The morphofunctional approach in paleontology

The principle of actualism is regarded as the major principle in morphofunctional studies of fossil organisms, which is based on comparisons of evolutionary series of both extinct and extant taxa. The objects and specificity of morphofunctional studies in paleontology are discussed. The revelation of relationships between morphological and functional archetypes are considered to be the major task of these studies. The ecosystem approach, constrains on actualistic reconstruction imposed by various morphofunctional modi, hierarchy of functions at different levels of structural organization and at different phylogenetic stages are considered. It is shown that parallel development and the mosaic pattern of characters are accounted for by general morphogenetic mechanisms and heterochronies.     

Coordinated Optimization of Visual Cortical Maps (I) Symmetry-based Analysis

In the primary visual cortex of primates and carnivores, functional architecture can be characterized by maps of various stimulus features such as orientation preference (OP), ocular dominance (OD), and spatial frequency. It is a long-standing question in theoretical neuroscience whether the observed maps should be interpreted as optima of a specific energy functional that summarizes the design principles of cortical functional architecture. A rigorous evaluation of this optimization hypothesis is particularly demanded by recent evidence that the functional architecture of orientation columns precisely follows species invariant quantitative laws. Because it would be desirable to infer the form of such an optimization principle from the biological data, the optimization approach to explain cortical functional architecture raises the following questions: i) What are the genuine ground states of candidate energy functionals and how can they be calculated with precision and rigor? ii) How do differences in candidate optimization principles impact on the predicted map structure and conversely what can be learned about a hypothetical underlying optimization principle from observations on map structure? iii) Is there a way to analyze the coordinated organization of cortical maps predicted by optimization principles in general? To answer these questions we developed a general dynamical systems approach to the combined optimization of visual cortical maps of OP and another scalar feature such as OD or spatial frequency preference. From basic symmetry assumptions we obtain a comprehensive phenomenological classification of possible inter-map coupling energies and examine representative examples. We show that each individual coupling energy leads to a different class of OP solutions with different correlations among the maps such that inferences about the optimization principle from map layout appear viable. We systematically assess whether quantitative laws resembling experimental observations can result from the coordinated optimization of orientation columns with other feature maps.     

It is normal for classification approaches to be diverse

It is asserted that the postmodern concept of science, unlike the classical ideal, presumes necessary existence of various classification approaches (schools) in taxonomy, each corresponding to a particular aspect of consideration of the "taxic reality". They are set up by diversity of initial epistemological and ontological backgrounds which fix in a certain way a) fragments of that reality allowable for investigation, and b) allowable methods of exploration of the fragments being fixed. It makes it possible to define a taxonomic school as a unity of the above backgrounds together with consideration aspect delimited by them. Two extreme positions of these backgrounds could be recognized in recent taxonomic thought. One of them follows the scholastic tradition of elaboration of a formal and, hence, universal classificatory method ("new typology", numerical phenetics, pattern cladistics). Another one asserts dependence of classificatory approach on the judgment of the nature of taxic reality (natural philosophy, evolutionary schools of taxonomy). Some arguments are put forward in favor of significant impact of evolutionary thinking onto the theory of modern taxonomy. This impact is manifested by the correspondence principle which makes classificatory algorithms (and hence resulting classifications) depending onto initial assumptions about causes of taxic diversity. It is asserted that criteria of "quality" of both classifications proper and classificatory methods can be correctly formulated within the framework of a particular consideration aspect only. For any group of organisms, several particular classifications are rightful to exist, each corresponding to a particular consideration aspect. These classifications could not be arranged along the "better-worse" scale, as they reflect different fragments of the taxic reality. Their mutual interpretation depends on degree of compatibility of background assumptions and of the tasks being resolved. Extensionally, classifications are compatible as much as they coincide by context and hierarchical structure of included taxa. Intentionally, typological classifications are compatible if included taxa are comparable by their diagnoses, while phylogenetic classifications are compatible if the included taxa are ascribed monophyletic status. A brief consideration is given to the "new phylogenetics" (= "genophyletics") as to a classificatory approach aimed at elaboration of parsimonious phylogenetic hypotheses based on molecular biology data and employing numerical methods of cladistic analysis. This approach is shown to borrows some phenetic ideas and revives scholastic principle of unified classificatory basis. It is supposed that, in a time, biological classification would get escaping from plethora of positivistic ideas (including those being developed by nowaday cladistics) and would assimilate (revive) more actively holistic worldview.     

Phosphorylation of Ion channels

The introduction of highly specific reagents such as enzymes and inhibitors directly into living cells has proven to be a powerful tool in studying the modulation of cellular activity by protein phosphorylation. The use of exogenous kinases can be thought of as a pharmacological approach: this demonstrates that phosphorylation can produce modulation, but does not address the question of whether the cell actually uses this mechanism under normal physiological conditions. The complementary approach, the introduction of highly specific inhibitors such as R subunit or PKI, does ask whether endogenous kinase activity is necessary for a given physiological response. Together these two approaches have provided rather compelling evidence that cAMP-dependent and calcium/phospholipid-dependent protein phosphorylations can regulate membrane excitability. In several cases single-channel analysis has allowed the demonstration that an ion channel itself or something very close to the channel is the phosphorylation target, and it seems reasonable to assume that this will also be the case for many if not all of the other systems described above. Have any general principles emerged from the results to date? Certainly it seems clear that protein phosphorylation regulates not one but many classes of ion channels. As summarized in the Table, different channels can be modulated in different cells, some channels are activated while others are inhibited, and in some cells more than one channel is subject to modulation by phosphorylation. The list in the Table is probably not yet complete, and indeed it is not inconceivable that all ion channels can under appropriate conditions be regulated by phosphorylation. What aspect of channel function is altered by phosphorylation? The total membrane current, I, carried by a particular species of ion channel is given by Npi, where N is the number of active channels in the membrane, p is the probability that an individual channel will be open, and i is the single-channel current. In principle a change in I, the quantity measured in whole cell experiments, could be caused by a change in any one (or more) of the parameters, N, p or i (see Fig. 1). In the two cases in which single-channel measurements have allowed this question to be investigated, changes in N (Shuster et al., 1985) and p (Ewald et al., 1985) have been observed. Here again it seems unlikely that any one mechanism operates in all cases, and it would not be surprising to find that phosphorylation of some other channel results in a change in i.(ABSTRACT TRUNCATED AT 400 WORDS)     

Classical and non-classical taxonomy: where does the boundary pass?

Rise of non-classical science during XX century had certain influence upon development of biological taxonomy. Scientific pluralism (especially normative naturalism of Laudan), contrary to positivist and early post-positivist treatments, made taxonomy acknowledged scientific discipline of its own right. The present state of some schools of taxonomy makes it possible to consider them as a part of non-classical science and constituting the non-classical taxonomy. The latter is characterized by the following most important features. Ontological substantiation of both classificatory approaches and particular classifications is requested which invalidates such formal approaches as nominalistic and phenetic (numerical) schools. This substantiation takes a form of content-wise background preferably causal models which include certain axioms and presumptions about taxonomic diversity being studied, together with its causes, and thus define initial conditions of classificatory procedures. From this viewoint, phylogenetic classificatory approach is the most developed part of non-classical taxonomy. The entire taxonomic diversity is structured into several aspects of different levels of generality, each being outlined by a particular consideration aspect. The latter makes personal knowledge constituting an irremovable part of any scientific statement about taxonomic diversity, thus opposition of "objectively" and "subjectively" elaborated classifications becomes vague. Interrelation of various species concepts corresponding to its different consideration aspects is described by uncertainty relation principle. Classificatory algorithms are to be compatible with the conditions of a background model to ensure particular classifications obtained by their means are interpretable within the same model: this is provided by the correspondence principle. Classification is considered as a taxonomic hypothesis, i.e. a conjectural judgement about structure of particular fragment of taxonomic diversity considered within given consideration aspect; wich is to be forwarded and tested according to certain rules. Recognition of different aspects of taxonomic diversity makes it "legal" to elaborate several classifications of equal status, each reflecting a particular aspect of a fixed fragment of that diversity. This viewpoint makes classical ideas of the "ultimate" Natural (whatever might be its definition) or the best reference systems futile. In general, any pretension of an approach to be "the best" in reflecting taxonomic divesrity is contr-productive. Instead, elaboration of particular spectra of complementary classifications becomes the main task of non-classical taxonomy which describes in sum the entire taxonomic diversity. So, not opposition but correct mutual interpretation of such classifications and uniting them into the comprehensive picture of taxonomic diversity become focal points of non-classical taxonomy.     

Transfer of Natural Micro Structures to Bionic Lightweight Design Proposals

The abstraction of complex biological lightweight structure features into a producible technical component is a funda- mental step within the transfer of design principles from nature to technical lightweight solutions. A major obstacle for the transfer of natural lightweight structures to technical solutions is their peculiar geometry. Since natural lightweight structures possess irregularities and often have extremely complex forms due to elaborate growth processes, it is usually necessary to simplify their design principles. This step of simplification/abstraction has been used in different biomimetic methods, but so far, it has an arbitrary component, i.e. it crucially depends on the competence of the person who executes the abstraction. This paper describes a new method for abstraction and specialization of natural micro structures for technical lightweight compo- nents. The new method generates stable lightweight design principles by using topology optimization within a design space of preselected biological archetypes such as diatoms or radiolarian. The resulting solutions are adapted to the technical load cases and production processes, can be created in a large variety, and may be further optimized e.g. by using parametric optimization.     

Replaceability of amino acids and the self-facilitation of evolution

The self-facilitating aspect of evolution is formulated in terms of measures of amino acid replaceability. The incorporation of highly replaceable amino acids into a protein increases the rate at which it can incorporate highly irreplaceable amino acids. The reality of self-facilitation is supported by sequence data which imply that silent mutations which change the replaceability of codons are subject to selection. There are a number of interesting implications for the dependence of evolutionary rate on protein diversity and variability. In general, the incorporation of low information value amino acids into a protein increases the maximum rate at which the value of the information in the protein can increase.     

Bayesian Computation Emerges in Generic Cortical Microcircuits through Spike-Timing-Dependent Plasticity

The principles by which networks of neurons compute, and how spike-timing dependent plasticity (STDP) of synaptic weights generates and maintains their computational function, are unknown. Preceding work has shown that soft winner-take-all (WTA) circuits, where pyramidal neurons inhibit each other via interneurons, are a common motif of cortical microcircuits. We show through theoretical analysis and computer simulations that Bayesian computation is induced in these network motifs through STDP in combination with activity-dependent changes in the excitability of neurons. The fundamental components of this emergent Bayesian computation are priors that result from adaptation of neuronal excitability and implicit generative models for hidden causes that are created in the synaptic weights through STDP. In fact, a surprising result is that STDP is able to approximate a powerful principle for fitting such implicit generative models to high-dimensional spike inputs: Expectation Maximization. Our results suggest that the experimentally observed spontaneous activity and trial-to-trial variability of cortical neurons are essential features of their information processing capability, since their functional role is to represent probability distributions rather than static neural codes. Furthermore it suggests networks of Bayesian computation modules as a new model for distributed information processing in the cortex.     

Bootstrapping model of the origin of life

The origin of life is analyzed in terms of the self-facilitating aspect of evolution. According to the self-facilitation (or bootstrap) principle the structure of biological systems becomes increasingly suited to effective evolutionary search through the process of evolution. The principle may be extended to primitive collections of polymers with catalytic properties. The origin of the code may be based on a form of bootstrapping evolution. Once a primitive code appeared it could become more sophisticated through a multi-coding mechanism together with classical Darwinian mechanisms. The bootstrapping principle is also formulated in terms of the fluctuation-instability framework of Prigogine, Nicolis, and Babloyantz. Primitive collections of polymers accumulate evolution-enhancing redundancies which tend to reduce the extent to which they change when destabilized by fluctuation, but which increase the chances that these changes will lead to new predominant regimes. We show that the bootstrapping of evolutionary amenability is accompanied by the accumulation of a thermodynamic load, that is, a free energy cost which reduces the mechanistic efficiency. The bootstrapping effect suggests that the origin of life is most fruitfully approached as a long process during which the capacity to evolve facilitates itself in a step by step fashion rather than as a series of low probability events.     

The minimalist grammar of action

Language and action have been found to share a common neural basis and in particular a common 'syntax', an analogous hierarchical and compositional organization. While language structure analysis has led to the formulation of different grammatical formalisms and associated discriminative or generative computational models, the structure of action is still elusive and so are the related computational models. However, structuring action has important implications on action learning and generalization, in both human cognition research and computation. In this study, we present a biologically inspired generative grammar of action, which employs the structure-building operations and principles of Chomsky's Minimalist Programme as a reference model. In this grammar, action terminals combine hierarchically into temporal sequences of actions of increasing complexity; the actions are bound with the involved tools and affected objects and are governed by certain goals. We show, how the tool role and the affected-object role of an entity within an action drives the derivation of the action syntax in this grammar and controls recursion, merge and move, the latter being mechanisms that manifest themselves not only in human language, but in human action too.     

The Development and Structure of the Generative Cell Wall in Polygonatum simizui

The developmental structure and components of the generative cell wall in Polygonatum sirnizui Kitag were studied by means of cytochemical and electron microscope observation. The early generative cell wall separating the generative and vegetative cytoplasm contains callose and cellulose. From the time when the generative cell detaches from the intine untill it is freely suspended in the cytoplasm of the vegetative cell, the wall becomes progressively thinner and does not show the specific fluorescence when stained with aniline blue and cai- cofluor white although it remains PAS positive. At later developmental stage when the generative cell moves into the pollen tube but before its initiation of mitosis, an envelope with weak PAS positive reaction appears on the surface of the cell. Its morphological nature is similar to that of the sperm cell discribed as the "periplasm”. This study proves that a cell wall is present in the generative cell of Polygonatum simizui throughout the developmental process, althrough changes in structure and components of the wall may occur. The properties of the generative cell wall at different stages, its significance in differentiation between generative and vegetative cytoplasm and translocation of nutrient materials, and the possible mechanism of the detachment of the generative cell from the intine are the subjects to discussion.     

Measurement and meaning in biology

Measurement--the assignment of numbers to attributes of the natural world--is central to all scientific inference. Measurement theory concerns the relationship between measurements and reality; its goal is ensuring that inferences about measurements reflect the underlying reality we intend to represent. The key principle of measurement theory is that theoretical context, the rationale for collecting measurements, is essential to defining appropriate measurements and interpreting their values. Theoretical context determines the scale type of measurements and which transformations of those measurements can be made without compromising their meaningfulness. Despite this central role, measurement theory is almost unknown in biology, and its principles are frequently violated. In this review, we present the basic ideas of measurement theory and show how it applies to theoretical as well as empirical work. We then consider examples of empirical and theoretical evolutionary studies whose meaningfulness have been compromised by violations of measurement-theoretic principles. Common errors include not paying attention to theoretical context, inappropriate transformations of data, and inadequate reporting of units, effect sizes, or estimation error. The frequency of such violations reveals the importance of raising awareness of measurement theory among biologists.     

Ultrastructure of the Pollen Grain and Taxonomy

Abstract

The fine structure of mature pollen grains of several Monocotyle-dons and Dicotyledons plants was studied at the electron microscope. It was observed that inside the pollen grain each generative cell is always clearly separated from romaining cytoplasmic portions. The ways by which the generative cell is delimited are vary in systematically different plants. There may be either a cell wall, quite similar to the one MARUYAMA (1965) reported in the pollen of Tradescantia paludosa. He believed, it to be of a pectocellulosic nature, or a passage from a wall to a two-layered membrane. Multiple membranes, or simply two-layered ones have also been found. These different structures seems to be related to the possible evolutionary trends of the pollen grain. The most primitive forms have grains with an evidently walled generative cell, while in the more evolued ones, there is only a two layered membrane. The fact that in both Monocotyledons and Dicotyledons the generative cell in the more primitive species has a distinct wall, while in the most advanced types it has a double membrane, is very interesting from a phylogenetic point of view.     

A model for the evolution and control of generative apomixis

A model is presented for the evolution and control of generative apomixis—a collective term for apomixis in animals and diplosporous apomixis in flowering plants. Its development takes into account data obtained from studies of apomictic-like processes in sexual organisms and in non-apomictic parthenogens, as well as data obtained from studies of generative apomicts. This approach provides insights into the evolution and control of generative apomixis that cannot be obtained from studies of generative apomicts alone. It is argued that the control of the avoidance of meiotic reduction during egg production in generative apomicts resides at a single locus, the identity of which can vary between lineages. This variation accounts for the observed variation between taxa in the pattern of avoidance of meiotic reduction. The affected locus contains a wild-type allele that codes for meiotic reduction and excess copies of a mutant allele that codes for its avoidance. The dominance relationship between these is determined by their ratio and by the environment. Environmental differences between female generative cells and somatic cells are such that the phenotypic expression of the mutant allele is favoured in the former, while that of the wild-type allele is favoured in the latter. This is important, for the locus is also involved in the control of mitosis which would be disrupted by the expression of the mutant allele in somatic cells. The requirement to maintain a viable pattern of growth and development explains why the wild-type allele is retained by generative apomicts, and this in turn explains why the ability to produce meiotically reduced eggs is retained by facultative forms and why it appears to be suppressed in, rather than absent from, obligate forms. The requirement for excess copies of the mutant allele in generative cells explains why generative apomicts are typically polyploid, as this condition provides a simple and effective means of generating the correct balance of mutant and wild-type alleles. Environmental effects can also lead to the dominance relationship between wild-type and mutant alleles varying between generative cells. In plants, this can lead to the apomixis gene being expressed, and thus to meiotic reduction being avoided, in only some ovules. Meiotically reduced, as well as meiotically unreduced, eggs are produced when this occurs. If compatible and viable pollen is available the meiotically reduced eggs may be fertilized, resulting in these organisms reproducing as facultative apomicts. It is argued that the control and evolution of parthenogenesis in generative apomicts varies between taxa. In some, the parthenogenetic initiation of embryos may result from the acquisition of a parthenogenesis gene or genes; but there is no reason to believe that this is either a general or a common requirement. Indeed, in some it may be an ancestral trait, these apomicts differing from their sexual ancestors in the ability to mature, rather than in the ability to initiate, embryos from unfertilized eggs; or it may result from physiological or developmental changes induced, for example, by polyploidization, hybridization, or the avoidance of meiotic reduction. In some plants it may be induced by pollination (without fertilization) or by the activity of a developing endosperm. Although it is argued that most generatively apomictic lineages may have acquired this form of reproduction relatively easily, by the acquisition of a mutation at a single locus, it is argued that newly initiated lineages may often be reproductively inefficient. These will begin to accumulate mutations that improve the efficiency of apomictic reproduction. Thus several loci may be involved in the control of generative apomixis in established lineages, even though only a single locus was involved in its initiation in these lineages. Care must be taken to distinguish between these initiator and modifier genes when considering the evolution of generative apomixis. Finally, it is argued that although generatively apomictic lineages have easily acquired this form of reproduction, its evolution in some taxa may be so difficult, requiring the acquisition of mutations simultaneously at two or more loci, that these may never acquire it. Thus, evidence obtained from taxa that have successfully made the transition from sexual reproduction to generative apomixis that its evolution was straightforward should not be used as evidence that its evolution will always be relatively easily achieved. Its uneven taxonomic distribution indicates that it is much more easily evolved by some taxonomic groups than by others.     

First,do no harm: Generalized procreative non‐maleficence

New reproductive technologies allow parents some choice over their children. Various moral principles have been suggested to regulate such choices. This article starts from a discussion of Julian Savulescu's Principle of Procreative Beneficence (PPB), according to which parents ought to choose the child expected to have the best quality of life, before combining two previously separate lines of attack against this principle. First, it is suggested that the appropriate moral principles of guiding reproductive choices ought to focus on general wellbeing rather than prioritizing that of the child and, second, that they ought to be non‐maximizing (e.g. seeking the ‘good enough’ or to avoid harm). Though neither of these suggestions is entirely novel, combining them results in a new, and arguably more plausible, principle to regulate procreative choices, which I call the Principle of Generalized Procreative Non‐Maleficence (PGPNM). According to this principle, the primary obligation on parents is not to cause harm to other people through their reproductive choices.     

A transformational-grammar approach to the study of the regulation of gene expression

An important problem in biology is the lack of a set of common principles unifying biological knowledge. We propose generative grammar for constructing an integrative paradigm for the understanding of genome organization and the regulation of gene expression. Linguistic terms in molecular biology are defined. A genetic syntactic structure is defined as being equivalent to a sentence. The hypotheses for the grammar of genome structure are: (i) the "grammaticality" of the linguistic approach studies the "regulability" of genome structures; (ii) the "regulability" of genetic structures is independent from their specific biochemical meaning and (iii) the dynamics of regulation is implicit in the genome structure. A general structure is presented for the grammar; the application of phase-structure rules is justified by the existence of lexical categories. Transformational rules are utilized to represent loops of regulation. Negative inducible, positive repressible, positive inducible and negative repressible alternative mechanisms of regulation are represented, by four transformational rules, and the application of these rules is established by two principles. Finally, this approach is compared to other linguistic applications in molecular biology.     

Generative cell composition and its relation to male plastid inheritance patterns inMedicago sativa

Summary Genetic studies have recently shown that plastids are inherited biparentally in alfalfa; yet most crosses produce high frequencies of progenies containing only paternal plastids, and certain genotypes have been characterized as relatively strong or weak transmitters of male plastids. The objective of the present study was to determine whether the structure of generative cells differs among genotypes known to differ in male plastid transmission pattern. Using the techniques of serial ultrathin sectioning and three-dimensional reconstruction, we found that mature generative cells of the genotypes investigated have basically similar morphology, and contain numerous plastids in each end of the spindle shaped cell. Since the morphological variation that does occur is as great within a genotype as it is between genotypes, it does not appear that generative cell structure can be used to predict male plastid transmission behavior in a particular genotype. The number of mitochondria in generative cells, which is much less than that of plastids, varies considerably among genotypes. However, comparable genetic studies between genotypes are not yet available on male mitochondrial inheritance in alfalfa.     

Steady-State Differential Dose Response in Biological Systems

In pharmacology and systems biology, it is a fundamental problem to determine how biological systems change their dose-response behavior upon perturbations. In particular, it is unclear how topologies, reactions, and parameters (differentially) affect the dose response. Because parameters are often unknown, systematic approaches should directly relate network structure and function. Here, we outline a procedure to compare general non-monotone dose-response curves and subsequently develop a comprehensive theory for differential dose responses of biochemical networks captured by non-equilibrium steady-state linear framework models. Although these models are amenable to analytical derivations of non-equilibrium steady states in principle, their size frequently increases (super) exponentially with model size. We extract general principles of differential responses based on a model’s graph structure and thereby alleviate the combinatorial explosion. This allows us, for example, to determine reactions that affect differential responses, to identify classes of networks with equivalent differential, and to reject hypothetical models reliably without needing to know parameter values. We exemplify such applications for models of insulin signaling.