An Evolutionary Textual Environment

This article introduces the notion of evolutionary textual environment as the outcome of a digital experiment. The experiment consisted of transforming a digital archive of Fernando Pessoa’s Book of Disquiet into a changing textual space sustained by role-playing interactions. As conceptual and technical artifact, this living archive expresses an innovative model not only for the literary acts of reading, editing and writing, but also for reimagining the book as a network of reconfigurable and dynamic texts, structures, and actions. The programmed features of the LdoD Archive can be used in multiple activities, including leisure reading, study, analysis, advanced research, and creative writing. Through the integration of computational tools in a simulation space, this collaborative archive provides an open exploration of the procedurality of the digital medium itself. The “unfinished machine” metaphor suggests the open-endedness both of the evolving textual environment and of the computational modeling of literary performativity that sustains the whole experiment.

Variation at Spike position 142 in SARS-CoV-2 Delta genomes is a technical artifact caused by dropout of a sequencing amplicon

Public SARS-CoV-2 genomes from the Delta lineage show complex and confusing patterns of mutations at Spike codon 142, and at another nearby position, Spike codon 95. It has been hypothesised that these represent recurrent mutations with interesting evolutionary dynamics, and that these mutations may affect viral load. Here we show that these patterns, and the relationship with viral load, are artifacts of sequencing difficulties in this region of the Delta genome caused be a deletion in the binding site for the 72_RIGHT primer of the ARTIC V3 schema. Spike G142D should be considered a lineage-defining mutation of Delta.

Variation at Spike position 142 in SARS-CoV-2 Delta genomes is a technical artifact caused by dropout of a sequencing amplicon

Public SARS-CoV-2 genomes from the Delta lineage show complex and confusing patterns of mutations at Spike codon 142, and at another nearby position, Spike codon 95. It has been hypothesised that these represent recurrent mutations with interesting evolutionary dynamics, and that these mutations may affect viral load. Here we show that these patterns, and the relationship with viral load, are artifacts of sequencing difficulties in this region of the Delta genome caused be a deletion in the binding site for the 72_RIGHT primer of the ARTIC V3 schema. Spike G142D should be considered a lineage-defining mutation of Delta.

The Epistemology of Biomimetics: The Role of Models and of Morphogenetic Principles

Form follows function, but it does not follow from function. Form is not derivable from the latter. To realize a desired technical function, a form must first be found that is able to realize it at all. Secondly, the question arises as to whether an envisaged form realizes the function in an appropriate way. Functions are multiply realizable—various different forms can bear the very same function. One needs to find a form of a technical artifact that realizes an envisaged function sufficiently efficient, robust, or whatever criteria might be imposed. This paper scrutinizes biomimetics as one way to find a good solution to the realization problem. Drawing on an approach from the philosophy of simulations, it reconstructs the biomimetic relation as being mediated by a theoretical model. It is shown that the robustness of the functioning system is usually reached in different ways in biological and in technological systems, which explains differences in morphogenetic mechanisms or principles found in these fields. This reconstruction helps to understand problems with robustness in synthetic biology that occur when technical design principles are implemented in a biological system. The mimetic relation between the biological and the technical realm is found to be asymmetric.

A docência como profissão: O portfólio como dispositivo e política de formação docente no estágio supervisionado em educação física

The goal of this article is to analyze if the portfolio in teacher education policies and in the Supervised Internship (SI) in Physical Education (PE) constitutes a formative device and to contributes to the professionalization of teaching. This qualitative, documentary research used content analysis of Curriculum Guidelines for Teacher Education and 12 portfolios produced by PE interns from a public university in Brazil. The results integrate narratives of the interns' portfolios, identified by axes: diagnostic evaluation and teaching learning. Policies are interpreted with attention to the portfolio that was treated as a technical artifact of controlled rational activity (tensioning the notion of professionalization). We concluded that the use of portfolios expanded and differed from that foreseen by the literature and the current teacher education policy. Portfolio in SI in PE emerges as a possible open and flexible training device, which is consistent with the professionalization of teaching.

André Bazin's Eternal Returns: An Ontological Revision

The recent publication of André Bazin's Écrits complets (2018), an enormous two-volume edition of 3000 pages which increases ten-fold Bazin's available corpus, provides opportunities for renewed reflection on, and possibly for substantial revisions of, this key figure in film theory. On the basis of several essays, I propose a drastic rereading of Bazin's most explicitly philosophical notion of “ontology.” This all too familiar notion, long settled into a rather dust-laden couple (“Bazin and ontology”) nonetheless retains its fascination. Rather than attempting to provide a systematic reworking of this couple along well established lines, particularly those defined by realism and indexicality, this article proposes to shift the notion of ontology in Bazin from its determination as actual existence toward a more radical concept of ontology based on the notion of mimesis, particularly as articulated, in a Heideggerian mode, by Philippe Lacoue-Labarthe. This more properly ontological concept, also paradoxically and radically improper, is shown to be at work already in Bazin's texts, and it allows us to see that far from simplistically naturalizing photographic technology, Bazin does the contrary: he technicizes nature. If Bazin says that the photograph is a flower or a snowflake, he also implies that, like photographs, these are likewise a kind of technical artifact, an auto-mimetic reproduction of nature. Bazin likewise refers to film as a kind of skin falling away from the body of History, an accumulating pellicule in which nature and history disturbingly merge. This shifted perspective on Bazin's thinking is extended further in reference to Georges Didi-Huberman on the highly mimetic creatures known as phasmids, insects that mimic their environement. I extend this into the dynamic notion of eternal return, an implicit dimension of Bazin's thinking, clarified here in reference to Giorgio Agamben and the “immemorial image” which, like Bazin's “Death Every Afternoon,” presents an eminently repeatable deathly image, an animated corpse-world that can be likened to hell.

Technical artifact drives apparent deviation from Hardy-Weinberg equilibrium at CCR5-∆32 and other variants in gnomAD

Following an earlier report suggesting increased mortality due to homozygosity at the CCR5-∆32 allele1, Wei and Nielsen recently suggested a deviation from Hardy-Weinberg Equilibrium (HWE) observed in public variant databases as additional supporting evidence for this hypothesis2. Here, we present a re-analysis of the primary data underlying this variant database and identify a pervasive genotyping artifact, especially present at long insertion and deletion polymorphisms. Specifically, very low levels of contamination can affect the variant calling likelihood models, leading to the misidentification of homozygous individuals as heterozygous, and thereby creating an apparent depletion of homozygous calls, which is especially prominent at large insertions and deletions. The deviation from HWE observed at CCR5-∆32 is a consequence of this specific genotyping error mode rather than a signature of selective pressure at this locus.

scRNABatchQC: multi-samples quality control for single cell RNA-seq data

Summary Single cell RNA sequencing is a revolutionary technique to characterize inter-cellular transcriptomics heterogeneity. However, the data are noise-prone because gene expression is often driven by both technical artifacts and genuine biological variations. Proper disentanglement of these two effects is critical to prevent spurious results. While several tools exist to detect and remove low-quality cells in one single cell RNA-seq dataset, there is lack of approach to examining consistency between sample sets and detecting systematic biases, batch effects and outliers. We present scRNABatchQC, an R package to compare multiple sample sets simultaneously over numerous technical and biological features, which gives valuable hints to distinguish technical artifact from biological variations. scRNABatchQC helps identify and systematically characterize sources of variability in single cell transcriptome data. The examination of consistency across datasets allows visual detection of biases and outliers. Availability and implementation scRNABatchQC is freely available at https://github.com/liuqivandy/scRNABatchQC as an R package. Supplementary information Supplementary data are available at Bioinformatics online.

Immunocytochemical Labeling of Rhabdomeric Proteins inDrosophilaPhotoreceptor Cells Is Compromised by a Light-dependent Technical Artifact

Drosophila photoreceptor cells are employed as a model system for studying membrane protein transport. Phototransduction proteins like rhodopsin and the light-activated TRPL ion channel are transported within the photoreceptor cell, and they change their subcellular distribution in a light-dependent way. Investigating the transport mechanisms for rhodopsin and ion channels requires accurate histochemical methods for protein localization. By using immunocytochemistry the light-triggered translocation of TRPL has been described as a two-stage process. In stage 1, TRPL accumulates at the rhabdomere base and the adjacent stalk membrane a few minutes after onset of illumination and is internalized in stage 2 by endocytosis after prolonged light exposure. Here, we show that a commonly observed crescent shaped antibody labeling pattern suggesting a fast translocation of rhodopsin, TRP, and TRPL to the rhabdomere base is a light-dependent antibody staining artifact. This artifact is most probably caused by the profound structural changes in the microvillar membranes of rhabdomeres that result from activation of the signaling cascade. By using alternative labeling methods, either eGFP-tags or the self-labeling SNAP-tag, we show that light activation of TRPL transport indeed results in fast changes of the TRPL distribution in the rhabdomere but not in the way described previously.