‘Snakes and Ladders’ – ‘Therapy’ as Liberation in Nagarjuna and Wittgenstein’s Tractatus

This paper reconsiders the notion that Nagarjuna and Wittgenstein’s Tractatus may only be seen as comparable under a shared ineffability thesis, that is, the idea that reality is impossible to describe in sensible discourse. Historically, Nagarjuna and the early Wittgenstein have both been widely construed as offering either metaphysical theories or attempts to refute all such theories. Instead, by employing an interpretive framework based on a ‘resolute’ reading of the Tractatus, I suggest we see their philosophical affinity in terms of a shared conception of philosophical method without proposing theses. In doing so, this offers us a new way to understand Nagarjuna’s characteristic claims both to have ‘no views’ (Mūlamadhyamakakārikā 13.8 and 27.30) and refusal to accept that things exist ‘inherently’ or with ‘essence’ (svabhāva). Therefore, instead of either a view about the nature of a mind-independent ‘ultimate reality’ or a thesis concerning the rejection of such a domain, I propose that we understand Nagarjuna’s primary aim as ‘therapeutic’, that is, concerned with the dissolution of philosophical problems. However, this ‘therapy’ should neither be confined to the psychotherapeutic metaphor nor should it be taken to imply a private enlightenment only available to philosophers. Instead, for Nagarjuna and Wittgenstein, philosophical problems are cast as a source of disquiet for all of us; what their work offers is a soteriology, a means towards our salvation

Altitudinal variation in soil organic carbon stock in coniferous subtropical and broadleaf temperate forests in Garhwal Himalaya

<p>Abstract</p> <p>Background</p> <p>The Himalayan zones, with dense forest vegetation, cover a fifth part of India and store a third part of the country reserves of soil organic carbon (SOC). However, the details of altitudinal distribution of these carbon stocks, which are vulnerable to forest management and climate change impacts, are not well known.</p> <p>Results</p> <p>This article reports the results of measuring the stocks of SOC along altitudinal gradients. The study was carried out in the coniferous subtropical and broadleaf temperate forests of Garhwal Himalaya. The stocks of SOC were found to be decreasing with altitude: from 185.6 to 160.8 t C ha^-1and from 141.6 to 124.8 t C ha^-1in temperature (<it>Quercus leucotrichophora</it>) and subtropical (<it>Pinus roxburghii</it>) forests, respectively.</p> <p>Conclusion</p> <p>The results of this study lead to conclusion that the ability of soil to stabilize soil organic matter depends negatively on altitude and call for comprehensive theoretical explanation</p

Synaptic scaffold evolution generated components of vertebrate cognitive complexity

The origins and evolution of higher cognitive functions, including complex forms of learning, attention and executive functions, are unknown. A potential mechanism driving the evolution of vertebrate cognition early in the vertebrate lineage (550 million years ago) was genome duplication and subsequent diversification of postsynaptic genes. Here we report, to our knowledge, the first genetic analysis of a vertebrate gene family in cognitive functions measured using computerized touchscreens. Comparison of mice carrying mutations in each of the four Dlg paralogs showed that simple associative learning required Dlg4, whereas Dlg2 and Dlg3 diversified to have opposing functions in complex cognitive processes. Exploiting the translational utility of touchscreens in humans and mice, testing Dlg2 mutations in both species showed that Dlg2\u27s role in complex learning, cognitive flexibility and attention has been highly conserved over 100 million years. Dlg-family mutations underlie psychiatric disorders, suggesting that genome evolution expanded the complexity of vertebrate cognition at the cost of susceptibility to mental illness

Structure and Age Jointly Influence Rates of Protein Evolution

What factors determine a protein's rate of evolution are actively debated. Especially unclear is the relative role of intrinsic factors of present-day proteins versus historical factors such as protein age. Here we study the interplay of structural properties and evolutionary age, as determinants of protein evolutionary rate. We use a large set of one-to-one orthologs between human and mouse proteins, with mapped PDB structures. We report that previously observed structural correlations also hold within each age group – including relationships between solvent accessibility, designabililty, and evolutionary rates. However, age also plays a crucial role: age modulates the relationship between solvent accessibility and rate. Additionally, younger proteins, despite being less designable, tend to evolve faster than older proteins. We show that previously reported relationships between age and rate cannot be explained by structural biases among age groups. Finally, we introduce a knowledge-based potential function to study the stability of proteins through large-scale computation. We find that older proteins are more stable for their native structure, and more robust to mutations, than younger ones. Our results underscore that several determinants, both intrinsic and historical, can interact to determine rates of protein evolution

“Positive” Results Increase Down the Hierarchy of the Sciences

The hypothesis of a Hierarchy of the Sciences with physical sciences at the top, social sciences at the bottom, and biological sciences in-between is nearly 200 years old. This order is intuitive and reflected in many features of academic life, but whether it reflects the “hardness” of scientific research—i.e., the extent to which research questions and results are determined by data and theories as opposed to non-cognitive factors—is controversial. This study analysed 2434 papers published in all disciplines and that declared to have tested a hypothesis. It was determined how many papers reported a “positive” (full or partial) or “negative” support for the tested hypothesis. If the hierarchy hypothesis is correct, then researchers in “softer” sciences should have fewer constraints to their conscious and unconscious biases, and therefore report more positive outcomes. Results confirmed the predictions at all levels considered: discipline, domain and methodology broadly defined. Controlling for observed differences between pure and applied disciplines, and between papers testing one or several hypotheses, the odds of reporting a positive result were around 5 times higher among papers in the disciplines of Psychology and Psychiatry and Economics and Business compared to Space Science, 2.3 times higher in the domain of social sciences compared to the physical sciences, and 3.4 times higher in studies applying behavioural and social methodologies on people compared to physical and chemical studies on non-biological material. In all comparisons, biological studies had intermediate values. These results suggest that the nature of hypotheses tested and the logical and methodological rigour employed to test them vary systematically across disciplines and fields, depending on the complexity of the subject matter and possibly other factors (e.g., a field's level of historical and/or intellectual development). On the other hand, these results support the scientific status of the social sciences against claims that they are completely subjective, by showing that, when they adopt a scientific approach to discovery, they differ from the natural sciences only by a matter of degree

Comparative genome analysis of PHB gene family reveals deep evolutionary origins and diverse gene function

<p>Abstract</p> <p>Background</p> <p>PHB (Prohibitin) gene family is involved in a variety of functions important for different biological processes. PHB genes are ubiquitously present in divergent species from prokaryotes to eukaryotes. Human PHB genes have been found to be associated with various diseases. Recent studies by our group and others have shown diverse function of PHB genes in plants for development, senescence, defence, and others. Despite the importance of the PHB gene family, no comprehensive gene family analysis has been carried to evaluate the relatedness of PHB genes across different species. In order to better guide the gene function analysis and understand the evolution of the PHB gene family, we therefore carried out the comparative genome analysis of the PHB genes across different kingdoms.</p> <p>Results</p> <p>The relatedness, motif distribution, and intron/exon distribution all indicated that PHB genes is a relatively conserved gene family. The PHB genes can be classified into 5 classes and each class have a very deep evolutionary origin. The PHB genes within the class maintained the same motif patterns during the evolution. With<it> Arabidopsis</it> as the model species, we found that PHB gene intron/exon structure and domains are also conserved during the evolution. Despite being a conserved gene family, various gene duplication events led to the expansion of the PHB genes. Both segmental and tandem gene duplication were involved in Arabidopsis PHB gene family expansion. However, segmental duplication is predominant in Arabidopsis. Moreover, most of the duplicated genes experienced neofunctionalization. The results highlighted that PHB genes might be involved in important functions so that the duplicated genes are under the evolutionary pressure to derive new function.</p> <p>Conclusion</p> <p>PHB gene family is a conserved gene family and accounts for diverse but important biological functions based on the similar molecular mechanisms. The highly diverse biological function indicated that more research needs to be carried out to dissect the PHB gene function. The conserved gene evolution indicated that the study in the model species can be translated to human and mammalian studies.</p

The evolutionary significance of polyploidy

Polyploidy, or the duplication of entire genomes, has been observed in prokaryotic and eukaryotic organisms, and in somatic and germ cells. The consequences of polyploidization are complex and variable, and they differ greatly between systems (clonal or non-clonal) and species, but the process has often been considered to be an evolutionary 'dead end'. Here, we review the accumulating evidence that correlates polyploidization with environmental change or stress, and that has led to an increased recognition of its short-term adaptive potential. In addition, we discuss how, once polyploidy has been established, the unique retention profile of duplicated genes following whole-genome duplication might explain key longer-term evolutionary transitions and a general increase in biological complexity