A case for resurrecting lost species—review essay of Beth Shapiro’s, “How to Clone a Mammoth: The Science of De-extinction”

The title of Beth Shapiro’s ‘How to Clone a Mammoth’ contains an implicature: it suggests that it is indeed possible to clone a mammoth, to bring extinct species back from the dead. But in fact Shapiro both denies this is possible, and denies there would be good reason to do it even if it were possible. The de-extinct ‘mammoths’ she speaks of are merely ecological proxies for mammoths—elephants re-engineered for cold-tolerance by the addition to their genomes of a few mammoth genes. Shapiro’s denial that genuine species de-extinction is possible is based on her assumption that resurrected organisms would need to be perfectly indistinguishable from the creatures that died out. In this article I use the example of an extinct New Zealand wattlebird, the huia, to argue—contra Shapiro—that there are compelling reasons to resurrect certain species if it can be done. I then argue—again, contra Shapiro—that synthetically created organisms needn’t be perfectly indistinguishable from their genetic forebears in order for species de-extinction to be successful.     

The Politics and Regulation of Anger in Urban China

Negative emotions such as anger, and community responses to their expression are culturally and politically conditioned, including by dominant medical discourse on anger’s somatic and psychic effects. In this article I examine local genres of anger expression in Beijing, China, particularly among marginalized workers, and address culturally specific responses to them. Through majie (rant), xiangpi ren (silenced rage), and nande hutu (muddledness as a more difficult kind of smartness), workers strategically employ anger to seek redress for injustices and legitimate their moral indignation while challenging official psychotherapeutic interventions. Those who seek to regulate anger, mostly psychosocial workers acting as arm’s-length agents of the state, use mixed methods that draw on Western psychotherapy and indigenous psychological resources to frame, medicalize or appease workers’ anger in the name of health and social stability. I demonstrate how the two processes—anger expression and responses to it—create tensions and result in an ambiguous and multivalent social terrain which Chinese subjects must negotiate and which the state attempts to govern. I argue that the ambivalence and multi-valence of anger expressions and state-sponsored reactions to them render this emotion both subversive vis-à-vis power and subject to manipulations that maintain social order.     

Control and consequences of <Emphasis Type="Italic">Spartina</Emphasis> spp. invasions with focus upon San Francisco Bay

Maritime Spartina spp. are powerful ecosystem engineers that accrete sediment, define shorelines, create habitat, and generate prodigious primary productivity both where they are native and where they have been introduced. Invasive Spartina spp. can compete vigorously with native species, diminish biota, change hydrology, and confound human uses of estuaries. Herbicides have been effective in controlling several Spartina spp. invasions. One of the most recent successes is a 15-year campaign that has virtually eliminated S. alterniflora from the large, century-old invasion in Willapa Bay, WA, USA. Hybridization between native and introduced Spartina spp. has created new species and hybrid swarms. In San Francisco Bay, CA, USA (SF Bay) a complicated situation continues to play out from the purposeful introduction of S. alterniflora, which hybridized with native California cordgrass, S. foliosa. The hybrids spread rapidly and led to a long list of environmental problems, which led to an herbicide program that was successful in greatly diminishing the hybrid and saving the open mud habitat of migratory shorebirds. However, it was belatedly realized that the non-migratory, endangered Ridgeway’s rail uses the tall, dense hybrid Spartina as a surrogate for habitat that was lost during the twentieth century to urbanization and agricultural transformation of marshes around SF Bay. This realization has made difficult the simultaneous management of hybrid Spartina, wildlife conservation, and marsh restoration in San Francisco Bay. Restoration of native vegetation could satisfy the multiple goals of preserving open mud and conserving Ridgeway’s rail.     

Invasive <Emphasis Type="Italic">Tamarix</Emphasis> (Tamaricaceae) in South Africa: current research and the potential for biological control

Most species of Tamarix originate in Eurasia and at least five species have become invasive around the world, including South Africa. However, T. usneoides is indigenous to southern Africa, where the potential for biological control of the invasive species is being investigated. Recent research on the invasive species is reviewed here with particular reference to these South African biocontrol efforts. The successful biological control programme against invasive Tamarix in the USA, using several species of “Tamarisk beetle”, is being used as a guide for the South African research. The South African programme is complicated by firstly, the presence of the indigenous T. usneoides which raises the precision of host-specificity required, and secondly, the introduced and indigenous Tamarix have a high intrinsic value for phytoremediation of mine tailings dams in South Africa. The phylogenetic proximity of these Tamarix species to each other has contributed to this challenge, which has nevertheless been successfully addressed by molecular techniques used to separate the species. In addition, classical morphological techniques have been used to separate the Tamarisk beetles, so that now they can generally be matched to Tamarix tree species. Overall, it is concluded that given the broad knowledge now available on the ecology and identity of both the trees and their biocontrol agents, the prospects for successful biological control of Tamarix in South Africa are good.     

Rethinking the role of theory in exploratory experimentation

To explain their role in discovery and contrast them with theory-driven research, philosophers of science have characterized exploratory experiments in terms of what they lack: namely, that they lack direction from what have been called “local theories” of the target system or object under investigation. I argue that this is incorrect: it’s not whether or not there is direction from a local theory that matters, but instead how such a theory is used to direct an experiment that matters. Appealing to contemporary exploratory experiments that involve the use of experimental techniques—specifically, examples where scientists explore the interaction of neural activity and human behavior by magnetically stimulating brains—I argue that local theories of a target system can inform auxiliary hypotheses in exploratory experiments, which direct these experiments. These examples illustrate how local theories can direct the exploration of target systems where researchers do not aim to evaluate these theories.     

The management of “quality”: class decomposition and racial formation in a Chicago factory

Workplace training offers a distinctly explicit and uniquely articulate site for the ethnography of the capital–labor relation as an ideological phenomenon, where the everyday work of hegemony is shown to be deeply grounded in the everyday hegemony of work. In this ethnographic account of a factory classroom devoted to introducing production workers to the precepts of Total Quality Management and training them in Statistical Process Control, the neoliberal reform of the labor process—which sought to accomplish a class decomposition of the company’s workforce in favor of an individualizing regime of workers’ personal responsibility and accountability for various quality control operations—repeatedly provoked the company’s Latino workers into angry and vociferous expressions of antagonism to management. Indeed, insofar as the management’s efforts to reform labor by decomposing the workforce as a class formation merely intensified the prevailing preconditions of their racial formation, they thereby only exacerbated anew the Latino workers’ antagonism as workers to the terms of their subordination. Thus, the generic (ostensibly race-neutral) reform of the labor process initiated under the aegis of “Total Quality Management” implicated the presumed management of “quality” in a concomitant reconfiguration of what was, effectively, a contemporary regime of racial management.     

Genome: Origins and evolution of the term

The appearance of a new scientific term is a significant event in the human cognitive process and the result of the realization of the separateness of an object or a phenomenon. Our article concentrates on the origins of basic genetic terms, such as genetics, gene, genotype, genome, gene pool, and genomics. We propose using the term karyogenomics for the special direction of genomics related to the study of the organization and evolution of eukaryotic genomes by means of modern chromosome analysis, as well as by full genome sequencing.     

Enthalpy–entropy compensation and the isokinetic temperature in enzyme catalysis

Enthalpy–entropy compensation supposes that differences in activation enthalpy ?H ^? for different reactions (or, typically in biochemistry, the same reaction catalysed by enzymes obtained from different species) may be compensated for by differences in activation entropy ?S ^?. At the isokinetic temperature the compensation is exact, so that all samples have the same activity. These ideas have been controversial for several decades, but examples are still frequently reported as evidence of a real phenomenon, nearly all of the reports ignoring or discounting the possibility of a statistical artefact. Even for measurements in pure chemistry artefacts occur often, and they are almost inescapable in enzyme kinetics and other fields that involve biological macromolecules, on account of limited stability and the fact that kinetic equations are normally valid only over a restricted range of temperature. Here I review the current status and correct an error in a recent book chapter.     

Survey of potential factors involved in the low frequency of CP5 and CP8 expression in <Emphasis Type="Italic">Staphylococcus aureus</Emphasis> isolates from mastitis of dairy cattle from Argentina,Chile, and Uruguay

Staphylococcus aureus produces capsular polysaccharides (CPs) both in vivo and under defined culture conditions being serotypes 5 and 8 the most prevalent. S. aureus isolates that fail to produce CP5 or CP8 are defined as non-typeable (NT). Loss of capsule expression, however, may lead to S. aureus persistence in a chronically infected host. The prevalence of NT strains of S. aureus isolated from bovine mastitis varies according to the geographic origin of the strain. The aims of this work were to detect phenotypically and genotypically the capsular profile of 144 S. aureus isolated from bovine mastitis in Argentina, Chile, and Uruguay and explore the factors that are considered to be associated with capsule expression as presence of IS257, IScap, and agr typing of non-related collection. The detection of the IS257, IScap, cap genes, and agr typing was performed using PCR. The detection and quantification of capsular polysaccharide production were performed by ELISA assays. We found that 96% of the S. aureus isolates investigated carried cap5(8) genes but over 75% of strains do not express capsule in the three countries studied. However, only 6 isolates from Argentina carried the IScap element that totally suppressed the expression of the capsule, suggesting that other factors could influence on CP expression. Moreover, the agrI/NT association was statistically significant suggesting that this profile is a phenomenon observed not only in other parts of the world but also in our region.     

Larval aquatic and terrestrial mites infesting parthenogenetic <Emphasis Type="Italic">Ischnura hastata</Emphasis> (Odonata: Coenagrionidae) from the Azores islands

We report here the prevalence of parasitism by water mites (Arrenurus sp.) and terrestrial mites (Leptus killingtoni) on parthenogenetic Ischnura hastata (Odonata: Coenagrionidae) from the Azores islands. Leptus killingtoni was only found on the island of Pico, and the prevalence of infestation was highly variable among the different ponds studied, ranging from 0 to 41%. Leptus killingtoni was observed on three of the four odonate species from the archipelago: I. hastata, I. pumilio, and Sympetrum fonscolombii, all of them new hosts for this species. Aquatic mites have been found parasitizing I. hastata females on the island of São Miguel. The prevalence of mite parasitism by Arrenurus sp. on I. hastata was very low, ranging from 12% (2003) to 1% (2008), and in most of the studied ponds, no mites were found attached to females. Although I. hastata coexists with a sexual congener species in the Azores (I. pumilio), they are syntopic in only a small fraction of ponds. Therefore, a comparison between I. hastata and I. pumilio was insufficient to test the predictions of the Red Queen Hypothesis, and further research on parasitism rates in both species needs to be done. In any case, the low prevalence of mite parasitism found in the Azores, coupled with the fact that most of the populations in the archipelago are almost free from competitors and predators, could explain the persistence of these I. hastata parthenogenetic populations, despite their low levels of genetic variation.     

Biogeography of North Pacific <Emphasis Type="Italic">Isoëtes</Emphasis> (Isoëtaceae) inferred from nuclear and chloroplast DNA sequence data

Recent advances in phylogenetics indicate that reticulate evolution has played an important role in the emergence of Isoëtes species in the North Pacific region. However, the biogeographical origin of the North Pacific Isoëtes species remains contentious. We present a fossilcalibrated phylogeny of species from the North Pacific region based on molecular data. Within this framework, we discuss their ancestral areas and biogeographical history. North Pacific Isoëtes are divided into two clades: clade I, consisting of East Asian, Papua New Guinean, and Australian species, and clade II, consisting of West Beringian and western North American species. Within clade I, Australian Isoëtes species were an early divergent group, and Papua New Guinea’s species form a sister clade to the East Asian species. Biogeographical reconstructions suggest an Australasian origin for the East Asian species that arose through long-distance dispersal during the late Oligocene. Within clade II, I. asiatica from West Beringia forms a clade with I. echinospora and I. muricata from Alaska. Western North America was the area of origin for the dispersal of Isoëtes species to West Beringia via the Bering land bridge during the late Miocene. Our study identifies the biogeographic origin of the North Pacific Isoëtes and suggests long-distance dispersal as the most likely explanation for their intercontinental distribution.     

<Emphasis Type="Italic">Phragmites</Emphasis><Emphasis Type="Italic">australis</Emphasis> as a model organism for studying plant invasions

The cosmopolitan reed grass Phragmites australis (Poaceae) is an intensively studied species globally with a substantial focus in the last two decades on its invasive populations. Here we argue that P. australis meets the criteria to serve as a model organism for studying plant invasions. First, as a dominant species in globally important wetland habitats, it has generated significant pre-existing research, demonstrating a high potential for funding. Second, this plant is easy to grow and use in experiments. Third, it grows abundantly in a wide range of ecological systems and plant communities, allowing a broad range of research questions to be addressed. We formalize the designation of P. australis as a model organism for plant invasions in order to encourage and standardize collaborative research on multiple spatial scales that will help to integrate studies on the ecology and evolution of P. australis invasive populations, their response to global environmental change, and implications for biological security. Such an integrative framework can serve as guidance for studying invasive plant species at the population level and global spatial scale.     

Characterisation of seven <Emphasis Type="Italic">Inocybe</Emphasis> ectomycorrhizal morphotypes from a semiarid woody steppe

Ectomycorrhizas (ECM) of Inocybe species (Inocybaceae, Basidiomycota) formed by three host plant species (Populus alba, Salix rosmarinifolia and Pinus nigra) in a semiarid woody steppe of Hungary were studied. To identify the fungal partners, we performed phylogenetic analyses of nucleotide sequences for the internal transcribed spacer region of nuclear DNA (nrDNA ITS) together with sequences gained from public databases. Seven Inocybe ectomycorrhiza morphotypes were morpho-anatomically characterised. Five morphotypes were identified (I. phaeoleuca, I. psammophila, I. semifulva, I. splendens and I. subporospora), whereas two morphotypes represented unidentified Inocybe species. Differences were discernible among the morphotypes, and they showed general anatomical characteristics of Inocybe ECM, such as the slightly organised plectenchymatic mantle (types A, B and E and the gelatinous C). The ECM of I. subporospora and I. phaeoleuca were detected from the introduced Pinus nigra. These two fungi are probably native to the area but capable of forming a novel ectomycorrhizal association with the invasive host.     

The evolution of cultivated potatoes

In the first stages of potato evolution in the northern Andes, diploid cultivated species of theSolanum stenotomum complex were selected, in all probability, from wild progenitors in theS. brevicaule complex. TetraploidSolanum tuberosum ssp.andigena arose by fusion of unreduced gametes of a parent in theS. stenotomum complex with those of an unidentified wild species having actinomorphic calyces. Unreduced male gametes of several diploid species fertilized eggs of ssp. andigena leading to extensive introgression.Solanum tuberosum ssp.tuberosum probably originated from a cross between ssp.andigena as staminate parent and an unidentified wild species which contributed cytoplasmic sterility factors encoded in mitochondria and/or plastids having a distinctive type of DNA. Derivatives of this hybridization, which may have occurred in northwestern Argentina, evolved to ssp. tuberosum in southern Chile and southern Argentina. In the 1570’s ssp.andigena was imported to Europe and spread from there to become a major crop with worldwide distribution. In the 1840's it was essentially eliminated by late blight,Phytophthora infestans.Solanum tuberosum ssp.tuberosum was introduced from Chile into North America and Europe in the late 1800's, and in turn achieved a worldwide distribution, filling the vacated agricultural niche of ssp.andigena. The differences between ssp.andigena and ssp.tuberosum in South America are sufficient that the two could reasonably be considered to be separate species. Since the 1960’s the two taxa have been hybridized often in breeding programs. Neotuberosum, a northern-adapted strain of ssp. andigena, has been selected to mimic ssp.tuberosum. Substitution back-cross products have been produced that have the chromosomal genes of ssp.tuberosum combined with cytoplasmic factors of Andean species. These breeding activities are blurring the distinctions between the two subspecies throughout much of the world, though they remain distinct in their native areas in South America.     

<Emphasis Type="Italic">Humulus lupulus</Emphasis> L., a very popular beer ingredient and medicinal plant: overview of its phytochemistry,its bioactivity,and its biotechnology

Humulus lupulus L. (Cannabaceae), commonly named hop, is widely grown around the world for its use in the brewing industry. Its female inflorescences (hops) are particularly prized by brewers because they produce some secondary metabolites that confer bitterness, aromas and antiseptic properties to the beer. These sought-after metabolites include terpenes and sesquiterpenes, found in essential oil, but also prenylated phenolic compounds, mainly acylphloroglucinols (bitter acids) from the series of α-acids (humulone derivatives). These metabolites have shown numerous biological activities, including among others, antimicrobial, sedative and estrogenic properties. This review provides an inventory of hop’s chemistry, with an emphasis on the secondary metabolites and their biological activities. These compounds of biological interest are essentially produced in female inflorescences, while other parts of the plant only synthetize low quantities of them. Lastly, our article provides an overview of the research in plant biotechnology that could bring alternatives for hops metabolites production.     

Larvae of the exotic predatory ladybird <Emphasis Type="Italic">Platynaspidius maculosus</Emphasis> (Coleoptera: Coccinellidae) on citrus trees: prey aphid species and behavioral interactions with aphid-attending ants in Japan

An aphidophagous ladybird, Platynaspidius maculosus (Weise) (Coleoptera: Coccinellidae), is originally distributed in China, Taiwan, and Vietnam. The ladybird has recently intruded into the southern and central parts of Japan. The present study found that the larvae of this ladybird preyed on three aphid species, Aphis spiraecola, Aphis gossypii, and Toxoptera citricidus (all Hemiptera: Aphididae), feeding on young shoots of various Citrus species in August to early October in Shizuoka Prefecture, central Japan. Laboratory rearing of the sampled larvae confirmed that the larvae completed their development (adult emergence) by consuming each of the three aphid species. The ladybird larvae were observed foraging in aphid colonies attended by one of the four ants, Lasius japonicus, Pristomyrmex punctatus, Formica japonica, and Camponotus japonicus (all Hymenoptera: Formicidae). Field observations revealed that the foraging/feeding larvae were almost completely ignored by honeydew-collecting ants even when they physically contacted each other. Thus, in Japan, the larvae of the exotic ladybird exploit colonies of the three aphid species attended by one of the four ant species on many Citrus species. On the basis of the results, I discuss the possibility of the ladybird’s reproduction on citrus trees in Japan, probable adaptations of the ladybird larvae to aphid-attending ants, and potential impacts of the ladybird on native insect enemies attacking ant-attended aphids on citrus.     

The ontology of organisms: Mechanistic modules or patterned processes?

Though the realm of biology has long been under the philosophical rule of the mechanistic magisterium, recent years have seen a surprisingly steady rise in the usurping prowess of process ontology. According to its proponents, theoretical advances in the contemporary science of evo-devo have afforded that ontology a particularly powerful claim to the throne: in that increasingly empirically confirmed discipline, emergently autonomous, higher-order entities are the reigning explanantia. If we are to accept the election of evo-devo as our best conceptualisation of the biological realm with metaphysical rigour, must we depose our mechanistic ontology for failing to properly “carve at the joints” of organisms? In this paper, I challenge the legitimacy of that claim: not only can the theoretical benefits offered by a process ontology be had without it, they cannot be sufficiently grounded without the metaphysical underpinning of the very mechanisms which processes purport to replace. The biological realm, I argue, remains one best understood as under the governance of mechanistic principles.     

In stark contrast to widespread declines along the Scotia Arc,a survey of the South Sandwich Islands finds a robust seabird community

The South Sandwich Islands, in the South Atlantic Ocean, are a major biological hot spot for penguins and other seabirds, but their remoteness and challenging coastlines preclude regular biological censuses. Here we report on an extensive survey of the South Sandwich Islands, the first since the late 1990s, which was completed through a combination of direct counting, GPS mapping, and interpretation of high-resolution commercial satellite imagery. We find that the South Sandwich Islands host nearly half of the world’s Chinstrap Penguin (Pygoscelis antarctica) population (1.3 million breeding pairs), as well as c. 95,000 breeding pairs of Macaroni Penguins (Eudyptes chrysolophus), and several thousand breeding pairs of Gentoo Penguins (Pygoscelis papua). Despite being at the northern edge of their breeding range, we found an unexpectedly large (≥125,000 breeding pairs) population of Adélie Penguins (Pygoscelis adeliae). Additionally, we report that nearly 1900 pairs of Southern Giant Petrels (Macronectes giganteus) breed in the South Sandwich Islands, 4 % of the global population, almost all of which are found on Candlemas Island. We find that the South Sandwich Islands have not experienced the same changes in penguin abundance and distribution as the rest of the Scotia Arc and associated portions of the western Antarctic Peninsula. This discovery adds important context to the larger conversation regarding changes to penguin populations in the Southern Ocean.     

Metal hyperaccumulating Brassicaceae from the ultramafic area of Yahyalı in Kayseri province,Turkey

Many of the plants found in serpentine areas are endemics and they may accumulate Ni at high concentration. High accumulation of Cr is rare, or in some views, never properly demonstrated. Generally, a very small proportion of any serpentine flora shows high accumulation of Ni, in some serpentine areas Ni accumulators are completely absent. There are approximately 570 hyperaccumulator plant species found on earth, 450 of them are Ni hyperaccumulators. A few of the Ni accumulators have potential for phytoremediation or phytomining. In the present study, 19 different Brassicaceae members growing in serpentine habitats in the district of Yahyal?, Kayseri province, Turkey viz., members of genera Aethionema, Alyssum, Arabis, Heldreichia, Hesperis, Iberis, Isatis, Microthlaspi, Odontarrhena, Pseudosempervivum and Thlaspi were investigated. Nickel concentrations in the soil and underground and aboveground parts of plants were determined by using ICP-OES. It was observed that Ni concentrations of seven taxa (Odontarrhena muralis, O. oxycarpa, Isatis cappadocica subsp. cappadocica, Microthlaspi perfoliatum, Pseudosempervivum sempervivum, Thlaspi triangulare, Thlaspi rosulare) reach the threshold criterion of 1,000 mg kg^?1 for Ni hyperaccumulation. In this study Ni concentrations in aboveground tissues of I. cappadocica subsp. cappadocica are determined as 5,587 mg kg^?1 (in dry weight). Accordingly, it is suggested that this taxon be added to the list of Ni hyperaccumulator plants.     

The genus <Emphasis Type="Italic">Lindera</Emphasis>: a source of structurally diverse molecules having pharmacological significance

Lindera plants not only have good ornamental and economic uses but also have great medicinal and therapeutic values. The genus Lindera consists of approximately 100 species that are widely distributed in tropical and subtropical areas throughout the world. This extensive geographical distribution allows Lindera plants to produce diverse secondary metabolites having novel structures. Phytochemical investigations have shown that Lindera plants produce 341 constituents, including sesquiterpenoids, alkaloids, butanolides, lucidones, flavonoids, and phenylpropanoids. Moreover, some Lindera plants show significant chemotaxonomic reference under family Lauraceae and tribe Litseae. Although Lindera plants have various pharmacological and biological properties, their anticancer, antihypertensive, anti-inflammatory, and analgesic properties have been focused in many studies. Butanolides and lucidones have shown great potential in developing anticancer agents while aporphine alkaloids have shown great potential in developing antiarthritic and antinociceptive agents. However, these compounds need to be assessed further by performing in-depth and systematic research.