Phylogenetic hypotheses, taxonomic sameness and the reference of taxon names

When scientists use a taxon name like Mammalia, it is important that they talk about the same thing. But, what does it mean to be the same thing in different phylogenetic hypotheses? And, how is taxonomic reference maintained across hypotheses? Here, we discuss the differences between real and hypothetical clades, and how such a distinction relates to the sameness problem. Since hypotheses influence how we perceive things and pursue science, we find it important to have a functioning nomenclatural system for clades as perceived in phylogenetic hypotheses. As a solution to the sameness problem for such clades, we argue that a taxon name does not primarily refer to a single clade that somehow mirror the reality of branches in the tree of life. Instead we suggest that a taxon name refers to a set, or natural kind, of counterfactual and reconstructed clades.     

The state of the pores in functioning sieve plates

Summary Electron microscopy of Helianthus stem and Saxifraga sarmentosa stolon after first plunging the material into boiling water indicates that the natural condition of the sieve plate pores is to be plugged fairly compactly with slime substance. Electron microscopy of pre-wilted plants demonstrates the same thing. These and other arguments indicate that the slime-filled condition of the pores is not an artifact induced by enzyme action or turgor release, nor is it a consequence of rapid translocation of slime; it is the natural state. This conclusion, very damaging to the pressure-flow hypothesis, is favourable to the electroosmotic theory.     

Four Applications of a Bivariate Pareto Distribution

The following model, of “latent structure” type, is considered: in each subpopulation, X and Y are random variables drawn independently from the same exponential distribution, and the parameter of the exponential distribution varies between subpopulations with a Gamma density. Over the whole population, X and Y are then positively correlated, and jointly have a bivariate PARETO distribution. Four examples show how this distribution is useful in analysing ordered contingency tables in which the two dimensions can be regarded as alternative measures of the same thing: the injuries to the two drivers in a road accident, or the severity of a lesion present in a patient as assessed by two physicians, for instance. Two extensions are considered: (a) allowing X and Y to have Gamma distributions, with each subpopulation having the same shape parameter but different scale parameters; (b) allowing the scale parameter for Y to be correlated with the scale parameter for X, rather than being identical to it. A new bivariate distribution with three shape parameters is derived, expressed in terms of a generalised hypergeometric function.     

Dreamwork as Etymology

This essay proposes that etymology, the study of word roots, presents analogies with dreamwork, although parallels between them must be carefully framed. Quoting Freud and the seventh century encyclopedist Isidore of Seville, weaknesses in their use of etymological arguments are identified. Theories forged from word origins should not blur distinctions between word and thing or force linguistic process into support of a preconceived theoretical project. To explore Freud's notion of contraries in words and dreams, examples are offered of single Indo-European word roots capable of engendering divergent or contradictory modern meanings, as well as examples of divergent or contradictory modern meanings for words that have two or more derivations, e.g., the English word dream and French rêve. Tracing a place-name (Campidoglio) in an actual dream demonstrates that etymology and dreamwork are both reconstructive processes that should avoid determinism, accept uncertainty, and respect complexity.     

The Intelligent Egg, and How It Got That Way: from Genes to Genius in a Few Easy Lessons

A seed has no flowers or leaves, and an egg no fingers or lungs. Yet plants and animals not only have these things but they resemble their parents in detail throughout their bodies. Something is inherited, but what is it? Life is based on the activities of cells. An organism has large numbers of them—a human has trillions! Cells live as separate units, which enables them each to do its own thing within its particular organ, but to be an organism they must work together. A cell can only detect its immediate local environment, but that includes various kinds of signals or information from nearby or far away within the body—or even from the external environment. It is by being local but responding globally in this way that an egg becomes an organism, an organism manages its way through life, and organisms make up species and ecosystems that interact with each other. The evolution of these abilities has produced the glorious array of living forms that populate the world. In these ways, an egg may have no thoughts but is a highly intelligent being.     

On concept formation in systematics

In his “Grundzüge einer Theorie der phylogenetischen Systematik”, Hennig (1950 ) cited three philosophers: the leading empiricist Rudolf Carnap, the conventionalist Hugo Dingler, and the somewhat more obscure empiricist Theodor Ziehen. David Hull characterized Hennig's “Grundzüge” as one long argument against idealistic morphology. It will here be argued that Hennig attacked idealistic morphology (synonymous with “systematic” morphology) for its mode of concept formation. Building on Carnap and Ziehen, who both looked back on Ernst Cassirer, Hennig argued that the “generic”, “thing” or “class” concept of traditional nomothetic science must be replaced with Cassirer's “relation concept.” According to Hennig, such “emancipation” of systematics from the Aristotelian “species” concept would also allow transcendence from the distinction of idiographic from nomothetic sciences, thus preserving the unity of science. However, the establishment of relations in the construction of a system of order presupposes entities that can be, or are, related. Relations presuppose relata, which in modern systematics are best conceptualized (at least at the supraspecific level) not as Aristotelian classes, nor as individuals as was argued by Hennig and Ziehen, but as tokens of natural kinds. © The Willi Hennig Society 2006.     

Distinguishing "or" from "and" and the case for historical identification

The adequacy of a probabilistic interpretation must be judged according to the nature of the event, or thing, being inferred. For example, conditional (frequency) probability is not admissible in the inference of phylogeny, because basic statements of common ancestry do not fulfill the requirements of the relations specified by the probability calculus. The probabilities of the situation peculiar to the time and place of origin of species are unique. Moreover, according to evolutionary theory, an event of species diversification is necessarily unique, because species are parts of a replicator continuum—species arise from ancestral species. Also, these probabilities cannot be ascertained, because the relevant situation cannot be repeated—it is unique. Finally, the applicability of conditional (frequency) probability is denied, because events of common ancestry have already occurred—there is nothing to predict. However, hypotheses of species relationships can be identified objectively according to the degree to which they have survived simultaneous testing with critical evidence, not with generally confirming evidence. The most parsimonious hypothesis of species relationships represents the least disconfirmed, best supported, proposition among the alternatives being compared. That hypothesis does not, however, deserve any special epistemological status beyond serving as the focus of the next round of testing.     

Information processing,computation, and cognition

Computation and information processing are among the most fundamental notions in cognitive science. They are also among the most imprecisely discussed. Many cognitive scientists take it for granted that cognition involves computation, information processing, or both – although others disagree vehemently. Yet different cognitive scientists use ‘computation’ and ‘information processing’ to mean different things, sometimes without realizing that they do. In addition, computation and information processing are surrounded by several myths; first and foremost, that they are the same thing. In this paper, we address this unsatisfactory state of affairs by presenting a general and theory-neutral account of computation and information processing. We also apply our framework by analyzing the relations between computation and information processing on one hand and classicism, connectionism, and computational neuroscience on the other. We defend the relevance to cognitive science of both computation, at least in a generic sense, and information processing, in three important senses of the term. Our account advances several foundational debates in cognitive science by untangling some of their conceptual knots in a theory-neutral way. By leveling the playing field, we pave the way for the future resolution of the debates’ empirical aspects.     

Impact of herbal medicines on physical impairment

The usefulness of recording physical impairment during intervention studies in chronic low back patients has been questioned. A re-analysis of all of our studies investigating aqueous extracts of Harpagophytum procumbens and a proprietary ethanolic Salix extract for chronic non-specific low back pain revealed that the “physical impairment” component of the Arhus low back pain index changed very little during treatment despite appreciable changes in the other two components, “pain” and “disability”, over time. For comparison, we also extracted data from the literature on the topical use of capsaicin, which showed the same thing. There may be little to lose from omitting the time-consuming assessments of “physical impairment” in studies of the (primarily analgesic) effectiveness of herbal preparations.     

Documenting DNA in the dust

I bought a robotic vacuum cleaner this summer and set it to work. Although my initial expectations were not high, my robot (christened Buddy) finished its cleaning cycle, and then insistently demanded that I empty its dust collection box. As I took the box out, my jaw dropped. I live in a modern house, we don't have pets, and I like to think that I keep it reasonably dust free. But, there was much dust in that box. And when I ran it again 2 days later, the same thing happened. And indeed, every 2 days, Buddy dutifully goes to work, and sucks up a similarly impressive quantity. It's remarkable, and naturally begs the question of where it all comes from? Some is externally derived, entering the house with us or through open windows. Some is clearly fibres shed from clothes, furniture etc. Then there's the skin cells and hair we shed. But at least part is derived from the host of smaller organisms that live in and around our homes, many of which are arthropods (Butte & Heinzow 2002 ). I suspect almost all readers are aware that some smaller animals live in our houses – even those who live in the modern urban houses will have occasionally encountered the odd drosophila, silverfish or spider. But I suspect that prior to reading Madden et al.'s article in this issue of Molecular Ecology (Madden et al. 2017 ), few of you will have appreciated the true diversity, which, it turns out, is huge.     

The spirit of the gift,the price of potency: a Maussian model of the Southeast Asian state of Luwu

This rereading of Mauss's The gift shifts the focus of discussion from the Maori hau to another example: tanoana (potency) among the Toraja (To Pamona) of Central Sulawesi. This potency animates an exchange with (human) gods that is at once gift and purchase (maoli). By tracing the intersection of this Maussian literature with that on the animist foundation of the Southeast Asian state, I analyse the nature of potent gifts that serve as a form of social currency in a ‘spiritual economy’ tying centre with (Toraja) periphery in the kingdom of Luwu. This ‘money’, imbued with royal potency, is a medium for the payment of debt only and not a medium of exchange, which gives ‘purchases’ made with it the characteristics of a ‘gift’ and also an opportunity to extract tribute. The Maussian analysis of the blurring of person and thing, and of persons and spirits, thus offers new insight into the nature of political power in the Southeast Asian state.     

The Untold Sacrifice: The Monotony and Incompleteness of Self-Sacrifice in Northeast Brazil

There is no such thing as an accidental sacrifice. Sacrifice is always pre-meditated, and if not entirely goal-oriented, at the very least inherently meaningful as a process in itself. This paper is about how we might begin to understand sacrifices that do not conform to these rules. It concerns the question: does sacrifice exist outside of its (often) dramatic, self-conscious elaboration? Within the Brazilian Catholic tradition everyday life – ideally characterised by monotonous, undramatic, acts of self-giving – is ‘true sacrifice’. For ordinary Catholics, the challenge is not how to self-sacrifice, but how to make one's mundane life of self-sacrifice visible whilst keeping one's gift of suffering ‘free’. In this paper I describe, ethnographically, the work entailed as one of ‘revelation’ and use the problems thrown up to reflect upon both the limits and advantages of Western philosophical versus anthropological understandings of Christian sacrificial practices to date.     

PCNA binding through a conserved motif

Proliferating cell nuclear antigen (PCNA) has recently been identified as a target for the binding of several proteins. The cell cycle regulatory protein, p21, and the replication endonuclease, Fen1, have already been described as competing for PCNA binding. Two recent reports have identified DNA (cytosine-5)methyltransferase (MCMT) and the DNA repair endonuclease XPG as binding to PCNA.^1,2 The remarkable thing about these interactions is that they all seem to occur through a conserved motif that is likely to contact the same site on PCNA. This has fascinating implications for a regulatory network linking these diverse protein functions. BioEssays 20 :195–199, 1998. © 1998 John Wiley & Sons, Inc.     

Effects of a predatory fish (Galaxias olidus) on the structure of intermittent stream pool communities in southeast Australia

Abstract The impact of predation over a 3 week period by the small (mean length 53 mm) salmoniform fish, Galaxias olidus, on the invertebrate communities in the still summer pools of an intermittent stream in southeastern Australia was tested using enclosures that incorporated both deep and shallow habitat areas. Twenty G. olidus, a key generalist predator in the system studied, were enclosed for 3 weeks in 1.5 × 1.7 m enclosures. Galaxias olidus was found to reduce significantly the distribution and abundance of air-breathing nektonic species. In contrast, the abundance of non-air-breathing nektonic species increased in the presence of fish in the deep areas of the enclosures. There was no significant impact offish predation on species richness, total abundance, epibenthic or interstitial species. The most likely reason for the general lack of response to the presence of fish by epibenthic and interstitial species is the availability of abundant spatial refugia from predation within the complex substrate of the stream. In contrast, air-breathing nektonic species are vulnerable to predation by fish due to the lack of refuges in the open water. Increases in the abundance of non-air-breathing nektonic species in the presence of fish may be related to reductions in the abundance of predatory dytiscid beetles. Significant differences between deep and shallow habitats were observed in total abundance and species richness, and in the abundances of air-breathing nektonic and epibenthic species, suggesting that physicochemical factors play a key role in determining invertebrate distribution within stream pools.     

A toxic imbalance of Hsp70s in Saccharomyces cerevisiae is caused by competition for cofactors

Molecular chaperones are responsible for managing protein folding from translation through degradation. These crucial machines ensure that protein homeostasis is optimally maintained for cell health. However, ‘too much of a good thing’ can be deadly, and the excess of chaperones can be toxic under certain cellular conditions. For example, overexpression of Ssa1, a yeast Hsp70, is toxic to cells in folding‐challenged states such as [PSI+]. We discovered that overexpression of the nucleotide exchange factor Sse1 can partially alleviate this toxicity. We further argue that the basis of the toxicity is related to the availability of Hsp70 cofactors, such as Hsp40 J‐proteins and nucleotide exchange factors. Ultimately, our work informs future studies about functional chaperone balance and cautions against therapeutic chaperone modifications without a thorough examination of cofactor relationships.     

Homology as a relation of correspondence between parts of individuals

The recognition of correspondences has long been a fundamental activity among systematists. Advocates ofNaturphilosophie, such as Lorenz Oken, drew far-fetched analogies between taxonomic groups and all sorts of other things, including the Persons of the Trinity. They treated change through time either as analogous to an ontogeny or as the product of divinely instituted laws of nature. Darwin changed things by making the taxonomic units strictly historical, implying that they are not classes but rather individuals in a broad metaphysical sense. That means that taxa are concrete, particular things, or wholes made up of parts which are themselves individuals, and that there are no laws of nature for them. Homology is a relationship of correspondence between parts of organisms that are also parts of populations and lineages. It is not a relationship of similarity, and unlike similarity it is transitive. Analogy is a relationship of correspondence between parts of organisms that are members of classes, and is not necessarily due to function. Taxa, like other individuals, can change indefinitely, and the only thing that they must share is a common ancestor. They do not share an essence, Platonic Idea orBauplan, although “conservative characters” may be widespread in them. Iterative homology likewise is a relationship of correspondence, but the nature of that correspondence remains unclear. The difficulties of the homology concept can be overcome by treating phylogenetics and comparative biology in general as historical narrative. From the 46th “Phylogenetisches Symposium”, Jena, Germany, November 20–21, 2004. Theme of the symposium: “Evolutionary developmental biology—new challenges to the homology concept”.     

Interdependence of welfare outcome measures and potential confounding factors on finishing pig farms

The factors influencing the observed prevalence of some welfare outcome measures were investigated as part of a larger project examining the feasibility and benefits of incorporating on-farm welfare outcome assessments into UK Pig Farm Assurance Schemes. All finishing pigs (>40 kg) on six farms that had pens containing 25 pigs or less were assessed for dirtiness, body lesions, tail lesions, bursitis, lameness, oral behaviour and pigs requiring hospitalisation. The overall small number of significant correlations between the measures across all farms (29 out of a possible 120) and the lack of a significant correlation between any pair of measures on all six or even five farms suggests that no measure can be reliably replaced by another. On the three farms with the highest farm prevalence of dirtiness there were significant negative correlations between pen prevalences of dirtiness and recorded tail and/or body lesions (p < 0.02). The prevalence of pigs requiring hospitalisation was positively correlated with lameness on four farms (p < 0.001) and tail lesions on three farms (p < 0.005). Using a univariate general linear model the time of observation was only found to correlate with one measure, the dirtiness of the pigs (p = 0.004), with the prevalence of dirtiness in pens on the three ‘dirtiest’ farms increasing as the day progressed. There was no effect of the stocking density, group size, time since feeding and time since straw provision on the prevalence of any of the outcome measures. It is recommended that to prevent bias in the recording of tail and body lesions farm assurance assessments are conducted on pigs with a prevalence for dirtiness of less than 17%. Lower prevalences of dirtiness are more likely to occur on some farms first thing in the morning.     

Antibiotics potentiating potential of catharanthine against superbug Pseudomonas aeruginosa

Multidrug resistance (MDR) put an alarming situation like preantibiotic era which compels us to invigorate the basic science of anti-infective chemotherapy. Hence, the drug resistant genes/proteins were explored as promising drug targets. Keeping this thing in mind, proteome of Pseudomonas aeruginosa PA01 was explored, which resulted in the identification of tripartite protein complexes (MexA, MexB, and OprM) as promising drug target for the screening of natural and synthetic inhibitors. The purpose of present investigation was to explore the drug resistance reversal potential mechanism of catharanthine isolated from the leaves of Catharanthus roseous. Hence, the test compound catharanthine was in silico screened using docking studies against the above receptors, which showed signi?cant binding affinity with these receptors. In order to validate the in silico findings, in vitro evaluation of the test compound was also carried out. In combination, catharanthine reduced the minimum inhibitory concentration MIC of tetracycline (TET) and streptomycin up to 16 and 8 folds, respectively. Further, in time kill assay, catharanthine in combination with TET reduced the cell viability in concentration dependent manner and was also able to reduce the mutation prevention concentration of TET. It was also deduced that drug resistance reversal potential of catharanthine was due to inhibition of the efflux pumps.     

Framing the ethical and legal issues of human artificial gametes in research,therapy, and assisted reproduction: A German perspective

Recent results from studies on animals suggest that functional germ cells may be generated from human pluripotent stem cells, giving rise to three possibilities: research with these so‐called artificial gametes, including fertilization experiments in vitro; their use in vivo for therapy for the treatment of human infertility; and their use in assisted reproductive technologies in vitro. While the legal, philosophical, and ethical questions associated with these possibilities have been already discussed intensively in other countries, the debate in Germany is still at its beginning. A systematic and detailed analysis of the legal framework in Germany is provided with regard to the three possibilities, including the applicable statutory laws as well as the constitutional law. The question emerges as to whether the statutory laws as well as the constitution justify a distinction to be made between embryos of artificial and natural origin. This question is subject to philosophical analysis, discussing the distinction between person and thing, dignity and price, personality and property, and nature and technique. As a result, the criterion of naturalness alone may not be sufficient to differentiate between embryos of natural and artificial origin, and other criteria need to be identified.     

Turkish nationalism and the Kurdish question

This article addresses the ways in which Turkish nationalism has perceived the Kurdish question. It is shown that both Turkish nationalism and the Kurdish question have passed through some paradigmatic moments in the twentieth century. This, I argue, has shaped the way that the Kurdish question has been perceived by Turkish nationalism. While the Kurdish question had been seen by Turkish nationalism mostly in terms of a fatal rivalry between the backward, pre-modern and tribal past and the prosperous present in the first half of the century, it was perceived in terms of a tension between the peripheral economy and national market in the fifties and sixties. In the 1970s, the Kurdish unrest was believed to be a product of communist incitement. Despite this impurity in perception, one thing has remained nearly unchanged for Turkish nationalism: Kurds could become Turkish. In other words, Turkish nationalism of the republican era has principally perceived Kurds as future-Turks. However, the signs in circulation at present indicate that the confidence of Turkish nationalism as to Kurds’ potential of becoming Turkish is not as firm as it used to be. At present, Turkish nationalism seems to be getting prepared to abandon its contention that Kurds are future-Turks.