This paper is intended to complement our previous works on the necessary existence of error-correcting codes endowing genomes with the ability of being regenerated, not merely copied. It sketchily recalls some fundamental definitions and results of information theory and error-correcting codes; provides an overview of our research; shows that the disjunction of replication and regeneration enlightens the divide between germinal and somatic cells; suggests that some phenomena referred to as epigenetic may possibly find an (...) explanation within the framework of error-correcting codes; points out some difficulties, especially those related to sexual reproduction; criticizes the template-replication paradigm, and prompts geneticists to become familiar with information theory. (shrink)

Barbieri introduced and developed the concept of organic codes. The most basic of them is the genetic code, a set of correspondence rules between otherwise unrelated sequences: strings of nucleotides on the one hand, polypeptidic chains on the other hand. Barbieri noticed that it implies ‘coding by convention’ as arbitrary as the semantic relations a language establishes between words and outer objects. Moreover, the major transitions in life evolution originated in new organic codes similarly involving conventional rules. Independently, (...) dealing with heredity as communication over time and relying on information theory, we asserted that the conservation of genomes over the ages demands that error-correcting codes make them resilient to casual errors. Moreover, the better conservation of very old parts of the genome demands that they result from combining successively established nested codes such that the older an information, the more numerous component codes protect it. Barbieri’s concept of organic code and that of genomic error-correcting code may seem unrelated. We show however that organic codes actually entail error-correcting properties. Error-correcting, in general, results from constraints being imposed on a set of sequences. Mathematical equalities are conveniently used in communication engineering for expressing constraints but error correction only needs that constraints exist. Biological sequences are similarly endowed with error-correcting ability by physical-chemical or linguistic constraints, thus defining ‘soft codes’. These constraints are moreover presumably efficient for correcting errors. Insofar as biological sequences are subjected to constraints, organic codes necessarily involve soft codes, and their successive onset results in the nested structure we hypothesized. Organic codes are generated and maintained by means of molecular ‘semantic feedback loops’. Each of these loops involves genes which code for proteins, the enzymatic action of which controls a function needed for the protein assembly. Taken together, thus, they control the assembly of their own structure as instructed by the genome and, once closed, these loops ensure their own conservation. However, the semantic feedback loops do not prevent the genome lengthening. It increases both the redundancy of the genome and the information quantity it bears, thus improving the genome reliability and the specificity of the enzymes, which enables further evolution. (shrink)

Communication is an important feature of the living world that mainstream biology fails to adequately deal with. Applying two main disciplines can be contemplated to fill in this gap: semiotics and information theory. Semiotics is a philosophical discipline mainly concerned with meaning; applying it to life already originated in biosemiotics. Information theory is a mathematical discipline coming from engineering which has literal communication as purpose. Biosemiotics and information theory are thus concerned with distinct and complementary possible meanings of the word (...) ‘communication’. Since literal communication needs to be secured so as to enable semantics being communicated, information theory is a necessary prerequisite to biosemiotics. Moreover, heredity is a purely literal communication process of capital importance fully relevant to literal communication, hence to information theory. A short introduction to discrete information theory is proposed, which is centred on the concept of redundancy and its use in order to make sequences resilient to errors. Information theory has been an extremely active and fruitful domain of researches and the motor of the tremendous progress of communication engineering in the last decades. Its possible connections with semantics and linguistics are briefly considered. Its applications to biology are suggested especially as regards error-correcting codes which are mandatory for securing the conservation of genomes. Biology needs information theory so biologists and communication engineers should closely collaborate. (shrink)

Since the beginning of the XX-th century, it became increasingly evident that information, besides matter and energy, is a major actor in the life processes. Moreover, communication of information has been recognized as differentiating living things from inanimate ones, hence as specific to the life processes. Therefore the sciences of matter and energy, chemistry and physics, do not suffice to deal with life processes. Biology should also rely on sciences of information. A majority of biologists, however, did not change their (...) mind and continued to describe life in terms of chemistry and physics. They merely borrowed some vocabulary from the information sciences. The first science of information available to biological applications, semiotics, appeared at the end of the XIX-th century. It is a qualitative and descriptive science which stemmed from efforts of linguists and philosophers to understand the human language and is thus mainly concerned with semantics. Applying semiotics to biology resulted in today’s Biosemiotics. Independently, an explosive expansion of communication engineering began in the second half of the XX-th century. Besides tremendous progresses in hardware technology, it was made possible by the onset of a science of literal communication: Information Theory (Shannon, Bell Syst Tech J 27:379–457, 623–656, 1948). Literal communication consists of faithfully transporting a message from a place to another, or from an instant to another. Because the meaning of a message does not matter for its transportation, information theory ignores semantics. This restriction enables defining information as a measurable quantity on which a mathematical theory of communication is founded. Although lacking implementation means at its beginning, information theory became later very successful for designing communication means. Modern ones, like mobile phones, can be thought of as experimentally proving the relevance and accuracy of information theory since their design and operation heavily rely on it. Information theory is plainly relevant to biological functions which involve literal communication, especially heredity. This paper is intended to compare the two approaches. It shows that, besides obvious differences, they have some points in common: for instance, the quantitative measurement of information obeys Peirce’s triadic paradigm. They also can mutually enlighten each other. Using information theory, which is closer to the basic communication mechanisms, may appear as a preliminary step prior to more elaborated investigations. Criticizing genetics from outside, information theory furthermore reveals that the ability of the template-replication paradigm to faithfully conserve genomes is but a prejudice. Heredity actually demands error-correcting means which impose severe constraints to the living world and must be recognized as biological facts. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Commentary on “Loopholes, Gaps, and What Is Held Fast”Lorraine Code (bio)Keywordsepistemology, incredulity, knowing other people, memory, testimonyNancy Potter’s compelling essay points to some of the limitations of the theoretical apparatus that the post-positivist empiricist epistemologies of the Anglo-American mainstream make available for evaluating experiential memory claims in general, and “false memory syndrome” in particular. The loopholes and gaps in these theories of knowledge push urgent questions about testimony, trust, (...) and the politics of knowledge into a prominent place on the agendas of successor epistemology projects. These politics are enacted in societies whose dominant rhetoric privileges eye-witness evidence and “knowledge by acquaintance” as sources of objective knowledge, yet whose practices of incredulity—of granting and withholding acknowledgement to testimonial knowledge claims—expose power-saturated structures of dominance and subordination and of arbitrarily uneven distributions of epistemic authority. 1For classical empiricists and their successors, perception, memory and testimony, hierarchically ordered with perception on top, count as the principal sources of empirical knowledge. This ordering maps the relative reliability of the processes, with perception ranking as most stable, reliable and secure, memory coming second on all of these scores, and testimony ranking a poor third, closer to opinion, hearsay and rumor than to the other more respectable sources. Perception, for these theories, is “immediate” in that it is direct, bare, uncontaminated either by the particularities of the perceiving subject or of the perceptual event: from its presumed (but contestable) immediacy, all the rest follows. Memory counts as perception at one remove, its reliability a function of the relative “vividness” of the perceptions it commemorates. The esteem commonly claimed for eye-witness testimony derives from this conception of memory, which is believed to ground the testimony because of its presumed proximity to “immediate” perception. Yet testimony, even in its restricted “knowledge by description” form, tends by contrast with perception and memory to be a shaky affair; and as the temporal distance between event and testimony increases, so knowledge of matters unavailable to direct observation fares less and less well in classical and post-positivist epistemologies. A distrust of testimony is at once understandable and odd, because so small a proportion both of communal and of “individual” knowledge indeed derives from first-hand observations and experiences: most of it comes from testimony in an extended sense that encompasses books, teachings, media reports, all of the sources and resources on which both secular and scholarly knowledge relies for much of its substance. This expanded construction of the term runs alongside [End Page 255] the first-personal “testimonial” sense that is more plainly operative in discussions of false memory syndrome which, despite its experiential source, is often likewise contested on grounds that discredit the “privileged access” status that these same epistemologies claim for experience at first hand.Epistemologists commonly assimilate testimony to monologic, observational knowledge, deriving its constitutive features from instances where a testimonial utterance can pose as another perception—this time an auditory one—in a personal set of knowledge-producing observations (e.g., Fricker 1987). Because the speaker may be lying or mistaken, the process may fail to transmit knowledge; but this failure can be read as a simple perceptual error or a misremembering. Such approaches ignore the constitutive function of an interpreter/listener in fostering or thwarting testimonial knowledge to subsume it, too, much under an observational model. Indeed, not only do they separate the knower from the known and the process of knowing, as Potter observes, they also separate the knower from other knowers to guard against their influencing (= contaminating) the knowledge-production process. Experiences where an interlocutor actually enables the production of knowledge do not figure in such analyses, 2 whose effect is to suggest that giving or hearing testimony invokes no more significant moral-political issues than do acts of perceiving tables and chairs: that hearing, like seeing, is believing. (Norman Malcolm’s analysis of memory, which Potter cites, would also underwrite such a view of testimony.) Yet standard empiricist and post-positivist epistemologies generate an inquisitorial model of eliciting testimony in which the more generalized “testimony” in the knowledge that people acquire from books, media reports, conversation, reference sources recedes from... (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Reviewed by:Women Philosophers: Genre and the Boundaries of PhilosophyLorraine CodeCatherine Villanueva Gardner. Women Philosophers: Genre and the Boundaries of Philosophy. Boulder, CO: Westview, 2003. Pp. xv + 198. Paper, $22.00.In a tradition which "trains us to read purely for content" (xii), Catherine Gardner wonders how to read the philosophy of five women who write in "non-standard philosophical forms" (xiii): Mechthild of Magdeburg's poetry, Christine de Pisan's allegory, Catharine Macaulay's (...) epistolary form, and Mary Wollstonecraft's and George Eliot's fiction. Asking how these authors' gender and their works' genre bear on their exclusion from canonical philosophy with its reliance on rigorous argument unsullied by stylistic considerations, she argues that form is integral to understanding philosophy, and can impede its recognition as philosophy. Specifically, she wonders what these historical writings can offer present-day feminist ethics?Gardner's readings and her thesis about style and genre as conditions of philosophical legitimacy are provocative. She urges "reading past" forms deemed inhospitable to moral truth—such as Macaulay's epistolary style (44-45)—to encounter the author as moral philosopher, and explain her invisibility as such. Eliot's philosophy "demands the form of a novel" (123), she proposes, and Wollstonecraft's principles of style "are ultimately principles of morality as well" (92). More complex is the poetically articulated moral epistemology in Mechthild's The Flowing Light, with God, speaking through Mechthild, as its author (154-56). Because these forms—epistolary, allegorical, mystical-poetic, fictional—have been most accessible to women, Gardner urges feminists to consider how these authors' gender bears on their exclusion from moral philosophy. Owing to women's "greater capacity for emotion and... weaker capacity for reason" (155), mystics such as Mechthild were deemed well-suited to write as they did; yet works attributed to God stand immune to philosophical argument. Macaulay's thoughts on government and social reform were judged secondary to her "feminine" ones about educating women for marriage and domesticity (26-27). Gardner is persuaded and persuasive about the philosophical stature of the works she discusses. Yet if a thinker's gender denies her philosophical status, how can she bypass those exclusionary structures—even if, like Eliot, she chooses a male name? If a work's genre removes it from the sustained argumentative debate that is the hallmark of western philosophy, how can it claim a place there?There are no easy answers, but the questions spark numerous others. Perplexing is Gardner's contention that these women are ignored because they defy norms of style and method. But how would she classify Plato's dialogues, Voltaire's Candide, Pascal's and Nietzsche's aphorisms, Wittgenstein's numbered propositions,or Sartre's, Camus' (and Beauvoir's) philosophical novels, given their maverick styles? Style alone cannot effect or explain the exclusions she deplores. More puzzling are Gardner's conceptions of standard method and dominant form (e.g., 24, 120, 175), since she does not elaborate, apart from indicating that both require rigorous prose argument. But formal and methodological orthodoxy varies historically, as in the influence of scholasticism, for Christine, which receives no mention, or Gardner's ahistorical suggestion that the absence of a "normative subject as an independent, autonomous individual" (171) is a lacuna in Mechthild's work. Why would a thirteenth-century writer presuppose an Enlightenment subject? These issues demand attention in a work of historical scholarship.A different question troubles the method discussion. The author regrets certain women's exclusion from the canon despite the philosophical nature of their work, maintaining that [End Page 215] works whose styles/forms diverge from the standard count, nonetheless, as philosophy. These women demonstrate that philosophy need not be couched in formal argument: poetry, allegory, novels can also articulate philosophical theories. But—if my reading is correct—here Gardner is inconsistent. She commends the philosophy in Macaulay's Letters, claiming it "can and does contain the sort of sustained argument... uncontroversially identifiable as... philosophical" (44), and makes similar claims for Wollstonecraft and Eliot. But in legitimating these works by received standards of argument after all, Gardner weakens the force of her claims that philosophy—good philosophy—need not be presented in orthodox form, thus... (shrink)

Journalistic codes of ethics from 55 countries were analyzed for their discussions of errors and corrections. The sample includes codes from press councils, broadcast media outlets, newspa...

There is ongoing controversy as to whether the genome is a representing system. Although it is widely recognised that DNA carries information, both correlating with and coding for various outcomes, neither of these implies that the genome has semantic properties like correctness or satisfaction conditions, In the Scope of Logic, Methodology, and the Philosophy of Sciences, Vol. II. Kluwer, Dordrecht, pp. 387–400). Here a modified version of teleosemantics is applied to the genome to show that it does indeed have semantic (...) properties – there is representation in the genome. The account differs in three respects from previous attempts to apply teleosemantics to genes. It emphasises the role of the consumer of representations. It rejects the standard assumption that genetic representation can be used to explain the course of an organism’s development. And it identifies the explanatory role played by representational properties of the genome. A striking consequence of this account is that other inheritance systems could also be representational. Thus, a version of the parity thesis is accepted. However, the criteria for being an inheritance system are demanding, so semantic properties are not ubiquitous. (shrink)

Major codes adopted by newspapers in recent years show marked similarities to the statements of purpose found in the first (and only) issue of Benjamin Harris? Public Occurrences Both Forreign and Domestick, published in Boston in 1690. This essay compares the front page statement by Harris with seven other statements about the role or responsibility of the press: The Associated Press Managing Editors Association ?Code of Ethics for Newspapers and their Staffs''; the 1947 report of the Commission on Freedom (...) of the Press; the American Society of Newspaper Editors 1923 Canons of Journalism and 1975 Statement of Principles; the Society of Professional Journalists, Sigma Delta Chi Code of Ethics; a memorandum to the staff of The New York Times by A.M. Rosenthal when he became managing editor in 1969; and an article by former Knight?Ridder executive Don Carter. Recurring themes include an emphasis on gathering and reporting news with accuracy, objectivity, truthfulness, and completeness. In addition, Harris led the way with his promises to correct errors when they occur and to allay false rumors and replace them with substantive information. Harris? stated goals, according to this essay, would sit quite comfortably on many American newspaper editorial pages today. (shrink)

This article argues that basic ethical principles of U.S. journalism as described in the Society of Professional Journalists' Code of Ethics are the result of, and a response to, cognitive bias and error. Cognitive biases and errors necessitate journalistic best practices to correct or attenuate them. Social cognitive processes explored include stereotyping, confirmation bias, and attribution. These concepts are noteworthy because each may be activated by the practice of journalism, and each has been shown to be susceptible to attenuation (...) through specific practices. The article concludes with ideas for integrating cognition into journalism education. (shrink)

Cultural differences occur in the use of categories to aid accurate recall of information. This study investigated whether culture also contributed to false (erroneous) memories, and extended cross-cultural memory research to Turkish culture, which is shaped by Eastern and Western influences. Americans and Turks viewed word pairs, half of which were categorically related and half unrelated. Participants then attempted to recall the second word from the pair in response to the first word cue. Responses were coded as correct, as blanks, (...) or as different types of errors. Americans committed more categorical errors than did Turks, and Turks mistakenly recalled more non-categorically related list words than did Americans. These results support the idea that Americans use categories either to organize information in memory or to support retrieval strategies to a greater extent than Turks and suggest that culture shapes not only accurate recall but also erroneous distortions of memory. (shrink)

Correspondence analysis of 28 proteomes selected to span the entire realm of prokaryotes revealed universal biases in the proteins’ amino acid distribution. Integral Inner Membrane Proteins always form an individual cluster, which can then be used to predict protein localisation in unknown proteomes, independently of the organism’s biotope or kingdom. Orphan proteins are consistently rich in aromatic residues. Another bias is also ubiquitous: the amino acid composition is driven by the GþC content of the first codon position. An unexpected bias (...) is driven, in many proteomes, by the AANbox of the genetic code, suggesting some functional biochemical relationship between asparagine and lysine. Less-significant biases are driven by the rare amino acids, cysteine and tryptophan. Some allow identification of species-specific functions or localisation such as surface or exported proteins. Errors in genome annotations are also revealed by correspondence analysis, making it useful for quality control and correction. (shrink)

The authors have retracted this article [1] because they found a fundamental mistake in the methodology that is not correctable at this time. This mistake is found in the methodology and the derivation of the model with Tukey and Huber’s losses. Because of the error, the findings in the article are not reliable. All authors agree to this retraction.

English grammar error correction algorithm refers to the use of computer programming technology to automatically recognize and correct the grammar errors contained in English text written by nonnative language learners. Classification model is the core of machine learning and data mining, which can be applied to extracting information from English text data and constructing a reliable grammar correction method. On the basis of summarizing and analyzing previous research works, this paper expounded the research status and significance of English grammar (...) error correction algorithm, elaborated the development background, current status, and future challenges of the classification model, introduced the methods and principles of feature extraction method and dynamic residual structure, constructed a basic model for English grammar error correction based on the classification model, analyzed the classification model and translation model of English grammar error correction, proposed the English grammar error correction algorithm based on the classification model, performed the analyses of the model architecture and model optimizer of the grammar error correction algorithm, and finally conducted a simulation experiment and its result analysis. The study results show that, with the continuous increase of training samples and the continuous progress of learning process, the proposed English grammar error correction algorithm based on the classification model will continue to increase its classification accuracy, further refine its recognition rules, and gradually improve correction efficiency, thereby reducing processing time, saving storage space, and streamlining processing flow. The study results of this paper provide a certain reference for the further research on English grammar error correction algorithm based on the classification model. (shrink)

The generation of patterns and the diversity of cell types in a multicellular organism require differential gene regulation. At the heart of this process are enhancers or cis‐regulatory modules (CRMs), genomic regions that are bound by transcription factors (TFs) that control spatio‐temporal gene expression in developmental networks. To date, only a few CRMs have been studied in detail and the underlying cis‐regulatory code is not well understood. Here, we review recent progress on the genome‐wide identification of CRMs with chromatin (...) immunoprecipitation of TF‐DNA complexes followed by microarrays (ChIP‐on‐chip). We focus on two computational approaches that have succeeded in predicting the expression pattern driven by a CRM either based on TF binding site preferences and their expression levels, or quantitative analysis of CRM occupancy by key TFs. We also discuss the current limits of these methods and highlight some of the key problems that have to be solved to gain a more complete understanding of the structure and function of CRMs. (shrink)

Relying on the universality of quantum mechanics and on recent results known as the “threshold theorems,” quantum information scientists deem the question of the feasibility of large‐scale, fault‐tolerant, and computationally superior quantum computers as purely technological. Reconstructing this question in statistical mechanical terms, this article suggests otherwise by questioning the physical significance of the threshold theorems. The skepticism it advances is neither too strong (hence is consistent with the universality of quantum mechanics) nor too weak (hence is independent of technological (...) contingencies). *Received June 2009; revised August 2009. †To contact the author, please write to: Department of History and Philosophy of Science, College of Arts and Sciences, Indiana University, Bloomington, IN 47405; e‐mail: [email protected]. (shrink)

Journal Name: Semiotica Issue: Ahead of print.

Correct chromosome segregation in mitosis relies on chromosome biorientation, in which sister kinetochores attach to microtubules from opposite spindle poles prior to segregation. To establish biorientation, aberrant kinetochore–microtubule interactions must be resolved through the error correction process. During error correction, kinetochore–microtubule interactions are exchanged (swapped) if aberrant, but the exchange must stop when biorientation is established. In this article, we discuss recent findings in budding yeast, which have revealed fundamental molecular mechanisms promoting this “swap and stop” process for (...) error correction. Where relevant, we also compare the findings in budding yeast with mechanisms in higher eukaryotes. Evidence suggests that Aurora B kinase differentially regulates kinetochore attachments to the microtubule end and its lateral side and switches relative strength of the two kinetochore–microtubule attachment modes, which drives the exchange of kinetochore–microtubule interactions to resolve aberrant interactions. However, Aurora B kinase, recruited to centromeres and inner kinetochores, cannot reach its targets at kinetochore–microtubule interface when tension causes kinetochore stretching, which stops the kinetochore–microtubule exchange once biorientation is established. (shrink)

Living organisms are exposed to numerous influencing factors. This holds also true for their infrastructures that are processing and transducing information like endocrine networks or nerval channels. Therefore, the ability to compensate for noise is crucial for survival. An efficient mechanism to neutralise disturbances is instantiated in form of parallel complementary communication channels exerting antagonistic effects at their common receivers. Different signal processing types share the ability to suppress noise, to widen the system’s regulation capacity, and to provide for variable (...) gains while leaving the transferred signal to a large extent unchanged. (shrink)

Inspired by the recent trends in education towards learner autonomy with their emphasis on the interests and desires of the students, and borrowing ideas from philosophy (particularly ethics), the present study is an attempt to investigate the discrepancy in the findings of the studies addressing error correction in L2 writing instruction, and suggest the (oft-neglected) students’ beliefs, interests and wants as what can point the way out of confusion. To this end, a questionnaire was developed and 56 advanced adult (...) EFL learners were asked to complete the questionnaire. The opinions of 20 EFL teachers were also collected using another questionnaire. Twenty-three of the students and 13 of the teachers were then interviewed in an attempt to collect explanations for their answers in the questionnaires. The results indicated that all the learners wanted the errors in their writings to be corrected. About 90 percent of them believed that all the errors in their writings should be corrected and only less than 10 percent of them agreed that there is no need to correct all the errors and that only “important” errors should be rectified. On the contrary, of the teachers who participated in the study, only 20 percent believed that all the errors in the students’ writings should be corrected. While most of the interviewed students attributed their preference of choice to feeling more confident and efficient in learning when they can recognize all the errors in their written assignments, most of the teachers believed that by correcting important errors (and not all errors), learners can get the most of their writings. Given the incongruity between teachers’ and (advanced) students’ beliefs over writing error correction, and considering advanced students as legitimate decision makers for their own learning, some suggestions are offered for EFL writing teachers. -/- . (shrink)

In 2004 Atserias, Kolaitis, and Vardi proposed $\text {OBDD}$ -based propositional proof systems that prove unsatisfiability of a CNF formula by deduction of an identically false $\text {OBDD}$ from $\text {OBDD}$ s representing clauses of the initial formula. All $\text {OBDD}$ s in such proofs have the same order of variables. We initiate the study of $\text {OBDD}$ based proof systems that additionally contain a rule that allows changing the order in $\text {OBDD}$ s. At first we consider a proof (...) system $\text {OBDD}$ that uses the conjunction rule and the rule that allows changing the order. We exponentially separate this proof system from $\text {OBDD}$ proof system that uses only the conjunction rule. We prove exponential lower bounds on the size of $\text {OBDD}$ refutations of Tseitin formulas and the pigeonhole principle. The first lower bound was previously unknown even for $\text {OBDD}$ proofs and the second one extends the result of Tveretina et al. from $\text {OBDD}$ to $\text {OBDD}$.In 2001 Aguirre and Vardi proposed an approach to the propositional satisfiability problem based on $\text {OBDD}$ s and symbolic quantifier elimination $ algorithms). We augment these algorithms with the operation of reordering of variables and call the new scheme $\text {OBDD}$ algorithms. We notice that there exists an $\text {OBDD}$ algorithm that solves satisfiable and unsatisfiable Tseitin formulas in polynomial time, but we show that there are formulas representing systems of linear equations over $\mathbb {F}_2$ that are hard for $\text {OBDD}$ algorithms. Our hard instances are satisfiable formulas representing systems of linear equations over $\mathbb {F}_2$ that correspond to checksum matrices of error correcting codes. (shrink)

The problem of initializing phase in a quantum computing system is considered. The initialization of phases is a problem when the system is initially present in a superposition state as well as in the application of the quantum gate transformations, since each gate will introduce phase uncertainty. The accumulation of these random phases will reduce the effectiveness of the recently proposed quantum computing schemes. The paper also presents general observations on the nonlocal nature of quantum errors and the expected performance (...) of the recently proposed quantum error-correction codes that are based on the assumption that the errors are either bit-flip or phase-flip or both. It is argued that these codes cannot directly solve the initialization problem of quantum computing. (shrink)

Quantum computers are hypothetical quantum information processing (QIP) devices that allow one to store, manipulate, and extract information while harnessing quantum physics to solve various computational problems and do so putatively more efficiently than any known classical counterpart. Despite many ‘proofs of concept’ (Aharonov and Ben–Or 1996; Knill and Laflamme 1996; Knill et al. 1996; Knill et al. 1998) the key obstacle in realizing these powerful machines remains their scalability and susceptibility to noise: almost three decades after their conceptions, experimentalists (...) still struggle to maintain useful quantum coherence in QIP devices with more than a pair of qubits (e.g., Blatt and Wineland 2008). This slow progress has prompted debates on the feasibility of quantum computers, yet the quantum information community has dismissed the skepticism as “ideology” (Aaronson 2004), claiming that the obstacles are merely technological (Kaye et al. 2007, 240). In a recent paper (Hagar 2009) I’ve argued that such a skepticism with respect to the feasibility of quantum computers need not be deemed ideological at all, and that the aforementioned ‘proofs of concept’ are physically suspect. Using analogies from the foundations of classical statistical mechanics (SM), I’ve also argued that instead of active error correction, the appropriate framework for debating the feasibility of large–scale, fault–tolerant and computationally superior quantum computers should be the project of error avoidance: rather than trying to constantly ‘cool down’ the QIP device and prevent its thermalization, one should try to locate those regions in the device’s state space which are thermodynamically ‘abnormal’, i.e., those regions in the device’s state space which resist thermalization regardless of external noise. This paper is intended as a further contribution to the debate on the feasibility of large–scale, fault–tolerant and computationally superior quantum computers. Relying again on analogies from the foundations of classical SM, it suggests a skeptical conjecture and frames it in the ‘passive’, error avoidance, context.. (shrink)

In this paper we describe some first steps for bringing the framework of branching space-times to bear on quantum information theory. Our main application is quantum error correction. It is shown that branching space-times offers a new perspective on quantum error correction: as a supplement to the orthodox slogan, ``fight entanglement with entanglement'', we offer the new slogan, ``fight indeterminism with indeterminism''.

In this paper we describe some first steps for bringing the framework of branching space-times to bear on quantum information theory. Our main application is quantum error correction. It is shown that branching space-times offers a new perspective on quantum error correction: as a supplement to the orthodox slogan, ``fight entanglement with entanglement'', we offer the new slogan, ``fight indeterminism with indeterminism''.

In his interesting comment on my recent article, “The Appeals Process as a Means of Error Correction,” Edward Schwartz makes two criticisms of my analysis. The criticisms have essentially to do with my assumption that an appeals court judge will base his or her decisions only on what happened at trial, and not on any inference that can be drawn from the fact that an appeal was brought. Before explaining why I do not find Schwartz's criticisms problematic, it will (...) be helpful for me to restate the main features of the model that I examined in the article. (shrink)

In this paper we describe some first steps for bringing the framework of branching space-times (BST) to bear on quantum information theory. Our main application is quantum error correction. It is shown that BST offers a new perspective on quantum error correction: as a supplement to the orthodox slogan, “fight entanglement with entanglement”, we offer the new slogan, “fight indeterminism with indeterminism”.

In lieu of an abstract, here is a brief excerpt of the content:Philosophy, Psychiatry, & Psychology 11.1 (2004) 65-70 [Access article in PDF] Top-Down and Bottom-Up in Delusion Formation Jakob Hohwy Keywords delusions, top-down, bottom-up, predictive coding Some delusions may arise as responses to unusual experiences (Davies et al. 2001; Maher 1974;). The implication is that delusion formation in some cases involves some kind of bottom-up mechanism—roughly, from perception to belief. Delusion formation may also involve some kind of top-down mechanism. (...) This could be in the shape of a patient's flawed background beliefs, or biases, which somehow modulate perception or ensure delusional interpretations of experience. There is little agreement about what kind of mechanism is primary in delusion formation, or, indeed, what the particular mechanisms and their neural substrates might be.In the evaluation of top-down and bottom-up mechanisms in delusion formation, a number of conceptual questions should be addressed (Davies and Coltheart 2000). For example, if there is an experiential component, why is a hypothesis with a delusional explanation of the unusual experience seen as relevant? Why do the subjects come to believe it tenaciously? How come some unusual experiences do not develop into delusions?A number of empirical findings also need to be taken into account: for example, the damage to the autonomic system in Capgras delusion (Ellis et al. 1997), the decreased ability for fast error correction in schizophrenia (Frith and Done 1989), modulation of activity in parietal cortex in delusions of alien control and other passivity experiences (Blakemore, Oakley, and Frith 2003), and also in schizophrenia, the increased sensitivity to self-produced stimuli, such as tickling oneself (Blakemore et al. 2000) and the sound of one's own voice (Ford et al. 2001).Theory choice can also be guided by philosophical doctrines about, for example, the nature of belief, the constitutive role of rationality, and intersubjectivity and the nature of judgements about the external world. It is natural, however, to let beliefs about philosophical doctrine be secondary to empirical findings and conceptual issues.The distinction between bottom-up and top-down mechanisms is particularly sharp in John Campbell's (2001) account of delusions and in Tim Bayne and Elisabeth Pacherie's (2004) discussion of Campbell. In this discussion, top-down approaches are associated with the general philosophical doctrine of rationalism, and bottom-up approaches with the philosophical doctrine of empiricism. Campbell's account is top-down because he posits delusional framework beliefs that arise directly as a result of brain damage or malfunction, and that work in some top-down fashion on the interpretation of experience. Bayne [End Page 65] and Pacherie convincingly defend empiricism against Campbell's rationalist account. Among their many other objections, they briefly puzzle about how a delusional framework belief (e.g., that one's spouse is an impostor) in a top-down fashion could cause the damage to the autonomic system seen in the Capgras and Cotard delusions (2004, 1). I think this is a very important objection because skin conductance data are part of the evidence for the bottom-up hypothesis concerning the Capgras delusion. We could add to this, for example, that it is mysterious how belief in a top-down fashion could cause people with schizophrenia to be worse at fast error correction than normal controls, to be better at tickling themselves than normal controls, and to have an increased response to the sound of their own voice.On the other hand, although the skin conductance response (SCR) evidence suggests a bottom-up approach to the Capgras delusion, it does not explain the character of the subjective experience that is hypothesized to give rise to the delusional belief: reduced SCR is not part of the experience itself (thanks to Ian Gold for discussion of this). Something more is required to give a full account of the type of experience that gives rise to the delusion. Further, as they stand, most bottom-up accounts are unable to account for why reality testing fails for beliefs based on these experiences.Neither rationalism nor empiricism on their own seem able to address the conceptual questions while paying... (shrink)

This paper presents a new take on how argument dependencies in natural language are established and constrained. The paper starts with a rather standard view that (quantificational) argument dependencies are operator-variable dependencies. The interesting twist the paper offers is to eliminate the need for syntax that serves to enforce what the operator-variable dependencies are. Instead the role of ensuring grammatical and generally unambiguous forms is taken up by semantics imposing what are dependency requirements for any interpretation to go through at (...) evaluation time. With this viewpoint there emerges an essential need for localities as the hiding of (embedded) expression material, together with a (limited) form of garbage collection to release grammatical resources used in the current locality for reuse in subsequent localities. (shrink)

In quantum computing, where algorithms exist that can solve computational problems more efficiently than any known classical algorithms, the elimination of errors that result from external disturbances or from imperfect gates has become the ...

This study examines how a Purkinje cell receives its appropriate olivary error signal during the learning of compound movements. We suggest that the Purkinje cell only reinforces those target pyramidal cells which already participate in the movement, subsequently reducing any repeated error signal, such as its own climbing fiber input, [simpson et al.; smith].

The Italian code of medical deontology recently approved stipulates that physicians have the duty to inform the patient of each unwanted event and its causes, and to identify, report and evaluate adverse events and errors. Thus the obligation to supply information continues to widen, in some way extending beyond the doctor-patient relationship to become an essential tool for improving the quality of professional services.

Recent investigations have revealed 1) that the isochores of the human genome group into two super‐families characterized by two different long‐range 3D structures, and 2) that these structures, essentially based on the distribution and topology of short sequences, mold primary chromatin domains (and define nucleosome binding). More specifically, GC‐poor, gene‐poor isochores are low‐heterogeneity sequences with oligo‐A spikes that mold the lamina‐associated domains (LADs), whereas GC‐rich, gene‐rich isochores are characterized by single or multiple GC peaks that mold the topologically associating domains (...) (TADs). The formation of these “primary TADs” may be followed by extrusion under the action of cohesin and CTCF. Finally, the genomic code, which is responsible for the pervasive encoding and molding of primary chromatin domains (LADs and primary TADs, namely the “gene spaces”/“spatial compartments”) resolves the longstanding problems of “non‐coding DNA,” “junk DNA,” and “selfish DNA” leading to a new vision of the genome as shaped by DNA sequences. (shrink)

This paper sheds light on the shift that is taking place from the practice of ‘coding’, namely developing programs as conventional in the software community, to the practice of ‘curing’, an activity that has emerged in the last few years in Deep Learning (DL) and that amounts to curing the data regime to which a DL model is exposed during training. Initially, the curing paradigm is illustrated by means of a study-case on autonomous vehicles. Subsequently, the shift from coding to (...) curing is analysed taking into consideration the epistemological notions, central in the philosophy of computer science, of function, implementation, and correctness. First, it is illustrated how, in the curing paradigm, the functions performed by the trained model depend much more on dataset curation rather than on the model algorithms which, in contrast with the coding paradigm, do not comply with requested specifications. Second, it is highlighted how DL models cannot be considered implementations according to any of the available definitions of implementation that follow an intentional theory of functions. Finally, it is argued that DL models cannot be evaluated in terms of their correctness but rather in their experimental computational validity. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Philosophy, Psychiatry, & Psychology 11.1 (2004) 65-70 [Access article in PDF] Top-Down and Bottom-Up in Delusion Formation Jakob Hohwy Keywords delusions, top-down, bottom-up, predictive coding Some delusions may arise as responses to unusual experiences (Davies et al. 2001; Maher 1974;). The implication is that delusion formation in some cases involves some kind of bottom-up mechanism—roughly, from perception to belief. Delusion formation may also involve some kind of top-down mechanism. (...) This could be in the shape of a patient's flawed background beliefs, or biases, which somehow modulate perception or ensure delusional interpretations of experience. There is little agreement about what kind of mechanism is primary in delusion formation, or, indeed, what the particular mechanisms and their neural substrates might be.In the evaluation of top-down and bottom-up mechanisms in delusion formation, a number of conceptual questions should be addressed (Davies and Coltheart 2000). For example, if there is an experiential component, why is a hypothesis with a delusional explanation of the unusual experience seen as relevant? Why do the subjects come to believe it tenaciously? How come some unusual experiences do not develop into delusions?A number of empirical findings also need to be taken into account: for example, the damage to the autonomic system in Capgras delusion (Ellis et al. 1997), the decreased ability for fast error correction in schizophrenia (Frith and Done 1989), modulation of activity in parietal cortex in delusions of alien control and other passivity experiences (Blakemore, Oakley, and Frith 2003), and also in schizophrenia, the increased sensitivity to self-produced stimuli, such as tickling oneself (Blakemore et al. 2000) and the sound of one's own voice (Ford et al. 2001).Theory choice can also be guided by philosophical doctrines about, for example, the nature of belief, the constitutive role of rationality, and intersubjectivity and the nature of judgements about the external world. It is natural, however, to let beliefs about philosophical doctrine be secondary to empirical findings and conceptual issues.The distinction between bottom-up and top-down mechanisms is particularly sharp in John Campbell's (2001) account of delusions and in Tim Bayne and Elisabeth Pacherie's (2004) discussion of Campbell. In this discussion, top-down approaches are associated with the general philosophical doctrine of rationalism, and bottom-up approaches with the philosophical doctrine of empiricism. Campbell's account is top-down because he posits delusional framework beliefs that arise directly as a result of brain damage or malfunction, and that work in some top-down fashion on the interpretation of experience. Bayne [End Page 65] and Pacherie convincingly defend empiricism against Campbell's rationalist account. Among their many other objections, they briefly puzzle about how a delusional framework belief (e.g., that one's spouse is an impostor) in a top-down fashion could cause the damage to the autonomic system seen in the Capgras and Cotard delusions (2004, 1). I think this is a very important objection because skin conductance data are part of the evidence for the bottom-up hypothesis concerning the Capgras delusion. We could add to this, for example, that it is mysterious how belief in a top-down fashion could cause people with schizophrenia to be worse at fast error correction than normal controls, to be better at tickling themselves than normal controls, and to have an increased response to the sound of their own voice.On the other hand, although the skin conductance response (SCR) evidence suggests a bottom-up approach to the Capgras delusion, it does not explain the character of the subjective experience that is hypothesized to give rise to the delusional belief: reduced SCR is not part of the experience itself (thanks to Ian Gold for discussion of this). Something more is required to give a full account of the type of experience that gives rise to the delusion. Further, as they stand, most bottom-up accounts are unable to account for why reality testing fails for beliefs based on these experiences.Neither rationalism nor empiricism on their own seem able to address the conceptual questions while paying... (shrink)

Both patched versions of the Bostrom/Kulczycki simulation argument contain serious objective errors, discovered while attempting to formalize them in predicate logic. The English glosses of both versions involve badly misleading meanings of vague magnitude terms, which their impressiveness benefits from. We fix the errors, prove optimal versions of the arguments, and argue that both are much less impressive than they originally appeared. Finally, we provide a guide for readers to evaluate the simulation argument for themselves, using well-justified settings of the (...) argument parameters that have simple, accurate statements in English, which are easier to understand and critique than the statements in the original paper. (shrink)