外显子和内含子的序列复杂性

引入了两个新的关于序列复杂性的测度,并以此为指标分析比较了结构基因序列中的外显子和内含子的复杂性差异。     

Beyond “beyond GDP indicators:” The need for reflexivity in science for governance

“Beyond GDP” initiatives flag the limits of the quantitative indicators of progress currently used for governance. Focusing on the quality assessment of quantitative information used for governance, we use some of the conceptual tools of theoretical ecology and evolutionary biology in order to identify the pre-analytical choices that determine the usefulness and pertinence of a model. Starting from the definition of a model as a formal representation of a specific and necessarily subjective observation, we show that the production of indicators is the final result of a series of decisions on what to observe and how. These choices, in turn, depend on the narrative, or set of narratives, adopted. Narratives provide causality and context to knowledge claims and are needed to select the indicators to be used for policy. Moving beyond the GDP debate requires reflexivity, that is, awareness of the key role that pre-analytical choices play in the definition of both the relevance of the chosen perceptions and narratives (determined by the normative stands of different actors – who defines wellbeing?), and the usefulness of the chosen models and data (determined by the pertinence of the resulting representation – how to measure wellbeing?). Reflexivity is essential in order to take into account the purposes for which different indicators were created and to define new purposes for the “beyond GDP” indicators.     

Intractable mixtures and the origin of life

Attempts to model the spontaneous chemistry which presumably preceded the origin of life on Earth commonly result in the production of intractably complex mixtures of organic compounds. It is, therefore, difficult to understand how any kind of evolutionary process might have begun. A number of potential solutions to this well-known and frustrating problem have been offered in the literature over the years. The present contribution briefly reviews and evaluates some of the more promising possibilities.     

The practical modelling of context-dependent causal processes--a recasting of Robert Rosen's thought

This paper is a critical recasting of some of Robert Rosen's thought. It is argued that a lot of the thrust of Rosen's work can be better understood when recast in terms of the context dependency of causal models. When recast in this way, I seek to highlight how his thought does not lead to the abandonment of formal modelling and a descent into relativism, but a more careful and rigours science of complex systems. This also sheds light on several aspects of modelling, including the need for multiple models, the nature of modelling noise, and why adaptive systems cause particular problems to modellers. In this way, I hope to decrease researchers fear that, by taking Rosen's criticisms seriously, they would have to abandon the realm of acceptable science.     

Alterations in peripheral joint muscle force control in adults with musculoskeletal disease,injury, surgery,or arthroplasty: A systematic review and meta-analysis

PurposeTo systematically review and analyse whether musculoskeletal conditions affect peripheral joint muscle force control (i.e. magnitude and/or complexity of force fluctuations).MethodsA literature search was conducted using MEDLINE, CINAHL and SPORTDiscus databases (from inception-8th April 2021) for studies involving: 1) participants with musculoskeletal disease, injury, surgery, or arthroplasty in the peripheral joints of the upper/lower limb; 2) comparison with an unaffected control group or unaffected contralateral limb; and 3) measures of the magnitude and/or complexity of force fluctuations during targeted isometric contractions. The methodological quality of studies was evaluated using a modified Downs and Black Quality Index. Studies were combined using the standardized mean difference (SMD) in a random-effects model.Results14 studies (investigating 694 participants) were included in the meta-analysis. There was a significant effect of musculoskeletal conditions on peripheral joint muscle force coefficient of variation (CV; SMD = 0.19 [95 % CI 0.06, 0.32]), whereby individuals with musculoskeletal conditions exhibited greater CV than controls. Subgroup analyses revealed that CV was only greater: 1) when comparison was made between symptomatic and asymptomatic individuals (rather than between affected and contralateral limbs; SMD = 0.22 [95 % CI 0.07, 0.38]); 2) for conditions of the knee (SMD = 0.29 [95 % CI 0.14, 0.44]); and 3) for ACL injury post-surgery (SMD = 0.56 [95 % CI 0.36, 0.75]).ConclusionMusculoskeletal conditions result in an increase in peripheral joint muscle force CV, with this effect dependent on study design, peripheral joint, and surgical status. The greater force CV is indicative of decreased force steadiness and could have implications for long-term tissue health/day-to-day function.     

Reduction, integration and emergence in biochemical networks

Most studies of molecular cell biology are based upon a process of decomposition of complex biological systems into their components, followed by the study of these components. The aim of the present paper is to discuss, on a physical basis, the internal logic of this process of reduction. The analysis is performed on simple biological systems, namely protein and metabolic networks. A multi-sited protein that binds two ligands x and y can be considered the simplest possible biochemical network. The organization of this network can be described through a comparison of three systems, i.e. XY, X and Y. X and Y are component sub-systems that collect states x(i) and y(j), respectively, i.e. protein states that have bound either i molecules of x (whether or not these states have also bound y), or j molecules of y (whether or not these states have bound x). XY is a system made up of the specific association of X and Y that collects states x(i)y(j). One can define mean self-informations per node of the network, , and . Reduction of the system XY into its components is possible if, and only if, ,is equal to the sum of and . If is smaller than the sum of and , the system is integrated, for it has less self-information than the set of its components X and Y. It can also occur that , be larger than the sum of and . Hence, the system XY displays negative integration and emergence of self-information relative to its components X and Y. Such a system is defined as complex. Positive or negative integration of the system implies it cannot be reduced to its components. The degree of integration can be measured by a function , called mutual information of integration. In the case of enzyme networks, emergence of self-information is associated with emergence of catalytic activity. Moreover, if the enzyme reaction is part of a metabolic sequence, its mutual information of integration can be increased by an effect of context of this sequence.     

External and internal complexity of complex adaptive systems

We introduce concepts of external and internal complexity to analyze the relation between an adaptive system and its environment. We apply this theoretical framework to the construction of models in a cognitive system and the selection between hypotheses through selective observations performed on a data set in a recurrent process and propose a corresponding neural network architecture.     

Soft Picture of Lateral Heterogeneity in Biomembranes

Standard methods of characterization of electron paramagnetic resonance (EPR) spectra of spin-labeled biomembranes limit the resolution of lateral heterogeneity to only two or three domain types. This disables examination of the structure—function relationship in complex membranes, which might be composed of a larger number of different domain types. To enable exploration of this kind, a new approach based on analysis of EPR spectra with multi-run, hybrid evolutionary optimization is proposed here. From the multiple runs a quasi-continuous distribution of membrane spectral parameters (order parameter, proportion of spectral component, polarity correction factor, rotational correlation time and broadening constant) can be constructed and presented by a new presentation technique CODE (colored distribution of EPR spectral parameters). Through this the concept of a soft picture of membrane heterogeneity is introduced, in contrast to the standard discrete domain picture. The soft characterization method, established on synthetic spectra, was used to examine the lateral heterogeneity of liposome membranes as well as of membranes of neutrophils from healthy and asthmatic horses. In liposome membranes the determined number of domain types was the same as already established by standard procedures of EPR spectra line-shape interpretation. In membranes of neutrophils a quasi-continuous distribution of membrane domain properties was detected by the new method.