What is Autonomy?

A system is autonomous if it uses its own information to modify itself and its environment to enhance its survival, responding to both environmental and internal stimuli to modify its basic functions to increase its viability. Autonomy is the foundation of functionality, intentionality and meaning. Autonomous systems accommodate the unexpected through self-organizing processes, together with some constraints that maintain autonomy. Early versions of autonomy, such as autopoiesis and closure to efficient cause, made autonomous systems dynamically closed to information. This contrasts with recent work on open systems and information dynamics. On our account, autonomy is a matter of degree depending on the relative organization of the system and system environment interactions. A choice between third person openness and first person closure is not required

A Note on Emergence in Multi-Agent String Processing Systems

We propose a way to define (and, in a certain extent, even to measure) the phenomenon of emergence which appears in a complex system of interacting agents whose global behaviour can be described by a language and whose components (agents) can also be associated with grammars and languages. The basic idea is to identify the "linear composition of behaviours" with "closure under basic operations", such as the AFL (Abstract Families of Languages) operations, which are standard in the theory of formal languages

Foodborne Staphylococcus Aureus: Identification and Enterotoxin Production in Milk and Cheese.

Onemocnění z potravin (alimentární onemocnění) vyvolaná bakteriemi jsou stále aktuálním tématem v celosvětovém měřítku. Abychom zajistili výrobu zdravotně nezávadných potravin, je potřeba nových poznatků o virulenci patogenů, které by doplnily již známé skutečnosti o jejich růstu a přeživání v potravinách. Také potřebujeme vyvíjet rychlé a citlivé metody na detekci těchto patogenů. Dizertační práce popisuje metodu na detekci S. aureus v potravinách, která je založená na PCR v reálném čase ve spojení s namnožením v selektivním médium. Dále pojednává o vlivu environmentálních faktorů na růst S. aureus a tvorbu enterotoxinů v mléce a sýrech. Vyvinuli jsme rychlou a citlivou metodu na detekci S. aureus v potravinách s použitím selektivního namnožení a PCR v reálném čase. Nově vyvinutá metoda umožnila detekci S. aureus na druhý den od přijetí vzorku. Tato metoda může být použita jako rychlejší, citlivějsí a vysoce specifická alternativní metoda ke konvenční mikrobiologické metodě. Zkoumali jsme vliv tří různých teplot, 8°C, 12°C a 20°C na růst S. aureus a tvorbu enterotoxinu D v pasterizovaném mléce a na růst, expresi genu sed a tvorbu enterotoxinu D v tekutém médiu s extraktem z mozku a srdce (BHI). Experimenty byly prováděny v malých skleněných fermentorech po 6 dní. Genová exprese byla sledována pomocí qRT-PCR a tvorba enterotoxinu D byla měřena pomocí imunologické metody ELISA. Růstová křivka v BHI měla stejný průběh při 20°C a 12°C, ale v při 12°C začal růst se spožděním. Při 8°C nebyl pozorován žádný růst. Růst S. aureus v mléce byl ve srovnání s BHI menší. sed mRNA byla detekována při 20°C po 4 hodinách a při 12°C po 7 hodinách a produkce enterotoxinu se objevila v exponenciální fázi růstu. V mléce se produkce SED při 20°C a při 12°C objevila dříve, ale celkové množství vyprodukovaného SED bylo nižší než v BHI. Při 8°C nebyla pozorována žádná produkce SED stejně jako v BHI. Dále byl zkoumán společný vliv nízké teploty 12°C a přítomnosti kompetitivní doprovodné mikroflóry pocházející ze surového mléka na růst S. aureus a produkci enterotoxinu v pasterizovaném mléce. Byl pozorován inhibiční účinek na růst a produkci enterotoxinů a vliv kompetice byl výraznější než vliv nízké teploty. Produkce enterotoxinu byla nízká a odpovídala růstu. Snížením množství doprovodné mikroflóry a zvýšením inokula došlo pouze k nepatrnému zvýšení produkce enterotoxinu. V další fázi byly dva různé typy sýrů zaočkovány S. aureus za účelem simulace sekundární kontaminace při výrobě sýrů. Vzorky byly odebírány v průběhu 4 týdnů. Kritické faktory jako jsou kompetitivní mikrofóra nebo pH, které jsou zodpovědné za regulaci virulence S. aureus byly sledovány. Snažili jsem se rozlišit situace při kterých: (i) není pozorován růst, ale objevuje se produkce enterotoxinu a (ii) dochází k růstu ale bez produkce enterotoxinu.Foodborne diseases caused by bacteria are an actual issue worldwide. To produce food, which is safe for human consumption, data about food-borne pathogen virulence is required to complement the already existing knowledge about the bacterial growth and survival in food. There is also a growing need for rapid and sensitive methods to detect these pathogens. In this dissertation, the real-time PCR-based method for the detection of S. aureus in food using selective enrichment and the impact of environmental factors on S. aureus growth and enterotoxin production in milk and cheese are described. We developed a rapid and sensitive method for the detection of S. aureus in food using selective enrichment and a new species-specific real-time PCR. The method facilitated the detection of S. aureus on the next day after the sample reception. This method can be used for S. aureus detection as a faster, highly specific, and more sensitive alternative to the microbiological method. We investigated the effect of three different temperatures, 8°C, 12°C and 20°C on S. aureus growth and SED production in pasteurized milk and on growth, sed gene expression and SED production in Brain heart infusion. The experiments were performed in small-scale fermentors for six days and gene expression was followed by qRT-PCR. SED production was measured using Enzyme-Linked ImmunoSorbent Assay (ELISA). In BHI the growth pattern was the same at 20°C and 12°C but delayed in the latter. At 8°C there was no growth. In milk, growth was lower compared to BHI. sed mRNA was detected at 20°C and 12°C after 4 and 7 hours respectively in BHI and the production occurred during the exponential phase of growth. In milk the SED production at 20°C and 12°C occurred earlier in growth but a lower total amount was produced compared to BHI. At 8°C, there was no SED production like in BHI. The combined effect of low temperature, 12°C, and the presence of competing background microflora derived from raw milk on the growth of S. aureus and SED production in pasteurized milk was further investigated. An inhibitory effect on S. aureus growth and enterotoxin production was observed and the impact of competition was greater than the impact of low temperature. The enterotoxin production was low and correlated with the growth. By lowering the amount of competing microflora and increasing the inoculation level of S. aureus, only a slight increase in enterotoxin production occurred. In the next stage, two different cheese matrices were inoculated with S. aureus to simulate a post-contamination scenario in cheese manufacture. Samples were collected over period of 4 weeks. Critical food factors, like competing microflora and pH, which are responsible for down- and up-regulation of the virulence of S. aureus, were monitored. We tried to indentify if there are situations in which: (i) no growth but enterotoxin formation is observed, and (ii) growth and no enterotoxin formation occurs.

Darwin's Rainbow: Evolutionary radiation and the spectrum of consciousness

Evolution is littered with paraphyletic convergences: many roads lead to functional Romes. We propose here another example - an equivalence class structure factoring the broad realm of possible realizations of the Baars Global Workspace consciousness model. The construction suggests many different physiological systems can support rapidly shifting, sometimes highly tunable, temporary assemblages of interacting unconscious cognitive modules. The discovery implies various animal taxa exhibiting behaviors we broadly recognize as conscious are, in fact, simply expressing different forms of the same underlying phenomenon. Mathematically, we find much slower, and even multiple simultaneous, versions of the basic structure can operate over very long timescales, a kind of paraconsciousness often ascribed to group phenomena. The variety of possibilities, a veritable rainbow, suggests minds today may be only a small surviving fraction of ancient evolutionary radiations - bush phylogenies of consciousness and paraconsciousness. Under this scenario, the resulting diversity was subsequently pruned by selection and chance extinction. Though few traces of the radiation may be found in the direct fossil record, exaptations and vestiges are scattered across the living mind. Humans, for instance, display an uncommonly profound synergism between individual consciousness and their embedding cultural heritages, enabling efficient Lamarkian adaptation

Ensamblaje de genes y transformación genética para la bioproducción de las feromonas sexuales de polilla Z11-16:OH y Z11-16:OAc en el hongo filamentoso Penicillium digitatum

[ES] La utilización de feromonas de insectos destaca como una alternativa sostenible frente al uso tradicional de pesticidas en el control integral de plagas. Actualmente, las feromonas sexuales están siendo eficientemente aplicadas en el control de diversas especies de lepidópteros, tales como Helicoverpa armigera o Lobesia botrana, capaces de atacar cultivos de alto valor. Sin embargo, su producción industrial se basa en métodos químicos sumamente costosos, que, usualmente, requieren reactantes peligrosos y generan subproductos perjudiciales para el medio ambiente. Por tanto, se ha propuesto el desarrollo y aplicación de biofactorías como método de producción sostenible de feromonas de insecto. Hasta el momento, diversas pruebas de concepto han demostrado la potencial utilización de las plantas como biofactorías. En este contexto, los esfuerzos de nuestro grupo de investigación se han centrado en la aplicación de herramientas de la biología sintética para la biosíntesis de feromonas sexuales de polilla en Nicotiana benthamiana. Por otro lado, los hongos filamentosos podrían facilitar la producción optimizada y comercialmente viable de estas feromonas, dado que se utilizan como biofactorías industriales ampliamente estandarizadas, con elevada diversidad metabólica y capacidad de producción de metabolitos secundarios. El objeto de este trabajo, por tanto, es desarrollar una primera prueba de concepto en la obtención de un hongo filamentoso capaz de expresar las enzimas requeridas en la síntesis de las feromonas sexuales de polilla Z11-16:OH y Z11-16:OAc. Concretamente, se ha generado una ruta genética constituida por una desaturasa (AtrΔ11), una reductasa (HarFAR) y una acetiltransferasa (EaDAcT) mediante el método de clonación Fungal Braid (FB). FB es una nueva rama, específica de hongos, de la tecnología Golden Braid, sistema que permite el ensamblaje modular y estandarizado de los elementos necesarios en la ingeniería genética de plantas y hongos. Mediante la transformación genética mediado por Agrobacterium tumefaciens (ATMT), las construcciones multigénicas resultantes han sido subsecuentemente introducidas en el genoma del hongo Penicillium digitatum. Finalmente, la verificación de los transformantes ha sido llevada a cabo mediante amplificación por PCR. Como resultado, se han seleccionado candidatos Z11-16:OH positivos para el futuro análisis de expresión de la feromona mediante microextracción en fase sólida (HS-SPME) acoplada a cromatografía de gases/masas (GC-MS).[EN] Pheromone-based strategies stand out as environmentally benign alternatives to traditional pesticides for insect pest management. Sex pheromones are already been employed for the control of pest lepidopteran species, such as Helicoverpa armigera or Lobesia botrana, that attack high-value crops. However, current approaches for sex pheromones production at an industrial level relies on high-cost chemical methods that often require harmful reactants and generate hazardous waste. Thus, it has been proposed the use of biological factories as a sustainable way to produce insect pheromones. So far, proof-of-concept studies have proven the feasibility of using plants as biological factories. In this regard, our group efforts have been focused on the application of synthetic biology tools for the production of moth sex pheromones in Nicotiana benthamiana. On the other hand, filamentous fungi could greatly ease pheromone mass production in an optimized and commercially feasible way because they are well-established industrial biofactories with high metabolic diversity and capacity to produce secondary metabolites. The aim of this project is to generate an initial demonstration of genetic engineered filamentous fungi expressing a set of three enzymes for the production of Z11-16:OH and Z11-16:OAc moth sex pheromones. For this purpose, a designed pathway involving a desaturase (AtrΔ11), a fatty acyl reductase (HarFAR) and an acetyltransferase (EaDAcT) has been assembled using the FungalBraid (FB) cloning methodology. FB is a fungal-specific new branch of the GoldenBraid technology, which allows the modular and standardized assembly of the genetic elements required for genetic engineering of plants and fungi. Resultant multigenic constructs have then been integrated into Penicillium digitatum genome through the Agrobacterium tumefaciens-mediated transformation (ATMT). Finally, transformants verification was accomplished through PCR analysis. As a result, positive candidates for Z11-16:OH production have been selected for future pheromone expression analysis via Headspace Solid Phase Microextraction (HS-SPME) coupled to gas chromatography-mass spectrometer (GC-MS).Ropero Pérez, C. (2020). Ensamblaje de genes y transformación genética para la bioproducción de las feromonas sexuales de polilla Z11-16:OH y Z11-16:OAc en el hongo filamentoso Penicillium digitatum. http://hdl.handle.net/10251/147455TFG