Low birth weight, maternal birth-spacing decisions, and future reproduction

The aim of this study is an analysis of the possible adaptive consequences of delivery of low birth weight infants. We attempt to reveal the cost and benefit components of bearing small children, estimate the chance of the infants’ survival, and calculate the mothers’ reproductive success. According to life-history theory, under certain circumstances mothers can enhance their lifetime fitness by lowering the rate of investment in an infant and/or enhancing the rate of subsequent births. We assume that living in a risky environment and giving birth to a small infant may involve a shift from qualitative to quantitative production of offspring. Given high infant mortality rates, parents will have a reproductive interest in producing a relatively large number of children with a smaller amount of prenatal investment. This hypothesis was tested among 650 Gypsy and 717 non-Gypsy Hungarian mothers. Our study has revealed that 23.8% of the Gypsy mothers had low birth weight (<2,500 g) children, whose mortality rate is very high. These mothers also had more spontaneous abortions and stillbirths than those with normal weight children. As a possible response to these reproductive failures, they shortened birth spacing, gaining 2–4 years across their reproductive lifespan for having additional children. Because of the relatively short interbirth intervals, by the end of their fertility period, Gypsy mothers with one or two low birth weight infants have significantly more children than their ethnic Hungarian counterparts. They appear to compensate for handicaps associated with low birth weights by having a larger number of closely spaced children following the birth of one or more infants with a reduced probability of survival. The possible alternative explanations are discussed, and the long-term reproductive benefits are estimated for both ethnic groups.     

An Answer to Schrödinger’s What Is Life?

That semiosis is specific to the living world is the cornerstone of biosemiotics. For checking an information-theoretic interpretation of this statement already proposed at the 2009 Biosemiotics Gathering in Prague, it is first attempted here to answer a question asked by Kupiec and Sonigo in Ni Dieu ni Gène (2000) on what differentiates living objects and those resulting from a geophysical process. Similar questions were asked by Schr?dinger in his essay What Is Life? where the emphasis was laid on the relationship of the atomic scale of the genes and the macroscopic scale of living beings. This essay was published in 1944, before information was introduced as a scientific entity, at a time when DNA was not yet identified as the vector of heredity. We undertake answering some of these questions, arguing that the living world is made of organisms, i.e., of assemblies possessing in a genome the information needed for their replication and their maintenance while the inanimate world only contains aggregates. In short, a biological process keeps its order through the use of information. For defining order, it is proposed that an orderly object can be produced by a construction (e.g., the copy of a template) using available data within some given context. In other words, replicating an orderly object does not bring new information into its context. Order in this meaning appears as specific to the living world, at variance with the inanimate world which is basically disorderly. A better understanding of what separates the living world from the inanimate world results: the use of information is the distinguishing feature which defines their border. Any living thing contains a symbolic information, referred to as its genome, inscribed into DNA molecules. This genome can indeed be copied but, its support being embedded in the physical world, it incurs disturbances which result in symbol errors. Keeping its order thus needs endowing any genome with error correction ability: it must belong to a redundant code, i.e., a set of sequences separated by some minimum distance. The larger its minimum distance, the more immune to errors are the elements of a code. Then genomes become as distinct as to ensure order. Identity and specificity result. Although conservative according to the above definition of order, the living world actually exhibits an extreme diversity which even tends to increase as evolution proceeds. In sharp contrast, homogeneity and monotony are observed in the inanimate world, assumed however non-conservative. In order to solve this paradox and justify the proposed definition of order, it is argued that the error-correcting means which ensure the conservation of genomes fail with some low, but non-zero, probability. Although very infrequent, regeneration errors result in genomes largely different from the initial ones; and the correction mechanisms conserve the mutated genomes just as the original ones. The operation of life changes scales, since the regeneration errors which originate in atomic events have observable consequences at the macroscopic scale.     

Information dynamics in living systems: prokaryotes, eukaryotes, and cancer

Background

Living systems use information and energy to maintain stable entropy while far from thermodynamic equilibrium. The underlying first principles have not been established.

Findings

We propose that stable entropy in living systems, in the absence of thermodynamic equilibrium, requires an information extremum (maximum or minimum), which is invariant to first order perturbations. Proliferation and death represent key feedback mechanisms that promote stability even in a non-equilibrium state. A system moves to low or high information depending on its energy status, as the benefit of information in maintaining and increasing order is balanced against its energy cost. Prokaryotes, which lack specialized energy-producing organelles (mitochondria), are energy-limited and constrained to an information minimum. Acquisition of mitochondria is viewed as a critical evolutionary step that, by allowing eukaryotes to achieve a sufficiently high energy state, permitted a phase transition to an information maximum. This state, in contrast to the prokaryote minima, allowed evolution of complex, multicellular organisms. A special case is a malignant cell, which is modeled as a phase transition from a maximum to minimum information state. The minimum leads to a predicted power-law governing the in situ growth that is confirmed by studies measuring growth of small breast cancers.

Conclusions

We find living systems achieve a stable entropic state by maintaining an extreme level of information. The evolutionary divergence of prokaryotes and eukaryotes resulted from acquisition of specialized energy organelles that allowed transition from information minima to maxima, respectively. Carcinogenesis represents a reverse transition: of an information maximum to minimum. The progressive information loss is evident in accumulating mutations, disordered morphology, and functional decline characteristics of human cancers. The findings suggest energy restriction is a critical first step that triggers the genetic mutations that drive somatic evolution of the malignant phenotype.     

Origin and evolution of life and intellect from the point of view of information processing]

Beginning of life and intellect on the Earth is determined by the fact that synthesis of semantic information about algorithms of chemical transformation for appointed classes of chemical compounds is not accompanied by the information synthesis, but is controlled by chance in genetic material. Genetic information as memorizing accidental choice always arises as a result of the environment interaction, when memorizing realization in the form of repeated reproduction occurs on the basis of processes radically different from those which created initial genetic chance. Such stepped synthesis of information has hierarchical character and it is described by entropy of different dimensions. Entropy is determined by conditional probabilities. Therefore as a form of life becomes complicated, the entropy is decreased within the limits of the given hierarchical step. The part of entropy depending on the number of elements of the system (cells, individuals, etc.) always increases in the memorizing process, i. e. life defines the maximum of entropy production (but not the minimum like in nature). This fact settles paradoxes of chance in Darwinism: as a result of entropy decrease within higher hierarchical step the simbiotic processes for more complex forms of life can arise with great probability. For instance, rapidity of evolution of human brain given by supplementary chance in the mechanism of fecundation under the conditions of biochemical pressure of androgenes both, on the brain development and on muscular force at the same time. Synthesis of information in the brain is determined by the same principles, but extremums of the thermo-dynamic potential (their analogues in logic) are based on an arbitrary system of axioms. As a whole life and intellect are not fluctuations pointed against entropy increases, but they arose according to spontaneous process of entropy development.     

Neural assemblies and laminar interactions in the cerebral cortex

 Neural assemblies are assumed to become organized and to operate within the cerebral cortex, and so must be constrained by the cytological and physiological properties of this laminated structure. A hypothesis of such assemblies is presented, based on important details of neuronal architecture and physiology in different cortical laminae. Laminae II, III and VI, which are the origin and termination of most cortico-cortical projections, are regarded as the site of storage of most of the information encoded by assemblies – a neuronal ‘library’. Laminae II and III are the most sensitive coincidence detectors, and therefore probably initiate the process of assembly formation. However, these three laminae have very low levels of spontaneous activity in the waking state, and so active cell assemblies cannot base their functioning on these laminae alone. Lamina V pyramidal cells have a much higher level of spontaneous activity. Thus, indirect pathways between ‘library’ cells, via lamina V pyramidal cells, are likely to be more secure than direct ones. It is proposed that direct links between ‘library’ cells become stabilized by Hebbian strengthening, once the recipient ‘library’ cell has been ‘primed’ by neural activity transmitted indirectly via lamina V neurones. Thus lamina V neurones could catalyse the process of assembly formation. Given this proposal, lamina V cells, in their interaction with ‘library’ cells, would code information in terms of precisely timed individual impulses, but would employ a code based on slower frequency changes in their descending influences upon neural centres in the brainstem and spinal cord. Predictions for single unit and electrographic experiments are discussed. Received: 30 November 1995/Accepted in revised form: 3 June 1996     

A calculation of the probability of spontaneous biogenesis by information theory.

The Darwin-Oparin-Haldane “warm little pond” scenario for biogenesis is examined by using information theory to calculate the probability that an informational biomolecule of reasonable biochemical specificity, long enough to provide a genome for the “protobiont”, could have appeared in 10⁹ years in the primitive soup. Certain old untenable ideas have served only to confuse the solution of the problem. Negentropy is not a concept because entropy cannot be negative. The role that negentropy has played in previous discussions is replaced by “complexity” as defined in information theory. A satisfactory scenario for spontaneous biogenesis requires the generation of “complexity” not “order”. Previous calculations based on simple combinatorial analysis over estimate the number of sequences by a factor of 10⁵. The number of cytochrome c sequences is about 3·8 × 10⁶¹. The probability of selecting one such sequence at random is about 2·1 ×10^?65. The primitive milieu will contain a racemic mixture of the biological amino acids and also many analogues and non-biological amino acids. Taking into account only the effect of the racemic mixture the longest genome which could be expected with 95 % confidence in 10⁹ years corresponds to only 49 amino acid residues. This is much too short to code a living system so evolution to higher forms could not get started. Geological evidence for the “warm little pond” is missing. It is concluded that belief in currently accepted scenarios of spontaneous biogenesis is based on faith, contrary to conventional wisdom.     

Distributions of activation energy barriers that produce stretched exponential probability distributions for the time spent in each state of the two state reaction A⇌B

Many biochemical reactions consist of the spontaneous fluctuation between two states: A⇌B. For example these two states could be a ligand bound to an enzyme and the ligand and the enzyme separated from each other. A typical case would be the unbinding of CO from myoglobin (Mb), namely, MbCO⇌Mb+CO. Another example is the fluctuation in the ion channel protein in the cell membrane between conformations that are closed to the passage of ions and those that are open to the passage of ions, namely, closed⇌open. Such chemical reactions can be described as two energy levels corresponding to the two states, separated by a distribution of activation energy barriers. Since a kinetic rate can be associated with each energy barrier, this is also equivalent to a distribution of kinetic rate constants. We derive the distribution of the kinetic rates that produces the stretched exponential probability distribution, exp(−at ^b ) where 0<b≤1, which has been observed for such reactions. We also derive the form of the cumulative probability distribution when the pathways connecting the states have minimum or maximum rate constants.     

Information storing by biomagnetites

Since the discovery of the presence of biogenic magnetites in living organisms, there have been speculations on the role that these biomagnetites play in cellular processes. It seems that the formation of biomagnetite crystals is a universal phenomenon and not an exception in living cells. Many experimental facts show that features of organic and inorganic processes could be indistinguishable at nanoscale levels. Living cells are quantum “devices” rather than simple electronic devices utilizing only the charge of conduction electrons. In our opinion, due to their unusual biophysical properties, special biomagnetites must have a biological function in living cells in general and in the brain in particular. In this paper, we advance a hypothesis that while biomagnetites are developed jointly with organic molecules and cellular electromagnetic fields in cells, they can record information about the Earth’s magnetic vector potential of the entire flight in migratory birds.     

Chance vs. necessity in living systems: a false antinomy

The concepts of order and randomness are crucial to understand 'living systems' structural and dynamical rules. In the history of biology, they lay behind the everlasting debate on the relative roles of chance and determinism in evolution. Jacques Monod [1970] built a theory where chance (randomness) and determinism (order) were considered as two complementary aspects of life. In the present paper, we will give an up to date version of the problem going beyond the dichotomy between chance and determinism. To this end, we will first see how the view on living systems has evolved from the mechanistic one of the 19th century to the one stemming from the most recent literature, where they emerge as complex systems continuously evolving through multiple interactions among their components and with the surrounding environment. We will then report on the ever increasing evidence of "friendly" co-existence in living beings between a number of "variability generators", fixed by evolution, and the "spontaneous order" derived from interactions between components. We will propose that the "disorder" generated is "benevolent" because it allows living systems to rapidly adapt to changes in the environment by continuously changing, while keeping their internal harmony.     

An oscillator cell cycle model needs no first or second chance event

Theoretical data is presented to support the view that a limit cycle oscillator model of the cell cycle (as originally described) which accounts for random triggering of replication, can also accomodate the experimental results which have caused the supporters of the Transition Probability model to introduce the occurrence of yet a second chance event. In particular, it explains why the addition of a suboptimal amount of mitogen in a split dose alters the probability of triggering at each treatment but, generally, has little effect on the delay before the initiation of S-phase. It is also confirmed that, other than in some exceptional circumstances, lowering the probability of triggering in the oscillator model may have little effect on the minimum “intermitotic” time (as required by the evidence of the Transition Probability proponents) and, moreover, the oscillator concept provides reason why this should be so.     

The problem of transition from the chemical to the biological evolution: some possible solutions

On the basis of evidence that several low-molecular-weight substances as well as enzymes are compartmentalised within the so-called soluble phase of the cell, and other considerations, it is argued that DNA may not contain information for certain types of organisation found in living cells. It may be necessary for a cell to possess the "non-DNA-controlled" organisation for performance of its minimum functions; such organisation would then also serve as a "template" for its appearance in the daughter cell. The problem of transition from chemical to biological evolution (that is, the formation of the "first cell") may be essentially the problem of emergence of such intracellular organisation for which information may not reside in DNA. Two possible mechanisms through which this may have happened are stated.     

The relationship between sperm DNA fragmentation,free radicals and antioxidant capacity with idiopathic repeated pregnancy loss

More than two consecutive miscarriages in less than 20 weeks of gestation is defined as recurrent spontaneous miscarriage. Various causes such as uterine anatomical anomalies, genetic factors, and infectious and endocrine disorders have been reported for RPL. However, approximately 50% of the causes are unknown, which can be due to male factors. Several studies have been done on semen parameters to determine the unknown causes and risk factors for miscarriages, however, only studying common semen parameters have not been sufficient. In this study, the relationship between sperm DNA fragmentation, the amount of free radicals, and total antioxidant capacity (TAC) in semen have been considered as a risk factor for spontaneous miscarriage. Semen samples were collected from 42 men whose partners had a history of spontaneous miscarriage and 42 fertile men as the control group. Volume, pH, viscosity, concentration, and motility of semen, as well as sperm morphology were measured. Sperm DNA fragmentation was analyzed by the sperm chromatin structure assay (SCSA) and TUNEL methods, the amount of sperm free radicals was measured by the luminescence method and the total amount of semen antioxidant was measured using the TAC kit. The results have shown that sperm motility in the experimental group was significantly less than the control group (P?=?0.001). The percentage of sperm DNA fragmentation and the amount of free radicals in the experimental group were significantly higher than the control group (P?<?0.001). The total amount of antioxidant was lower in the experimental group compared to the control. Spouses of men with lower sperm motility and higher DNA fragmentation had a higher chance of spontaneous miscarriage when compared to the control group. The results of this study support the hypothesis that sperm DNA fragmentation is a major contributor to spontaneous miscarriage.The relationship between SDF, ROS and TAC with RPL.     

Observations on variations in electrical conductivity of pure demineralized water: modification (”activation”) of conductivity by low-frequency, low-level alternativing electric fields

 Piccardi and Capel-Boute have previously indicated a number of physical parameters which describe the physico-chemical evolution of pure water over time. Electrical conductivity is such a parameter. Experiments have been carried out in order to investigate correlations between the conductivity of pure water and various parameters. Based earlier work by Halla and Novotny we used an electrical voltage (5 V) of weak frequency (3.4 KHz) to ”activate” water. Results have been positive, the stimulus producing an increase of 10% in electrical conductivity. A biomass test with this water confirmed the observations of Violet that such water produced an increase in vegetation. Measurements of the electrical conductivity of pure water over time showed that ”external phenomena” acted upon control water but did not act upon ”activated” water. In a third series of experiments, water from the same source was put in two bottles: the first was a screened one and the second was a normal one. In this experiment, the influence of variations in electrical atmospheric fields on variations in the electrical conductivity of pure water was confirmed. Received: 11 August 1997 / Accepted: 26 September 1997     

The structure of photosystem I and evolution of photosynthesis

Oxygenic photosynthesis is the principal producer of both oxygen and organic matter on earth. The primary step in this process--the conversion of sunlight into chemical energy--is driven by four multi-subunit membrane protein complexes named photosystem I, photosystem II, cytochrome b(6)f complex and F-ATPase. Photosystem I generates the most negative redox potential in nature and thus largely determines the global amount of enthalpy in living systems. The recent structural determination of PSI complexes from cyanobacteria and plants sheds light on the evolutionary forces that shaped oxygenic photosynthesis. The fortuitous formation of our solar system in a space plentiful of elements, our distance from the sun and the long time of uninterrupted evolution enabled the perfection of photosynthesis and the evolution of advanced organisms. The available structural information complements the knowledge gained from genomic and proteomic data to illustrate a more precise scenario for the evolution of life systems on earth.     

Gedanken zum Schutz der biologischen Vielfalt. Globales Unwissen contra Biodiversität

A professional approach to conservation of biodiversity requires good knowledge, but we do not even know anywhere near how many species do occur on earth. We even know less on the conservation status of the living world. Factors threatening biodiversity are many and diverse. In addition to key problems such as human population growth, or ever increasing and unsustainable use of resources, effective biodiversity conservation is also hampered by massive lack of knowledge, a growing gap of trained taxonomists and ecologists, bureaucracy, politics and serious misinterpretation of important issues affecting biodiversity. In order to reduce the knowledge gap, the need to catalogue and conserve the diversity of live on earth must be seen as an important global challenge and must be funded with appropriate resources accordingly.     

Creating Prebiotic Sanctuary: Self-Assembling Supramolecular Peptide Structures Bind and Stabilize RNA

Any attempt to uncover the origins of life must tackle the known ‘blind watchmaker problem’. That is to demonstrate the likelihood of the emergence of a prebiotic system simple enough to be formed spontaneously and yet complex enough to allow natural selection that will lead to Darwinistic evolution. Studies of short aromatic peptides revealed their ability to self-assemble into ordered and stable structures. The unique physical and chemical characteristics of these peptide assemblies point out to their possible role in the origins of life. We have explored mechanisms by which self-assembling short peptides and RNA fragments could interact together and go through a molecular co-evolution, using diphenylalanine supramolecular assemblies as a model system. The spontaneous formation of these self-assembling peptides under prebiotic conditions, through the salt-induced peptide formation (SIPF) pathway was demonstrated. These peptide assemblies possess the ability to bind and stabilize ribonucleotides in a sequence-depended manner, thus increase their relative fitness. The formation of these peptide assemblies is dependent on the homochirality of the peptide monomers: while homochiral peptides (L-Phe-L-Phe and D-Phe-D-Phe) self-assemble rapidly in aqueous environment, heterochiral diastereoisomers (L-Phe-D-Phe and D-Phe-L-Phe) do not tend to self-assemble. This characteristic consists with the homochirality of all living matter. Finally, based on these findings, we propose a model for the role of short self-assembling peptides in the prebiotic molecular evolution and the origin of life.     

赣南稀土矿开发区生态环境遥感动态监测与评估

稀土矿业的发展在促进区域经济发展的同时,也对生态环境带来影响。为研究江西赣南稀土矿产开发及其对生态环境的影响,采用SPOT1/2/5、Landsat7和ALOS等多源遥感数据,对该区域2000—2010年稀土矿开发进行遥感动态监测。采用面向对象的方法对研究区进行生态系统分类,同时结合回溯法可较好地减少伪变化,并可快速地提取稀土矿开采区的变化信息。通过分析发现赣南稀土矿开采集中分布在几个主要的乡镇,从2000年至2010年这10年间整体上呈增加的趋势,但前5年主要体现为扩张,后5年复垦的力度在加强。新增的稀土矿矿区在开发过程中破坏的生态系统类型主要为林地,而废弃稀土矿区通过治理后主要恢复成耕地。稀土矿开采对植被覆盖、生物量、土地退化以及景观的破碎化都有一定的影响。同时稀土矿开采可能引发水体流失、山体滑坡等环境问题和风险。     

Wikipedia as an encyclopaedia of life

In a 2003 essay E. O. Wilson outlined his vision for an “encyclopaedia of life” comprising “an electronic page for each species of organism on Earth”, each page containing “the scientific name of the species, a pictorial or genomic presentation of the primary type specimen on which its name is based, and a summary of its diagnostic traits.” Although biodiversity informatics has generated numerous online resources, including some directly inspired by Wilson’s essay (e.g., iSpecies and EOL), we are still some way from the goal of having available online all relevant information about a species, such as its taxonomy, evolutionary history, genomics, morphology, ecology, and behaviour. While the biodiversity community has been developing a plethora of databases, some with overlapping goals and duplicated content, Wikipedia has been slowly growing to the point where it now has over 100,000 pages on biological taxa. My goal in this essay is to explore the idea that, largely independent of the aims of biodiversity informatics and well-funded international efforts, Wikipedia has emerged as potentially the best platform for fulfilling E. O. Wilson’s vision.     

Removing exogenous information using pedigree data

Management of certain populations requires the preservation of its pure genetic background. When, for different reasons, undesired alleles are introduced, the original genetic conformation must be recovered. The present study tested, through computer simulations, the power of recovery (the ability for removing the foreign information) from genealogical data. Simulated scenarios comprised different numbers of exogenous individuals taking part of the founder population and different numbers of unmanaged generations before the removal program started. Strategies were based on variables arising from classical pedigree analyses such as founders’ contribution and partial coancestry. The efficiency of the different strategies was measured as the proportion of native genetic information remaining in the population. Consequences on the inbreeding and coancestry levels of the population were also evaluated. Minimisation of the exogenous founders’ contributions was the most powerful method, removing the largest amount of genetic information in just one generation. However, as a side effect, it led to the highest values of inbreeding. Scenarios with a large amount of initial exogenous alleles (i.e. high percentage of non native founders), or many generations of mixing became very difficult to recover, pointing out the importance of being careful about introgression events in populations where these are undesired.