最大信息熵原理与群体遗传平衡

建立了用最大信息熵原理推导群体遗传平衡定律的统一数学模型,并给出了模型的统一解,此解正是Hardy-Weinberg定律所给出的平衡群体的基因型频率,说明当群体信息熵达到最大时,群体基因型频率不再变化,即达到“平衡”。这证明了最大熵分布就是Hardy-Weinberg平衡分布。Hardy-Weinberg平衡定律与最大信息熵原理的内在一致性说明,杂交和随机交配是一个不可逆过程,使群体基因型信息熵增大,无序性增,是选择和近亲交配使群体的信息熵降低,有序性增加,育种过程实际就是调节群体信息熵的过程。过程信息熵的含义是表示一个概率分布的不确定性,最大熵原理意味着在一定的约束条件,选择具有最大不确定性的分布,从而其分布是最为随机的。最大熵原理在信息,工程,天文,地理,图像处理,模式识别等自然科学和社会科学领域都有广泛的成功应用,本文从群体遗传学角度证明了这一原理具有普遍适用性。熵是描述系统状态的函数,而最大熵原理则表明了系统发展变化的趋势,系统的最终状态必然是熵增加至最大值的状态,对于任何系统都是如此。因此,群体遗传系统的平衡定律可以统一用最大熵原理进行判定和描述;任意群体的基因型信息熵在随机交配世代传递时有不断增加的趋势;在一定约束条件下基因型信息熵达到最大值时,就称之为达到遗传平衡。本文将信息论原理应用于群体遗传学研究,揭示了基因信息熵的生物学意义,并表明可以用信息学和控制论的原理和方法来研究群体遗传学问题。     

关于最大信息熵原理与群体遗传平衡一致性的探讨

汪小龙等建立了用最大信息熵原理推导一个基因座上群体遗传平衡的统一数学模型,并给出了模型的最大值解,此解正是Hardy-Weinberg平衡定律所给出的基因型频率。这说明当群体基因型信息熵最大时,群体基因型频率不再变化,达到平衡状态,从而证明了最大信息熵原理与Hardy-Weinberg平衡定律具有一致性,同时指出这一结论可以推广至有迁移、突变、选择、遗传漂变、近亲交配的群体以及多个基因座情形。概括地说就是：最大信息熵原理与群体遗传平衡具有一致性。但是,他们仅仅证明了最大信息熵原理与一个基因座上Hardy-Weinberg平衡定律具有一致性,本文在这个范围内将其推广至多个基因座,且每一个基因座均为复等位基因情形。至于最大信息熵原理是否与其它的群体遗传平衡具有一致性,他们的结论仅仅是猜想,并未严格推导。事实上,要想将这种一致性推广到迁移、突变、随机漂变和近亲交配等群体,则不见得正确。      

Mapping the Information Landscape: Discerning Peaks and Valleys for Ecological Monitoring

We investigate previously unreported phenomena that have a potentially significant impact on the design of surveillance monitoring programs for ecological systems. Ecological monitoring practitioners have long recognized that different species are differentially informative of a system’s dynamics, as codified in the well-known concepts of indicator or keystone species. Using a novel combination of analysis techniques from nonlinear dynamics, we describe marked variation among spatial sites in information content with respect to system dynamics in the entire region. We first observed these phenomena in a spatially extended predator–prey model, but we observed strikingly similar features in verified water-level data from a NOAA/NOS Great Lakes monitoring program. We suggest that these features may be widespread and the design of surveillance monitoring programs should reflect knowledge of their existence.     

Entropy and the conceit of biodiversity management

Many conservation biologists and ecologists consider invasive species to be one of the greatest threats to biodiversity because their spread across biogeographical boundaries may endanger unique and localized expressions of biodiversity (whether species or communities). Consequently, they imagine a future, the ‘Homogocene’, in which a small set of species dominates ecosystems around the world, and they promote policies and practices to lessen the spread of these species. Here, we consider some thermodynamic dimensions of the efforts to maintain current biogeographical boundaries. We wish to explore an important conceptual analogy between thermodynamically‐closed systems and isolated biogeographical regions in ecology. The conceptual tools developed in the context of thermodynamic systems can be shown to have relevance in a wide variety of systems contexts. The ‘Maxwell's demon’ thought experiment suggests that entropy is best thought of as information‐relative rather than a ‘law of nature’. Adopting this Maxwellian thermodynamic approach to managing complexity can shed new light on the challenges of biodiversity management. To prevent the dispersion of invasive species, people must invest energy on a scale to counteract global trade and concomitant dispersal of species. We show that removing barriers to species interaction through globalization is akin to allowing a previously isolated thermal system to interact with its environment; in both cases, the system will tend towards mixing or ‘equilibrium’, and fighting this tendency is costly. Unless social and economic integration declines, the energetic input required to lessen the spread of invasive species will continue to grow.     

Population-level cure of colorectal cancer in Malta: An analysis of patients diagnosed between 1995 and 2004

AimThe aim of this study was to estimate the population-level ‘cure’ of Maltese colorectal cancer patients diagnosed between 1995 and 2004, and to estimate the median survival time for the ‘uncured’ patients.Methods and study populationAnalysis was conducted on 1470 cases registered by the Malta National Cancer Register between 1995 and 2004 and followed up to end of 2010. The mean age of the patients was 66.4 (95%CI 65.8–67.1), and the number of men and women were equal. Background mortality for 1995–2010 was extracted from publicly available life tables. A mixture model with Weibull survival distribution and identity link was used to model ‘cure’.ResultsThe overall ‘cured’ proportion for the patients diagnosed in 1995–1999 was 45.3% (95%CI 40.2–50.5) while the ‘cured’ proportion for the patients diagnosed in 2000–2004 was 52.3% (95%CI 47.2–57.5). Median survival time for the ‘uncured’ patients increased in the second calendar period from 1.25 years (95%CI 1.04–1.45) to 1.42 years (95%CI 1.15–1.76).ConclusionIn Malta, as in the rest of Europe, improvements have been made in short- and long-term survival over the 15-year period under study. To continue this improvement, differences by age that still persist must be investigated and efforts focused to reduce any gaps between Malta and other European countries.     

植物微卫星分子标记中无效等位基因检测方法的比较与应用

微卫星分子标记因其开发便捷、突变率高、成本较低等优势一直被广泛应用于群体遗传学、保护生物学和分子生态学研究中。近年来二代测序技术、多重PCR方法以及毛细管电泳等新技术的发展和完善,极大地提高了微卫星分子标记的开发和使用效率并降低了使用成本。但是在开展微卫星实验过程中普遍存在的无效等位基因(或称为哑等位基因,null alleles）会对研究结果造成偏差,是微卫星分子标记应用中的最大缺陷之一。然而,长期以来无效等位基因的检测问题并未受到研究者的足够重视。本文通过对国内外相关文献查阅,在对无效等位基因有一个较为深入和全面认识的基础上,对目前无效等位基因的主要检测方法进行全面的介绍和深入的比较。最后,结合研究实例总结出植物微卫星分子标记研究中无效等位基因检测的有效办法。     

Linking ecological and social systems in cities: urban planning in Finland as a case

The loss of urban green space as a result of urbanization threatens the overall biodiversity of urban areas, and prompts us to consider the importance of existing urban nature more carefully. Because urban ecological systems are in intense interaction with human-social systems, it is fruitful to create an interdisciplinary research and planning framework to ensure the maintenance of biodiversity in urban areas. For this purpose, we adapted a suitable theoretical and conceptual scheme for the setting of Finnish urban development, which provides an example of a situation where a lot of nature has so far remained inside and around urban area. The adapted scheme focuses on the land use change as a result of urban land use planning and development, and may provide a way to address the important variables and feedback mechanisms between information flowing from ecological systems and drivers from the social system. Furthermore, we outlined a more specific framework around the Finnish urban detailed planning process in order to study the interactions between these systems further. After addressing ecology-oriented questions of quantity, quality and needs of urban nature, and human-oriented drivers, such as flow and incorporation of information, knowledge, values and institutions, we identified several challenges in integrating the components of ecological and social systems. Creating common conceptual ground for different actors and disciplines, improving communication in the process, matching contradictory values and perceptions, and improving stakeholder participation would be in the best interest of nature and people of urban areas.     

生态化学计量学在水生态系统中的研究与应用

生态化学计量学主要是研究碳、氮、磷等元素在各种生态过程中平衡的一门科学,其核心问题是揭示生物体元素组成的差异对生态功能的影响。由于生态化学计量学研究可以把生态实体的各个层次在元素水平上统一起来,因此生态化学计量学已成为许多生态系统的新兴研究工具。目前,生态化学计量学的研究与应用已深入到生态学的各个层次(分子、细胞、个体、种群、群落、生态系统及区域等不同尺度)。该文围绕生态化学计量学的两个重要组成理论,并结合笔者近年来的研究,归纳总结了生态化学计量学在水生态系统中的研究与应用及未来研究重点,希望有助于推动我国生态化学计量学在水生态系统中的应用研究。     

NOGEA: A Network-oriented Gene Entropy Approach for Dissecting Disease Comorbidity and Drug Repositioning

Rapid development of high-throughput technologies has permitted the identification of an increasing number of disease-associated genes (DAGs), which are important for understanding disease initiation and developing precision therapeutics. However, DAGs often contain large amounts of redundant or false positive information, leading to difficulties in quantifying and prioritizing potential relationships between these DAGs and human diseases. In this study, a network-oriented gene entropy approach (NOGEA) is proposed for accurately inferring master genes that contribute to specific diseases by quantitatively calculating their perturbation abilities on directed disease-specific gene networks. In addition, we confirmed that the master genes identified by NOGEA have a high reliability for predicting disease-specific initiation events and progression risk. Master genes may also be used to extract the underlying information of different diseases, thus revealing mechanisms of disease comorbidity. More importantly, approved therapeutic targets are topologically localized in a small neighborhood of master genes in the interactome network, which provides a new way for predicting drug-disease associations. Through this method, 11 old drugs were newly identified and predicted to be effective for treating pancreatic cancer and then validated by in vitro experiments. Collectively, the NOGEA was useful for identifying master genes that control disease initiation and co-occurrence, thus providing a valuable strategy for drug efficacy screening and repositioning. NOGEA codes are publicly available at https://github.com/guozihuaa/NOGEA.     

Statistical fluctuations in population bargaining in the ultimatum game: Static and evolutionary aspects

We explore the emergent behavior in heterogeneous populations where players negotiate via an ultimatum game: two players are offered a gift, one of them (the proposer) suggests how to divide the offer while the other player (the responder) can either accept or reject the deal. Rejection is detrimental to both players as it results in no earnings. In this context, our contribution is twofold: (i) we consider a population where the distribution of used strategies is constant over time and properties of the random payoff received by the players (average and higher moments) are reported from simple exact methods and corroborated by computer simulations; (ii) the evolution of a population is analyzed via Monte Carlo simulations where agents may change independently the proposing and accepting parameters of their strategy depending on received payoffs. Our results show that evolution leads to a stationary state in which wealth (accumulated payoff) is fairly distributed. As time evolves, an increase in average payoff and a simultaneous variance decrease is observed when we use a dynamics based on a probabilistic version of the saying: “One should not comply with small earnings, but one's greed must be limited.”     

Biogenic Amines and Polyamines: Similar Biochemistry for Different Physiological Missions and Biomedical Applications

Biogenic amines are organic polycations derived from aromatic or cationic amino acids. All of them have one or more positive charges and a hydrophobic skeleton. Nature has evolved these molecules to play different physiological roles in mammals, but maintains similar patterns for their metabolic and intracellular handling. As deduced from this review, many questions still remain to be solved around their biochemistry and molecular biology, blocking our aims to control the relevant pathologies in which they are involved (cancer and immunological, neurological, and gastrointestinal diseases). Advances in this knowledge are dispersed among groups working on different biomedical areas. In these pages, we put together the most relevant information to remark how fruitful it can be to learn from Nature and to take advantage of the biochemical similarities (keyprotein structures and their regulation data on metabolic interplays and binding properties) to generate new hypothesis and develop different biomedical strategies based on biochemistry and molecular biology of these compounds.     

Remediation of ecosystems damaged by environmental contamination: Applications of ecological engineering and ecosystem restoration in Central and Eastern Europe

To investigate the applicability of ecological engineering to pollution problems prevalent in present-day Central and Eastern Europe, a SCOPE-UNEP sponsored workshop was held in Estonia in November 1995. The workshop was undertaken specifically to obtain information from and to train planners, managers and scientists in the region. These ‘countries in transition' face, in many respects, unique environmental problems as a result of their recent domination by a centralized planning government system. Twenty workshop findings that resulted from workshop presentations and subsequent discussion are presented. Six papers published as part of this special issue of Ecological Engineering, and summarized here, deal with the general principles of mineland restoration, acidification effects and mitigation in Poland, reestablishment of riparian buffer strips in Estonia, recovery of forests in the Black Triangle of Czechoslovakia and Poland, restoration after 10 years near the Chernobyl nuclear plant accident in the Ukraine, and studies on remediation of contaminated soils in Belarus.     

3D Primary Hepatocyte Culture Systems for Analyses of Liver Diseases,Drug Metabolism,and Toxicity: Emerging Culture Paradigms and Applications

Recent research has shown that the maintenance of relevant liver functions ex vivo requires models in which the cells exhibit an in vivo‐like phenotype, often achieved by reconstitution of appropriate cellular interactions. Multiple different models have been presented that differ in the cells utilized, media, and culture conditions. Furthermore, several technologically different approaches have been presented including bioreactors, chips, and plate‐based systems in fluidic or static media constituting of chemically diverse materials. Using such models, the ability to predict drug metabolism, drug toxicity, and liver functionality have increased tremendously as compared to conventional in vitro models in which cells are cultured as 2D monolayers. Here, the authors highlight important considerations for microphysiological systems for primary hepatocyte culture, review current culture paradigms, and discuss their opportunities for studies of drug metabolism, hepatotoxicity, liver biology, and disease.     

Ultrafast molecular dynamics of biofuel extraction for microalgae and bacteria milking: blocking membrane folding pathways to damaged lipid-bilayer conformations with nanomicelles

Cell milking is a 100% renewable green energy for CO₂ by extraction of biofuels inside the cytosol of photosynthetic micro-organisms as microalgae and bacteria. The cells are exposed to a hydrophobic solvent forming holes and cracks through their membranes from which the biofuels can leak out. In protein folding, the goal would be to find pathways to the unique functional protein conformer. However, in the lipid-bilayer interaction with the solvent for milking, the objective is to block the pathways for damaged membrane conformations of low free energy with undesired nanostructures, using the solvent properties, as shown with an ab initio structural bioinformatic model. Statistical thermodynamics is used to compute the free energy (including entropy) from the molecular dynamics trajectory of the biomolecular system with many conformational changes. This model can be extended to the general problem of biomolecules folding as for proteins and nucleic acids. Using an adaptation of the Einstein diffusion law, the conformational change dynamics of the lipid bilayer depends on the two diffusion coefficients of the solvent: D₁ before the irreversible folding transition time and the much smaller D₂ thereafter. In contrast to the n-hexane and n-heptane hydrocarbons of smaller size, the residual D₂?=?4.7?×?10^?7?cm²/s of the n-decane solvent, with the highest partition coefficient among the three extractors, is the only to present a D₂ value that is significantly below the critical threshold of 10^?6?cm²/s. Therefore, the membrane would resist to long hydrocarbons and the exposed cells would remain viable for milking.     

Book Review Essay: Mary Angela Uwalaka. Ọfọ: Its Juridical and Linguistic Potency. Ibadan, Afrika-Link Books, 1996. 69 pages

Rev. Mother (Dr.) Mary Angela Uwalaka was a distinguished and devoted religious woman linguist. Her major area of research was Igbo syntax, where she made tremendous contributions, through published texts and scholarly articles towards the development of a unified Igbo language and the field of Linguistics. As a renowned scholar, her research interest was not limited to Linguistics only. In the words of Prof. Ben Elugbe, her colleague at the University of Ibadan where Mother Uwalaka worked until her demise in January 7 2007, she also “found time and ability to work and publish in the areas of religion and Igbo culture.” Ọfọ: Its Juridical and Linguistic Potency, which we shall review here, is an evidence that Uwalaka’s interests extended to other areas of Igbo studies, apart from the Igbo language.     

Viewing brain processes as Critical State Transitions across levels of organization: Neural events in Cognition and Consciousness,and general principles

In this theoretical and speculative essay, I propose that insights into certain aspects of neural system functions can be gained from viewing brain function in terms of the branch of Statistical Mechanics currently referred to as “Modern Critical Theory” [Stanley, H.E., 1987. Introduction to Phase Transitions and Critical Phenomena. Oxford University Press; Marro, J., Dickman, R., 1999. Nonequilibrium Phase Transitions in Lattice Models. Cambridge University Press, Cambridge, UK]. The application of this framework is here explored in two stages: in the first place, its principles are applied to state transitions in global brain dynamics, with benchmarks of Cognitive Neuroscience providing the relevant empirical reference points. The second stage generalizes to suggest in more detail how the same principles could also apply to the relation between other levels of the structural-functional hierarchy of the nervous system and between neural assemblies. In this view, state transitions resulting from the processing at one level are the input to the next, in the image of a ‘bucket brigade’, with the content of each bucket being passed on along the chain, after having undergone a state transition. The unique features of a process of this kind will be discussed and illustrated.