Adaptation and Natural Selection revisited.

In Adaptation and Natural Selection, George C. Williams linked the distinction between group and individual adaptation with the distinction between group and individual selection. Williams' Principle, as we will call it, says that adaptation at a level requires selection at that level. This is a necessary but not a sufficient condition; for example, group adaptation requires group selection, but the fact that group selection influences a trait's evolution does not suffice for the resulting trait frequency to be a group adaptation. What more is required? In this paper, we describe an answer to this question that has been developed in multilevel selection theory. We also discuss an alternative framework for defining units of adaptation that violates Williams' Principle.

Social semantics: toward a genuine pluralism in the study of social behaviour.

Pluralism is the coexistence of equivalent theoretical frameworks, either because they are historically entrenched or because they achieve separate insights by viewing the same process in different ways. A recent article by West et al. [Journal of Evolutionary Biology (2007) vol. 20, 415-432] attempts to classify the many equivalent frameworks that have been developed to study the evolution of social behaviour. This article addresses shortcomings in the West et al.'s article, especially with respect to multilevel selection, in a common effort to maximize the benefits of pluralism while minimizing the semantic costs.

Use of dry powder inhalers in COPD.

INTRODUCTION: This was a study of 30 chronic obstructive pulmonary disease (COPD) patients to assess the ease of use and preference of four dry powder inhalers -- accuhaler, aerolizer, handihaler, turbohaler -- the accuhaler and turbohaler are multidose devices, whereas the aerolizer and handihaler are single dose devices. METHOD: None of the subjects had previous experience of dry powder inhalers. The correct technique for each inhaler was divided into 12 steps including one critical step that if not performed would result in no drug delivery. Subjects were shown the correct technique for each inhaler in a random order and were assessed immediately and 1 h later. Each subject was asked to rank the four devices for preference and ease of use, as well as to assess how comfortable it felt to inhale through the device using a visual analogue scale. RESULTS: The numbers of perfect scores were not significantly different between devices, but the number of fatal errors that would result in no drug delivery was significantly more common in single dose devices (p < 0.01). There were significant differences in the rankings of each device (Friedman test, p < 0.005) with the turbohaler being ranked first most often and the handihaler last. The turbohaler scored highest for comfort of inhalation and the accuhaler lowest, but differences were small. CONCLUSIONS: In COPD patients starting on dry powder inhalers, multidose devices appear to be preferred, have fewer problems and are easier to use effectively.

Replica Ornstein-Zernike self-consistent theory for mixtures in random pores.

We present a self-consistent integral equation theory for a binary liquid in equilibrium with a disordered medium, based on the formalism of the replica Ornstein-Zernike (ROZ) equations. Specifically, we derive direct formulas for the chemical potentials and the zero-separation theorems (the latter provide a connection between the chemical potentials and the fluid cavity distribution functions). Next we solve a modified-Verlet closure to ROZ equations, which has built-in parameters that can be adjusted to satisfy the zero-separation theorems. The degree of thermodynamic consistency of the theory is also kept under control. We model the binary fluid in random pores as a symmetrical binary mixture of nonadditive hard spheres in a disordered hard-sphere matrix and consider two different values of the nonadditivity parameter and of the quenched matrix packing fraction, at different mixture concentrations. We compare the theoretical structural properties as obtained through the present approach with Percus-Yevick and Martinov-Sarkisov integral equation theories, and assess both structural and thermodynamic properties by performing canonical standard and biased grand canonical Monte Carlo simulations. Our theory appears superior to the other integral equation schemes here examined and provides reliable estimates of the chemical potentials. This feature should be useful in studying the fluid phase behavior of model adsorbates in random pores in general.

Extra-articular migration of the patellar component following total knee arthroplasty.

Complications related to patellar resurfacing are well recognized. We present an unusual case where the patellar button, after separating from the patella, extruded from the knee joint to lie within the extra-articular soft tissues.

One-step purification of recombinant proteins using a nanomolar-affinity streptavidin-binding peptide, the SBP-Tag.

We describe the use of the SBP-tag, a new streptavidin-binding peptide, for both the one-step purification and the detection of recombinant proteins. The SBP-tag sequence is 38 amino acids long and binds to streptavidin with an equilibrium dissociation constant of 2.5 nM. We demonstrate that a single-step purification of SBP-tagged proteins from bacterial extract yields samples that are more pure than those purified using maltose-binding protein or the His-tag. The capacity of the immobilized streptavidin used to purify SBP-tagged proteins is about 0.5 mg per milliliter of matrix, which is high enough to isolate large quantities of proteins for further study. Also, the elution conditions from the streptavidin column are very mild and specific, consisting of the wash buffer plus biotin. This combination of high-affinity, high-yield, mild elution conditions, and simplicity of use makes the SBP-tag suitable for high-throughput protein expression/purification procedures, including robotically manipulated protocols with microtiter plates. Additionally, the SBP-tag can be used for detection since a wide variety of streptavidin-conjugated fluorescent and enzymatic systems are commercially available. We also present a new, rapid, method for the measurement of protein-protein, protein-peptide, or protein-small molecule equilibrium dissociation constants that require as little as 1 fmol of labeled protein. We call this method the spin-filter binding inhibition assay.

The use of mRNA display to select high-affinity protein-binding peptides.

We report the use of "mRNA display," an in vitro selection technique, to identify peptide aptamers to a protein target. mRNA display allows for the preparation of polypeptide libraries with far greater complexity than is possible with phage display. Starting with a library of approximately 10(13) random peptides, 20 different aptamers to streptavidin were obtained, with dissociation constants as low as 5 nM. These aptamers function without the aid of disulfide bridges or engineered scaffolds, yet possess affinities comparable to those for monoclonal antibody-antigen complexes. The aptamers bind streptavidin with three to four orders of magnitude higher affinity than those isolated previously by phage display from lower complexity libraries of shorter random peptides. Like previously isolated peptides, they contain an HPQ consensus motif. This study shows that, given sufficient length and diversity, high-affinity aptamers can be obtained even from random nonconstrained peptide libraries. By engineering structural constraints into these ultrahigh complexity peptide libraries, it may be possible to produce binding agents with subnanomolar binding constants.

Random mutagenesis by PCR.

Error-prone PCR (EP-PCR) is the method of choice for introducing random mutations into a defined segment of DNA that is too long to be chemically synthesized as a degenerate sequence. Using EP-PCR, the 5' and 3' boundaries of the mutated region may be defined by the choice of PCR primers. Accordingly, it is possible to mutagenize an entire gene or merely a segment of a gene. The average number of mutations per DNA fragment can be controlled as a function of the number of EP-PCR doublings performed. The EP-PCR technique described here is for a 400-bp sequence, and an Alternate Protocol is for a library. EP-PCR takes advantage of the inherently low fidelity of Taq DNA polymerase, which may be further decreased by the addition of Mn2+, increasing the Mg2+ concentration, and using unequal dNTP concentrations.

Religious groups as adaptive units.

This essay provides a sketch of religion as a set of biologically and culturally evolved adaptations that enable human groups to function as adaptive units. Recent developments in evolutionary biology make such a group-level interpretation of religion more plausible than in the past. A brief survey of relevant concepts is followed by a relatively detailed interpretation of Calvinism as a religious system in which explicit behavioral prescriptions, beliefs about God and his relationship with people, and numerous social control mechanisms combined to change the city of Geneva from a collection of warring factions to a unified population.

Artificial ecosystem selection.

Artificial selection has been practiced for centuries to shape the properties of individual organisms, providing Darwin with a powerful argument for his theory of natural selection. We show that the properties of whole ecosystems can also be shaped by artificial selection procedures. Ecosystems initiated in the laboratory vary phenotypically and a proportion of the variation is heritable, despite the fact that the ecosystems initially are composed of thousands of species and millions of individuals. Artificial ecosystem selection can be used for practical purposes, illustrates an important role for complex interactions in evolution, and challenges a widespread belief that selection is most effective at lower levels of the biological hierarchy.

Population viscosity and the evolution of altruism.

The term population viscosity refers to limited dispersal, which increases the genetic relatedness of neighbors. This effect both supports the evolution of altruism by focusing the altruists' gifts on relatives of the altruist, and also limits the extent to which altruism may emerge by exposing clusters of altruists to stiffer local competition. Previous analyses have emphasized the way in which these two effects can cancel, limiting the viability of altruism. These papers were based on models in which total population density was held fixed. We present here a class of models in which population density is permitted to fluctuate, so that patches of altruists are supported at a higher density than patches of non-altruists. Under these conditions, population viscosity can support the selection of both weak and strong altruism.

Constructing high complexity synthetic libraries of long ORFs using in vitro selection.

We present a method that can significantly increase the complexity of protein libraries used for in vitro or in vivo protein selection experiments. Protein libraries are often encoded by chemically synthesized DNA, in which part of the open reading frame is randomized. There are, however, major obstacles associated with the chemical synthesis of long open reading frames, especially those containing random segments. Insertions and deletions that occur during chemical synthesis cause frameshifts, and stop codons in the random region will cause premature termination. These problems can together greatly reduce the number of full-length synthetic genes in the library. We describe a strategy in which smaller segments of the synthetic open reading frame are selected in vitro using mRNA display for the absence of frameshifts and stop codons. These smaller segments are then ligated together to form combinatorial libraries of long uninterrupted open reading frames. This process can increase the number of full-length open reading frames in libraries by up to two orders of magnitude, resulting in protein libraries with complexities of greater than 10(13). We have used this methodology to generate three types of displayed protein library: a completely random sequence library, a library of concatemerized oligopeptide cassettes with a propensity for forming amphipathic alpha-helical or beta-strand structures, and a library based on one of the most common enzymatic scaffolds, the alpha/beta (TIM) barrel.

Artificial selection of microbial ecosystems for 3-chloroaniline biodegradation.

We present a method for selecting entire microbial ecosystems for bioremediation and other practical purposes. A population of ecosystems is established in the laboratory, each ecosystem is measured for a desired property (in our case, degradation of the environmental pollutant 3-chloroaniline), and the best ecosystems are used as 'parents' to inoculate a new generation of 'offspring' ecosystems. Over many generations of variation and selection, the ecosystems become increasingly well adapted to produce the desired property. The procedure is similar to standard artificial selection experiments except that whole ecosystems, rather than single individuals, are the units of selection. The procedure can also be understood in terms of complex system theory as a way of searching a vast combinatorial space (many thousands of microbial species and many thousands of genes within species) for combinations that are especially good at producing the desired property. Ecosystem-level selection can be performed without any specific knowledge of the species that comprise the ecosystems and can select ensembles of species that would be difficult to discover with more reductionistic methods. Once a 'designer ecosystem' has been created by ecosystem-level selection, reductionistic methods can be used to identify the component species and to discover how they interact to produce the desired effect.

In vitro selection of functional nucleic acids.

In vitro selection allows rare functional RNA or DNA molecules to be isolated from pools of over 10(15) different sequences. This approach has been used to identify RNA and DNA ligands for numerous small molecules, and recent three-dimensional structure solutions have revealed the basis for ligand recognition in several cases. By selecting high-affinity and -specificity nucleic acid ligands for proteins, promising new therapeutic and diagnostic reagents have been identified. Selection experiments have also been carried out to identify ribozymes that catalyze a variety of chemical transformations, including RNA cleavage, ligation, and synthesis, as well as alkylation and acyl-transfer reactions and N-glycosidic and peptide bond formation. The existence of such RNA enzymes supports the notion that ribozymes could have directed a primitive metabolism before the evolution of protein synthesis. New in vitro protein selection techniques should allow for a direct comparison of the frequency of ligand binding and catalytic structures in pools of random sequence polynucleotides versus polypeptides.

Multilevel selection and the social transmission of behavior.

Many evolutionary models assume that behaviors are caused directly by genes. An implication is that behavioral uniformity should be found only in groups that are genetically uniform. Yet, the members of human social groups often behave in a uniform fashion, despite the fact that they are genetically diverse. Behavioral uniformity can occur through a variety of psychological mechanisms and social processes, such as imitation, consensus decision making, or the imposition of social norms. We present a series of models in which genes code for social transmission rules, which in turn govern the behaviors that are adopted. Transmission rules can evolve in randomly formed groups that concentrate phenotypic variation at the between-group level, favoring the evolution of altruistic behaviors and other group-advantageous traits. In addition, a direct bias toward adopting altruistic behaviors can evolve. Our models begin to show how group selection can be a strong force in human evolution, despite the absence of extreme genetic variation among groups.

Neuromuscular organization of avian flight muscle: Morphology and contractile properties of motor units in the pectoralis (pars thoracicus) of pigeon (Columba livia).

We used acid digestion and glycogen depletion to determine fascicle organization, fiber morphology, and physiological and anatomical features of individual motor units of an in-series muscle, the pectoralis (pars thoracicus) of the pigeon (Columba livia). Most fascicles are attached at one end to connective tissue. Average fiber length in the four regions examined range from 42% to 66% of average fascicle length. More than 65% of fibers are blunt at one end of a fascicle and taper intrafascicularly. Fibers with blunt-blunt endings range from 13% to 31% of the population in different regions; taper-taper fibers range from 2% to 17%. Pigeon pectoralis fibers are distinguished histochemically into fast-twitch glycolytic (FG) and fast-twitch oxidative-glycolytic (FOG) populations. Three units composed of FG fibers (FG units) contract more quickly than three units composed of FOG fibers (FOG units) (range 31-37 vs 47-62 msec), produce more tetanic force (0.11-0.32 vs 0.02-0.05 N) and are more fatigable (<18% initial force vs >50% after repeated stimulation). Most motor units are confined to one of the four muscle regions. Territory of two FOG units is <30% of parent fascicle length. Territories of other units spanned parent fascicles; most fibers in these units do not extend the full fascicle length. Compared to FG units, FOG units have lower maximum innervation ratios and density indices (ratio of depleted/total FOG fibers in territory 8-14% vs 58-76% for FG units). These differences support the hypothesis that FG units are organized to produce substantial force and power for takeoff, landing and other ballistic movements whereas FOG units are suited for sustained flight when power requirements are reduced. Implications of findings for understanding the control of in-series muscles and the use of connective tissue elastic elements during wing movements are discussed. J.Morphol. 236:179-208, 1998. © 1998 Wiley-Liss, Inc.

Optimal foraging, specialization, and a solution to Liem's paradox.

Species that appear highly specialized on the basis of their phenotype (e.g., morphology, behavior, and physiology) also sometimes act as ecological generalists. This apparent paradox has been used to argue against the importance of competition as a diversifying evolutionary force. We provide an alternative explanation based on optimal foraging theory. Some resources are intrinsically easy to use and are widely preferred, while others require specialized phenotypic traits on the part of the consumer. This asymmetry allows optimally foraging consumers to evolve phenotypic specializations on nonpreferred resources without greatly compromising their ability to use preferred resources. The evolution of phenotypic specialization on nonpreferred resources can be driven by competition, but the specialists act as ecological generalists whenever their preferred resources are available. Our model identifies at least three different concepts of specialization that need to be distinguished, based on diet, prey utilization efficiencies, and phenotypic adaptations. The relationships among these concepts are complex and often counterintuitive. Specialists should often reject the very resources that they have evolved traits to use. The most extreme phenotypic specializations should occur in the absence of a trade-off between using preferred and nonpreferred resources. Our model may explain why extreme phenotypic-specializations evolve more often in fish communities than in terrestrial vertebrate communities and provides a mechanism whereby species can coexist in stable communities despite common preferences for some resources.