Epistemic, Evolutionary, and Physical Conditions for Biological Information

The necessary but not sufficient conditions for biological informational concepts like signs, symbols, memories, instructions, and messages are (1) an object or referent that the information is about, (2) a physical embodiment or vehicle that stands for what the information is about (the object), and (3) an interpreter or agent that separates the referent information from the vehicle’s material structure, and that establishes the stands-for relation. This separation is named the epistemic cut, and explaining clearly how the stands-for relation is realized is named the symbol-matter problem. (4) A necessary physical condition is that all informational vehicles are material boundary conditions or constraints acting on the lawful dynamics of local systems. It is useful to define a dependency hierarchy of information types: (1) syntactic information (i.e., communication theory), (2) heritable information acquired by variation and natural selection, (3) non-heritable learned or creative information, and (4) measured physical information in the context of natural laws. High information storage capacity is most reliably implemented by discrete linear sequences of non-dynamic vehicles, while the execution of information for control and construction is a non-holonomic dynamic process. The first epistemic cut occurs in self-replication. The first interpretation of base sequence information is by protein folding; the last interpretation of base sequence information is by natural selection. Evolution has evolved senses and nervous systems that acquire non-heritable information, and only very recently after billions of years, the competence for human language. Genetic and human languages are the only known complete general purpose languages. They have fundamental properties in common, but are entirely different in their acquisition, storage and interpretation.     

The measurement problem in artificial world models

The only epistemic relations between the world and organisms are established through evolution by natural selection, and learning by observation and measurement. In physics, measurements map an open domain of physical structure to a closed set of symbols. A basic problem in simulating evolution and measurement is that neither activity can be adequately formalized. Artificial world models based on programmable computers require a formalized domain of symbols in which the concepts of evolution and measurement are limited. The measurement problem also bears on the questions of the relation of computation to physics and to formal symbol systems and on what sense dissipationless computation is a useful concept.     

How do plant growth substances work? II

Abstract. This article continues the discussion on sensitivity prompted by the publication of an earlier paper by the author in 1981. It is indicated that appropriate measurements of sensitivity can help uncover the function of growth substances in development. The experimental constraints which are necessary for unambiguous measurements of sensitivity are outlined and it is shown that a specific sensitivity measurement, termed control strength, would most readily clarify function and help obviate controversy. Methods for measuring control strength which deal with the problem of compartmentalization are considered and it is suggested that stochastic variation in single cell biochemistry might provide a constraint on the accuracy of control strength determinations.     

Key Innovations: Further Remarks on the Importance of Morphology in Elucidating Systematic Relationships and Adaptive Radiations

The present paper is an argument in support of the continued importance of morphological systematics and a plea for improving molecular phylogenetic analyses by addressing explicit character transformations. We use here the inference of key innovations and adaptive radiations to demonstrate why morphological systematics is still relevant and necessary. After establishing that theories of phylogenetic relationship offer robust explanatory bases for discussing evolutionary diversification, the following topics are addressed: (1) the inference of key innovations grounded in phylogenetic analyses; (2) the epistemic distinction between character ‘mapping’ and relevant evidence in systematic and evolutionary studies; and (3) key innovations in molecular phylogenetics. We emphasize that the discovery of key innovations, in fossil or extant taxa, further strengthens the importance of morphology in systematic and evolutionary inferences, as they reveal scenarios of character transformation that have led to asymmetrical sister-group diversification. Our main conclusion is that understanding characters in and of themselves, when properly contextualized systematically, is what evolutionary biologists should be concerned with, whereas the analysis of tree topology alone, in which statistical nodal support measures are the sole indicators of phylogenetic affinity, does not lead to a fuller understanding of key innovations.     

The semiotics of control and modeling relations in complex systems

We provide a conceptual analysis of ideas and principles from the systems theory discourse which underlie Pattee's semantic or semiotic closure, which is itself foundational for a school of theoretical biology derived from systems theory and cybernetics, and is now being related to biological semiotics and explicated in the relational biological school of Rashevsky and Rosen. Atomic control systems and models are described as the canonical forms of semiotic organization, sharing measurement relations, but differing topologically in that control systems are circularly and models linearly related to their environments. Computation in control systems is introduced, motivating hierarchical decomposition, hybrid modeling and control systems, and anticipatory or model-based control. The semiotic relations in complex control systems are described in terms of relational constraints, and rules and laws are distinguished as contingent and necessary functional entailments, respectively. Finally, selection as a meta-level of constraint is introduced as the necessary condition for semantic relations in control systems and models.     

Aorta in vivo parameter identification using an axial force constraint

It was shown in a previous study by Stålhand et al. (2004) that both material and residual strain parameters for an artery can be identified noninvasively from an in vivo clinical pressure–diameter measurement. The only constraints placed on the model parameters in this previous study was a set of simple box constraints. More advanced constraints can also be utilized, however. These constraints restrict the model parameters implicitly by demanding the state of the artery to behave in a specified way. It has been observed in vitro that the axial force is nearly invariant to the pressure at the physiological operation point. In this paper, we study the possibility to include this behaviour as a constraint in the parameter optimization. The method is tested on an in vivo obtained pressure–diameter cycle for a 24-year-old human. Presented results show that the constrained parameter identification procedure proposed here can be used to obtain good results, and we believe that it may be applied to account for other observed behaviours as well.     

Improved distance analysis in RNA using network-editing techniques for overcoming errors due to spin diffusion

Multispin magnetization transfer, or spin diffusion, is a significant source of error in NOESY-derived distance measurements for the determination of nucleic acid solution structures. The BD-NOESY and CBD-NOESY experiments, which allow the measurement of interproton distances with greatly reduced contributions from spin diffusion, have been adapted to structural analysis in RNA oligonucleotides. The techniques are applied to a lead-dependent ribozyme (LZ2). We demonstrate the measurement of both aromatic proton–aromatic proton NOEs free of spin diffusion involving the intervening ribose moieties and aromatic proton–ribose proton NOEs free of the efficient cross-relaxation within the ribose ring. In LZ2, the accuracy and precision of the resulting distances are significantly improved. We also find that, by allowing the use of longer mixing times with greater sensitivity, the experimental attenuation of spin diffusion in RNA increases the distance range of interactions that can be analyzed. This effect permits measurement of important long-range distances in LZ2 that are not accessible with standard techniques. Thus, these techniques allow the simultaneous optimization of the number, accuracy, and precision of distance constraints used for RNA structure determinations.     

Why don't zebras have machine guns? Adaptation, selection, and constraints in evolutionary theory

In an influential paper, Stephen Jay Gould and Richard Lewontin (1979) contrasted selection-driven adaptation with phylogenetic, architectural, and developmental constraints as distinct causes of phenotypic evolution. In subsequent publications Gould (e.g., 1997a,b, 2002) has elaborated this distinction into one between a narrow "Darwinian Fundamentalist" emphasis on "external functionalist" processes, and a more inclusive "pluralist" emphasis on "internal structuralist" principles. Although theoretical integration of functionalist and structuralist explanations is the ultimate aim, natural selection and internal constraints are treated as distinct causes of evolutionary change. This distinction is now routinely taken for granted in the literature in evolutionary biology. I argue that this distinction is problematic because the effects attributed to non-selective constraints are more parsimoniously explained as the ordinary effects of selection itself. Although it may still be a useful shorthand to speak of phylogenetic, architectural, and developmental constraints on phenotypic evolution, it is important to understand that such "constraints" do not constitute an alternative set of causes of evolutionary change. The result of this analysis is a clearer understanding of the relationship between adaptation, selection and constraints as explanatory concepts in evolutionary theory.     

Genetics of Powdery Mildew Resistance in Barley

A comprehensive, critical review on the present knowledge regarding the genetics of resistance of barley to the powdery mildew fungus is presented. The review deals with six kinds of resistance: Race-specific resistance; Mlo resistance; partial resistance; induced resistance; passive resistance; and non-host resistance. Most of the sections are subdivided into: phenotype of the interaction; resistance mechanisms; and genetics. A distinction is made between three groups of genes involved in the defense of plants to diseases: those that serve exclusively to mediate resistance; those that are mobilized to strengthen the plants' defense; and those that serve exclusively functions other than disease defense, but may bring about resistance. The more than 200 gene symbols assigned to race-specific mildew resistance genes over time are summarized and revised to 85 symbols that may be considered valid.     

Regulation of the Escherichia coli rrnB P2 promoter

The seven rRNA operons in Escherichia coli each contain two promoters, rrn P1 and rrn P2. Most previous studies have focused on the rrn P1 promoters. Here we report a systematic analysis of the activity and regulation of the rrnB P2 promoter in order to define the intrinsic properties of rrn P2 promoters and to understand better their contributions to rRNA synthesis when they are in their natural setting downstream of rrn P1 promoters. In contrast to the conclusions reached in some previous studies, we find that rrnB P2 is regulated: it displays clear responses to amino acid availability (stringent control), rRNA gene dose (feedback control), and changes in growth rate (growth rate-dependent control). Stringent control of rrnB P2 requires the alarmone ppGpp, but growth rate-dependent control of rrnB P2 does not require ppGpp. The rrnB P2 core promoter sequence (-37 to +7) is sufficient to serve as the target for growth rate-dependent regulation.     

Regulation of β-1,4-Endoglucanase Synthesis in Thermomonospora fusca

In Thermomonospora fusca YX, endocellulase synthesis varies over a 100-fold range depending on the carbon source used. This study shows that the variation is caused by two regulatory mechanisms: an induction mechanism that increases the rate of endocellulase synthesis about 20-fold and a growth rate-dependent repression mechanism that changes the rate of synthesis over a 6-fold range in both induced and noninduced cells. In T. fusca, endocellulase synthesis can be induced by cellulose, cellobiose, or cellodextrin. Cellulase is involved in inducer generation from cellulose. Growth rate-dependent repression can be reversed by limiting cultures for carbon, nitrogen, or, to a lesser extent, phosphorus. Further evidence for two separate regulatory mechanisms is provided by the isolation of mutants (CC-1 and CC-2) whose endocellulases are synthesized constitutively but are still sensitive to growth rate-dependent repression. These conclusions about total endocellulase synthesis were extended to the individual endocellulases by showing that three T. fusca endocellulases are coordinately regulated.     

Measuring coral reef community metabolism using new benthic chamber technology

Accurate measurement of coral reef community metabolism is a necessity for process monitoring and in situ experimentation on coral reef health. Traditional methodologies used for these measurements are effective but limited by location and scale constraints. We present field trial results for a new benthic chamber system called the Submersible Habitat for Analyzing Reef Quality (SHARQ). This large, portable incubation system enables in situ measurement and experimentation on community-scale metabolism. Rates of photosynthesis, respiration, and calcification were measured using the SHARQ for a variety of coral reef substrate types on the reef flat of South Molokai, Hawaii, and in Biscayne National Park, Florida. Values for daily gross production, 24-h respiration, and net calcification ranged from 0.26 to 6.45 g O₂ m^–2 day^–1, 1.96 to 8.10 g O₂ m^–2 24 h^–1, and 0.02 to 2.0 g CaCO₃ m^–2 day^–1, respectively, for all substrate types. Field trials indicate that the SHARQ incubation chamber is an effective tool for in situ isolation of a water mass over a variety of benthic substrate types for process monitoring, experimentation, and other applications.     

WildSpan: mining structured motifs from protein sequences

Background  

Automatic extraction of motifs from biological sequences is an important research problem in study of molecular biology. For proteins, it is desired to discover sequence motifs containing a large number of wildcard symbols, as the residues associated with functional sites are usually largely separated in sequences. Discovering such patterns is time-consuming because abundant combinations exist when long gaps (a gap consists of one or more successive wildcards) are considered. Mining algorithms often employ constraints to narrow down the search space in order to increase efficiency. However, improper constraint models might degrade the sensitivity and specificity of the motifs discovered by computational methods. We previously proposed a new constraint model to handle large wildcard regions for discovering functional motifs of proteins. The patterns that satisfy the proposed constraint model are called W-patterns. A W-pattern is a structured motif that groups motif symbols into pattern blocks interleaved with large irregular gaps. Considering large gaps reflects the fact that functional residues are not always from a single region of protein sequences, and restricting motif symbols into clusters corresponds to the observation that short motifs are frequently present within protein families. To efficiently discover W-patterns for large-scale sequence annotation and function prediction, this paper first formally introduces the problem to solve and proposes an algorithm named WildSpan (sequential pattern mining across large wildcard regions) that incorporates several pruning strategies to largely reduce the mining cost.     

Development and mechanistic explanation

Within modern philosophy of biology the topic of mechanistic explanation has become a central theme for critical discussion. The neo-mechanical philosophers have developed accounts that emphasize intervention and manipulation as the central epistemic tools that allow gaining epistemic access upon the mechanisms and have argued that the processes of inter-field integration across disciplines can be understood through the analysis of mechanisms spanning multiple levels. In this paper I revisit current proposals on mechanistic explanation in order to show some of their limitations when dealing with developmental mechanisms. I basically argue that (i) developmental mechanisms cannot be accommodated within a framework centered upon the mutual manipulation principle, (ii) the distinction between causal relations vs. constitutive relations cannot be easily demarcated within developmental biology and (iii) the notion of "part" underlying the neo-mechanical accounts on explanation is not suitable for developmental biology.     

Early response of Abies balsamea seedlings to artificially created openings

Abstract. Small-scale canopy openings are being increasingly recognized for their importance in boreal forest stand development. Yet more work is necessary to understand their effects on seedling growth. This study investigated the effect of different degrees of canopy opening (all trees cut, conifers cut, conifers girdled and control quadrats) in different stand types on Abies balsamea seedling recruitment, growth and architecture. The lack of a treatment effect on seedling establishment suggests that gaps primarily affect advance regeneration. In the first year after treatment the seedlings in the cut blocks (both conifer cut and all trees cut) responded with an increase in height growth. Changes in the leader to lateral branch ratio were also significant. Continued architectural change in terms of number of branches produced did not occur until after two years had passed. Although not significantly different from the control, increases can be observed in all measurements for the girdled treatment. It is therefore concluded that the growth response of advance regeneration is more important following canopy opening than new seedling recruitment and that seedling performance is greatest where degree of opening is greatest.     

Propagating aleatory and epistemic uncertainty in land cover change prediction process

An objective of satellite remote sensing is to predict or characterize the land cover change (LCC) over time. Sometimes we are capable of describing the changes of land cover with a probability distribution. However, we need sufficient knowledge about the natural variability of these changes, which is not always possible. In general, uncertainties can be subdivided into aleatory and epistemic. The main problem is that classical probability theory does not make a clear distinction between aleatory and epistemic uncertainties in the way they are represented, i.e., both of them are described with a probability distribution. The aim of this paper is to propagate the aleatory and epistemic uncertainty associated with both input parameters (features extracted from satellite image object) and model structure of LCC prediction process using belief function theory. This will help reducing in a significant way the uncertainty about future changes of land cover. In this study, the changes prediction of land cover in Cairo region, Egypt for next 16 years (2030) is anticipated using multi-temporal Landsat TM5 satellite images in 1987 and 2014. The LCC prediction model results indicated that 15% of the agriculture and 6.5% of the desert will be urbanized in 2030. We conclude that our method based on belief function theory has a potential to reduce uncertainty and improve the prediction accuracy and is applicable in LCC analysis.