Automata, Living and Non-Living: Descartes' Mechanical Biology and His Criteria for Life

Despite holding to the essential distinction between mind and body, Descartes did not adopt a life-body dualism. Though humans are the only creatures which can reason, as they are the only creatures whose body is in an intimate union with a soul, they are not the only finite beings who are alive. In the present note, I attempt to determine Descartes' criteria for something to be 'living.' Though certain passages associate such a principle with the presence of a properly functioning heart, I show that there are important reasons for also understanding life in terms of a degree of complexity of design.     

Nestbox orientation: a species-specific influence on occupation and breeding success in woodland passerines

Capsule Nestbox orientation has species-specific influences on nestbox occupation and breeding success for woodland passerines.

Aims To determine if nestbox orientation had an influence upon nestbox selection or breeding success for three co-occurring woodland passerines.

Methods We analysed 15 consecutive years of breeding data (1990–2004) from 295 nestboxes in the UK using circular statistical analyses to examine the influence of orientation upon nestbox occupation and breeding success for three species, Blue Tit Cyanistes caeruleus, Great Tit Parus major and Pied Flycatcher Ficedula hypoleuca.

Results The three species used nestboxes of all orientations during the 15-year period. The frequency of nestbox occupation by Great Tits correlated with orientation (the mean number of nests in boxes oriented south-southwest was lower than the mean number of nests in boxes facing other directions). There was no such relationship for Blue Tits or Pied Flycatchers. Nestbox orientation influenced the breeding success of Pied Flycatcher (the mean number of young to fledge from boxes oriented south-southwest was lower than from boxes facing other directions). There was no such relationship for Blue or Great Tits.

Conclusion Nestbox orientation can be an important influence on occupation and breeding success, but this differed between species. Intriguingly, although the directionality reduced nestbox occupation (Great Tit) and breeding success (Pied Flycatcher) was the same (south-southwest), there was a disparity in the influence of orientation for Great Tit (orientation influenced the frequency of occupation but not success) and Pied Flycatcher (orientation did not influence occupation but did affect success). We discuss these disparities, considering the possible influences of mating strategy, breeding phenology, nestbox microclimate and offspring quality.     

Transforming Signs. Iconicity and Indexicality in Russian Healing and Magic

In this article, the ethnography of magic and healing in contemporary Russia is analyzed using the basic concepts of Peircian semiotics. Indigenous terms of affliction used in magical diagnostics of misfortunes, as well as pantomimic gestures in hand healing are regarded as iconic and indexical signs. Their mode of signification is pragmatic presentation rather than textual representation, which underlies their capacity to effect transformations in consciousness. It is shown, however, that it is cultural conventions of their symbolic meanings that form these signs as icons and indexes.     

Signs and Instruments: The Convergence of Aristotelian and Kantian Intuitions in Biosemiotics

Biosemiotics—a discipline in the process of becoming established as a new research enterprise—faces a double task. On the one hand it must carry out the theoretical and experimental investigation of an enormous range of semiotic phenomena relating organisms to their internal components and to other organisms (e.g., signal transduction, replication, codes, etc.). On the other hand, it must achieve a philosophical re-conceptualization and generalization of theoretical biology in light of the essential role played by semiotic notions in biological explanation and modeling. This paper attempts to contribute to the second task by tracing some aspects of the historical evolution of explanatory models in biology. In so doing, a parallel can be drawn between the present status of biosemiotics and that of physics during the early decades of the last century. By following the career of the concept instrument (organon) in Aristotelian science, we revisit historical stages of the antithetical (but often complementary) roles of mechanical and teleological forms of explanation. The impact of the introduction of the organic codes in biology is seen to be somewhat analogous to that of the introduction of the quantum of action in physics. Faced with intractable empirical facts, physicists combined experimental results and bold philosophical speculation to create quantum physics—a wider, deeper framework that accommodates the new facts through a wholesale reformulation of the classical ideas. Essential to this development was the articulation of the epistemic functions of instruments, which was absent from classical physics. Similarly, the consideration of the role of instruments in biology may lead to a synthesis of Aristotelian and Kantian intuitions within a wider framework capable of joining now separate perspectives, such as Jablonka’s four-fold view of inheritance information, Barbieri’s theory of artifactual copymakers and codemakers, and recently developed models of causation based on the idea of manipulative interventions.

On the Semio-Mathematical Nature of Codes

The relational structure of RNA, DNA, and protein bears an interesting similarity to the determination problem in category theory. In this paper, we present this deep-structure similarity and use it as a springboard for discussing some abstract properties of coding in various systems. These abstract properties, in turn, may shed light on the evolution of the DNA world from a semiotic perspective. According to the perspective adopted in this paper, living systems are not information processing systems but “meaning-making” systems. Therefore, what flows in the genetic system is not “information” but “value.” We define meaning, meaning-making, and value and then use these terms to explain the abstract dynamics of coding, which can illuminate many forms of sign-mediated activities in biosystems.     

On some recent insights in Integral Biomathics

This paper summarizes the results in Integral Biomathics obtained to this moment and provides an outlook for future research in the field.     

Very Simple Models, the Self-Modifying Automata and Chain of Self-Modifying Automata, Can Explain Self-Referential Properties of Living Beings

Very often, living beings seem able to change their functioning when external conditions vary. In order to study this property, we have devised abstract machines whose internal organisation changes whenever the external conditions vary. The internal organisations of these machines (or programs), are as simple as possible, functions of discrete variables. We call such machines self-modifying automata.These machines stabilise after any transient steps when they go indefinitely through a loop called p-cycle or limit cycle of length p. More often than not, the p in the cycle is equal to one and the cycle reduces to a fixed point.In this case the external value (v) can be considered as the index of function f such as: f_v(v)^–v and the machine has the property of self-replication and to be self-referential. Many authors, in computer and natural science, consider that self-referential objects are a main concept in comprehension of perception, behaviour and associations.In the third part, we have studied chains of automata. Only one automaton changes its internal organisation at each step. Chains of automata have better performances than single self-modifying automata: Higher frequency of fixed point occurrence and a shorter transient length. The performances of the chains of automata improve when the value of their internal states increases whereas the performances of single automata decrease.     

Virtual Speakers, Virtual Audiences: Agency, Audience and Constraint in an Online Chat Community

A participant-observer approach was used to explore an online chat community. The chat room was defined in terms of its construction and maintenance of speaker identities, and the user-chat room interface was examined with the aim of exploring how notions of selfhood can be better understood. Chat room audiences were then discussed within the framework of delineating different levels of virtual audiences and outlining processes by which these different levels interact. Finally, formal and informal discursive constraints were explored, and conclusions drawn on the ways that chat room users deal with constraints on their chat activity. Implications for understanding internet communication as well as discourse in general are discussed.     

A Psychology of Ghosts: The Regime of the Self and the Reinvention of Spirits in Indonesia and Beyond

The afterlife is currently being psychologised on a global scale. Based on a comparison of recent transformations in the reality of ghosts in eastern Indonesia and in contemporary Hollywood ghost series, this paper explores the links between spirits and changing conceptions of self in a global world. In Indonesia, ghosts are becoming traumatised, while in the West spirits increasingly struggle with emotional problems. In different ways, the paper suggests, spirits are becoming implicated in the globalisation of an interiorised and psychologised understanding of what it means to be human. As humans are encouraged to think of themselves as psychological beings, human spirits and ghosts are reinvented in a variety of ways—East and West. I argue that, ironically, it is the very hegemony of the powerful discourses and institutions that drive the globalisation of a psychological understanding of the self into ever more contexts and locations that is leading to these new forms of re-enchantment. The new kinds of ghosts that are currently emerging in the folds of global governmentality do so, it would seem, not in spite of the power of governmental reason, but by virtue of it.     

Chromobodies to Quantify Changes of Endogenous Protein Concentration in Living Cells

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Highlights

• •Chromobodies are stabilized by antigen binding in live cells.
• •Monitoring changes of endogenous protein levels in living cells with chromobodies.
• •Broadly applicable system to generate turnover-accelerated chromobodies.
• •Quantification of time- and dose-dependent compound effects.

     

The Importance of Being Serious: Subjectivity and Adulthood in Kenya

While anthropological scholarship on the life course transitions of young people has aimed to contribute to theories of structure and agency, social reproduction and change, it has done so relatively independently from the anthropological literature on subject formation. This paper explores how subjectivity – how people feel, think, and experience – is implicated in grappling with life course transitions. It addresses how ‘being serious’ is considered a critical adult competency and its achievement delineates a key life transition that young women in western Kenya variously resent and value, resist and seek. The analysis illuminates ways in which people grapple with their own subjectivity as a problem as well as a project, and how such problems and projects of subjectivity are problems and projects of social reproduction. I argue that taking account of such subjective transformations can augment political economy analysis of meanings and modes of life.     

Too Lonely to Die Alone: Internet Suicide Pacts and Existential Suffering in Japan

Most striking in the recent rise of suicide in Japan are the increase in suicide among young Japanese and the emergence of Internet suicide pacts. An ethnography of suicide-related Web sites reveals a distinctive kind of existential suffering among visitors that is not reducible to categories of mental illness and raises questions regarding the meaning of an individual “choice” to die, when this occurs in the context of an intersubjective decision by a group of strangers, each of whom is too afraid to die alone. Anthropology’s recent turn to subjectivity enables analyses of individual suffering in society that provide a more nuanced approach to the apparent dichotomy between agency and structure and that connect the phenomenon of suicide in Japan to Japanese conceptions of selfhood and the afterlife. The absence of ikigai [the worth of living] among suicide Web site visitors and their view of suicide as a way of healing show, furthermore, that analyses of social suffering must be expanded to include questions of meaning and loss of meaning and, also, draw attention to Japanese conceptions of self in which relationality in all things, including the choice to die, is of utmost importance.

Building momentum for systems and synthetic biology in India

Biological systems are inherently noisy. Predicting the outcome of a perturbation is extremely challenging. Traditional reductionist approach of describing properties of parts, vis-a-vis higher level behaviour has led to enormous understanding of fundamental molecular level biology. This approach typically consists of converting genes into junk (knock-down) and garbage (knock-out) and observe how a system responds. To enable broader understanding of biological dynamics, an integrated computational and experimental strategy was formally proposed in mid 1990s leading to the re-emergence of Systems Biology. However, soon it became clear that natural systems were far more complex than expected. A new strategy to address biological complexity was proposed at MIT (Massachusetts Institute of Technology) in June 2004, when the first meeting of synthetic biology was held. Though the term ‘synthetic biology’ was proposed during 1970s (Szybalski in Control of gene expression, Plenum Press, New York, 1974), the usage of the original concept found an experimental proof in 2000 with the demonstration of a three-gene circuit called repressilator (Elowitz and Leibler in Nature, 403:335–338, 2000). This encouraged people to think of forward engineering biology from a set of well described parts.     

Phylogenetic and phenotypic originality and abundance in a cerrado plant community

The originality of a species is how much that species contributes to the rarity of traits in a community. Here we tested the relation between abundance and both phylogenetic and phenotypic originality. We measured nine traits associated with defence against herbivory, as well as phylogenetic information and abundance for woody plant species in a woodland cerrado in southeastern Brazil. About 90% of the species accounted for about 50% of the phylogenetic and phenotypic originality: most woody species had low originality. Abundance was related to tougher leaves, lower specific leaf area and lower originality based on nutritional quality. Our results suggest that herbivory may reduce the abundance of species with low resistance to herbivory and with different nutritional quality. Nevertheless, abundance was not related to either phylogenetic or phenotypic originality, so extinction of rare species may not endanger overall community function as long as more abundant species are retained. We argue that this is a consequence of the low complementarity of a large number of woody species.     

冷冻电子显微学在结构生物学研究中的现状与展望

冷冻电子显微学近年来在电子显微镜的硬件设备及结构解析的软件算法等方面取得了多个重要的技术突破,正在成为结构生物学研究的重要技术手段,为越来越多的生物学研究者所重视.冷冻电子显微学的技术特点决定了它所具备的一些独特优势和发展方向,同时作为一个正在迅速发展的科学技术领域,需要多学科的交叉促进.本文主要介绍冷冻电子显微学的研究现状及面临的技术挑战,并提出未来可能实现结构生物学与细胞生物学不同尺度的研究在冷冻电子显微学技术上融合的新方法.     

Chemical complementarity between immune receptors and cancer mutants,independent of antigen presentation protein binding,is associated with increased survival rates

Uterine cancer has been associated with a T-cell immune response that leads to increased survival. Therefore, we used several bioinformatics approaches to explore specific interactions between T-cell receptor (TCR) and tumor mutant peptide sequences. Using endometrioid uterine cancer exome files from the The Cancer Genome Atlas database, we obtained tumor resident V-J recombinations for the T-Cell Receptor alpha gene (TRA). The charged-based, chemical complementarity for each patient''s LRP2 or TTN mutant amino acids (AAs) and the recovered, TRA complementarity determining region-3 (CDR3) sequences was calculated, allowing a division of patients into complementary and noncomplementary groups. Complementary groups with TTN mutants had increased disease-free survival and increased expression of complement genes. Furthermore, the survival distinction based on CDR3-mutant peptide complementarity was independent of programmatically assessed HLA class II binding and was not observable based on the CDR3 AA chemical features alone. The above approach provides a potential, highly efficient method for identifying TCR targets in uterine cancer and may aid in the development of novel prognostic tools.