Lessons in Software Evolution Learned by Listening to Smalltalk

The biggest challenge facing software developers today is how to gracefully evolve complex software systems in the face of changing requirements. We clearly need software systems to be more dynamic, compositional and model-centric, but instead we continue to build systems that are static, baroque and inflexible. How can we better build change-enabled systems in the future? To answer this question, we propose to look back to one of the most successful systems to support change, namely Smalltalk. We briefly introduce Smalltalk with a few simple examples, and draw some lessons for software evolution. Smalltalk's simplicity, its reflective design, and its highly dynamic nature all go a long way towards enabling change in Smalltalk applications. We then illustrate how these lessons work in practice by reviewing a number of research projects that support software evolution by exploiting Smalltalk's design. We conclude by summarizing open issues and challenges for change-enabled systems of the future.

Three linked enzyme loci in fishes: implications in the evolution of vertebrate chromosomes.

A three-point linkage group comprised of loci coding for adenosine deaminase (ADA), glucose-6-phosphate dehydrogenase (G6PDH), and 6-phospho-gluconate dehydrogenase (6PGD) is described in fish of the genus Xiphophorus (Poeciliidae). The alleles at loci in this group were shown to assort independently from the alleles at three other loci--isocitrate dehydrogenase 1 and 2, and glyceraldehyde-3-phosphate dehydrogenase 1. Alleles at the latter three loci also assort independently from each other. Data were obtained by observing the segregation of electrophoretically variant alleles in reciprocal backcross hybrids derived from crosses between either X. helleri guentheri or X. h. strigatus and X. maculatus. The linkage component of chi2 was significant (less than 0.01) in all crosses, indicating that the linkage group is conserved in all populations of both species of Xiphophorus examined. While data from X. h. guentheri backcrosses indicate the linkage relationship ADA--6%--G6PDH--24%--6PGD, and ADA--29%--6PGD (30% when corrected for double crossovers), data from backcrosses involving strigatus, while supporting the same gene order, yielded significantly different recombination frequencies. The likelihood of the difference being due to an inversion could not be separated from the possibility of a sex effect on recombination in the present data. The linkage of 6PGD and G6PDH has been shown to exist in species of at least three classes of vertebrates, indicating the possibility of evolutionary conservation of this linkage.

In vivo Evolution of CMY-2 to CMY-33 β-Lactamase in Escherichia coli ST131: Characterization of an Acquired Extended-Spectrum AmpC (ESAC) Conferring Resistance to Cefepime.

Cefepime is frequently prescribed to treat infections caused by AmpC-producing Gram-negative bacteria. CMY-2 is the most common plasmid-mediated AmpC (pAmpC) β-lactamase. Unfortunately, CMY variants conferring enhanced cefepime resistance are reported. Here, we describe the evolution of CMY-2 to an extended-spectrum AmpC (ESAC) in clonally identical E. coli isolates obtained from a patient. The CMY-2-producing E. coli (CMY-2-Ec) was isolated from a wound. Thirty days later, one CMY-33-producing E. coli (CMY-33-Ec) was detected in bronchoalveolar lavage. Two weeks before the isolation of CMY-33-Ec, the patient received cefepime.CMY-33-Ec and CMY-2-Ec were identical by rep-PCR, being of hyperepidemic ST131, but showed different β-lactam MICs (e.g., cefepime 16 vs. ≤0.5 μg/ml). Identical CMY-2-Ec isolates were also found in a rectal swab. CMY-33 differs from CMY-2 by a Leu293-Ala294 deletion. Expressed in E. coli DH10B, both CMYs conferred resistance to ceftazidime (≥256 μg/ml), but cefepime MICs were higher for CMY-33 than CMY-2 (8 vs. 0.25 μg/ml). The kcat/Km or kinact/KI (μM(-1) s(-1)) indicated that CMY-33 possesses an ESBL-like spectrum compared to CMY-2 (cefoxitin: 0.2 vs. 0.4; ceftazidime: 0.2 vs. not measurable; cefepime: 0.2 vs. not measurable; tazobactam 0.0018 vs. 0.0009). Using molecular modeling, we show that a widened active site (∼4 Å shift) may play a significant role in enhancing cefepime hydrolysis. This is the first in vivo demonstration of a pAmpC that under cephalosporin treatment expands its substrate spectrum resembling an ESBL. The prevalence of CMY-2-Ec isolates is rapidly increasing worldwide, therefore awareness that cefepime treatment may select for resistant isolates is critical.

Training project management complexity in postgraduate and continuing education programs: a learning strategy in the eshe (European Space of Higher Education) framework

The objective of this paper is to address the methodological process of a teaching strategy for training project management complexity in postgraduate programs. The proposal is made up of different methods —intuitive, comparative, deductive, case study, problem-solving Project-Based Learning— and different activities inside and outside the classroom. This integration of methods motivated the current use of the concept of “learning strategy”. The strategy has two phases: firstly, the integration of the competences —technical, behavioral and contextual—in real projects; and secondly, the learning activity was oriented in upper level of knowledge, the evaluating the complexity for projects management in real situations. Both the competences in the learning strategy and the Project Complexity Evaluation are based on the ICB of IPMA. The learning strategy is applied in an international Postgraduate Program —Erasmus Mundus Master of Science— with the participation of five Universities of the European Union. This master program is fruit of a cooperative experience from one Educative Innovation Group of the UPM -GIE-Project-, two Research Groups of the UPM and the collaboration with other external agents to the university. Some reflections on the experience and the main success factors in the learning strategy were presented in the paper

Training project management complexity in postgraduate and continuing education programs: a learning strategy in the eshe (European Space of Higher Education) framework

The objective of this paper is to address the methodological process of a teaching strategy for training project management complexity in postgraduate programs. The proposal is made up of different methods —intuitive, comparative, deductive, case study, problem-solving Project-Based Learning— and different activities inside and outside the classroom. This integration of methods motivated the current use of the concept of ―learning strategy‖. The strategy has two phases: firstly, the integration of the competences —technical, behavioral and contextual—in real projects; and secondly, the learning activity was oriented in upper level of knowledge, the evaluating the complexity for projects management in real situations. Both the competences in the learning strategy and the Project Complexity Evaluation are based on the ICB of IPMA. The learning strategy is applied in an international Postgraduate Program —Erasmus Mundus Master of Science— with the participation of five Universities of the European Union. This master program is fruit of a cooperative experience from one Educative Innovation Group of the UPM -GIE-Project-, two Research Groups of the UPM and the collaboration with other external agents to the university. Some reflections on the experience and the main success factors in the learning strategy were presented in the paper.

Towards Understanding Reasoning Complexity in Practice

Although the computational complexity of the logic underlying the standard OWL 2 for the Web Ontology Language (OWL) appears discouraging for real applications, several contributions have shown that reasoning with OWL ontologies is feasible in practice. It turns out that reasoning in practice is often far less complex than is suggested by the established theoretical complexity bound, which reflects the worstcase scenario. State-of-the reasoners like FACT++, HERMIT, PELLET and RACER have demonstrated that, even with fairly expressive fragments of OWL 2, acceptable performances can be achieved. However, it is still not well understood why reasoning is feasible in practice and it is rather unclear how to study this problem. In this paper, we suggest first steps that in our opinion could lead to a better understanding of practical complexity. We also provide and discuss some initial empirical results with HERMIT on prominent ontologies

Lempel-Ziv complexity in schizophrenia: A MEG study

Objective The neurodevelopmental–neurodegenerative debate is a basic issue in the field of the neuropathological basis of schizophrenia (SCH). Neurophysiological techniques have been scarcely involved in such debate, but nonlinear analysis methods may contribute to it. Methods Fifteen patients (age range 23–42 years) matching DSM IV-TR criteria for SCH, and 15 sex- and age-matched control subjects (age range 23–42 years) underwent a resting-state magnetoencephalographic evaluation and Lempel–Ziv complexity (LZC) scores were calculated. Results Regression analyses indicated that LZC values were strongly dependent on age. Complexity scores increased as a function of age in controls, while SCH patients exhibited a progressive reduction of LZC values. A logistic model including LZC scores, age and the interaction of both variables allowed the classification of patients and controls with high sensitivity and specificity. Conclusions Results demonstrated that SCH patients failed to follow the “normal” process of complexity increase as a function of age. In addition, SCH patients exhibited a significant reduction of complexity scores as a function of age, thus paralleling the pattern observed in neurodegenerative diseases. Significance Our results support the notion of a progressive defect in SCH, which does not contradict the existence of a basic neurodevelopmental alteration. Highlights ► Schizophrenic patients show higher complexity values as compared to controls. ► Schizophrenic patients showed a tendency to reduced complexity values as a function of age while controls showed the opposite tendency. ► The tendency observed in schizophrenic patients parallels the tendency observed in Alzheimer disease patients.

Characteristic time in quasispecies evolution

Estudio del tiempo en que un fenotipo alcanza un estado estacionario

Complexity in the Optimisation of ATM Performance Metrics

Today's motivation for autonomous systems research stems out of the fact that networked environments have reached a level of complexity and heterogeneity that make their control and management by solely human administrators more and more difficult. The optimisation of performance metrics for the air traffic management system, like in other networked system, has become more complex with increasing number of flights, capacity constraints, environmental factors and safety regulations. It is anticipated that a new structure of planning layers and the introduction of higher levels of automation will reduce complexity and will optimise the performance metrics of the air traffic management system. This paper discusses the complexity of optimising air traffic management performance metrics and proposes a way forward based on higher levels of automation.

Assessing the effects of complexity in cross-temporal transferability of species distribution modelling predictions using palaeobotanical data

Valoración de la transferencia temporal de los modelos de distribución de especies para su aplicación en nuestros días utilizando datos paleobotánicos Corilus avellana y Alnus glutinosa.