An axiomatic explanation of complete self-reproduction

A similarity between the concepts of reproduction and explanation is observed which implies a similarity between the less well understood concepts of complete self-reproduction and complete self-explanation. These latter concepts are shown to be independent from ordinary logical-mathematical-biological reasoning, and a special form of complete self-reproduction is shown to be axiomatizable. Involved is the question whether there exists a function that belongs to its own domain or range. Previously, Wittgenstein has argued, on intuitive grounds, that no function can be its own argument. Similarly, Rosen has argued that a paradox is implied by the notion of a function which is a member of its own range. Our result shows that such functions indeed are independent from ordinary logical-mathematical reasoning, but that they need not imply any inconsistencies. Instead such functions can be axiomatized, and in this sense they really do exist. Finally, the introduced notion of complete self-reproduction is compared with “self-reproduction” of ordinary biological language. It is pointed out that complete self-reproduction is primarily of interest in connection with formal theories of evolution.     

Suggestion for a possible approach to molecular biology

A hypothetical “self-reproducing living molecule” has been recently frequently discussed in the literature. A physical theory of such a molecule is tentatively outlined. The relational, rather than the quantitative, aspects of the process are emphasized. The process of synthesis of such a molecule from its components is considered as a transition of a complex system between two quantum-mechanical states. The requirement that a “living molecule” should be able to multiply only by self-reproduction but not by a formationde novo leads to the conclusion that the above mentioned transition is a forbidden one. A constellation of conditions under which the forbiddenness is lifted by the presence of an already existing “living molecule” is suggested. The outlined mechanism leads to the conclusion that the property of self-reproduction does not so much reside in the self-reproducing molecule itself as in its relations to other molecules of a system.     

Theoretical Assessment of Public Health Impact of Imperfect Prophylactic HIV-1 Vaccines with Therapeutic Benefits

This paper presents a number of deterministic models for theoretically assessing the potential impact of an imperfect prophylactic HIV-1 vaccine that has five biological modes of action, namely “take,” “degree,” “duration,” “infectiousness,” and “progression,” and can lead to increased risky behavior. The models, which are of the form of systems of nonlinear differential equations, are constructed via a progressive refinement of a basic model to incorporate more realistic features of HIV pathogenesis and epidemiology such as staged progression, differential infectivity, and HIV transmission by AIDS patients. The models are analyzed to gain insights into the qualitative features of the associated equilibria. This allows the determination of important epidemiological thresholds such as the basic reproduction numbers and a measure for vaccine impact or efficacy. The key findings of the study include the following (i) if the vaccinated reproduction number is greater than unity, each of the models considered has a locally unstable disease-free equilibrium and a unique endemic equilibrium; (ii) owing to the vaccine-induced backward bifurcation in these models, the classical epidemiological requirement of vaccinated reproduction number being less than unity does not guarantee disease elimination in these models; (iii) an imperfect vaccine will reduce HIV prevalence and mortality if the reproduction number for a wholly vaccinated population is less than the corresponding reproduction number in the absence of vaccination; (iv) the expressions for the vaccine characteristics of the refined models take the same general structure as those of the basic model.     

Reactions chimiques couplees considerees en tant que filtres passe-bande

An investigation is made as to whether or not the existence of a band-pass filter function, analogous to that in electronics, can be proved from the fundamental laws of chemical kinetics. The problem is important for better understanding of the preference of certain biological rhythms to others. It is shown with simple examples that such behavior is possible for a number of systems of coupled chemical reactions far enough from the thermodynamic equilibrium. It is of interest to generalize this behavior since it could conceivably play a role in the transmission of “usable information” in biology.      

On the mathematical theory of rumor spread

The applicability of the theory of random nets to the theory of rumor spread is shown. In particular the “weak connectivity” of the net appears as the saturation fraction of “knowers” in a thoroughly mixed population through which a message diffuses where each knower tells the message to a finite average number of individuals. Further it is shown how the time course equation of rumor spread, where time is measured by the number of “removes” from the starters, can be translated into an ordinary continuous time course equation if the distribution of the telling intervals is known.     

Eradication of cross-contaminated cell lines: A call for action

This “white paper” was prepared and widely disseminated in an attempt to sound an alarm about the long-term existence of a grave, unresolved and growing problem that affects a significant portion of biomedical research, namely, the use of misidentified and cross-contaminated cell cultures. The “white paper” shows how bold action could bring about a profession-wide change in practice that would prevent further erosion. Misidentification and inter- and intra-specific cross-contamination of mammalian cell cultures used in research continues as a widespread problem despite an awareness that dates back more than 45 years. Awareness of the problem has led to a good understanding of the causes of cross-contamination and appropriate preventive measures. It has also led to the application of robust methods for the authentication of cell lines. Yet the problem continues unabated. Estimates of the incidence of research papers flawed by the use of misidentified and cross-contaminated cell cultures approximate 15–20%. The gravity of the situation calls for a strategy that would deliver a remedial message of authentication to virtually all cell culture researchers and also ensure compliance with the message. At the core of the strategy proposed herein is having cell line authentication as a condition for the award of research grants and for the publication of research findings.     

An exact method for the computation of the connectivity of random nets

The problem of finding the “weak connectivity” of a random net is reduced to one involving a Markov process. This provides a mathematically exact treatment of the problem which had previously been treated by an approximation, whose justification was not rigorous. The exact method allows in principle not only the calculation of the “weak connectivity”, but also of the “strong connectivity”, and, in general, the probability that from a randomly selected neuron in the net there exist paths to a specified number of neurons. The computations become exceedingly involved for large nets.     

Chain processes and their biophysical applications: Part I. General theory

A mathematical theory applicable to the biological effects of radiations as chain processes is developed. The theory may be interpreted substantially as a “hit theory” involving the concepts of “sensitive volume” or “target area”. The variability of the sensitivity of the organism to the radiation and its capacity of recovery between single hits is taken into account. It is shown that in a continuous irradiation of a biological aggregate in which the effect of each single hit cannot be observed, recovery and variation of sensitivity are formally equivalent to each other so that a discrimination between these two phenomena is possible only by discontinuous irradiation or by using different radiation intensities. Methods for the calculation of the “number of hits” and for the determination of the kinetics of the processes from “survival curves” or similar experimental data are given. The relation between the recovery and the Bunsen-Roscoe law is discussed. The case in which the injury of the organism is dependent on the destruction of more than one “sensitive volume” is also considered.     

Source-sink landscape theory and its ecological significance

Exploring the relationships between landscape pattern and ecological processes is the key topic of landscape ecology, for which, a large number of indices as well as landscape pattern analysis model were developed. However, one problem faced by landscape ecologists is that it is hard to link the landscape indices with a specific ecological process. Linking landscape pattern and ecological processes has become a challenge for landscape ecologists. “Source” and “sink” are common concepts used in air pollution research, by which the movement direction and pattern of different pollutants in air can be clearly identified. In fact, for any ecological process, the research can be considered as a balance between the source and the sink in space. Thus, the concepts of “source” and “sink” could be implemented to the research of landscape pattern and ecological processes. In this paper, a theory of sourcesink landscape was proposed, which include: (1) In the research of landscape pattern and ecological process, all landscape types can be divided into two groups, “source” landscape and “sink” landscape. “Source” landscape contributes positively to the ecological process, while “sink” landscape is unhelpful to the ecological process. (2) Both landscapes are recognized with regard to the specific ecological process. “Source” landscape in a target ecological process may change into a “sink” landscape as in another ecological process. Therefore, the ecological process should be determined before “source” or “sink” landscape were defined. (3) The key point to distinguish “source” landscape from “sink” landscape is to quantify the effect of landscape on ecological process. The positive effect is made by “source” landscape, and the negative effect by “sink” landscape. (4) For the same ecological process, the contribution of “source” landscapes may vary, and it is the same to the “sink” landscapes. It is required to determine the weight of each landscape type on ecological processes. (5) The sourcesink principle can be applied to non-point source pollution control, biologic diversity protection, urban heat island effect mitigation, etc. However, the landscape evaluation models need to be calibrated respectively, because different ecological processes correspond with different source-sink landscapes and evaluation models for the different study areas. This theory is helpful to further study landscape pattern and ecological process, and offers a basis for new landscape index design. __________ Translated from Acta Ecologica Sinica, 2006, 26(5): 1444–1449 [译自: 生态学报]     

Interactions among biological systems: An analysis of asymptotic stability

An analysis of the interactions among asymptotically stable dynamical systems is formulated by making use of the dynamical system theory. Some results coming from previous mathematical analyses have been slightly modified to take into account some typical biological constraints as the boundedness properties of the solutions. In particular it has been shown that when the “coupling” among the subsystems is “loose” enough (in a sense that has to be made mathematically precise) the asymptotic behaviour of a complex system is the same of that of its individual components. The mathematical theory has been used to analyze two systems of biological significance: the coupling among chemical reactions and the stability properties of a 4-dimensional system describing the kinetics of a chemical transmitter.     

Sexes,species, and genomes: why males and females are not like humans and chimpanzees

This paper describes, analyzes, and critiques the construction of separate “male” and “female” genomes in current human genome research. Comparative genomic work on human sex differences conceives of the sexes as like different species, with different genomes. I argue that this construct is empirically unsound, distortive to research, and ethically questionable. I propose a conceptual model of biological sex that clarifies the distinction between species and sexes as genetic classes. The dynamic interdependence of the sexes makes them “dyadic kinds” that are not like species, which are “individual kinds.” The concept of sex as a “dyadic kind” may be fruitful as a remedy to the tendency to conceive of the sexes as distinct, binary classes in biological research on sex more generally.     

J D Bernal (1901–1971) in perspective

Conclusion We must conclude that the sub-title of Bernal’s “The Social Function of Science” — “What science does: what science could do” is still the relevant challenge and indicates Bernal’s chief contribution, besides the foundation of molecular biology to our civilization. It is manifest that resources spent on armaments are a monstrous pathological symptom of our social structure. The ancient problem of “what is property” and what may be “owned” and by whom or by what organs of society is awakening.     

Circumscription of Malvaceae (Malvales) as determined by a preliminary cladistic analysis of morphological, anatomical, palynological, and chemical characters

We report a phylogenetic analysis of “core” Malvales (Tiliaceae, Sterculiaceae, Bombacaceae, and Malvaceae) based on morphological, anatomical, palynological, and chemical features. The results of the analyses lead to the conclusion that Tiliaceae, Sterculiaceae, and Bombacaceae, as variously delimited, are paraphyletic; only the Malvaceae are likely monophyletic. The genera of “core” Malvales form a well-defined clade. Genera of “Tiliaceae” constitute the basal complex within “core” Malvales. The “Sterculiaceae” (most genera)+ “Bombacaceae” + Malvaceae form a clade on the basis of a monadelphous androecium; “Bombacaceae”+ Malvaceae also form a clade, which is diagnosable on the basis of monoloculate anthers. It is clear that the traditional classification, with its arbitrarily delimited evolutionary grades, is unsatisfactory, especially if one seeks to reflect phylogeny accurately. Thus, Malvaceae is redefined to refer to the most recent common ancestor of plants previously considered to be “Tiliaceae,” “Sterculiaceae,” “Bombacaceae,” and Malvaceae, and all of the descendants of that ancestor. This broadly circumscribed Malvaceae can be diagnosed by several presumed synapomorphies, but we draw special attention to the unusual floral nectaries that are composed of densely packed, multicellular, glandular hairs on the sepals (or less commonly on the petals or androgynophore).     

Psychological Altruism Vs. Biological Altruism: Narrowing The Gap With The Baldwin Effect

This paper defends the position that the supposed gap between biological altruism and psychological altruism is not nearly as wide as some scholars (e.g., Elliott Sober) insist. Crucial to this defense is the use of James Mark Baldwin's concepts of “organic selection”and “social heredity” to assist in revealing that the gap between biological and psychological altruism is more of a small lacuna. Specifically, this paper argues that ontogenetic behavioral adjustments, which are crucial to individual survival and reproduction, are also crucial to species survival. In particular, it is argued that human psychological altruism is produced and maintained by various sorts of mimicry and self-reflection in the aid of both individual and species survival. The upshot of this analysis is that it is possible to offer an account of psychological altruism that is closelytethered to biological altruism without reducing entirely the former to thelatter.     

A “lookup table” schema for synthetic biological patterning

A schema is proposed by which the three-dimensional structure and temporal development of a biological organism might be encoded and implemented via a genetic “lookup table”. In the schema, diffusive morphogen gradients and/or the global concentration of a quickly diffusing signal index sets of kinase genes having promoters with logarithmically diminished affinity for the signal. Specificity of indexing is enhanced via concomitant expression of phosphatases undoing phosphorylation by “neighboring” kinases of greater affinity. Combinations of thus-selected kinases in turn jointly activate, via multiple phosphorylation, a particular enzyme from a virtual, multi-dimensional array thereof, at locations and times specified within the “lookup table”. In principle, such a scheme could be employed to specify arbitrary gross anatomy, surface pigmentation, and/or developmental sequencing, extending the burgeoning toolset of the nascent field of synthetic morphology. A model of two-dimensional surface coloration using this scheme is specified, and LabVIEW software for its exploration is described and made available.     

Regulatory considerations when developing biological products

The Center for Biologics Evaluation and Research, whose regulatory authority includes monoclonal antibodies, cytokines, vaccines, toxins and somatic cellular therapies, communicates to sponsors issues for consideration in the development of biological products through the publication of “Points to Consider” and “Guideline” documents. This paper summarizes the available “Points to Consider” and “Guideline” documents and outlines recommendations from these documents for characterizing the cells used to produce biological products.     

The advantages and disadvantages of being introduced

Introduced species, those dispersed outside their natural ranges by humans, now cause almost all biological invasions, i.e., entry of organisms into habitats with negative effects on organisms already there. Knowing whether introduction tends to give organisms specific ecological advantages or disadvantages in their new habitats could help understand and control invasions. Even if no specific species traits are associated with introduction, introduced species might out-compete native ones just because the pool of introduced species is very large (“global competition hypothesis”). Especially in the case of intentional introduction, high initial propagule pressure might further increase the chance of establishment, and repeated introductions from different source populations might increase the fitness of introduced species through hybridization. Intentional introduction screens species for usefulness to humans and so might select for rapid growth and reproduction or carry species to suitable habitats, all which could promote invasiveness. However, trade offs between growth and tolerance might make introduced species vulnerable to extreme climatic events and cause some invasions to be transient (“reckless invader hypothesis”). Unintentional introduction may screen for species associated with human-disturbed habitats, and human disturbance of their new habitats may make these species more invasive. Introduction and natural long-distance dispersal both imply that species have neither undergone adaptation in their new habitats nor been adapted to by other species there. These two characteristics are the basis for many well-known hypotheses about invasion, including the “biotic resistance”, “enemy release”, “evolution of increased competitive ability” and “novel weapon” hypotheses, each of which has been shown to help explain some invasions. To the extent that biotic resistance depends upon local adaption by native species, altering selection pressures could reduce resistance and promote invasion (“local adaptation hypothesis”), and restoring natural regimes could reverse this effect.     

Abstract mathematical molecular biology: II some relational consequences of the “one gene-one enzyme” hypothesis

Following the program outlined in a previous paper (Bull. Math. Biophysics,23, 237–260, 1961), a further abstract study is made of some simple relational systems which possess some properties of living organisms. It is shown that the “one gene-one enzyme” hypothesis leads to the conclusion that either all genes are built of the same chemical building blocks, or that at least all genes have a number of building blocks in common. A consistent relational application of the “one gene-one enzyme” hypothesis leads moreover to the conclusion that replication is not an inherent property of a gene. Rather there must be a set of enzymes which “copy” the genes. The number of enzymes in this set must be less than the number of genes and therefore the activity of those “copying” enzymes cannot be absolutely specific.     

Question 9: Prospects for the Construction of Artificial Cells or Protocells

The construction of artificial cells or protocells that are a simplified version of contemporary cells will have implications for both the understanding of the origins of cellular Life and the design of “cell-like” chemical factories. In this short communication, we discuss the progress and remaining issues related to the construction of protocells from metabolic products. We further outline the de novo design of a simple chemical system that mimics the functional properties of a living cell without being composed of molecules of biological origin, thereby addressing issues related to Life’s origins. Presented at: International School of Complexity—4th Course: Basic Questions on the Origins of Life; “Ettore Majorana” Foundation and Centre for Scientific Culture, Erice, Italy, 1–6 October 2006.     

Question 7: Biosynthesis of Phosphatidic Acid in Liposome Compartments – Toward the Self-Reproduction of Minimal Cells

Self-reproduction is one of main properties that define living cells. In order to explore the self-reproduction process for the study of early cells, and to develop a research line somehow connected to the origin of life, we have built up a constructive ‘synthetic cells (minimal cells)’ approach. The minimal cells approach consists in the investigation of the minimal number of elements to accomplish simple cell-like processes – like self-reproduction. Such approach belongs to the field of synthetic biology. The minimal cells are reconstructed from a totally reconstituted cell-free protein synthesis system (PURESYSTEM) and liposome compartments as containers. Based on this approach, we synthesized two membrane proteins (enzymes), GPAT and LPAAT, which are involved in the phosphatidic acid biosynthesis in bacteria. Both membrane proteins were successfully synthesized by PURESYSTEM encapsulated inside POPC liposomes. Additionally, the enzymatic activity of GPAT was restored by mixing the expressed enzyme with lipid and by forming liposomes in situ. Through these experimental evidences, here we present a possible model to achieve self-reproduction in minimal cells. Our results would contribute to the idea that early cells could have been built by an extremely small number of genes. Presented at the International School of Complexity – 4th Course: Basic Questions on the Origins of Life; “Ettore Majorana” Foundation and Centre for Scientific Culture, Erice, Italy, 1–6 October 2006.