The logic of identity and copy for computational artefacts

Defining identity for entities is a longstanding logical problem in philosophy, and it has resurfaced in current investigations within the philosophy of technology. The problem has not yet been explored for the philosophy of information, and of Computer Science in particular. This paper provides a logical analysis of identity and copy for computational artefacts. Identity is here understood as the relation holding between an instance of a computational artefact and itself. By contrast, the copy relation holds between two distinct computational artefacts. We distinguish among exact, inexact and approximate copies. We use process algebra to provide suitable formal definitions of these relations, using in particular the notion of bisimulation to define identity and exact copies, and simulation for inexact and approximate copies. Equivalence is unproblematic for identical computational artefacts at each individual time and for inexact copies; we will examine to which extent the formal constraints on identity criteria discussed in the literature are satisfied by our approach. As for inexact and approximate copy, they are intended as a weakening of the identity relation in that equivalence and other constraints on identity are violated. The proposed approach also suggests a computable treatment of identity and copy checking

Infringing software property rights : ontological, methodological, and ethical questions

This paper contributes to the computer ethics debate on software ownership protection by examining the ontological, methodological, and ethical problems related to property right infringement that should come prior to any legal discussion. The ontological problem consists in determining precisely what it is for a computer program to be a copy of another one, a largely neglected problem in computer ethics. The methodological problem is defined as the difficulty of deciding whether a given software system is a copy of another system. And the ethical problem corresponds to establishing when a copy constitutes, or does not constitute, a property right infringement. The ontological problem is solved on the logical analysis of abstract machines, and the latter are argued to be the appropriate level of abstraction for software at which the methodological and the ethical problems can be successfully addressed

Copying safety and liveness properties of computational artefacts

This paper shows how safety and liveness properties are not necessarily preserved by different kinds of copies of computational artefacts and proposes procedures to preserve them, which are consistent with ethical analyses on software property rights infringement. Safety and liveness are second-order properties that are crucial in the definition of the formal ontology of computational artefacts. Software copies are analysed at the level of their formal models as exact, inexact and approximate copies, according to the taxonomy in []. First, it is explained how exact copies are the only kind of copies that preserve safety and liveness properties, and how inexact and approximate copies do not necessarily preserve them. Secondly, two model checking algorithms are proposed to verify whether inexact and approximate copies actually preserve safety and liveness properties. Essential properties of termination, correctness and complexity are proved for these algorithms. Finally, contraction and expansion algorithmic operations are defined, allowing for the automatic design of safety- and liveness-preserving approximate copies. As a conclusion, the relevance of the present logical analysis for the ongoing debates in miscomputation and computer ethics is highlighted

On malfunctioning software

Artefacts do not always do what they are supposed to, due to a variety of reasons, including manufacturing problems, poor maintenance, and normal wear-and-tear. Since software is an artefact, it should be subject to malfunctioning in the same sense in which other artefacts can malfunction. Yet, whether software is on a par with other artefacts when it comes to malfunctioning crucially depends on the abstraction used in the analysis. We distinguish between “negative” and “positive” notions of malfunction. A negative malfunction, or dysfunction, occurs when an artefact token either does not (sometimes) or cannot (ever) do what it is supposed to. A positive malfunction, or misfunction, occurs when an artefact token may do what is supposed to but, at least occasionally, it also yields some unintended and undesirable effects. We argue that software, understood as type, may misfunction in some limited sense, but cannot dysfunction. Accordingly, one should distinguish software from other technical artefacts, in view of their design that makes dysfunction impossible for the former, while possible for the latter

KSHV gB associated RGD interactions promote attachment of cells by inhibiting the potential migratory signals induced by the disintegrin-like domain

Background: Kaposi's sarcoma-associated herpesvirus (KSHV) glycoprotein B (gB) is not only expressed on the envelope of mature virions but also on the surfaces of cells undergoing lytic replication. Among herpesviruses, KSHV gB is the only glycoprotein known to possess the RGD (Arg-Gly-Asp) binding integrin domain critical to mediating cell attachment. Recent studies described gB to also possess a disintegrin-like domain (DLD) said to interact with non-RGD binding integrins. We wanted to decipher the roles of two individually distinct integrin binding domains (RGD versus DLD) within KSHV gB in regulating attachment of cells over cell migration

Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

A major use of the 1000 Genomes Project (1000GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants. © 2014 Macmillan Publishers Limited. All rights reserved

High Differentiation among Eight Villages in a Secluded Area of Sardinia Revealed by Genome-Wide High Density SNPs Analysis

To better design association studies for complex traits in isolated populations it's important to understand how history and isolation moulded the genetic features of different communities. Population isolates should not “a priori” be considered homogeneous, even if the communities are not distant and part of a small region. We studied a particular area of Sardinia called Ogliastra, characterized by the presence of several distinct villages that display different history, immigration events and population size. Cultural and geographic isolation characterized the history of these communities. We determined LD parameters in 8 villages and defined population structure through high density SNPs (about 360 K) on 360 unrelated people (45 selected samples from each village). These isolates showed differences in LD values and LD map length. Five of these villages show high LD values probably due to their reduced population size and extreme isolation. High genetic differentiation among villages was detected. Moreover population structure analysis revealed a high correlation between genetic and geographic distances. Our study indicates that history, geography and biodemography have influenced the genetic features of Ogliastra communities producing differences in LD and population structure. All these data demonstrate that we can consider each village an isolate with specific characteristics. We suggest that, in order to optimize the study design of complex traits, a thorough characterization of genetic features is useful to identify the presence of sub-populations and stratification within genetic isolates

Identification of a founder BRCA2 mutation in Sardinia

Sardinian population can be instrumental in defining the molecular basis of cancer, using the identity-by-descent method. We selected seven Sardinian breast cancer families originating from the northern-central part of the island with multiple affected members in different generations. We genotyped 106 members of the seven families and 20 control nuclear families with markers flanking BRCA2 locus at 13q12–q13. The detection of a common haplotype shared by four out of seven families (60%) suggests the presence of a founder BRCA2 mutation. Direct sequencing of BRCA2 coding exons of patients carrying the shared haplotype, allowed the identification of a ‘frame-shift’ mutation at codon 2867 (8765delAG), causing a premature termination-codon. This mutation was found in breast cancer patients as well as one prostate and one bladder cancer patient with shared haplotype. We then investigated the frequency of 8765delAG in the Sardinian breast cancer population by analysing 270 paraffin-embedded normal tissue samples from breast cancer patients. Five patients (1.7%) were found to be positive for the 8765delAG mutation. Discovery of a founder mutation in Sardinia through the identity-by-descent method demonstrates that this approach can be applied successfully to find mutations either for breast cancer or for other types of tumours. © 2000 Cancer Research Campaig

Status of the multibeam S band receiver for the Sardinia Radio Telescope

We describe the development status of the S-band (3-4.5 GHz) seven-beam cryogenic receiver for the primary focus of the Sardinia Radio Telescope (SRT). The main scientific goals for the SRT at S-band include the search for new pulsars, the evaluation of the pulsar dispersion for gravitational wave measurements, the mapping of galactic supernova remnants, and the study of magnetic field of galaxy clusters