Integration of thermodynamic, quantum and hierarchical theories of information in the context of Peircean semiosis--a review.

I claim that Peirce's notion of information and sign iteration as an intermediation between potentialities that are actualized and actualities that are potentiated provides a suitable framework for interpretation of Zurek' Information gathering and using systems (IGUS). Moreover, this model can be extended to address the problem of quantum measurement (QM) since it allows exploring an alternative view based on IGUS understood as agents of internal measurement, beyond Copenhagen interpretation (CI) that invokes a classical observer that performs measurements and the "many worlds interpretation" (MWI) that rejects all sort of observers and measurements. This integrative view allows figuring out a hierarchy of IGUS-like systems of interpretation that explore new possibilities in the upper level analog boundary and consolidate actualized information in the lower level digital boundary.

Chronic functional constipation in children: adherence and factors associated with drug treatment.

OBJECTIVE: The aim of the present study was to evaluate the treatment adherence of children with chronic functional constipation. METHODS: The present study is a prospective and longitudinal study realized at a pediatric gastroenterology clinic of a Brazilian University Hospital, between August 2009 and October 2011. Rome III criteria and the Bristol Stool Scale were used to define constipation and to characterize feces, respectively. Drug treatment was prescribed for patients according to the protocols previously standardized in the clinic. Specific questionnaires, containing questions related to 1 dependent variable and independent variables were completed in the first and sixth months of the treatment. Independent variables related to the patients, their caregivers, the disease itself, and the therapeutic plan were analyzed and compared with the dependent variable (adherence to the treatment). Adherence was considered when the patient returned with >75% of the prescribed medicine containers empty. RESULTS: Fifty children participated in both the first and sixth months of treatment. The mean age of the sample was 77.6 ± 43.8 months and the mean age of the onset of symptoms was 18.8 ± 27.9 months. The adherence rate was 38% in the first month and 30% in the sixth month. Patients who were treated with polyethylene glycol had greater adherence than patients who were prescribed other laxatives, with statistical significance in the second moment of the study (P = 0.19 and P = 0.04, respectively). CONCLUSIONS: The study showed low adherence rates to drug treatment of constipation in children. It is necessary to seek new strategies to increase treatment adherence, while avoiding complications and reducing costs.

La dualidad anáoogo digital de la información s ejemplifica en el estudio de llas móleculas de rna / The Analog Digital Duality of Information is Exemplified by Studying RNA Molecules

Las investigaciones sobre las moléculas de RNA, han contribuido a precisar y formalizar la noción física de información considerada tanto en su aspecto analógico como digital. El dogma central de la biología molecular, restringe la noción de información al aspecto digital de la misma, y por tanto al copiado fiel de una cadena de símbolos en los procesos de replicación (DNA-DNA) y transcripción (DNA-RNA), e igualmente en la traducción a proteínas mediante el código genético. Esta visión genera la paradoja sobre qué surgió primero si DNA o proteínas, la cual se resuelve en parte recurriendo a la hipótesis según la cual existió un mundo prebiótico RNA, anterior a las proteínas codificadas genéticamente y al DNA. Esta hipótesis tiene soporte empírico sólido apoyado por los descubrimientos de la actividad catalítica de los RNA y el descubrimiento de estructuras RNA altamente conservadas en todos los seres vivos. Por otra parte, los modelos inspirados en la replicación de virus RNA y modelos computacionales que muestran la relación entre estructuras secundarias y secuencias lineales confirman las ventajas de la molécula RNA como modelo para el estudio del origen de la información genética, especialmente por su rol determinante en la aparición del código genético, el papel funcional en la expresión del mismo, la plasticidad estructural y la accesibilidad a las estructuras funcionales a partir de prácticamente cualquier cadena que se someta a ciclos de mutación y selección. Al proponer que la información digital requiere de la analógica para su aparición, no solamente se está contribuyendo a resolver problemas específicos de biología, sino que se trata de una propuesta que contribuye al entendimiento del sentido físico de dos medidas diferentes de información, la de Claude Shannon y la de Gregory Chaitin.

The study of RNA molecules have contributed to formalizing the physical notion of information considered in its dual nature analog and digital. The central dogma of molecular biology restricts the notion of information to its digital aspect and so to copying fidelity of symbol’s string during replication (DNA-DNA) and transcription (DNA-RNA), and also in translation to proteins, by means of a genetic code. This vision leads to the paradox about what molecule came first, DNA or proteins, that is solved by the hypotheses that postulates the existence of prebiotic RNA prior to the emergence of genetically encoded proteins and DNA. This hypothesis is based on solid empirical findings such as the discovery of catalytic RNA and RNA structures highly conserved in evolution and found in all living organisms. Besides, experimental models inspired on virus RNA replication and computational models that deal with the relations between secondary planar structures and linear sequences, confirm the advantages of RNA molecules to understand the origin of genetic information, due to their decisive role in the emergence of the genetic code, their functional role in gene expression, their structural plasticity and the accessibility of functional structures from any arbitrary sequence that undergoes cycles of mutation and selection. To state that the emergence of digital information requires the prior existence of analog information, not only contributes to solve specific problems of biology, but mainly contributes to advance in the understanding the physical meaning of the two different information measurements proposed by Claude Shannon and Gregory Chaitin.

Determining IgA and IgG antigliadin, IgA antitransglutaminase, and antiendomysial antibodies in monkey esophagus and in umbilical cord for diagnosis of celiac disease in developing countries.

OBJECTIVES: To assess the efficiency of determining IgA and IgG antigliadin antibodies (IgA- and IgG-AGA, respectively), antitransglutaminase (TgA), and anti-endomysial antibodies (AEA) in human umbilical cord (CO) and monkey esophagus for diagnosis of celiac disease; to determine the correlation between serological markers and celiac disease. PATIENTS AND METHODS: A total of 400 patients were divided in 3 groups: group 1 with 37 patients with celiac disease, group 2 with 208 patients with no enteropathies, and group 3 with 155 patients with other enteropathies. IgA-AGA, IgG-AGA, and TgA were assessed using enzyme-linked immunosorbent assay, whereas AEA was evaluated by indirect immunofluorescence. RESULTS: Sensitivity and specificity of IgA-AGA were 81.1% and 95.2%, of IgG-AGA 89.2% and 95.2%, of TgA 83.9% and 96.8%, of AEA-CO 87.9% and 100%, and of AEA of monkey esophagus 88.6% and 100%, respectively. Positive predictive values were 75.0%, 76.7%, 83.9%, and 100%. Negative predictive values were 96.6%, 98.0%, 96.8%, and 97.7% for IgA-AGA, IgG-AGA, TgA, and AEA, respectively. Multivariate analysis showed a strong association between AEA-CO and celiac disease and a good correlation with other markers (TgA, IgA-AGA, and IgG-AGA). CONCLUSIONS: TgA has been recommended for screening patients with celiac disease. Considering the similar sensitivity and specificity of IgA-AGA and TgA and their correlations in the multivariate analysis, both are applicable for this purpose. However, because TgA tests are highly costly and celiac disease is associated with IgA deficiency, the determination of IgA-AGA and IgG-AGA, followed by AEA-CO, is suitable for screening in developing countries, provided a cutoff point for these examinations is established. The results of antiendomysial antibodies in umbilical cord overlapped those in monkey esophagus. Therefore, umbilical cord should be used as a substrate instead of specimens from endangered species.

Analysis of tRNA abstract shapes of precursor/derivative amino acids in Archaea.

Wong's theory of the genetic code's origin states that because of historical constraints, codon assignment depends on the relation between precursor and derivative amino acids, a result of the coevolutionary process between amino acids' biosynthetic pathways and tRNAs. Based on arguments supporting the assumption that natural selection favors more stable and thus functionally constrained structures, we tested whether precursor and derivative tRNAs are equally evolved by measuring their structural parameters, thermostability and molecular plasticity. We also estimated the extent to which precursor and derivative tRNAs differ within Archaea. We used Archaea sequences of both precursor and derivative tRNAs in order to examine the plastic repertoires or sets of suboptimal structures at a defined free energy interval. We grouped secondary structures according to their helix nesting and adjacency using abstract shapes analysis. This clustering enabled us to infer a consensus sequence for all shapes that fit the clover leaf secondary structure [Giegerich, R., et al., Nucleic Acids Res 2004; 32 (16): 4843-51.]. This consensus sequence was then folded in order to retrieve a set of suboptimal structures. For each pair of precursor and derivative tRNAs, we compared these plastic repertoires based on the number of secondary structures, the thermostability of the minimum free energy structure and two structural parameters (base pair propensity (P) and mean length of helical stem structures (S)), which were measured for every representative secondary structure [Schultes, E.A., et al., J Mol Evol 1999; 49 (1): 76-83.]. We found that derivative tRNAs have fewer numbers of shapes, higher thermostability and more stable parameters than precursor tRNAs, a fact in full agreement with Wong's coevolution theory of the genetic code.

A semiotic framework for evolutionary and developmental biology.

This work aims at constructing a semiotic framework for an expanded evolutionary synthesis grounded on Peirce's universal categories and the six space/time/function relations [Taborsky, E., 2004. The nature of the sign as a WFF--a well-formed formula, SEED J. (Semiosis Evol. Energy Dev.) 4 (4), 5-14] that integrate the Lamarckian (internal/external) and Darwinian (individual/population) cuts. According to these guide lines, it is proposed an attempt to formalize developmental systems theory by using the notion of evolving developing agents (EDA) that provides an internalist model of a general transformative tendency driven by organism's need to cope with environmental uncertainty. Development and evolution are conceived as non-programmed open-ended processes of information increase where EDA reach a functional compromise between: (a) increments of phenotype's uniqueness (stability and specificity) and (b) anticipation to environmental changes. Accordingly, changes in mutual information content between the phenotype/environment drag subsequent changes in mutual information content between genotype/phenotype and genotype/environment at two interwoven scales: individual life cycle (ontogeny) and species time (phylogeny), respectively. Developmental terminal additions along with increment minimization of developmental steps must be positively selected.

Treatment of nonorganic recurrent abdominal pain: cognitive-behavioral family intervention.

OBJECTIVES: We evaluated the efficacy of cognitive-behavioral family intervention in the treatment of crises of pain in children with nonorganic recurrent abdominal pain (RAP) and the thresholds of pain for 17 body surface areas in these children. METHODS: A randomized clinical trial was undertaken with 32 children between the ages of 5.1 and 13.9 years with nonorganic RAP. A group of 15 patients, aged 9.9 +/- 2.2 years (11 girls), received standard pediatric care and cognitive-behavioral family intervention for treatment of pain crises. The control group of 17 children, aged 8.4 +/- 2.0 years (11 girls), received only standard pediatric care. These procedures were undertaken by general pediatricians over 4 monthly sessions. An analog visual scale was used to measure the frequency and intensity of the pain crises per month and a mechanical pressure algometer for the measurement of pain threshold. RESULTS: The median frequency of pain crises per month reported by patients at the 3 monthly cognitive-behavioral family intervention sessions was 15, 5, 2 and 2, respectively. In contrast, the median frequency for pain crises per month reported by the control group was 12, 8, 10 and 8, respectively. The difference between the intervention group and the controls was statistically significant for frequency of pain at the second, third and fourth visits. There was no statistical difference for intensity of pain or for measured pain thresholds between the control and the intervention group. CONCLUSIONS: The cognitive-behavioral family intervention reduced the frequency of pain crises of children with nonorganic RAP. This successful intervention was carried out by the intervention of general pediatricians.

Protein folding and evolution are driven by the Maxwell Demon activity of proteins.

In this paper we propose a theoretical model of protein folding and protein evolution in which a polypeptide (sequence/structure) is assumed to behave as a Maxwell Demon or Information Gathering and Using System (IGUS) that performs measurements aiming at the construction of the native structure. Our model proposes that a physical meaning to Shannon information (H) and Chaitin's algorithmic information (K) parameters can be both defined and referred from the IGUS standpoint. Our hypothesis accounts for the interdependence of protein folding and protein evolution through mutual influencing relationships mediated by the IGUS. In brief, IGUS activity in protein folding determines long term tendencies that emerge at the evolutionary time-scale.Thus, protein evolution is a consequence of measurements executed by proteins at the cellular level, where the IGUS imposes a tendency to attain a highly unique stable native form that promotes the updating of the information content. The folding kinetics observed is, thus, the outcome of an evolutionary process where the polypeptide-IGUS drives the evolution of its linear sequence. Finally, we describe protein evolution as an entropic process that tends to increase the content of mutual algorithmic information between the sequence and the structure. This model enables one: 1. To comprehend that full determination of the three-dimensional structure by the linear sequence is a tendency where satisfaction is only possible at thermodynamic equilibrium.2. To account for the observed randomness of the amino acid sequences. 3. To predict an alternation of periods of selection and neutral diffusion during protein evolutionary time.

On Maxwell's demons and the origin of evolutionary variations: an internalist perspective.

This paper defends an internalist perspective of selection based on the hypothesis that considers living evolutionary units as Maxwell's demons (MD) or Zurek's Information Gathering and Using Systems (IGUS). Individuals are considered as IGUS that extract work by means of measuring and recording processes. Interactions or measurements convert uncertainty about the environment (Shannon's information, H) into internalized information in the form of a compressed record (Chaitin's algorithmic complexity, K). The requirements of the model and the limitations inherent to its formalization are discussed. This approach offers an alternative view to the causes of evolutionary variations which goes beyond the classical Lamarckian-Darwinian controversy. I argue that random variations only apply near-to-equilibrium at the time organisms have attained structural closure, and that a speed up of mutation rates that facilitates the production of directed variations occurs far-from-equilibrium due to organisms' openness to the surrounding conditions. However, real organisms are located somewhere between the above two cases and thus, operate at an intermediate stage where there is a maximum efficiency of H/K conversion. In consequence, IGUS keep their autonomy and evolving capacity by compromising between external circumstances and inner constraints. This compromise is made possible by closure regulation. Likewise, this model explains why nature has favored the selection of agents capable of selectively recording a partial description of their environment.

La introducción del sujeto en las ciencias naturales o la rehabilitación del vitalismo / The incorporation of the subject in natural sciences or the revival of vitalism

The incorporaction of the subject in natural sciences or the revival of vitalism: the two classical rationalities Known as mechanistic and vitalist are examined according to the localization of the observers. Thus, the mechanistic approach is equated with an externalist perspective, while vitalism is shown to be congruent with an internalist outlook. The existence of natural internal observers , or agents that blong to the same scale of the observed objects, explanins the appearance of vialis approaches. Furthermore, an epistemological analysis of (form) is persented in order to explain the prevalence of the (formal cause) over the other aristotelian causes. The (formal cause) that explain an internal activity is recuperated as one examines the development of natural sciences.