The honey-bee “dance language” hypothesis and the foundations of biology and behavior

We have carried out a detailed analysis of the region of the hormone, which can be called an “active site”, that is essential for receptor binding and/or agonist activity, on the basis of structure-activity data of peptide hormones published in the literature. We find that one or more aromatic residues, often in a cluster, is present at the active sites of insulin, glucagon, adrenocorticotropin, gastrin, endorphins and angiotensin. Recognition of the functional importance of aromatic residues, combined with sequence comparisons and secondary structural predictions, enable us to identif active sites of nerve growth factor, somatostatin, calcitonin, parathyroid hormone and luteinizing hormone releasing hormone. Aromatic residues also appear to be essential for the function of nonpeptide hormones that act at the plasma membrane, and opiates. The apparently ubiquitous presence of aromatic groups at the active site of peptide hormones may facilitate understanding of the mechanism of action of hormones and provide insights into the design of hormone analogues.     

Info-gap robust-satisficing model of foraging behavior: do foragers optimize or satisfice?

In this note we compare two mathematical models of foraging that reflect two competing theories of animal behavior: optimizing and robust satisficing. The optimal-foraging model is based on the marginal value theorem (MVT). The robust-satisficing model developed here is an application of info-gap decision theory. The info-gap robust-satisficing model relates to the same circumstances described by the MVT. We show how these two alternatives translate into specific predictions that at some points are quite disparate. We test these alternative predictions against available data collected in numerous field studies with a large number of species from diverse taxonomic groups. We show that a large majority of studies appear to support the robust-satisficing model and reject the optimal-foraging model.     

The dark side of the “redundancy hypothesis” and ecosystem assessment

Intricacy of biotic interactions (predator-prey relationship, strength of food web links and other type of intra- and inter-specific relationships), as well as shifts in species functions in ecosystems, could affect the accuracy of predictions derived from the theory of redundancy of species, when applied to ecosystems assessment.This opinion paper is based on three main considerations: 1) some fundamental differences between ecological and engineering definition of “redundancy”, underlying the main concerns related to the use frameworks derived from economical or engineering disciplines, as the ecosystems services paradigm; 2) presence of empirical obstacles to establish whether two different species are fully or partially redundant. When species redundancy in a particular community is estimated using a matrix with species-specific functional traits, often forgetting potential biotic interactions not directly related to the trophic chains or neglecting the variability in strengths of the links connecting these species; and 3) recent evidence offered by studies that shed doubts on the validity of the ecological redundancy hypothesis.Finally, we claim that more attention must to be paid to intrinsic ecological aspects of ecosystem components (per se values rather than derived values), and a precautionary principle is necessary for decisions related to the assessment of ecosystems.     

Prion hypothesis: the end of the controversy?

Forty-three years have passed since it was first proposed that a protein could be the sole component of the infectious agent responsible for the enigmatic prion diseases. Many discoveries have strongly supported the prion hypothesis, but only recently has this once heretical hypothesis been widely accepted by the scientific community. In the past 3 years, researchers have achieved the 'Holy Grail' demonstration that infectious material can be generated in vitro using completely defined components. These breakthroughs have proven that a misfolded protein is the active component of the infectious agent, and that propagation of the disease and its unique features depend on the self-replication of the infectious folding of the prion protein. In spite of these important discoveries, it remains unclear whether another molecule besides the misfolded prion protein might be an essential element of the infectious agent. Future research promises to reveal many more intriguing features about the rogue prions.     

Selection and mutation in the “new” genetics: an emerging hypothesis

It has been anticipated that new, much more sensitive, next generation sequencing (NGS) techniques, using massively parallel sequencing, will likely provide radical insights into the genetics of multifactorial diseases. While NGS has been used initially to analyze individual human genomes, and has revealed considerable differences between healthy individuals, we have used NGS to examine genetic variation within individuals, by sequencing tissues “in depth”, i.e., oversequencing many thousands of times. Initial studies have revealed intra-tissue genetic heterogeneity, in the form of multiple variants of a single gene that exist as distinct “majority and “minority” variants. This highly specialized form of somatic mosaicism has been found within both cancer and normal tissues. If such genetic variation within individual tissues is widespread, it will need to be considered as a significant factor in the ontogeny of many multifactorial diseases, including cancer. The discovery of majority and minority gene variants and the resulting somatic cell heterogeneity in both normal and diseased tissues suggests that selection, as opposed to mutation, might be the critical event in disease ontogeny. We, therefore, are proposing a hypothesis to explain multifactorial disease ontogeny in which pre-existing multiple somatic gene variants, which may arise at a very early stage of tissue development, are eventually selected due to changes in tissue microenvironments.     

Mating behavior of the eucalyptus longhorned borer (Coleoptera: Cerambycidae) and the adaptive significance of long “horns”

Sexual dimorphism in insect antennal structure is often attributed to differences between the sexes in sensitivity to pheromones, the antennae of one sex being more elaborately structured (for example, plumose). Males of the family Cerambycidae (order Coleoptera) often have longer antennae than females, but of a similar general structure, suggesting that selective factors other than sensitivity to pheromones are at work. Both sexes of the eucalyptus longhorned borer, a cerambycid, were attracted to eucalyptus logs that were larval hosts. There, males located females by antennal contact, and male mating success therefore depended on the walking rate and width of the antennal spread. Elongate antennae may benefit males by increasing antennal spread width, but have no such advantage for females, suggesting an evolutionary explanation for sexual dimorphism.     

Is physiological performance optimized by thermoregulatory behavior?: a case study of the eastern fence lizard,Sceloporus undulatus

Eastern fence lizards (Sceloporus undulatus) exhibit a distinct thermal preference that might be related to the thermal optimum for physiological performance. Sprint speed and treadmill endurance of S. undulatus were insensitive to body temperature in the ranges of 28–38°C and 25–36°C, respectively. Both locomotor and digestive performances are optimized at the preferred body temperature of S. undulatus, but thermoregulatory behavior is more closely related to the thermal sensitivity of digestive performance than that of locomotor performance.     

Correction to: A critique of the capacitor-based “Transmembrane Electrostatically Localized Proton” hypothesis

Journal of Bioenergetics and Biomembranes -     

Evolution of female multiple mating: A quantitative model of the “sexually selected sperm” hypothesis

Explaining the evolution and maintenance of polyandry remains a key challenge in evolutionary ecology. One appealing explanation is the sexually selected sperm (SSS) hypothesis, which proposes that polyandry evolves due to indirect selection stemming from positive genetic covariance with male fertilization efficiency, and hence with a male's success in postcopulatory competition for paternity. However, the SSS hypothesis relies on verbal analogy with “sexy-son” models explaining coevolution of female preferences for male displays, and explicit models that validate the basic SSS principle are surprisingly lacking. We developed analogous genetically explicit individual-based models describing the SSS and “sexy-son” processes. We show that the analogy between the two is only partly valid, such that the genetic correlation arising between polyandry and fertilization efficiency is generally smaller than that arising between preference and display, resulting in less reliable coevolution. Importantly, indirect selection was too weak to cause polyandry to evolve in the presence of negative direct selection. Negatively biased mutations on fertilization efficiency did not generally rescue runaway evolution of polyandry unless realized fertilization was highly skewed toward a single male, and coevolution was even weaker given random mating order effects on fertilization. Our models suggest that the SSS process is, on its own, unlikely to generally explain the evolution of polyandry.     

On the free energy “cost of transition” in intermediary Metabolic processes and the evolution of cellular infrastructure

Certain questions are discussed regarding the evolution of spatial order in cellular metabolism. The treatment focuses on the significance of the transient phase (in steady-state transitions). For the purpose of simple, semi-quantitative analysis, an arbitrary metabolic process (multi-enzyme system) is modeled as a linear sequence of monomolecular reactions, governed by an initial “master reaction”. For such designs, explicit definition of the transient time τ may be obtained from previous studies; it is just a function of the K_m's and V_max's of the individual enzyme reactions. As indicated herein, the free energy “cost of transition” (ΔG)_τ, is related straightforwardly to the individual transient times of the multienzyme system. Using representations for K_m and V_max from a recent molecular enzyme-kinetic model (Somogyi & Damjanovich, 1971, 1975), the present report yields a novel expression for transient time, which depends explicitly on medium viscosity, enzyme concentration, and Boltzmann energy factor. It is seen that τ [and (ΔG)_τ] might be exceedingly large if a given metabolic process be pictured in complete communication with a bulk reaction-diffusion milieu in vivo. In general, excessive time delay and undue energy expenditures might arise from any of the following: (i) metabolic interferences due to pathway competition for common substrates; (ii) bulk motion; (iii) diffusional (viscosity) interference, e.g. that due to generalized Fickian diffusion. The situation would be acute particularly for cases where metabolites must be maintained at low intracellular concentration. It is recognized that living protoplasm may have obviated some of these difficulties and, concomitantly, economized on free energy by compartmentalizing much (if not all) of intermediary metabolism via multi-enzyme complexes and/or membrane-associated schemes. Experimental evidence lends support to such claim. The progression toward increased spatial organization is viewed here from the perspective of the following thermodynamic correlates of biological evolution: (a) increasing free energy dissipation and (b) increasing energetic efficiency. It is suggested that the evolution toward structuralization may be regarded simply as a trend toward increased “energetic profitableness” in cellular metabolism. In this context, a correspondence is proposed between real time and “thermodynamic time”. In conclusion, the basis of the thermodynamic approach to evolution is discussed.     

L-type calcium channel: Clarifying the “oxygen sensing hypothesis”

The heart is able to respond acutely to changes in oxygen tension. Since ion channels can respond rapidly to stimuli, the “ion channel oxygen sensing hypothesis” has been proposed to explain acute adaptation of cells to changes in oxygen demand. However the exact mechanism for oxygen sensing continues to be debated. Mitochondria consume the lion’s share of oxygen in the heart, fuelling the production of ATP that drives excitation and contraction. Mitochondria also produce reactive oxygen species that are capable of altering the redox state of proteins. The cardiac L-type calcium channel is responsible for maintaining excitation and contraction. Recently, the reactive cysteine on the cardiac L-type calcium channel was identified. These data clarified that the channel does not respond directly to changes in oxygen tension, but rather responds to cellular redox state. This leads to acute alterations in cell signalling responsible for the development of arrhythmias and pathology.     

On the evolution of protamines in bony Fish: Alternatives to the “Retroviral horizontal transmission” hypothesis

Fish protamines are highly specialized molecules which are responsible for chromatin condensation during the last stages of spermatogenesis (spermiogenesis). However, not all fish contain protamines in their sperm nuclei; rather, there seems to be a random distribution of protamines within this group. The origin of this sporadic presence of protamines in the sperm and its significance have not yet been precisely determined. In this paper we have conducted an exhaustive survey of the literature available on the different types of nuclear protein composition of the sperm of teleost fish in order to try to correlate these data with what is presently known about the taxonomy of this group. The results of this analysis have allowed us to make the following observations. The divergence between protamines and histones has occurred several times during the evolution of the bony fish. However, the relative frequency of this divergence is almost negligible during the differentiation of genera and species (intrafamily variation) and is very small during the differentiation of families (interfamily variation). Nevertheless, the divergence is very noticeable among the different orders. It is therefore possible to conclude from all this that the sporadic distribution of protamines in bony fish is not a random event as initially believed. Furthermore, such a heterogeneous distribution of protamines cannot be easily accounted for by a mechanism of horizontal retroviral transmission through repeated and independent acquisition of a prot amine gene as has been recently proposed (Jankowski, Stater, Dixon (1986) J Mol Evol 23:1–10). Rather, it could possibly be explained by a repeated and independent loss of the expression of the protamine gene (or loss of the gene itself) which mainly occurred during the diversification of the orders of this group.Correspondence to: J. Ausio     

A critique of the capacitor-based “Transmembrane Electrostatically Localized Proton” hypothesis

Journal of Bioenergetics and Biomembranes - In his Transmembrane Electrostatically Localized Proton hypothesis (TELP), James W. Lee has modeled the bioenergetic membrane as a simple capacitor....     

Some metabolic relationships between biopterin and folate: Implications for the “methyl trap hypothesis”

Tetrahydrobiopterin and the folate coenzymes can reciprocally interact in ways that would be useful to the metabolic pathways subserved by both of these coenzymes. Thus, through one of the reactions catalyzed by methylene tetrahydrofolate reductase, 5-CH₃-H₄-folate can regenerate BH₄ from q-BH₂ and q-BH₂ can provide an escape from the methyl trap.Special issue dedicated to Dr. Louis Sokoloff     

Seed plant phylogeny: Demise of the anthophyte hypothesis?

Recent molecular phylogenetic studies indicate, surprisingly, that Gnetales are related to conifers, or even derived from them, and that no other extant seed plants are closely related to angiosperms. Are these results believable? Is this a clash between molecules and morphology?