[Form structure and shape correspondence; a methodological treatise on the biological concept of wholeness].
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Biological Evolution↗
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[Possibilities of the future evolution of mankind from the biological viewpoint].
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Biological Evolution↗
Generic criticality in a model of evolution
Using Monte Carlo simulations, we show that for a certain model of biological evolution, which is driven by nonextremal dynamics, active and absorbing phases are separated by a critical phase. In this phase both the density of active sites rho(t) and the survival probability of spreading P(t) decay as t(-delta), where delta approximately 0.5. At the critical point that separates the active and critical phases delta approximately 0.29, which suggests that this point belongs to the so-called parity-conserving universality class. Such a classification is also supported by finite-size analysis. The model has infinitely many absorbing states and, except for a single point, has no apparent conservation law.
Journal Article↗
The evolution of treatment resistance: biologic implications.
The evolution of resistance of positive symptoms to antipsychotic therapy may represent a valuable means of subtyping schizophrenia. In contrast, resistance of negative symptoms and cognitive function to antipsychotic agents seems to be present from the first episode of psychotic symptoms and does not evolve over time to the same extent. If these findings are validated, this clearly points toward differences in the etiology of these components of schizophrenia. Data from a cohort of 223 patients with unsatisfactory responses to classical antipsychotic therapy are evaluated, at least 60% of whom responded to subsequent treatment with clozapine. Comparisons were made between the subgroups of patients with primary and delayed onset treatment resistance. Both subgroups responded to clozapine therapy, although better response was evident for patients with delayed resistance. The withdrawal of clozapine from patients who had previously been responsive to classical antipsychotic therapy was capable of inducing treatment resistance.
Antipsychotic Agents↗
[Nature of the optimum DNA code].
It is shown that the four-letter code of the messenger DNA sequences is optimal in the sense that it provides minimal volume of the total information < < stuffing > > of the cell. The optimal code holds true only for the simplest DNA. This fact is indirect evidence that these very DNAs were the object of < < construction > > at earlier stages of biological evolution.
DNA↗
Biological externalities and evolution: a comment.
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Animals↗
Search for optimal frequencies and amplitudes of therapeutic electrical carotid sinus nerve stimulation by application of the evolution strategy.
In humans, electrical, bipolar, bilateral carotid sinus nerve stimulation (CSNS; impulse duration 0.35 ms) was applied, using frequencies between 10 and 110 Hz and voltages between individual thresholds and maximal amplitudes of stimulation. Ten anginal patients and two hypertensive patients were studied at an interval of up to 12 years after implantation of electrodes and a radiofrequency receiver for chronic therapeutic CSNS. In search of combinations of frequency and voltage of CSNS, eliciting largest ("optimal") depressor responses of blood pressure and heart rate in the individual patient, Rechenberg's evolution strategy was applied. This strategy simulates mutation and selection of biological evolution. In each patient and on each test stimulation, a value of quality was computed from actual heart rate and blood pressure values as a selection criterion for the strategy. Either responses to uninterrupted CSNS were investigated, while stimulation parameters were adjusted every 3 min, according to the strategy, or responses to 3 min of CSNS after a change in stimulation parameters were compared to intercalated 3-min control periods. In each patient, one or more combined settings of frequency and voltage elicited "optimal" responses. In principle, "optimal" CSNS frequencies ranged between 35 and 105 Hz with large interindividual differences. Due to chronic implantation of electrodes and technical features of radiofrequency transmitted stimulation energy, interindividually different voltages led to an optimal response to CSNS. Also according to the present results, the frequency of CSNS has to be determined individually. It is concluded that the evolution strategy was applied successfully, because voltage and frequency settings leading to "optimal" responses were found within 90-180 min, whereas intraindividual systematic investigations would not be feasible due to their necessarily very long duration. So far, only short-term responses have been evaluated. A broader use of the strategy in other applications is encouraged, as for example in pacemaker optimization and especially in functional electrostimulation.
Adult↗
Philosophic perspectives: community, communications, and occupational disease causation.
The caste in which workers and occupational health practitioners find themselves is plagued by intertwined but separable conflicts. A Cartesian model of causation, useful in the demonologies of regulation and toxic torts, is not heuristic in the revisions of health care, worker's compensation, and disability systems, nor in the prevention of violence in the workplace. Outside the caste, science progresses beyond mind-body bifurcations, the adverse effects of which are magnified within the caste. An argument is made for an ecological concept of causation, drawn from Darwin's community approach to the web of causal factors in both cultural and biological evolution, subsequently stimulated and developed by G. H. Mead and by biologically oriented and sociologically oriented human ecologists for application in the workplace. The ecological model is found in occupational biomedicine as practiced by leaders as diverse as Tichauer and Selikoff. The model integrates environmental, lifestyle, and genetic vectors in a community system bonded by communication and embracing a view of work unbifurcated from other activities.
Causality↗
The role of plasticity in biological and cultural evolution.
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Adaptation, Biological↗
Chemical evolution and the origin of life: cumulative keyword subject index 1970-1986.
This cumulative subject index encompasses the subject indexes of the bibliographies on Chemical Evolution and the Origin of Life that were first published in 1970 and have continued through publication of the 1986 bibliography supplement. Early bibliographies focused on experimental and theoretical material dealing directly with the concepts of chemical evolution and the origin of life, excluding the broader areas of exobiology, biological evolution, and geochemistry. In recent years, these broader subject areas have also been incorporated as they appear in literature searches relating to chemical evolution and the origin of life, although direct attempts have not been made to compile all of the citations in these broad areas. The keyword subject indexes have also undergone an analogous change in scope. Compilers of earlier bibliographies used the most specific term available in producing the subject index. Compilers of recent bibliographies have used a number of broad terms relating to the overall subject content of each citation and specific terms where appropriate. The subject indexes of these 17 bibliographies have, in general, been cumulatively compiled exactly as they originally appeared. However, some changes have been made in an attempt to correct errors, combine terms, and provide more meaningful terms.
Exobiology↗
In vivo karyotypic evolution with altered biological characteristics in a case of neuroblastoma.
Molecular and biological analyses of a neuroblastoma case in which the original tumor contained a nodular region are described. No significant difference was observed between the nodular and the surrounding tumor tissue with respect to histopathologic examination, N-myc amplification, and trkA expression. However, flow cytometric analysis demonstrated that the nodular region consisted of a hypertetraploid clone, whereas the surrounding tissue mostly contained a hyperdiploid clone. Chromosome analysis showed that each clone had a similar chromosome acquisition pattern, suggesting that the hypertetraploid cells of the nodular region arose from the hyperdiploid cells of the surrounding tissue. Moreover, primary culture findings of the tumor cells showed that the responses to nerve growth factor or retinoic acid were different between the two. Collectively, this case suggests the possibility that neuroblastoma acquires novel biological characteristics through karyotypic evolution in vivo.
Abdominal Neoplasms↗
Hexahydro-1,3,5-trinitro-1,3,5-triazine transformation by biologically reduced ferrihydrite: evolution of Fe mineralogy, surface area, and reaction rates.
Microbial respiration of Fe(III) oxides has been shown to produce reduced Fe phases that are capable of transforming a variety of oxidized contaminants. Little data, however, are available on how these Fe phases evolve over time and how this evolution may affect their ability to reduce contaminants. Here,the evolution and reactivity of biologically reduced ferrihydrite were monitored over a period of 14 months. Solids were collected from a culture of Geobacter metallireducens (GS-15) thatwas incubated with ferrihydrite (as the electron acceptor) for 0, 7, 10, 20, 75, and 400 days. Mineralogical composition and surface area of the biologically reduced solids were characterized using Mössbauer spectroscopy, X-ray diffraction, and BET with N2 adsorption. By day 10, ferrihydrite began to transform, and a nanoparticle magnetite/maghemite phase, as well as two ferrous phases, was observed. One of the ferrous phases was identified as siderite, whereas the other could not be positively identified. Likely candidates, however, include Fe(OH)2(s) or an adsorbed Fe(II) species. Over the next few months, ferrihydrite was completely reduced and evolved into a mixture containing about 70% magnetite/maghemite, 19% siderite, and 11% of the second Fe(II) phase. The effect of incubation time on the reactivity of the biologically reduced solids was evaluated by measuring the kinetics of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) transformation. The only products observed were the three reduced nitroso products. Rate coefficients (k) for RDX transformation were dramatically influenced by incubation time with half-lives of about 1 month observed in the presence of solids incubated for 10 and 20 days, 3 months with solids incubated for 75 days, and negligible removal with solids incubated for 400 days. The loss of reactivity was not directly correlated to any one mineralogical variable but may be due to particle size or surface chemistry changes in the reactive Fe phase or to cell die-off and the accumulation of cell lysis products after consumption of the electron acceptor. The dramatic effect of incubation time on the rate of RDX removal highlights a potential limitation of studying complex systems, as we have here, in batch reactors and suggests that incubation time is an important variable to consider when measuring and comparing rates of contaminant reduction.
Biotransformation↗
From cofactor to enzymes. The molecular evolution of pyridoxal-5'-phosphate-dependent enzymes.
The pyridoxal-5'-phosphate (vitamin B(6))-dependent enzymes that act on amino acid substrates have multiple evolutionary origins. Thus, the common mechanistic features of B(6) enzymes are not accidental historical traits but reflect evolutionary or chemical necessities. The B(6) enzymes belong to four independent evolutionary lineages of paralogous proteins, of which the alpha family (with aspartate aminotransferase as the prototype enzyme) is by far the largest and most diverse. The considerably smaller beta family (tryptophan synthase beta as the prototype enzyme) is structurally and functionally more homogenous. Both the D-alanine aminotransferase family and the alanine racemase family consist of only a few enzymes. The primordial pyridoxal-5'-phosphate-dependent protein catalysts apparently first diverged into reaction-specific protoenzymes, which then diverged further by specializing for substrate specificity. Aminotransferases as well as amino acid decarboxylases are found in two different evolutionary lineages, providing examples of convergent enzyme evolution. The functional specialization of most B(6) enzymes seems to have already occurred in the universal ancestor cell before the divergence of eukaryotes, archebacteria, and eubacteria 1500 million years ago. Pyridoxal-5'-phosphate must have emerged very early in biological evolution; conceivably, metal ions and organic cofactors were the first biological catalysts. To simulate particular steps of molecular evolution, both the substrate and reaction specificity of existent B(6) enzymes were changed by substitution of active-site residues, and monoclonal pyridoxal-5'-phosphate-dependent catalytic antibodies were produced with selection criteria that might have been operative in the evolution of protein-assisted pyridoxal catalysis.
Amino Acid Isomerases↗
Environmental consequences of impact cratering events as a function of ambient conditions on Earth.
The end of the Mesozoic Era is defined by a dramatic floral and faunal turnover that has been linked with the Chicxulub impact event, thus leading to the realization that impact cratering can affect both the geologic and biologic evolution of Earth. However, the environmental consequences of an impact event and any subsequent biological effects rely on several factors, including the ambient environmental conditions and the extant ecosystem structures at the time of impact. Some of the severest environmental perturbations of the Chicxulub impact event would not have been significant in some periods of Earth history. Consequently, the environmental and biological effects of an impact event must be evaluated in the context in which it occurs.
Air↗
Evolution was chemically constrained.
The objective of this paper is to present a systems view of the major features of biological evolution based upon changes in internal chemistry and uses of cellular space, both of which it will be stated were dependent on the changing chemical environment. The account concerns the major developments from prokaryotes to eukaryotes, to multi-cellular organisms, to animals with nervous systems and a brain, and finally to human beings and their uses of chemical elements in space outside themselves. It will be stated that the changes were in an inevitable progression, and were not just due to blind chance, so that "random searching" by a coded system to give species had a fixed overall route. The chemical sequence is from a reducing to an ever-increasingly oxidizing environment, while organisms retained reduced chemicals. The process was furthered recently by human beings who have also increased the range of reduced products trapped on Earth in novel forms. All the developments are brought about from the nature of the chemicals which organisms accumulate using the environment and its changes. The relationship to the manner in which particular species (gene sequences) were coincidentally changed, the molecular view of evolution, is left for additional examination. There is a further issue in that the changes of the chemistry of the environment developed largely at equilibrium due to the relatively fast reactions there of the available inorganic chemicals. Inside cells, some of these same chemicals also came to equilibrium within compounds. All such equilibria reduced the variance (degrees of freedom) of the total environmental/biological system and its possible development. However, the more sophisticated organic chemistry, almost totally inside cells until humans evolved, is kinetically controlled and limited by the demands of cellular reduction necessary to produce essential chemicals and by the availability of certain elements and energy. Hence the variability of reductive cellular organic chemistry and its limitations in cells have to be considered separately. While as a whole they drive the oxidation of the environment, they also allow speciation within the major changes of organisms. Human beings have introduced recently new, virtually irreversible, inorganic and organic chemistry in the environment, much of it new modes of irreversible storage of reduced chemicals, and this is, we state, the last possible step of chemical evolution. We must attempt to evaluate its effect on organisms generally. It must be clear that all the changes and the original life forms are dependent upon energy as well as material capture and flow. We shall have to consider in which forms energy was available over the period of evolution, how it was usefully transformed, and the ways in which its sources changed.
Animals↗
Gene duplication, the evolution of novel gene functions, and detecting functional divergence of duplicates in silico.
Duplication of genes increases the amount of genetic material on which evolution can work and has been considered of major importance for the development of biological novelties or to explain important transitions that have occurred during biological evolution. Recently, much research has been devoted to the study of the evolutionary and functional divergence of duplicated genes. Since the majority of genes are part of gene families, there is considerable interest in predicting differences in function between duplicates and assessing the functional redundancy of genes within gene families. In this review, we discuss the strengths and limitations of both older and novel approaches to investigate the evolution of duplicated genes in silico.
Algorithms↗
Epidemiology and the web of causation: has anyone seen the spider?
'Multiple causation' is the canon of contemporary epidemiology, and its metaphor and model is the 'web of causation.' First articulated in a 1960 U.S. epidemiology textbook, the 'web' remains a widely accepted but poorly elaborated model, reflecting in part the contemporary stress on epidemiologic methods over epidemiologic theories of disease causation. This essay discusses the origins, features, and problems of the 'web,' including its hidden reliance upon the framework of biomedical individualism to guide the choice of factors incorporated in the 'web.' Posing the question of the whereabouts of the putative 'spider,' the author examines several contemporary approaches to epidemiologic theory, including those which stress biological evolution and adaptation and those which emphasize the social production of disease. To better integrate biologic and social understandings of current and changing population patterns of health and disease, the essay proposes an ecosocial framework for developing epidemiologic theory. Features of this alternative approach are discussed, a preliminary image is offered, and debate is encouraged.
Causality↗
Stability of discrete memory states to stochastic fluctuations in neuronal systems.
Noise can degrade memories by causing transitions from one memory state to another. For any biological memory system to be useful, the time scale of such noise-induced transitions must be much longer than the required duration for memory retention. Using biophysically-realistic modeling, we consider two types of memory in the brain: short-term memories maintained by reverberating neuronal activity for a few seconds, and long-term memories maintained by a molecular switch for years. Both systems require persistence of (neuronal or molecular) activity self-sustained by an autocatalytic process and, we argue, that both have limited memory lifetimes because of significant fluctuations. We will first discuss a strongly recurrent cortical network model endowed with feedback loops, for short-term memory. Fluctuations are due to highly irregular spike firing, a salient characteristic of cortical neurons. Then, we will analyze a model for long-term memory, based on an autophosphorylation mechanism of calcium/calmodulin-dependent protein kinase II (CaMKII) molecules. There, fluctuations arise from the fact that there are only a small number of CaMKII molecules at each postsynaptic density (putative synaptic memory unit). Our results are twofold. First, we demonstrate analytically and computationally the exponential dependence of stability on the number of neurons in a self-excitatory network, and on the number of CaMKII proteins in a molecular switch. Second, for each of the two systems, we implement graded memory consisting of a group of bistable switches. For the neuronal network we report interesting ramping temporal dynamics as a result of sequentially switching an increasing number of discrete, bistable, units. The general observation of an exponential increase in memory stability with the system size leads to a trade-off between the robustness of memories (which increases with the size of each bistable unit) and the total amount of information storage (which decreases with increasing unit size), which may be optimized in the brain through biological evolution.
Action Potentials↗