Brief Announcement: Persistent Software Combining

We study the performance power of software combining in designing recoverable algorithms and data structures. We present two recoverable synchronization protocols, one blocking and another wait-free, which illustrate how to use software combining to achieve both low persistence and synchronization cost. Our experiments show that these protocols outperform by far state-of-the-art recoverable universal constructions and transactional memory systems. We built recoverable queues and stacks, based on these protocols, that exhibit much better performance than previous such implementations

Artificial and Natural Genetic Information Processing

Conventional methods of genetic engineering and more recent genome editing techniques focus on identifying genetic target sequences for manipulation. This is a result of historical concept of the gene which was also the main assumption of the ENCODE project designed to identify all functional elements in the human genome sequence. However, the theoretical core concept changed dramatically. The old concept of genetic sequences which can be assembled and manipulated like molecular bricks has problems in explaining the natural genome-editing competences of viruses and RNA consortia that are able to insert or delete, combine and recombine genetic sequences more precisely than random-like into cellular host organisms according to adaptational needs or even generate sequences de novo. Increasing knowledge about natural genome editing questions the traditional narrative of mutations (error replications) as essential for generating genetic diversity and genetic content arrangements in biological systems. This may have far-reaching consequences for our understanding of artificial genome editing

Two genetic codes: Repetitive syntax for active non-coding RNAs; non-repetitive syntax for the DNA archives

Current knowledge of the RNA world indicates 2 different genetic codes being present throughout the living world. In contrast to non-coding RNAs that are built of repetitive nucleotide syntax, the sequences that serve as templates for proteins share—as main characteristics—a non-repetitive syntax. Whereas non-coding RNAs build groups that serve as regulatory tools in nearly all genetic processes, the coding sections represent the evolutionarily successful function of the genetic information storage medium. This indicates that the differences in their syntax structure are coherent with the differences of the functions they represent. Interestingly, these 2 genetic codes resemble the function of all natural languages, i.e., the repetitive non-coding sequences serve as appropriate tool for organization, coordination and regulation of group behavior, and the nonrepetitive coding sequences are for conservation of instrumental constructions, plans, blueprints for complex protein-body architecture. This differentiation may help to better understand RNA group behavioral motifs

Reactive Turing Machines

We propose reactive Turing machines (RTMs), extending classical Turing machines with a process-theoretical notion of interaction, and use it to define a notion of executable transition system. We show that every computable transition system with a bounded branching degree is simulated modulo divergence-preserving branching bisimilarity by an RTM, and that every effective transition system is simulated modulo the variant of branching bisimilarity that does not require divergence preservation. We conclude from these results that the parallel composition of (communicating) RTMs can be simulated by a single RTM. We prove that there exist universal RTMs modulo branching bisimilarity, but these essentially employ divergence to be able to simulate an RTM of arbitrary branching degree. We also prove that modulo divergence-preserving branching bisimilarity there are RTMs that are universal up to their own branching degree. Finally, we establish a correspondence between executability and finite definability in a simple process calculus

Computational Modalities of Belousov-Zhabotinsky Encapsulated Vesicles

We present both simulated and partial empirical evidence for the computational utility of many connected vesicle analogs of an encapsulated non-linear chemical processing medium. By connecting small vesicles containing a solution of sub-excitable Belousov-Zhabotinsky (BZ) reaction, sustained and propagating wave fragments are modulated by both spatial geometry, network connectivity and their interaction with other waves. The processing ability is demonstrated through the creation of simple Boolean logic gates and then by the combination of those gates to create more complex circuits

The Yogācāra Theory of Three Natures: Internalist and Non-Dualist Interpretations

According to Vasubandhu’s Trisvabhāvanirdeśa or Treatise on the Three Natures, experiential phenomena can be understood in terms of three natures: the constructed (parikalpita), the dependent (paratantra), and the consummate (pariniṣpanna). This paper will examine internalist and anti-internalist or non-dualist interpretations of the Yogācāra theory of the three natures of experience. The internalist interpretation is based on representationalist theory of experience wherein the contents of experience are logically independent of their cause and various interconnected cognitive processes continually create an integrated internal world-model that is transparent to the cognitive system that creates and uses it. In contrast, the anti-internalist interpretation begins, not from the constructed nature of experiential objects, but from the perfected nature of mind-world non-duality. This interpretation treats the distinctions between inside and outside, subject and object, mind and world as distinctions drawn within experience rather than between experience and something else. And experience here refers to the continuous dynamic interplay of factors constituting our sentient embodied (nāma-rūpa) existence. Having examined each interpretation, the paper will suggest some reasons to favor the non-dualist view

Claiming space outside dominant narratives: feminist strategies based upon freedom and diversity, alternative God-talk and criticizing structures of authority

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