浅论大陆漂移在生物进化中的作用

大陆漂移是地球诞生之后,在演化的过程中地壳表现出的一种肉眼看不见的缓慢、连续的水平运动现象。它是由奥地利地球物理学家魏格纳（Ａ．Ｌ．Ｗｅｇｅｎｅｒ）首先发现,于１９１５年发表的《海陆的起源》一书中首先提出的。他认为全球大陆在古生代石炭纪（距今３－５－２－８亿年）是一块统一的泛大陆,称原始大陆,后来到中生代（距今２－２５亿年－６５００万年）,这个原始大陆由于受太阳、月亮和地球自转各方面的作用,破裂成几块,硅铝层在硅镁层之上作水平运动,逐渐形成今日各大陆的水平位置。以后,人类在进一步研究地壳运动和…     

生物进化中的熵初探

１８６５年德国著名物理学家克劳修斯（Ｃｌａｕｓｉｕｓ,１８２２－１８８８）在创立了热力学第二定律的基础上,又提出熵（ｅｎｔｒｏｐｙ）这一重要的科学概念,进一步推动了力学理论的发展。随着生物进化论研究的不断深入,生物学家发现,熵并非仅限于物理学中的概念,在生物进化中,亦存在着熵的问题。目睹生物进化史,地球上的生物诞生迄今已有３５亿年的悠久历史,它是以３５亿年前最原始的生命体进化而来的。最原始的生命体至少经二,三亿年的历史形成原始原核生物,原始原核生物经过十五,六亿年的时间形成了真核单细胞生物,真核…     

基因突变的分子机制与生物进化

在自然群体中发现的遗传变异和物种之间的差异是人们普遍熟知的。同时我们都知道,最原始的生命非常小而且简单,可现在却有     

生物进化研究的回顾与展望

生物进化是自然科学的永恒之迷。随着历史的发展和科学的进步,生物进化思想从早期的萌芽,到自然选择学说、新达尔文主义,从现代综合理论,到分子进化的中性学说。再到新灾变论和点断平衡论等。当前,由于生物学各分支学科的飞速发展．它们就各自的研究对象在宏观和微观上不断地拓展和深入,并在不同的层次上形成了广泛的交叉、渗透和融合,现代的进化生物学研究从宏观的表型到微观的分子,从群体遗传改变的微进化到成种事件以及地史上生物类群谱系演化的宏进化,从直接的化石证据到基于形态性状、分子证据和环境变迁的综合推理,从基于遗传基础的比较基因组学到演化机理的进化发育生物学等。可以预见,在新的世纪里,在哲学和具体方法论(如系统论、控制论和信息论)的指导下,在生命科学、其他自然科学乃至社会科学工作者的通力合作下,综合遗传、发育和进化等研究领域的各种理论成果,生物进化理论即将出现也一定会出现的一个新的大综合和新的大统一。     

“生物进化-I”的教学组织

进化论是生物学中最大的统一理论,生物界的复杂现象只能在进化理论的基础上得到统一的解释。生物学各个学科无不贯穿着进化论的原则思想（张昀,1998）。从事生物进化研究的学者通过对生物进化的历程、原因、进化速率与方向等问题的研究,告诉人们生物界为什么丰富多彩,     

“生物进化-Ⅱ”的教学组织

<正>20世纪伟大的进化生物学家恩斯特·迈尔(Ernst Mayr)在他的著作《进化是什么》的开篇中写到:"进化是生物学中最重要的概念。如果不考虑进化的话,对生物学中任何为什么的问题都无法得出确切的答案"。不仅科学界需要理解进化,     

生物进化事件的出现及其规律：“天地生人”系列讲座（五）

古生物学家在研究化石的过程中,发现了这样一条规律：在长达几万年、几十万年、甚至几百万年的时间内,生物的形态往往处于停滞状态,至多只发生轻微的变化。这种现象在生物的进化史上是非常普遍的。古生物学家称它为“长期的形态停滞”现象。与此相对应,在生物的进化史...     

基于生物适应进化原理论证生物进化的动力

文章从现有主流生物进化理论存在的问题入手, 以生物适应进化原理为认识基础, 讨论生物进化的动力, 以求对生物进化机制有一个新的认识。在薛定谔“生命赖负熵生存”观点的指导下, 提出了“负熵流”包括能量流、物质流和信息流, 以及负熵流是生命生存和发育的动力的观点。作者在原有生物适应进化原理基础上, 修改完善并提出了“DNA、RNA和蛋白质在环境作用下的生物适应进化调控系统”理论, 并根据系统发育是个体发育的“积分”的观点, 推论得出生物与环境的负熵差引起的负熵流也是生命进化的动力, 对生物进化机制作出了新的理解。基于这样的生物进化机制的认识, 提出了“进化是一个子系统在其上一等级系统中, 将自身全部或部分信息遗传给下一代子系统, 并在其适应上一等级系统过程中, 产生一些新质, 终止一些旧质, 从而在其上一等级系统中得以延续的变化过程”的概念, 并探讨了一些与进化有关的其他争议问题。     

建立在化石证据之上的生物进化时间表

生物进化的两个最根本问题是 :最初生物的起源及不同物种的起源。关于最初生物的起源 ,主要有两种理论 ,一种是流传已久的神创论 ;另一种是近现代科学的推论。神创论在西方国家较为盛行 ,它起源于基督教的《圣经》 ,其主要思想是 :地球上的万事万物都是神创造的 ,并且是在 6天内完成的。这种论调早已经被自然科学的发现和进步所唾弃。因为它掩盖了自然界演化发展的真正规律 ,过分简化了生物界起源与进化的这样一个复杂而又漫长的过程。然而 ,近来西方的一些神创论的鼓吹者又别出心裁地提出 ,圣经中所说的“天” ,并非我们通常所指的 2 4小时…     

杆菌在平板上的生长模拟

在计算机上模拟了杆菌代谢产物对杆菌自身繁殖的影响。基于代谢产物对杆菌繁殖的影响,引入扩散速率（k0）,繁殖扩散时间比率（r＝Tr/Td）,代谢产物对繁殖的抑制系数（m）。在r－4时,对不同的m、k0组合进行了比较分析,得到较为满意的结果。用等高图和矢量图对代谢产物浓度进行了分析,得出结果为杆菌群落内部趋于平衡和稳定,群落边缘高度不平衡。     

Role of Utility and Inference in the Evolution of Functional Information

Functional information means an encoded network of functions in living organisms from molecular signaling pathways to an organism’s behavior. It is represented by two components: code and an interpretation system, which together form a self-sustaining semantic closure. Semantic closure allows some freedom between components because small variations of the code are still interpretable. The interpretation system consists of inference rules that control the correspondence between the code and the function (phenotype) and determines the shape of the fitness landscape. The utility factor operates at multiple time scales: short-term selection drives evolution towards higher survival and reproduction rate within a given fitness landscape, and long-term selection favors those fitness landscapes that support adaptability and lead to evolutionary expansion of certain lineages. Inference rules make short-term selection possible by shaping the fitness landscape and defining possible directions of evolution, but they are under control of the long-term selection of lineages. Communication normally occurs within a set of agents with compatible interpretation systems, which I call communication system. Functional information cannot be directly transferred between communication systems with incompatible inference rules. Each biological species is a genetic communication system that carries unique functional information together with inference rules that determine evolutionary directions and constraints. This view of the relation between utility and inference can resolve the conflict between realism/positivism and pragmatism. Realism overemphasizes the role of inference in evolution of human knowledge because it assumes that logic is embedded in reality. Pragmatism substitutes usefulness for truth and therefore ignores the advantage of inference. The proposed concept of evolutionary pragmatism rejects the idea that logic is embedded in reality; instead, inference rules are constructed within each communication system to represent reality, and they evolve towards higher adaptability on a long time scale.     

Could life have arisen in the primitive atmosphere?

Summary A recently proposed model for the origin of prebiotic progenitors of life in particles suspended in a primitive, specially organized atmosphere is considered critically. It is concluded that the physical and chemical framework of the new hypothesis conflicts with the conditions necessary for the evolution of the progenitors of life in the atmosphere of the early Earth. Therefore this model seems not to be a reasonable alternative to the Oparin thesis.     

Spatial electrical patterns in simulated neuronal dendrites

Steady state longitudinal distributions of (a) the density of channels conducting an inward transmembrane current of cations, (b) the submembrane concentrations of these cations, and (c) the resting membrane potential, were investigated in a phenomenological model of a cylinder-shaped dendritic process of the neuron. It was found that spatially non-uniform patterns of these distributions occur only if one of the following conditions held (i) an increase in the intracellular concentration of cations conducting an inward passive transmembrane current amplified the active efflux of those cations by the pump and attenuated their passive influx through the voltage dependent channels, with amplification of the efflux lower than attenuation of the influx; (ii) molecules of mobile channels bore a negative electrophoretic charge exposed to the intracellular space and were subject to lateral electrodiffusion in the membrane; (iii) the cations induced a further release of cations from intracellular stores. Numerical simulation studies of the membrane with Na and K channels and Na/K pumps with conditions (i) and (ii) have demonstrat-ed the possibility of the creation of inhomogeneous patterns in the neurites. These inhomogeneous patterns are dissipative structures (DSs), and they can be spatially periodic. Received: 23 October 1996 / Accepted: 21 May 1997     

The application of genetic algorithms in behavioural ecology, illustrated with a model of anti-predator vigilance

We develop a genetic algorithm (GA) approach to a well-known model of vigilance behaviour in a group of animals. We first demonstrate that the GA approach can provide a good match to analytic solutions to the original model. We demonstrate that a GA can be used to find the evolutionarily stable strategies in a model relevant to behavioural ecology where the fitness of each strategy is determined by the frequencies of different strategies in the population. We argue that the GA implementation demonstrates the combination of assumptions used to generate analytic solution to the original model can only be simultaneously satisfied under relatively restrictive conditions on the ecology of the species involved; specifically that group membership is very fluid but group size is conserved over timescales of individual foraging bouts. We further explore the sensitivity of model predictions to alternative choices in the implementation of the GA, and present advice for implementation and presentation of similar models. In particular, we emphasise the need for care in measuring the predictions of such models, so as to capture the intrinsic behaviour of the system and not the remnant of often arbitrarily chosen initial conditions. We also emphasise the potential for GA models to be more transparent about model assumptions regarding underlying biology than analytic models.     

Evolution in Lego ®: A Physical Simulation of Adaptation by Natural Selection

We describe a physical simulation of natural selection in a population of legorgs, six-segment model organisms. Legorg morphology is genetically specified by five alleles on each segment. Legorgs show a simple form of motility that could evolve in originally sessile animals. This motility, the ability to move horizontally on a smooth surface, depends on the morphology and interaction of the six segments that produce different patterns of locomotion. Legorgs are selected for motility and reproduce in proportion to fitness. After just five generations, the average population motility increases 2.5 times. Additionally, we describe a slightly less time-consuming simulation of legorg evolution, where fitness is assigned by comparison with a template. The calculation of gene pools is precisely the same as in the previous simulation and produces very robust increases in fitness during five generations. The simulation is designed as a classroom experiment to explore the mechanism of natural selection. A test of its learning efficiency by evaluating the students’ conception of central aspects of evolutionary theory before and after showed a significant improvement. The surprising power of natural selection in this very simple physical system may also be exploited in more advanced experiments.     

Entropy decrease associated to solute compartmentalization in the cell

We have deduced equations to quantify the entropy associated to the compartmentalization of components in eukaryotic cells as a function of cell and compartment volumes, and of the concentration of solutes. On the basis of known and plausible values of volume and solute concentrations and the deduced equations, we estimate that the contribution of compartmentalization to the decrease of entropy is approximately −14.4 × 10⁻¹⁴ J K⁻¹ cell⁻¹ (−0.7 J K⁻¹ L⁻¹) in the case of Saccharomyces cerevisiae, a typical eukaryotic cell, and approximately −49.6 × 10⁻¹⁴ J K⁻¹ cell⁻¹ (−1.0 J K⁻¹ L⁻¹) in the more complex Chlamydomonas reinhardtii. When compared with other potential contributing factors, such as the informational entropy of DNA and the conformational entropy of proteins, compartmentalization appears as an essential development that significantly decreased the entropy of living cells during biological evolution.     

The self-organization of speech sounds

The speech code is a vehicle of language: it defines a set of forms used by a community to carry information. Such a code is necessary to support the linguistic interactions that allow humans to communicate. How then may a speech code be formed prior to the existence of linguistic interactions? Moreover, the human speech code is discrete and compositional, shared by all the individuals of a community but different across communities, and phoneme inventories are characterized by statistical regularities. How can a speech code with these properties form? We try to approach these questions in the paper, using the "methodology of the artificial". We build a society of artificial agents, and detail a mechanism that shows the formation of a discrete speech code without pre-supposing the existence of linguistic capacities or of coordinated interactions. The mechanism is based on a low-level model of sensory-motor interactions. We show that the integration of certain very simple and non-language-specific neural devices leads to the formation of a speech code that has properties similar to the human speech code. This result relies on the self-organizing properties of a generic coupling between perception and production within agents, and on the interactions between agents. The artificial system helps us to develop better intuitions on how speech might have appeared, by showing how self-organization might have helped natural selection to find speech.     

Mammalian genes as molecular clocks?

Summary In analyzing the silent nucleotide substitutions in some mammalian mitochondrial mRNA coding genes, we had found that the frequency of each of the four nucleotides in rat, mouse, and cow, but not in humans, is the same in the silent third codon position (Lanave C, Preparata G, Saccone C, Serio G (1984) J Mol Evol 20:86-93). Because our findings for these three species were compatible with a stationary Markov process for the evolution of nucleotide sequences, we applied such a model to calculate the effective evolutionary silent substitution rate (v_s) and the divergence times among the species. In this paper we have analyzed the first and second codon positions in the same mammalian mitochondrial genes. We found that in the first and second codon positions the human mitochondrial genes satisfy the stationarity conditions. This has allowed us to use the stochastic model mentioned above to calculate the divergence times among mouse, rat, cow, and human. Furthermore, we have analyzed the silent substitution rate in one nuclear gene for these four mammals. We found that in this gene the effective silent substitution rate is about 3 times lower than in mitochondrial genes, and that humans are in this case stationary with respect to the other three mammals in the third codon position as well. Application of our Markov model to this latter gene yields divergence times consistent with our previous determinations.     

The curse of the pharaoh in space: free-living infectious stages and the evolution of virulence in spatially explicit populations

The idea that parasites with long-lived infective stages may evolve higher virulence has received considerable attention. This idea is called 'the curse of the pharaoh' because of the hypothesis that the death of Lord Carnavon was caused by very long-lived propagules of a highly virulent infectious disease. Here, we examined the evolution of diseases that transmit via free-living stages in a spatial context. We show that, if virulence evolves independently of transmission, long-lived infective stages can select for higher virulence. There is always the evolution of a finite transmission rate, which becomes higher when the infective stages are shorter lived. When a trade-off occurs between transmission and virulence, we show that there is no evidence for the curse of the pharaoh. Indeed, higher transmission and therefore virulence may be selected for by shorter rather than long-lived infective stages.