimmerer comments:Same species, same earth, different stories. Like Creation stories everywhere, cosmologies are a source of identity and orientation to the world. They tell us who we are. We are inevitably shaped by them no matter how distant they may be from our consciousness. One story leads to the generous embrace of the living world, the other to banishment. One woman is our ancestral gardener, a cocreator of the good green world that would be the home of her descendants. The other was an exile, just passing through an alien world on a rough road [...].1 [End Page 117]Cosmologies express collective imaginairies that have evolved over hundreds, even thousands of years. The Iroquois story recounted and rendered accessible by Kimmerer is one of countless creation stories that constitute an "important genre in many preliterate traditions" (Zolbrod 5). Kimmerer suggests that even though the Judeo-Christian creation story may have receded into the background of Western collective consciousness, it plays a role in the planet's devastation. What strikes the reader in the story of Skywoman is the centrality of reciprocity, of relation, and, as the woman's name indicates, the significance of the sky. While this might mean, on planet Earth, the atmosphere–the Earth's sky is blue because of the surrounding atmosphere–the implications of the sky's preponderance reach beyond the planetary into the cosmological. The "sky is not what is above. The sky is everywhere: it is the space and the reality of mixture and movement, the definite horizon starting from which everything has to draw itself" (Coccia 218-219) in order to breathe and live.In order to continue to breathe, breathe in the long-term, the long-term, that is, as Barbara Kingsolver put it in one of her poems, "from a tree's / way of thinking" (7), non-human kin's "way of thinking" will need to play a role in humans' self-understanding. Kyle Whyte underlines that it is not enough to respond with urgency to specific ecological crises (fires, flooding, etc.) alone, but, rather, "urgency must be aimed at addressing ecological and relational tipping points together":U.S. settler colonialism, for example, in a short period of time, inflicted displacement, drastic ecological changes, and lost or disrupted relationships with hundreds of species that indigenous peoples depended on through kinship ties for generations. These changes are more extreme than what many nonindigenous persons fear most about moving beyond... (shrink)

Two groups of plant viruses have DNA in their genomes. One group, the caulimoviruses, are non‐integrating retroviruses that package dsDNA in virions. The other group, the geminiviruses, package small circular ssDNA and include the only DNA viruses known with bipartite genomes. The regulation of transcription of these viruses is not well characterized, but recent work is beginning to yield interesting results. Regulatory sequences from these viruses function in cells of species that are not hosts of the virus and are (...) finding use in constitutive expression of chimeric genes in transformed plants. Development of vectors based on plant viruses requires further characterization at the molecular level of viral life cycles. (shrink)

The fine‐structure analyses of the nopaline synthase (nos) promoter which is active constitutively in a wide range of plant tissues reveal that a portion of the upstream essential region for maximal transcription is a potential Z‐DNA‐forming element. Z‐DNA sequences are found in almost all plant‐promoter regions, suggesting that these structural elements may play important roles in plant gene expression.

The discussion that follows rehearses some familiar arguments and replies from the Kripke/Putnam/Burge critique of the traditional Frege/Russell/Wittgenstein views on names and predicates. Its main contributions are, first, to introduce a novel way of individuating tokens of the same expression, (what we call “articulations”) second, to then revise standard views on deference, (as this notion is understood to pertain to securing access to meaning for potentially ignorant, and confused agents in the externalist tradition going back to Putnam and Burge) and (...) lastly, to emphasize the often conflated distinction between disambiguation and meaning fixing. Our line on deference is that it is not, and should not be conceived as, an intentional mental act, but rather indicates an historical chain of antecedent tokenings of the same expression. (shrink)

There is solid consensus among physicists and philosophers that, in gauge field theory, for a quantity to be physically meaningful or real, it must be gauge-invariant. Yet, every “elementary” field in the Standard Model of particle physics is actually gauge-variant. This has led a number of researchers to insist that new manifestly gauge-invariant approaches must be established. Indeed, in the foundational literature, dissatisfaction with standard methods for reducing gauge symmetries has been expressed: Spontaneous symmetry breaking is deemed conceptually dubious, while (...) gauge fixing suffers the same limitations and is subject to the same criticisms as coordinate choices in General Relativity. An alternative gauge-invariant proposal was recently introduced in the literature, the so-called “dressing field method” (DFM). It is a mathematically subtle tool, and unfortunately prone to be confused with simple gauge transformations, hence with standard gauge fixings. As a matter of fact, in the physics literature the two are often conflated, and in the philosophy community some doubts have been raised about whether there is any substantial difference between them. Clarifying this issue is of special significance for anyone interested in both the foundational issues of gauge theories and their invariant formulation. It is thus our objective to establish as precisely as possible the technical and conceptual distinctions between the DFM and gauge fixing. (shrink)

The form of higher plants is largely dependent upon cell division and expansion patterns. Taking a genetic approach, Takahashi et al.(1) have identified a regulatory molecule in Arabidopsis thaliana called DIMINUTO (DIM), which is involved in determining the degree and direction of plant cell expansion. Their extensive characterization of a dim mutant suggested a direct involvement of the DIM gene in regulating cell elongation, perhaps by modulating the expression of structural genes which determine the orientation and elasticity of the (...) cell wall. (shrink)

Arabidopsis thaliana is a small cruciferous weed which grows naturally, mainly in Europe. Because of its qualities of small size, rapid growth, low chromosome number and self‐fertilisation, I adapted it to aseptic growth in purified agar in sterile test‐tubes. I found that it secreted various substances into the medium, but not in type or amount likely to interfere with the expression of biosynthetic mutants. Following X‐irradiation of seed, I obtained a number of mutants, including several lethals. One lethal mutant I (...) discovered to be deficient in thiamine synthesis. It was the first biosynthetic mutant to be found in flowering plants. (shrink)

Possible world semantics considers not only what an expression actually refers to but also what it might have referred to in counterfactual circumstances. This has proven exceptionally useful both inside and outside philosophy. The way this is achieved is by using intensions. An intension of an expression is a function that assigns to each possible world the reference of the expression in that world. However, the specific intension of terms has been subject to frequent disputes. How is one to determine (...) the intension of a term? Carnap has shown how the intension of a term depends on the type of that term. Two-dimensional semantics has shown how intensions also depend on the actual state of affairs. I will show how, in addition, intensions are no less dependent on metaphysical criteria of identity. Furthermore, I will reveal how these three factors interact to fix the exact intension of a term. In other words, I propose an outline of the overall mechanism by which intensions are being fixed. (shrink)

Minimal predicates P satisfying a given first-order description φ(P) occur widely in mathematical logic and computer science. We give an explicit first-order syntax for special first-order ‘PIA conditions’ φ(P) which guarantees unique existence of such minimal predicates. Our main technical result is a preservation theorem showing PIA-conditions to be expressively complete for all those first-order formulas that are preserved under a natural model-theoretic operation of ‘predicate intersection’. Next, we show how iterated predicate minimization on PIA-conditions yields a language MIN(FO) equal (...) in expressive power to LFP(FO), first-order logic closed under smallest fixed-points for monotone operations. As a concrete illustration of these notions, we show how our sort of predicate minimization extends the usual frame correspondence theory of modal logic, leading to a proper hierarchy of modal axioms: first-order-definable, first-order fixed-point definable, and beyond. (shrink)

The new concept of lambda calculi with monotone inductive types is introduced byhelp of motivations drawn from Tarski's fixed-point theorem (in preorder theory) andinitial algebras and initial recursive algebras from category theory. They are intendedto serve as formalisms for studying iteration and primitive recursion ongeneral inductively given structures. Special accent is put on the behaviour ofthe rewrite rules motivated by the categorical approach, most notably on thequestion of strong normalization (i.e., the impossibility of an infinitesequence of successive rewrite steps). (...) It is shown that this key propertyhinges on the concrete formulation. The canonical system of monotone inductivetypes, where monotonicity is expressed by a monotonicity witness beinga term expressing monotonicity through its type, enjoys strong normalizationshown by an embedding into the traditional system of non-interleavingpositive inductive types which, however, has to be enriched by the parametricpolymorphism of system F. Restrictions to iteration on monotone inductive typesalready embed into system F alone, hence clearly displaying the differencebetween iteration and primitive recursion with respect to algorithms despitethe fact that, classically, recursion is only a concept derived from iteration. (shrink)

Many plants are adapted to flower at particular times of year, to ensure optimal pollination and seed maturation. In these plants flowering is controlled by environmental signals that reflect the changing seasons, particularly daylength and temperature. The response to daylength varies, so that plants isolated at higher latitudes tend to flower in response to long daylengths of spring and summer, while plants from lower latitudes avoid the extreme heat of summer by responding to short days. Such responses require a mechanism (...) for measuring time, and the circadian clock that regulates daily rhythms in behaviour also acts as the timer in the measurement of daylength. Plants from high latitudes often also show an extreme response to temperature called vernalisation in which flowering is repressed until the plant is exposed to winter temperatures for an extended time. Genetic approaches in Arabidopsis have identified a number of genes that control vernalisation and daylength responses. These genes are described and models presented for how daylength might regulate flowering by controlling their expression by the circadian clock. BioEssays 22:38–47, 2000. ©2000 John Wiley & Sons, Inc. (shrink)

Plant reproduction is vital for species survival, and is also central to the production of food for human consumption. Seeds result from the successful fertilization of male and female gametes, but our understanding of the development, differentiation of gamete lineages and fertilization processes in higher plants is limited. Germ cells in animals diverge from somatic cells early in embryo development, whereas plants have distinct vegetative and reproductive phases in which gametes are formed from somatic cells after the plant (...) has made the transition to flowering and the formation of the reproductive organs. Recently, novel insights into the molecular mechanisms underlying male germ‐line initiation and male gamete development in plants have been obtained. Transcriptional repression of male germ‐line genes in non‐male germ‐line cells have been identified as a key mechanism for spatial and temporal control of male germ‐line development. This review focuses on molecular events controlling male germ‐line development especially, on the nature and regulation of gene expression programs operating in male gametes of flowering plants. BioEssays 29:1124–1132, 2007. © 2007 Wiley Periodicals, Inc. (shrink)

The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. (...) The project also provides access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (shrink)