Cartography of the multiple formal systems of molecular autopoiesis: from the biology of cognition and enaction to anticipation and active inference.

A rich literature has grown up over the years that bears with autopoiesis, which tends to assume that it is a model, a theory, a principle, a definition of life, a property, refers to self-organization or even to hastily conclude that it is hylomorphic, hylozoist, in need of reformulation or to be overcome, making its status even more unclear. Maturana insists that autopoiesis is none of these and rather it is the causal organization of living systems as natural systems (NS) such that when it stops, they die. He calls this molecular autopoiesis (MA), which comprises two domains of existence: that of the self-producing organization (self-fabrication) and that of the structural coupling/enaction (cognition). Like all-NS in the universe, MA is amenable to be defined in theoretical terms, i.e. encoded in mathematical models and/or formal systems (FS). Framing the multiple formal systems of autopoiesis (FSA) into the Rosen's modeling relation (a process of bringing into equivalence the causality of NS and the inferential rules of FS), allows a classification of FSA into analytical categories, most importantly Turing machine (algorithmic) vs non-Turing machine (non-algorithmic) based, and FSA with a purely reactive mathematical image as cybernetic systems, i.e. feedbacks based, or conversely, as anticipatory systems making active inferences. It is thus the intent of the present work to advance the precision with which different FS may be observed to comply (preserve correspondence) with MA in its worldly state as a NS. The modeling relation between MA and the range of FS proposed as potentially illuminating their processes forecloses the applicability of Turing-based algorithmic computational models. This outcome indicates that MA, as modelled through Varela's calculus of self-reference or more especially through Rosen's (M,R)-system, is essentially anticipatory without violating structural determinism nor causality whatsoever, hence enaction may involve it. This quality may capture a fundamentally different mode of being in living systems as opposed to mechanical-computational systems. Implications in different fields of biology from the origin of life to planetary biology as well as in cognitive science and artificial intelligence are of interest.

Earth's Complexity Is Non-Computable: The Limits of Scaling Laws, Nonlinearity and Chaos.

Current physics commonly qualifies the Earth system as 'complex' because it includes numerous different processes operating over a large range of spatial scales, often modelled as exhibiting non-linear chaotic response dynamics and power scaling laws. This characterization is based on the fundamental assumption that the Earth's complexity could, in principle, be modeled by (surrogated by) a numerical algorithm if enough computing power were granted. Yet, similar numerical algorithms also surrogate different systems having the same processes and dynamics, such as Mars or Jupiter, although being qualitatively different from the Earth system. Here, we argue that understanding the Earth as a complex system requires a consideration of the Gaia hypothesis: the Earth is a complex system because it instantiates life-and therefore an autopoietic, metabolic-repair (M,R) organization-at a planetary scale. This implies that the Earth's complexity has formal equivalence to a self-referential system that inherently is non-algorithmic and, therefore, cannot be surrogated and simulated in a Turing machine. We discuss the consequences of this, with reference to in-silico climate models, tipping points, planetary boundaries, and planetary feedback loops as units of adaptive evolution and selection.

Subsurface and surface halophile communities of the chaotropic Salar de Uyuni.

Salar de Uyuni (SdU) is the biggest athalosaline environment on Earth, holding a high percentage of the known world Li reserves. Due to its hypersalinity, temperature and humidity fluctuations, high exposure to UV radiation, and its elevated concentration of chaotropic agents like MgCl2 , LiCl and NaBr, SdU is considered a polyextreme environment. Here, we report the prokaryotic abundance and diversity of 46 samples obtained in different seasons and geographical areas. The identified bacterial community was found to be more heterogeneous than the archaeal community, with both communities varying geographically. A seasonal difference has been detected for archaea. Salinibacter, Halonotius and Halorubrum were the most abundant genera in Salar de Uyuni. Different unclassified archaea were also detected. In addition, the diversity of two subsurface samples obtained at 20 and 80 m depth was evaluated and compared with the surface data, generating an evolutionary record of a multilayer hypersaline ecosystem.

Beyond planetary-scale feedback self-regulation: Gaia as an autopoietic system.

The Gaia hypothesis states that the Earth is an instance of life. However, appraisals of it tend to focus on the claim that life is a feedback self-regulator that controls Earth's chemistry and climate dynamics, yet, self-regulation by feedbacks is not a definitive characteristic of living systems. Here, we consider the characterization of biological systems as autopoietic systems (causally organized to self-produce through metabolic efficient closure) and then ask whether the Gaia hypothesis is a tractable question from this standpoint. A proof-of-concept based on Chemical Organization Theory (COT) and the Zero Deficiency Theorem (ZDT) applied on a simple but representative Earth's molecular reaction network supports the thesis of Gaia as an autopoietic system. We identify the formation of self-producing organizations within the reaction network, corresponding to recognizable scenarios of Earth's history. These results provide further opportunities to discuss how the instantiation of autopoiesis at the planetary scale could manifests central features of biological phenomenon, such as autonomy and anticipation, and what this implies for the further development of the Gaia theory, Earth's climate modelling and geoengineering.

Future climates: Markov blankets and active inference in the biosphere.

We formalize the Gaia hypothesis about the Earth climate system using advances in theoretical biology based on the minimization of variational free energy. This amounts to the claim that non-equilibrium steady-state dynamics-that underwrite our climate-depend on the Earth system possessing a Markov blanket. Our formalization rests on how the metabolic rates of the biosphere (understood as Markov blanket's internal states) change with respect to solar radiation at the Earth's surface (i.e. external states), through the changes in greenhouse and albedo effects (i.e. active states) and ocean-driven global temperature changes (i.e. sensory states). Describing the interaction between the metabolic rates and solar radiation as climatic states-in a Markov blanket-amounts to describing the dynamics of the internal states as actively inferring external states. This underwrites climatic non-equilibrium steady-state through free energy minimization and thus a form of planetary autopoiesis.

Prokaryotic and viral community structure in the singular chaotropic salt lake Salar de Uyuni.

Salar de Uyuni (SdU) is the largest hypersaline salt flat and the highest lithium reservoir on Earth. In addition to extreme temperatures and high UV irradiance, SdU has high concentrations of chaotropic salts which can be important factors in controlling microbial diversity. Here, for the first time we characterize the viral diversity of this hypersaline environment during the two seasons, as well as the physicochemical characteristics and the prokaryotic communities of the analysed samples. Most of the selected samples showed a peculiar physicochemical composition and prokaryotic diversity, mostly different from each other even for samples from locations in close proximity or the same season. In contrast to most hypersaline systems Bacteria frequently outnumbered Archaea. Furthermore, an outstanding percentage of members of Salinibacter sp., likely a species different from the cosmopolitan Salinibacter ruber, was obtained in most of the samples. Viral communities displayed the morphologies normally found in hypersaline environments. Two seasonal samples were chosen for a detailed metagenomic analysis of the viral assemblage. Both viral communities shared common sequences but were dominated by sample-specific viruses, mirroring the differences also observed in physicochemical and prokaryotic community composition. These metaviromes were distinct from those detected in other hypersaline systems analysed to date.

In-hospital and long-term outcomes of HIV-positive patients undergoing PCI according to kind of stent: a meta-analysis.

BACKGROUND: Pathogenesis of cardiovascular disease in HIV-positive patients is related to the interaction between traditional and HIV-specific factors. Limited data are available regarding the prognosis of HIV-positive patients undergoing percutaneous coronary intervention (PCI). METHODS: All observational studies evaluating the prognosis of HIV-positive patients treated with PCI were included. In-hospital and long-term major adverse cardiac events (MACE) [composite endpoint of all-cause death or myocardial infarction (MI)] were the primary endpoints, whereas in-hospital and long-term all-cause death, cardiovascular death, MI, stent thrombosis, target vessel revascularization (TVR), target lesion revascularization (TLR), and bleeding complications were the secondary ones. FINDINGS: In all, 1243 patients in nine studies were included, with a mean age of 54 years. Among them, 12% were female and 91% were admitted for acute coronary syndromes. In-hospital MACE occurred in 6.0% (5.4-6.6), death in 4.2% (2.6-5.9), and MI in 1.3% (0-2.8), whereas major bleeding occurred in 2.0% (1.7-2.3) of the patients. After 2 years (1.6-3.1), long-term MACE occurred in 17.4% (11.9-22.3), all-cause death in 8.7% (3.2-14.2), and MI in 7.8% (5.5-10.1) of the patients, whereas stent thrombosis and TVR in 3.4% (1.5-5.3) and 10.5% (7.5-13.4), respectively. In patients treated with drug-eluting stents (DES), the rate of long-term MACE was 22.3% (10.1-34.4), with an incidence of 4.9% (0.0-11.4) of MI and 5.7% (2.3-13.7, all 95% confidence intervals of TLR. INTERPRETATION: HIV-positive patients have a high risk of in-hospital and long-term MACE after PCI, partially reduced by the use of DES. Further studies on the risk of recurrent ischemic events with current generation stents are needed, to offer a tailored therapy in this high-risk population.

Beta-blocker therapy reduces mortality in patients with coronary artery disease treated with percutaneous revascularization: a meta-analysis of adjusted results.

AIMS: The long-term impact of beta blockers on prognosis in patients treated with contemporary therapies for coronary artery disease remains to be defined. METHODS AND RESULTS: All observational studies evaluating the impact of beta blockers in patients treated with coronary revascularization and contemporary therapies and adjusted with multivariate analysis were included. All-cause death was the primary endpoint, while Major Adverse Cardiac Events (MACE) (composite endpoint of all-cause death or myocardial infarction, MI) and MI were secondary endpoints. A total of 26 studies were included, with 863 335 patients. After 3 (1-4.3) years, long-term risk of all-cause death was lower in patients on beta blockers [odds ratio, OR 0.69 (0.66-0.72)], both for Acute Coronary Syndrome (ACS) [OR 0.60 (0.56-0.65)], and stable angina patients [OR 0.84 (0.78-0.91)], independently from ejection fraction [OR 0.64 (0.42-0.98) for reduced ejection fraction and OR 0.79 (0.69-0.91) for preserved ejection fraction]. The risk of long-term MACE was lower but NS for ACS patients treated with beta blockers [OR 0.83 (0.69-1.00)], as in stable angina. Similarly, risk of MI did not differ between patients treated with beta blockers or without beta blockers [OR 0.99 (0.89-1.09), all 95% confidence intervals]. Using meta-regression analysis, the benefit of beta blockers was increased for those with longer follow-up. The number needed to treat was 52 to avoid one event of all-cause death for ACS patients and 111 for stable patients. CONCLUSION: Even in percutaneous coronary intervention era, beta blockers reduce mortality in patients with coronary artery disease, confirming their protective effect, which was consistent for both ACS and stable patients indifferently of preserved or reduced ejection fraction.

Prokaryotic diversity and community composition in the Salar de Uyuni, a large scale, chaotropic salt flat.

Salar de Uyuni (SdU), with a geological history that reflects 50 000 years of climate change, is the largest hypersaline salt flat on Earth and is estimated to be the biggest lithium reservoir in the world. Its salinity reaches saturation levels for NaCl, a kosmotropic salt, and high concentrations of MgCL2 and LiCl, both salts considered important chaotrophic stressors. In addition, extreme temperatures, anoxic conditions, high UV irradiance, high albedo and extremely low concentrations of phosphorous, make SdU a unique natural extreme environment in which to contrast hypotheses about limiting factors of life diversification. Geophysical studies of brines from different sampling stations show that water activity is rather constant along SdU. Geochemical measurements show significant differences in magnesium concentration, ranging from 0.2 to 2M. This work analyses the prokaryotic diversity and community structure at four SdU sampling stations, selected according to their location and ionic composition. Prokaryotic communities were composed of both Archaea (with members of the classes Halobacteria, Thermoplasmata and Nanohaloarchaea, from the Euryarchaeota and Nanohaloarcheota phyla respectively) and Bacteria (mainly belonging to Bacteroidetes and Proteobacteria phyla). The important differences in composition of microbial communities inversely correlate with Mg2+ concentration, suggesting that prokaryotic diversity at SdU is chaotropic dependent.

Nitric oxide for anammox recovery in a nitrite-inhibited deammonification system.

The anaerobic ammonium oxidation (anammox) process is widely used for N-rich wastewater treatment. In the current research the deammonification reactor in a reverse order (first anammox, then the nitrifying biofilm cultivation) was started up with a high maximum N removal rate (1.4 g N m(-2) d(-1)) in a moving bed biofilm reactor. Cultivated biofilm total nitrogen removal rates were accelerated the most by anammox intermediate - nitric oxide (optimum 58 mg NO-N L(-1)) addition. Furthermore, NO was added in order to eliminate inhibition caused by nitrite concentrations (>50 mg [Formula: see text]) increasing [Formula: see text] (2/1, respectively) along with a higher ratio of [Formula: see text] (0.6/1, respectively) than stoichiometrical for this optimal NO amount added during batch tests. Planctomycetales clone P4 sequences, which was the closest (98% and 99% similarity, respectively) relative to Candidatus Brocadia fulgida sequences quantities increase to 1 × 10(6) anammox gene copies g(-1) total suspended solids to till day 650 were determined by quantitative polymerase chain reaction.

Comparison of sulfate-reducing and conventional Anammox upflow anaerobic sludge blanket reactors.

Autotrophic NH4(+) removal has been extensively researched, but few studies have investigated alternative electron acceptors (for example, SO4(2-)) in NH4(+) oxidation. In this study, sulfate-reducing anaerobic ammonium oxidation (SRAO) and conventional Anammox were started up in upflow anaerobic sludge blanket reactors (UASBRs) at 36 (±0.5)°C and 20 (±0.5)°C respectively, using reject water as a source of NH4(+). SO4(2-) or NO2(-), respectively, were applied as electron acceptors. It was assumed that higher temperature could promote the SRAO, partly compensating its thermodynamic disadvantage comparing with the conventional Anammox to achieve comparable total nitrogen (TN) removal rate. Average volumetric NH4(+)-N removal rate in the sulfate-reducing UASBR1 was however 5-6 times less (0.03 kg-N/(m(3) day)) than in the UASBR2 performing conventional nitrite-dependent autotrophic nitrogen removal (0.17 kg-N/(m(3) day)). However, the stoichiometric ratio of NH4(+) removal in UASBR1 was significantly higher than could be expected from the extent of SO4(2-) reduction, possibly due to interactions between the N- and S-compounds and organic matter of the reject water. Injections of N2H4 and NH2OH accelerated the SRAO. Similar effect was observed in batch tests with anthraquinone-2,6-disulfonate (AQDS). For detection of key microorganisms PCR-DGGE was used. From both UASBRs, uncultured bacterium clone ATB-KS-1929 belonging to the order Verrucomicrobiales, Anammox bacteria (uncultured Planctomycete clone Pla_PO55-9) and aerobic ammonium-oxidizing bacteria (uncultured sludge bacterium clone ASB08 "Nitrosomonas") were detected. Nevertheless the SRAO process was shown to be less effective for the treatment of reject water, compared to the conventional Anammox.

Arsenic thiolation and the role of sulfate-reducing bacteria from the human intestinal tract.

BACKGROUND: Arsenic (As) toxicity is primarily based on its chemical speciation. Although inorganic and methylated As species are well characterized in terms of metabolism and formation in the human body, the origin of thiolated methylarsenicals is still unclear. OBJECTIVES: We sought to determine whether sulfate-reducing bacteria (SRB) from the human gut are actively involved in the thiolation of monomethylarsonic acid (MMAV). METHODS: We incubated human fecal and colon microbiota in a batch incubator and in a dynamic gut simulator with a dose of 0.5 mg MMAV in the absence or presence of sodium molybdate, an SRB inhibitor. We monitored the conversion of MMAV into monomethyl monothioarsonate (MMMTAV) and other As species by high-performance liquid chromatography coupled with inductively coupled plasma mass spectrometry analysis. We monitored the sulfate-reducing activity of the SRB by measuring hydrogen sulfide (H2S) production. We used molecular analysis to determine the dominant species of SRB responsible for As thiolation. RESULTS: In the absence of sodium molybdate, the SRB activity-primarily derived from Desulfovibrio desulfuricans (piger)-was specifically and proportionally correlated (p < 0.01) to MMAV conversion into MMMTAV. Inactivating the SRB with molybdate did not result in MMAV thiolation; however, we observed that the microbiota from a dynamic gut simulator were capable of demethylating 4% of the incubated MMAV into arsenous acid (iAsIII), the trivalent and more toxic form of arsenic acid (iAsV). CONCLUSION: We found that SRB of human gastrointestinal origin, through their ability to produce H2S, were necessary and sufficient to induce As thiolation. The toxicological consequences of this microbial As speciation change are not yet clear. However, given the efficient epithelial absorption of thiolated methylarsenicals, we conclude that the gut microbiome-and SRB activity in particular-should be incorporated into toxicokinetic analysis carried out after As exposure.

Deammonification process start-up after enrichment of anammox microorganisms from reject water in a moving-bed biofilm reactor.

Deammonification via intermittent aeration in biofilm process for the treatment of sewage sludge digester supernatant (reject water) was started up using two opposite strategies. Two moving-bed biofilm reactors were operated for 2.5 years at 26 (+/- 0.5 degree C with spiked influent(and hence free ammonia (FA)) addition. In the first start-up strategy, an enrichment of anammox biomass was first established, followed by the development of nitrifying biomass in the system (R1). In contrast, the second strategy aimed at the enrichment of anammox organisms into a nitrifying biofilm (R2). The first strategy was most successful, reaching higher maximum total nitrogen (TN) removal rates over a shorter start-up period. For both reactors, increasing FA spiking frequency and increasing effluent concentrations of the anammox intermediate hydrazine correlated to decreasing aerobic nitrate production (nitritation). The bacterial consortium of aerobic and anaerobic ammonium oxidizing bacteria in the bioreactor was determined via denaturing gel gradient electrophoresis, polymerase chain reaction and pyrosequencing. In addition to a shorter start-up with a better TN removal rate, nitrite oxidizing bacteria (Nitrospira) were outcompeted by spiked ammonium feeding from R1.

T rypanosoma cruzi trans-sialidase as a multifunctional enzyme in Chagas' disease.

Trypanosoma cruzi trans-sialidase (TS) was identified three decades ago. TS catalyses a trans-glycosylation reaction, transferring SA from sialylated donors to the terminal galactose mucin-glycoconjugates, or non-mucin galactyosyl-glycoconjugates. It is an external surface protein that is also released from the parasite, displaying several binding properties in addition to its enzymatic function. TS structure has been solved and its catalytic properties are well known, providing tools for development of new inhibitors, as potential chemotherapeutic agents against Chagas' disease. However, there are still several unsolved questions regarding TS role in the biology of T. cruzi and in the pathology of Chagas' disease. In this review, we will describe the multifunctional roles of TS regarding the development of Chagas' disease and propose that these multiple functions have to be considered in future investigations aiming to use TS as a drug target.

Avaliação da precisão experimental em ensaios de competição de cultivares de soja / Experimental precision evaluation of soybean cultivar yield trials

Foram usados os dados de produtividade de grãos, de 216 ensaios de competição de cultivares de soja [Glycine max (L.) Merrill], realizados no Estado do Rio Grande do Sul, nos anos agrícolas 2003/2004, 2004/2005 e 2005/2006, com o objetivo de avaliar a acurácia seletiva e outras 15 estatísticas como medidas do grau de precisão experimental dos ensaios de soja. Os valores mínimo, máximo, média, desvio padrão e coeficiente de variação foram obtidos para 16 estatísticas de cada ensaio. A estatística acurácia seletiva, AS=(1-1/F)½, foi correlacionada com as demais estatísticas. Para cada faixa de precisão (baixa, moderada, alta e muito alta), segundo a estatística AS, foi obtida a frequência simples e relativa de ensaios para as diferentes categorias (ciclo, ano, significância entre blocos e entre genótipos) e no geral. Segundo esta estatística, 76,4 por cento dos ensaios de competição de cultivares de soja têm precisão alta e muito alta e apenas 6,9 por cento tem precisão baixa. A estatística acurácia seletiva é adequada para avaliar a precisão experimental dos ensaios de competição de genótipos de soja. Descartar ensaios apenas por ter coeficiente de variação muito alto é uma atitude desaconselhável.

Data of 216 soybean [Glycine max (L.) Merrill] yield trials conducted in the State of Rio Grande do Sul during the 2003/04, 2004/05 and 2005/06 were used in order to evaluate the selective accuracy and other 15 statistics as a measurement of the degree of experimental precision of soybean yield trials. The minimum, maximum, average standard deviation and variation coefficient were obtained of 16 statistics in each experiment. The statistics selective accuracy, SA=(1-1/F)½, was correlated with all others. For each precision class (low, moderate, high and very high) according to the selective accuracy, the simple and relative frequency were obtained for each different categories (growth duration, year, significance among blocks and among genotypes) and general frequencies. According to these selective accuracy statistics, 76.4 percent of the soybean yield trials have a high and very high degree of precision whereas and only 6.9 percent have a low precision. The statistics selective accuracy is adequate to evaluate the experimental precision of soybean yield trials. It is not advisable to discard results of experiments for having a variation coefficient considered as too high.

Fungicidas no controle da ferrugem asiática (Phakopsora pachyrhizi) e produtividade da soja / Fungicides on the control of soybean rust (Phakopsora pachyrhizi) and soybean yield

Neste trabalho, avaliou-se o efeito de fungicidas no desenvolvimento da ferrugem asiática, causada pelo fungo Phakopsora pachyrhizi, e na produtividade da soja. Os fungicidas foram pulverizados quando as plantas estavam no estádio de desenvolvimento R4. Utilizou-se a cultivar Fepagro-RS 10 e delineamento blocos ao acaso com quatro repetições e dez tratamentos. A avaliação da severidade da doença foi feita 30 dias após a pulverização, utilizando-se uma escala de notas de 0 a 5, considerando-se a porcentagem da área foliar infectada. Os tratamentos com os fungicidas azoxystrobin, difenoconazole + propiconazole, fluquinconazole, myclobutanil, pyraclostrobin + epoxiconazole, tebuconazole e trifloxistrobina + propiconazole, controlaram o patógeno em relação à testemunha, mostrando notas médias de severidade igual ou inferior a 2 e não diferiram entre si. O tratamento com difenoconazole (nota 3,05) controlou o patógeno, mas com nota inferior ao tratamento com carbendazin (nota 3,85) e à testemunha (nota 4,5). Todos os tratamentos mostraram produtividades superiores à testemunha, variando entre 14,5 por cento e 27,3 por cento. O peso de cem sementes foi superior ao da testemunha para todos os tratamentos (11,8 por cento a 14,4 por cento), com exceção do carbendazin (5,2 por cento).

Tratamento de sementes de soja com micronutrientes / Soybean seeds treated with micronutrients

Foram conduzidos dois experimentos na Estação Experimental de Júlio de Castilhos, RS, nos anos agrícolas 1990/91 e 1991/92, a fim de verificar a resposta da soja à aplicação de zinco, boro, molibdênio e cobalto nas sementes, em duas doses de calcário no solo Passo Fundo (LE). Utilizou-se o delineamento blocos ao acaso, em parcelas subdivididas com três repetições, estabelecendo-se nas parcelas duas doses de calcário (sem e com 17,7t/ha) e nas subparcelas formulações de zinco, boro, molibdênio e cobalto (0,875; 0,062; 0,150 e 0,012g/kg de sementes) aplicadas nas sementes junto com o inoculante. Os tratamentos constaram de testemunha, molibdênio e zinco isolados, combinados entre si e associados a boro e cobalto, nas formulações em forma de pó (Biocrop Soja) e fluída (fonte experimental MIQL 44-90A). Os resultados obtidos evidenciam que, na condição sem calcário, os tratamentos de sementes com molibdênio aumentam o rendimento de grãos. Na condição com calcário, não há resposta a aplicação dos micronutrientes.

The expenment was conducted in the Julio de Castilhos Experimental Station, RS, in 1990/91 and 1991/92 seasons. The effect of soybean seeds treated with zinc, boron, molybdenum and cobait, in two lime doses in Passo Fundo soil was evaluated. A completely randomized design with split plot with three replications was used. The lime doses formed the mam plots (zero and 17.71/ha) and zinc, boron, molybdenum and cobait formulation (0.875; 0.062; 0.150 and 0.012gkg of seeds) were the sub-plots. The treatments were contlol, molybdenum and zinc isolated and combinated with boron and cobait, with powder (Soybean Biocrop) and solution (MIQL 44-90A) formulation. The results indicate that withouth lime application, seeds treated with molybdenum had an increment in grain yield. However witht liming no difference in grain yield was observed.