Thermodynamic characteristics of a biological organism: Information value of a gene and of a protein as a measure of the efficiency and as an index of selective pressure

Summary For the treatment of the information exchanged by the biological system and the external world, the concept of information amount is not sufficient because of their remoteness from equilibrium states. Further explanations are, in fact, necessary about the effects of the reception of the message,i.e. its information value that is then necessary to define for each case. We have, therefore, defined the information value of a gene and of a protein and analysed a sample of about hundred genes looking for some significative regularity in the frequency of usage of codons and amino acids allowing us to individualize the salient characteristics of a translated sequence of codons. We have found that the most used amino acids have, on the average, a low information value and, for each amino acid type, the most used codons have a lower information value. Moreover, we can say that the composition in amino acids or in codons of a sequence useful for the biological systems is such that more frequent mutations cause the smaller variation in the phenotype. All that shows that our definitions well describe the system of transmission and reception of the information value in a biological organism and that they can be considered as an index of its efficiency,i.e. of its ability to minimize the effects of the mutation of the genotype on the phenotype. To speed up publication, the authors of this paper have agreed to not receive the proofs for correction.     

Thermodynamic optimality in some biochemical reactions

Summary In this short communication we discuss the possibility that anaerobic glycolisis and (aerobic) respiration, both for adenosine triphosphate (ATP) production, be chemical reactions that follow different thermodynamic-optimization criteria. The former reaction maximizing power output and the latter maximizing a function that represents an advantageous compromise between high power output and low entropy production. Our approach is by means of finite-time thermodynamics (FTT).     

Information value and information content in the evolutionary strategy of the genetic code

Summary In previous papers we defined the information value of a genetic code as a measure of its efficiency in the utilization of the information stored in the DNA molecule. Here the genetic codes which have been proposed to be intermediate steps in evolution are analysed in terms of information theory. The results show that evolution follows an optimization strategy between increasing the information content and decreasing the information value,i.e. in each evolutionary step the average information value per unitary information content decreases and at the same time the probability of nonsense mutations goes down as the code evolves. To speed up publication, the authors of this paper have agreed to not recive the proofs for correction.     

Chaotic dynamics in biological information processing: A heuristic outline

Summary A given but otherwise random environmental time series impinging on the input of a certain biological processor passes through with overwhelming probability practically undetected. A very small percentage of environmental stimuli, though, is ?captured? by the processor's nonlinear dissipative operator asinitial conditions, that is, assolutions of the processor's dissipative dynamics. The processor, then, is in such cases instrumental in compressing or abstracting those stimuli, thereby making the external world to collapse from a previous regime of a ?pure state? of suspended animation onto a set of stable eigenfunctions or ?categories?—chaotic strange attractors. The characteristics of this cognitive set depend on the operator involved and the hierarchical level where the abstraction takes place. In this paper we model the physics of such a cognitive process and the role that the thalamo-cortical pacemaker of the (human) brain plays in both stimulating the individual attractors and permutating them on a time division multiplexing basis. A synthesis of the Markovian processes taking place within each individual attractor-memory and the Markovian or semi-Markovian process involving the intermittent jumping among the different attractor-memories are discussed.

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Riassunto Una data ma casuale serie temporale ambientale che influisce sull'immissione di un determinato processore biologico passa con schiacciante probabilità praticamente inosservata. Una piccolissima percentuale di stimoli ambientali, tuttavia, è catturata dall'operatore dissipativo non lineare del processore comecondizioni iniziali, cioè comesoluzioni della dinamica dissipativa del processore. Il processore è quindi, in tali casi, strumentale nel comprimere o estrarre quegli stimoli, facendo perciò collassare il mondo esterno da un precedente regime di ?stato puro? ad animazione sospesa ad un gruppo di autofunzioni stabili o ?categorie?—attrattori caotici strani. Le caratteristiche di questo gruppo cognitivo dipendono dall'operatore coinvolto e dal livello gerarchico in cui l'estrazione ha luogo. In questo lavoro si modella la fisica di tale processo cognitivo e il ruolo che lo stimolatore talamo-corticale del cervello (umano) ha sia nello stimolare gli attrattori individuali che nel permutarli su una base che manda segnali multiplex a divisione temporale. Si discute una sintesi dei processi markoviani che hanno luogo all'interno di ogni attrattore-memoria individuale e il processo markoviano o semimarkoviano che interessa il salto intermittente tra i diversi attrattori-memoria.

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Резюме Временная последовательность на входе некоторого биологического процессора может иметь практически недетектируемую вероятность. Очень небольшой процент стимулов окружающей среды ?захватывается? нелинейным диссипативным оператором процессора как начальные условия, т.е. представляется как решение диссипативпой динамики процессора. Затем процессор обрабатывает внешние стимулы, вынуждая внешний мир коллапсировать из предыдущего режима ?чистого состояния? приостановленного оживления в систему собственных функций или ?категорий?. Характеристики зтой познавательной системы зависят от используемого оператора и иерархического уровня, на котором происходит абстрагирование. В зтой статье мы моделируем физику такого познавательного процесса. Обсуждается синтез марковских процессов, происходящий внутри отдельного злемента ?атрактор-память?, и марковский или полумарковский процесс, включающий пережежающиеся прыжки между различными злементами ?атракторпамять?.

     

Isotopic dimension in biology—A counterpart for quantum indeterminism?

Summary We suggest that the random distribution of stable isotopes may act as a contributing factor towards unpredictability and irreproducibility in living systems. In this respect isotopic randomness could act as a counterpart or competitor of the ?standard? quantum-mech cal indeterminism.     

Statistical and linguistic features of noncoding DNA: A heterogeneous «Complex system»

Summary We present evidence supporting the idea that the DNA sequence in genes containingnoncoding regions is correlated, and that the correlation is remarkably long range-indeed, base pairsthousands of base pairs distant are correlated. We do not find such a long-range correlation in the coding regions of the gene; we utilize this fact to build aCoding Sequence Finder algorithm, which uses statistical ideas to locate the coding regions of an unknown DNA sequence. We resolve the problem of the ?non-stationarity? feature of the sequence of base pairs (that the relative concentration of purines and pyrimidines changes in different regions of the mosaic-like chain) by describing a new algorithm calledDetrended Fluctuation Analysis (DFA). We address the claim of Voss that there is no difference in the statistical properties of coding and noncoding regions of DNA by systematically applying the DFA algorithm, as well as standard FFT analysis, to every DNA sequence (33 301 coding and 29 453 non-coding) in the entire GenBank database. We describe a simple model to account for the presence of long-range power law correlations (and the systematic variation of the scaling exponent α with evolution) which is based upon a generalization of the classic Lévy walk. Finally, we describe briefly some recent work showing that thenoncoding sequences have certain statistical features in common with natural languages. Specifically, we adapt to DNA the Zipf approach to analyzing linguistic texts, and the Shannon approach to quantifying the ?redundancy? of a linguistic text in terms of a measurable entropy function. We suggest that noncoding regions in eukaryotes may display a smaller entropy and larger redundancy than coding regions for plants and invertebrates, further supporting the possibility that noncoding regions of DNA may carry biological information. Paper presented at the I International Conference on Scaling Concepts and Complex Fluids, Copanello, Italy, July 4–8, 1994.     

Formulation and solution of the classical seashell problem

Summary Despite an extensive scholarly literature dating back to classical times, seashell geometries have hitherto resisted rigorous theoretical analysis, leaving applied scientists to adopt a directionless empirical approach toward classification. The voluminousness of recent palaeontological literature demonstrates the importance of this problem to applied scientists, but in no way reflects corresponding conceptual or theoretical advances beyond the XIX century thinking which was so ably summarized by Sir D’Arcy Wentworh Thompson in 1917. However, in this foundation paper for the newly emerging science of theoretical conchology, unifying theoretical considerations for the first time, permits a rigorous formulation and a complete solution of the problem of biological shell geometries. Shell coilingabout the axis of symmetry can be deduced from first principles using energy considerations associated with incremental growth. The present paper shows that those shell apertures which are incurved (?cowrielike?), outflared (?stromblike?) or even backturned (?Opisthostomoidal?) are merely special cases of a much broader spectrum of ?allowable? energy-efficient growth trajectories (tensile elastic clockspring spirals), many of which were widely used by Cretaceous ammonites. Energy considerations also dictate shell growthalong the axis of symmetry, thus seashell spires can be understood in terms of certain special figures of revolution (M?bius elastic conoids), the better-known coeloconoidal and cyrtoconoidal shell spires being only two special cases arising from a whole class of topologically possible, energy efficient and biologically observed geometries. The ?wires? and ?conoids? of the present paper are instructive conceptual simplifications sufficient for present purposes. A second paper will later deal with generalized tubular surfaces in three dimensions.

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Riassunto Malgrado un’ampia e dotta letteratura che risale ai tempi classici, la geometria delle conchiglie ha resistito fino ad ora ad analisi teoriche rigorose, quindi gli scienziati che si cimentano in questo campo hanno adottato un metodo empirico senza direttiva per quanto riguarda la classificazione. L’abbondanza della recente letteratura paleontologica dimostra l’importanza di questo problema per gli scienziati di questo campo, ma non riflette in alcun modo i corrispondenti progressi concettuali o teorici rispetto al pensiero del diciannovesimo secolo che venne cosí abilmente riassunto da Sir D’Arcy Wentworth Thompson nel 1917. Tuttavia, in questo lavoro fondamentale per la nuova scienza emergente di conchigliologia teorica, l’unificazione delle considerazioni teoriche permette una rigorosa formulazione e una completa soluzione del problema della geometria biologica delle conchiglie. L’avvolgimento delle conchiglieintorno all’asse di simmetria si deduce dai primi princípi usando considerazioni sull’energia associata alla crescita per aumento di dimensioni. Questo lavoro mostra che le aperture delle conchiglie che sono incurvate (di tipo ?cowrie?), allargate verso l’esterno (di tipo ?strombe?) o anche rivoltate all’indietro (di tipo ?opistostomoideo?) sono solamente casi speciali di uno spettro piú ampio di traiettorie di crescita efficienti d’energia ?permesse? (spirali tensili, elastiche a molla d’orologio), molte delle quali vennero estesamente usate dagli ammoniti del Cretaceo. Considerazioni d’energia dettano anche la crescita della conchiglialungo l’asse di simmetria, cosí le spirali delle conchiglie marine possono essere comprese nei termini di certe speciali figure di rivoluzione (conoidi elastici di M?bius), essendo i gusci meglio conosciuti delle conchiglie coeloconoidali e cyrtoconoidali soltanto due casi speciali che derivano da una intera classe di geometria topologicamente possibili, efficienti di energia e biologicamente osservate. I ?fili? e i ?conoidi? di questo lavoro sono istruttive semplificazioni concettuali sufficienti a questo scopo. Un secondo lavoro tratterà successivamente superfici tubolari generalizzate in tre dimensioni.

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Резюме Несмотря на большое количество литературы, до настоящего времени отсутствует строгий теоретический анализ геометрией морских раковин. Многотомность существующей палеонтологической литературы демонстрирует важность этой проблемы для прикладных ученых ине отражает соответствующих концептуальных и теоретических достижений после XIX века, которые были систематизированы Томсоном в 1917 г. Однако в этой фундаментальной работе по теоретической конхиологии были объединены теоретические рассмотрения, которые впервые позволили сформулировать и полностью решить проблему биологических геометрий морских раковин. Свертывание раковин спиралью вокруг оси симметрии можно получить из первых принципов, используя энергетические рассуждения, связанные с дифференциальным ростом. В настоящей статье показывается, что те отверстия раковин, которые являются искривленными, в форме раструба, или даже повернутыми назад, представляют просто частные случаи более широкого спектра ?разрешенных? траекторий роста. Энергетические рассуждения ткаже диктуют рост раковин вдоль оси симметрии, тонкое острие морских раковин можно понять в терминах некоторых специальных фигур вращения. ?Провода? и ?коноиды? настоящей статьи представляют поучительные концептуальные упрощения, достаточные для наших целей. Вторая статья будет посвящена трубчатым поверхностям в трех измерениях.

     

On the formation of dissipative spatial patterns of charge carriers in biosystems

Summary It is shown that in systems like large aggregates of biological molecules, population inversion of charge carriers, for example as produced by photoexcitation processes, may have competitive advantage beyond critical levels of excitation to produce ordered spatial structures (morphological transitions). In our analysis electromagnetic radiation transfers electrons from bonding states into a continuum of itinerant antibonding states in ap-type doped sample. In this system, in which energy is pumped continuously by an external source, the interplay of collective and dissipative processes can be responsible for the condensation of a self-organized spatially ordered structure. The study we present here is carried out resorting to the powerful nonequilibrium statistical operator method, thus showing that it can be provide a mechano-statistical formalism at the microscopic level for the treatment of Prigogine's synergetic dissipative structures. The authors of this paper have agreed to not receive the proofs for correction     

Hypothesis on the function of non-coding DNA and hnRNA

Summary Half-way through what North American scientists have nominated the ?Decade of the Brain?, the author brings to lights a completely new approach to the problem of the function of non-coding DNA and heterogeneous nuclear RNA whose role, for the moment, remains unknown. This allows the author to put forward an innovative hypothesis on intelligence and memory within the framework of a more logical and coherent unitarian vision of the structure and evolution of living things. The conjecture put forward in this paper, while plausible, has no experimental support. The Referees have expressed perplexity on this regard. Anyway, the Direction ofIl Nuovo Cimento considers it worthwhile to expose the readers to the challenge of this conjecture, hoping that it may trigger a lively debate. The author of this paper has agreed to not receive the proofs for correction.     

Chaotic dynamics of generating markov partitions and linguistic sequences mimicking Zipf’s law

Summary A chaotic dynamics model of creating Markovian strings of symbols as well as sequences of words is presented, and its possible relevance to Zipf’s law is discussed. Comparison from contemporary Greek prose as well as nucleotide sequences (strings) of mRNA Polymerase III and embryonic cDNA displaying a quasi-Zipf’s law behaviour is made. The order of generated Markovian strings as well as the information transferred between two symbolst steps apart (the ?transinformation?) is also estimated.

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Riassunto Si presenta un modello di dinamica caotica di creazione di stringhe markoviane di simboli, nonché di sequenze di parole e la sua attinenza alla legge di Zipf. Si fa un confronto dalla prosa greca contemporanea e da sequenze (stringhe) di nucleotidi di mRNA polimerasi III e cDNA embrionico che mostra un comportamento della legge di quasi-Zipf. Si calcola anche l’ordine delle stringhe markoviane generate e l’informazione trasferita tra due simboli spostati di passit (la ?transinformazione?).

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Резюме Предлагается модель хаотической динамики для образующихся Марковских цепочек символов, а также последовательностей слов. Обсуждается связь этой модели с законом Эипфа. Проводится сравнение с современнной греческой прозой, а также с последовательностями (цепочками) нуклеотидов mRNA полимеразы III и эмбриональных cDNA, обнаруживающих поведение, соответствующее закону квази-Эипфа. Определяется порядок образующихся Марковских цепочек, а также информация передаваемая на расстоянииt шагов между двумя символами.

     

On the kinks and dynamical phase transitions of α-helix protein chains

Summary Heuristic insights into a physical picture of Davydov's solitonic model of the one-dimensional protein chain are presented supporting the idea of a non-equilibrium competition between the Davydov phase and a complementary, dynamical-?ferroelectric? phase along the chain. The author of this paper has agreed to not receive the proofs for correction     

Chaos in nonlinear paradoxical games

Summary Paradoxical games are nonconstant sum conflicts, where individual and collective rationalities are at variance and refer to a dyadic antagonism where the contestants blackmail each other. The state space dynamics of a class of such games has been previously studied in the planar case of two variablesx ₁,x ₂ (representing the propensities of the two parties to cooperate), for which phase space portraits have been obtained for a wide range of control parameters. In this paper, we extend the analysis to 3 dimensions, by allowing two of these parameters (the so-called ?tempting factors?) to oscillate in time. We observe on a Poincaré surface of section that the invariant manifolds of twounstable fixed pointsU ₁ andU ₁ intersect, and form heteroclinic and homoclinic orbits. Thus, sufficiently close toU ₁ andU ₂, one finds ?horseshoe? chaos and extremely sensitive dependence to initial conditions. Moreover, since the equations of motion can be written in Hamiltonian form, all the known phenomena of periodic, quasi-periodic and chaotic orbits can be observed around twostable fixed points, where the two parties become ?deadlocked? in an inconclusive exchange that never ends. To speed up publication, the authors of this paper have agreed to not receive the proofs for correction.     

Isotopic biology

Summary A model of genetic code based on isotopic combinations of a single chemical element is discussed as a possible alternative to the ?usual? heteroatomic biology.

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Riassunto Si discute un modello di codice genetico basato su combinazioni isotopiche di un singolo elemento chimico come possibile alternativa all' ?usuale? biologia eteroatomica.

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Резюме Обсуждена модель генетического кода основанная на изотопических комбинациях одного и того же химического злемента. Данная модель представляет собой альтернативу ?обычной? гетероатомной биологии.

     

Stochastic resonance in perspective

Summary We outline the historical development of stochastic resonance (SR), a phenomenon in which the signal and/or the signal-to-noise ratio in a nonlinear system increase with increasing intensity of noise. We discuss basic theoretical ideas explaining and describing SR, and we review some revealing experimental data that place SR within the wider context of statistical physics. We emphasize the close relationship of SR to some effects that are well known in condensed-matter physics. Paper presented at the International Workshop ?Fluctuations in Physics and Biology: Stochastic Resonance, Signal Processing and Related Phenomena?, Elba, 5–10 June 1994.     

Energetics of social phenomena: Physics applied to evolutionary biology

Summary The potential usefulness of applications of two physical concepts to evolutionary biology was evaluated on ant societies. The optimization principle, which predicts a more efficient use of energy by more sophisticated societies, was contrasted to that of irreversible thermodynamics, predicting an increase in orderliness and thus an increase in energy consumption per unit of biomass. Our results on oxygen consumption measurements of ant colonies showed a complex and non-linear relationship between colony size and energy consumption per unit mass, that can be explained by irreversible thermodynamics and catastrophe theory, whereas an additional exponential inverse relationship may be explained by optimization principles. Thus, social complexity is related to energy consumption in a discontinuous manner, and seems to be bound by both negentropy content of a society and social-optimization mechanisms.     

A method to evaluate the relative weights of structural and functional constraints on a genome

Summary A method that numerically evaluates the relative influence of structural or functional constraints on the codon composition of a gene is presented. The method applies to any constraint provided that it can be translated intoa priori probability table of codon usage. The method is very easy to apply to different constraints and to different pools of sequences. Theoretical codon usage obtained from a linear combination of the various constraints was compared with experimental codon frequencies of several classes of genes taxonomically homogeneous and, applying a minimization tecnique, the relative weights of the examined constraints have been evaluated. The results show that a common strategy exists for all coding sequences even though most of the constraints are represented by different probability tables for different pools of genes. We also demonstrate that the method is reliable when it is applied to a single gene, so that it can also be used as a tool to predict the characteristics of a gene from its sequence.     

Computer simulation of water-plastocyanin interaction energy

Summary We have used a computer simulation method to calculate the interaction energy between water and a copper-containing protein, plastocyanin. The isoenergy maps obtained provide useful information on the hydration layer around the biomolecule. This method, furthermore, also leads to an estimation (6.4 ?) of the distance between the Cu²⁺ ion bound to plastocyanin and the nearest water molecule; on this basis we could rule out the possibility of the direct accessibility of water to the Cu²⁺ ion.

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Riassunto Si è usato un metodo di simulazione al calcolatore per calcolare l'energia d'interazione fra l'acqua ed una proteina contenente rame, la plastocianina. Le mappe iso-energetiche che ottenute forniscono informazioni utili sullo strato d'idratazione della biomolecola. Il metodo ha inoltre portato ad una stima (6.4 ?) della distanza fra lo ione Cu²⁺ legato alla plastocianina e la molecola d'acqua piú vicina; sulla base di questo risultato si esclude la possibilità di una diretta accessibilità dello ione Cu²⁺ all'acqua.

     

A lattice gas model for enzyme kinetics (a correlated walks' theory and variational procedures)

Summary We have shown that, by using a correlated walks' theory or variational procedures, for the lattice gas model we can find for enzyme kinetics some new equations, which in the limit of no interactions between sites reduce to the classical Michaelis-Henri equation. These new equations can be useful for the experimental investigation.