Baldwin Effect Research Articles

ChemInform Abstract: The Synthesis and Chemistry of Formylphosphonate

New methods of synthesis and reactions of formylphosphonate have been investigated. Attempts to deprotect the corresponding diethyl acetal with TiIV halides led instead to the formation of halo(ethoxy)methylphosphonates which undergo substitution reactions with a wide range of nucleophiles. The products of reactions of formylphosphonate with bifunctional nucleophiles are determined in most cases by Baldwin's Rules, while the imines derived from formylphosphonate undergo Diels-Alder reactions only in those cases which carry a strongly electron-withdrawing N-substitutent.

ACHANDRASURVEY OF FLUORESCENCE Fe LINES IN X-RAY BINARIES AT HIGH RESOLUTION

In this paper we present a comprehensive survey of 41 X-ray binaries (10 HMXBs and 31 LMXBs) with Chandra, with specific emphasis on the Fe K region and the narrow Fe Kalpha line, at the highest resolution possible. We find that: a) The Fe Kalpha line is always centered at 1.9387 +- 0.0016 Angstroms, compatible with Fe I up to Fe X; we detect no shifts to higher ionization states nor any difference between HMXBs and LMXBs. b) The line is very narrow, with FWHM < 5 mAngstroms, which means that the reprocessing material is not rotating at high speeds. c) Fe Kalpha fluorescence is present in all the HMXB in the survey while such emissions are very rare (~ 10% ) among LMXBs. d) The lack of Fe line emission is always accompanied by the lack of any detectable K edge. e) We obtain the empirical curve of growth of the equivalent width of the Fe Kalpha line versus the density column of the reprocessing material, i.e. EW_{Kalpha} vs N_{H}, and show that it is consistent with a reprocessing region spherically distributed around the compact object. f) We show that fluorescence in X-ray binaries follows the X-ray Baldwin effect. We interpret this finding as evidence of decreasing neutral Fe abundance with increasing X-ray illumination and use it to explain some spectral states of Cyg X-1 and as a possible cause of the lack of narrow Fe line emission in LMXBs. g) Finally, we study anomalous morphologies. We present the first evidence of a Compton shoulder in the HMXB X1908+075. Also the Fe Kalpha lines of 4U1700-37 and LMC X-4 present asymmetric wings suggesting the presence of highly structured stellar winds in these systems.

THE CORES OF THE Fe Kα LINES IN ACTIVE GALACTIC NUCLEI: AN EXTENDED CHANDRA HIGH ENERGY GRATING SAMPLE

We extend the study of the core of the Fe K$\alpha$ emission line at \sim 6.4 keV in Seyfert galaxies reported in Yaqoob & Padmanabhan (2004) using a larger sample observed by the Chandra High Energy Grating (HEG). Whilst heavily obscured active galactic nuclei (AGNs) are excluded from the sample, these data offer some of the highest precision measurements of the peak energy of the Fe K$\alpha$ line, and the highest spectral resolution measurements of the width of the core of the line in unobscured and moderately obscured ($N_{H}<10^{23} \ \rm cm^{-2}$) Seyfert galaxies to date. The Fe K$\alpha$ line is detected in 33 sources, and its centroid energy is constrained in 32 sources. In 27 sources the statistical quality of the data is good enough to yield measurements of the FWHM. We find that the distribution in the line centroid energy is strongly peaked around the value for neutral Fe, with over 80% of the observations giving values in the range 6.38--6.43 keV. Including statistical errors, 30 out of 32 sources ($\sim 94%$) have a line centroid energy in the range 6.35--6.47 keV. The mean equivalent width, amongst the observations in which a non-zero lower limit could be measured, was $53 \pm 3eV. The mean FWHM from the subsample of 27 sources was $2060 \pm 230 \ \rm km \ s^{-1}$. The mean EW and FWHM are somewhat higher when multiple observations for a given source are averaged. From a comparison with the H$\beta$ optical emission-line widths (or, for one source, Br$\alpha$), we find that there is no universal location of the Fe K$\alpha$ line-emitting region relative to the optical BLR. We confirm the presence of the X-ray Baldwin effect, an anti-correlation between the Fe K$\alpha$ line EW and X-ray continuum luminosity. The HEG data have enabled isolation of this effect to the narrow core of the Fe K$\alpha$ line.

Environmentally induced phenotypes and DNA methylation: how to deal with unpredictable conditions until the next generation and after

Organisms often respond to environmental changes by producing alternative phenotypes. Epigenetic processes such as DNA methylation may contribute to environmentally induced phenotypic variation by modifying gene expression. Changes in DNA methylation, unlike DNA mutations, can be influenced by the environment; they are stable at the time scale of an individual and present different levels of heritability. These characteristics make DNA methylation a potentially important molecular process to respond to environmental change. The aim of this review is to present the implications of DNA methylation on phenotypic variations driven by environmental changes. More specifically, we explore epigenetic concepts concerning phenotypic change in response to the environment and heritability of DNA methylation, namely the Baldwin effect and genetic accommodation. Before addressing this point, we report major differences in DNA methylation across taxa and the role of this modification in producing and maintaining environmentally induced phenotypic variation. We also present the different methods allowing the detection of methylation polymorphism. We believe this review will be helpful to molecular ecologists, in that it highlights the importance of epigenetic processes in ecological and evolutionary studies.

Baldwinian learning in clonal selection algorithm for optimization

Artificial immune systems are a kind of new computational intelligence methods which draw inspiration from the human immune system. Most immune system inspired optimization algorithms are based on the applications of clonal selection and hypermutation, and known as clonal selection algorithms. These clonal selection algorithms simulate the immune response process based on principles of Darwinian evolution by using various forms of hypermutation as variation operators. The generation of new individuals is a form of the trial and error process. It seems very wasteful not to make use of the Baldwin effect in immune system to direct the genotypic changes. In this paper, based on the Baldwin effect, an improved clonal selection algorithm, Baldwinian Clonal Selection Algorithm, termed as BCSA, is proposed to deal with optimization problems. BCSA evolves and improves antibody population by four operators, clonal proliferation, Baldwinian learning, hypermutation, and clonal selection. It is the first time to introduce the Baldwinian learning into artificial immune systems. The Baldwinian learning operator simulates the learning mechanism in immune system by employing information from within the antibody population to alter the search space. It makes use of the exploration performed by the phenotype to facilitate the evolutionary search for good genotypes. In order to validate the effectiveness of BCSA, eight benchmark functions, six rotated functions, six composition functions and a real-world problem, optimal approximation of linear systems are solved by BCSA, successively. Experimental results indicate that BCSA performs very well in solving most of the test problems and is an effective and robust algorithm for optimization.

Rapid adaptation: a new dimension for evolutionary perspectives in ecology

AbstractAlthough the study of adaptation is central to biology, two types of adaptation are recognized in the biological field: physiological adaptation (accommodation or acclimation; an individual organism's phenotype is adjusted to its environment) and evolutionary–biological adaptation (adaptation is shaped by natural selection acting on genetic variation). The history of the former concept dates to the late nineteenth and early twentieth centuries, and has more recently been systemized in the twenty‐first century. Approaches to the understanding of phenotypic plasticity and learning behavior have only recently been developed, based on cellular–histological and behavioral–neurobiological techniques as well as traditional molecular biology. New developments of the former concepts in phenotypic plasticity are discussed in bacterial persistence, wing di‐/polymorphism with transgenerational effects, polyphenism in social insects, and defense traits for predator avoidance, including molecular biology analyses. We also discuss new studies on the concept of genetic accommodation resulting in evolution of phenotypic plasticity through a transgenerational change in the reaction norm based on a threshold model. Learning behavior can also be understood as physiological phenotypic plasticity, associating with the brain–nervous system, and it drives the accelerated evolutionary change in behavioral response (the Baldwin effect) with memory stock. Furthermore, choice behaviors are widely seen in decision‐making of animal foragers. Incorporating flexible phenotypic plasticity and learning behavior into modeling can drastically change dynamical behavior of the system. Unification of biological sciences will be facilitated and integrated, such as behavioral ecology and behavioral neurobiology in the area of learning, and evolutionary ecology and molecular developmental biology in the theme of phenotypic plasticity.

Nature’s Genetic Gradients and the Clinical Phenotype

When God created the earth, he placed (modern) mankind in East Africa ≈200 000 years ago, as suggested by the phylogenetic and archeological studies.1,2 These hunter-gatherers populated the land and started to migrate, first to the west and southern tip of Africa and then north toward North Africa. Mankind gradually crossed the Arabian Peninsula to the Middle East and Eurasia. Then, over thousands of years of northerly movement, man crossed the Bering land bridge that connected Siberia to Alaska and migrated down to the Americas. This out-of-Africa migration took thousands of generations. It was interrupted by the Ice Age, which led to depopulation and isolation of the surviving population followed by the new waves of migrations, resulting in multiple founding populations.3 Articles see pages 552 and 558 At the genetic level, the tree of life was produced through replication of the genome. For the genome to replicate, cells are equipped with DNA polymerases to copy the parental DNA, which they do at blazing speeds.4 However, “no protein is perfect,” and neither are the DNA polymerases. So, the DNA polymerases commit occasional errors in copying the template (parental) DNA and incorporate wrong nucleotides into the new DNA strands. To correct the errors, nature afforded the cells with DNA repair enzymes, which are assigned the task of maintaining the integrity of the nucleotide pools before replication.5 Nevertheless, the process of DNA replication and editing, although exceedingly precise, is imperfect. The error rate of the DNA replication and editing machinery is estimated to be at 10−6 to 10−10 nucleotides incorporated into the new strand of DNA.6,7 The inheritance is forward. Therefore, the misincorporated nucleotides are passed on to the next generation, and with each generation, new errors in DNA replication are introduced. The occasional “errors of …

A hybrid genetic algorithm with the Baldwin effect

Here we present a new hybrid genetic algorithm (HGA) with the Baldwin effect. In the HGA, a local search is employed to change the fitness of individuals but the acquired improvements do not change the individual itself. This local search step exploits the Baldwin effect. Some numerical applications show that this algorithm can yield the global optimum more efficiently than commonly used HGAs. A theorem is presented that guarantees the convergence in probability of the new HGA.

Plasticity and language: an example of the Baldwin effect?

In recent years, many scholars have suggested that the Baldwin effect may play an important role in the evolution of language. However, the Baldwin effect is a multifaceted and controversial process and the assessment of its connection with language is difficult without a formal model. This paper provides a first step in this direction. We examine a game-theoretic model of the interaction between plasticity (represented by Herrnstein reinforcement learning) and evolution in the context of a simple language game. Additionally, we describe three distinct aspects of the Baldwin effect: the Simpson–Baldwin effect, the Baldwin expediting effect and the Baldwin optimizing effect. We find that a simple model of the evolution of language lends theoretical plausibility to the existence of the Simpson–Baldwin and the Baldwin optimizing effects in this arena, but not the Baldwin expediting effect.

PROBING THE ORIGINS OF THE C IV AND Fe Kα BALDWIN EFFECTS

We use UV/optical and X-ray observations of 272 radio-quiet Type 1 AGNs and quasars to investigate the CIV Baldwin Effect (BEff). The UV/optical spectra are drawn from the Hubble Space Telescope, International Ultraviolet Explorer and Sloan Digital Sky Survey archives. The X-ray spectra are from the Chandra and XMM-Newton archives. We apply correlation and partial-correlation analyses to the equivalent widths, continuum monochromatic luminosities, and alpha_ox, which characterizes the relative X-ray to UV brightness. The equivalent width of the CIV 1549 emission line is correlated with both alpha_ox and luminosity. We find that by regressing l_UV with EW(CIV) and alpha_ox, we can obtain tighter correlations than by regressing l_UV with only EW(CIV). Both correlation and regression analyses imply that l_UV is not the only factor controlling the changes of EW(CIV); alpha_ox (or, equivalently, the soft X-ray emission) plays a fundamental role in the formation and variation of CIV. Variability contributes at least 60% of the scatter of the EW(CIV)-l_UV relation and at least 75% of the scatter of the of the EW(CIV)-alpha_ox relation. In our sample, narrow Fe Kalpha 6.4 keV emission lines are detected in 50 objects. Although narrow Fe Kalpha exhibits a BEff similar to that of CIV, its equivalent width has almost no dependence on either alpha_ox or EW(CIV). This suggests that the majority of narrow Fe Kalpha emission is unlikely to be produced in the broad emission-line region. We do find suggestive correlations between the emission-line luminosities of CIV and Fe Kalpha, which could be potentially used to estimate the detectability of the Fe Kalpha line of quasars from rest-frame UV spectroscopic observations.

On the Physical Mechanism Underlying PC1 and Baldwin Effect in Quasars

Recent work (Baskin &amp; Laor 2004; Dong et al. 2009a, b) suggests that the Eddington ratio (l ≡ L/LEdd) is the origin of all the significant first-order object-to-object variations of quasar spectral properties from the zeroth-order similarity of AGN spectra; specifically, this includes the PC1 of Boroson &amp; Green (1992), the classic or inverse Baldwin effect (Baldwin 1977), and even blueshifting (i.e., blue asymmetry) of high-ionization emission lines (Dong et al. 2009c).

Epoxide‐Hydrolase‐Initiated Hydrolysis/Rearrangement Cascade of a Methylene‐Interrupted Bis‐Epoxide Yields Chiral THF Moieties without Involvement of a “Cyclase”

In contrast with electrophilic enzyme-catalysed cyclisations in terpenoid biosynthesis, cyclisations of tetrahydrofuran moieties found in several groups of natural products, such as annonaceous acetogenins, neurofurans and phytooxylipins, appear to proceed through a nucleophilic cascade mechanism starting from bis-epoxy fatty acid precursors. This hypothesis was verified by epoxide-hydrolase-catalysed hydrolytic ring-opening/cyclisation cascades starting from a methylene-interrupted meso-bis-epoxide model substrate, which furnished the corresponding THF products with excellent de and ee values. Molecular modelling showed that the points of enzyme attack were consistent with the stereospecificities of the enzymes, whereas the stereochemical courses of the cyclisation were solely governed by Baldwin's rules and did not invoke the involvements of a "cyclase".

Evolution and Learning: The Baldwin Effect Reconsidered. Bruce H. Weber and David J. Depew (Eds.). (2003, MIT Press.) $50 (hardcover), $25 (paper), 351 pages

Evolution and Learning: The Baldwin Effect Reconsidered. Bruce H. Weber and David J. Depew (Eds.). (2003, MIT Press.) $50 (hardcover), $25 (paper), 351 pages. ALife researchers have typically interpreted the Baldwin effect (BE) [2, 3] as a two-step evolution of the genetic acquisition of a learned trait without the Lamarckian mechanism: Individuals that have successfully adapted their own trait to the environment through their lifetime learning processes occupy the population (first step), and then the evolutionary path finds the innate trait that can replace the learned trait (second step) because of the cost of learning [17]. I think that this definition stemmed in part from the introduction of Hinton and Nowlan’s pioneering work [6] on the BE by Maynard-Smith in Nature [8]. However, what we first learn from this book is that the BE has been redefined several times and diversely interpreted in its more than 100-year history. This book is a collection of essays on this effect and related concepts, written by participants in an interdisciplinary conference on the emergence of mind and by several invited authors. It includes the history of the BE, its significance in language evolution or developmental biology, and its relationship to the evolution of consciousness or mind as an ultimate form of phenotypic plasticity. Recently, the BE and the role of phenotypic plasticity in evolution have been drawing much attention in evolutionary developmental biology; many experimental results on this effect have been reported [4, 13, 20]. Here, I summarize the topics in each chapter and then make several comments on what needs to be added, together with implications for further research on the BE in the ALife field. David J. Depew, one of the editors of this book, reviewed various versions of the BE defined by Baldwin himself, by the framers of the modern synthesis, and by the contemporary boosters of the BE such as Dennett and Deacon (Chapter 1). For example, according to Depew, natural selection is an indiscriminate force (rather than a creative force) that kills individuals before their reproduction (thus, adaptive learning keeps the individuals alive and determines evolution by securing genetic variations) in Baldwin’s original scenario of ‘‘organic selection’’ [2, 3]. On the other hand, the BE is merely a special case of Waddington’s genetic assimilation [18] for G. G. Simpson [14], who named the term ‘‘the Baldwin effect’’; however, he was skeptical about its significance. Depew states that, if the history of the BE is any guide, we should be cautious about dismissing these hypotheses just because they do not fit with existing interpretive schemes. Although Stephen M. Downes and Peter Godfrey-Smith are skeptical about the BE, they discuss the differences between these versions from several viewpoints. Downes classifies them by focusing on what kind of traits are considered and what kind of outcomes will be brought about as a result of the BE (Chapter 2). Godfrey-Smith compares the significance of several mechanisms that enable the ontogenetic adaptation (first step) to affect the acquisition of the innate trait (second step) among these versions (Chapter 3). He points out that the existence of similarity relations between genotypes can facilitate the genetic acquisition of the learned trait, but the niche construction induced by the ontogenetic adaptation is a more significant mechanism for the evolution of a novel trait that differs from the one previously acquired through the learning process. One of the controversial issues relating to the BE is language evolution, which includes both the cultural evolution of language and the evolution of language ability. Daniel Dennett and Terrence W. Deacon regard the BE or Baldwinian evolution as a key concept of language evolution; however, their scenarios are different. According to Dennett, the BE is essential to explain the genetic acquisition of a complex trait such as the innate ability for language acquisition, which is impossible

The Influence of Learning on Evolution: A Mathematical Framework

The Baldwin effect can be observed if phenotypic learning influences the evolutionary fitness of individuals, which can in turn accelerate or decelerate evolutionary change. Evidence for both learning-induced acceleration and deceleration can be found in the literature. Although the results for both outcomes were supported by specific mathematical or simulation models, no general predictions have been achieved so far. Here we propose a general framework to predict whether evolution benefits from learning or not. It is formulated in terms of the gain function, which quantifies the proportional change of fitness due to learning depending on the genotype value. With an inductive proof we show that a positive gain-function derivative implies that learning accelerates evolution, and a negative one implies deceleration under the condition that the population is distributed on a monotonic part of the fitness landscape. We show that the gain-function framework explains the results of several specific simulation models. We also use the gain-function framework to shed some light on the results of a recent biological experiment with fruit flies.

APF-guided adaptive immune network algorithm for robot path planning

Inspired by the mechanism of Jerne’s idiotypic network hypothesis, a new adaptive immune network algorithm (AINA) is presented through the stimulation and suppression between the antigen and antibody by taking the environment and robot behavior as antigen and antibody respectively. A guiding weight is defined based on the artificial potential field (APF) method, and the guiding weight is combined with antibody vitality to construct a new antibody selection operator, which improves the searching efficiency. In addition, an updating operator of antibody vi-tality is provided based on the Baldwin effect, which results in a positive feedback mechanism of search and accelerates the convergence of the immune network. The simulation and experimental results show that the proposed algorithm is characterized by high searching speed, good convergence performance and strong planning ability, which solves the path planning well in complicated environments.

Evolutionary significance of phenotypic accommodation in novel environments: an empirical test of the Baldwin effect.

When faced with changing environments, organisms rapidly mount physiological and behavioural responses, accommodating new environmental inputs in their functioning. The ubiquity of this process contrasts with our ignorance of its evolutionary significance: whereas within-generation accommodation of novel external inputs has clear fitness consequences, current evolutionary theory cannot easily link functional importance and inheritance of novel accommodations. One hundred and twelve years ago, J. M. Baldwin, H. F. Osborn and C. L. Morgan proposed a process (later termed the Baldwin effect) by which non-heritable developmental accommodation of novel inputs, which makes an organism fit in its current environment, can become internalized in a lineage and affect the course of evolution. The defining features of this process are initial overproduction of random (with respect to fitness) developmental variation, followed by within-generation accommodation of a subset of this variation by developmental or functional systems ('organic selection'), ensuring the organism's fit and survival. Subsequent natural selection sorts among resultant developmental variants, which, if recurrent and consistently favoured, can be inherited when existing genetic variance includes developmental components of individual modifications or when the ability to accommodate novel inputs is itself heritable. Here, I show that this process is consistent with the origin of novel adaptations during colonization of North America by the house finch. The induction of developmental variation by novel environments of this species's expanding range was followed by homeostatic channelling, phenotypic accommodation and directional cross-generational transfer of a subset of induced developmental outcomes favoured by natural selection. These results emphasize three principal points. First, contemporary novel adaptations result mostly from reorganization of existing structures that shape newly expressed variation, giving natural selection an appearance of a creative force. Second, evolutionary innovations and maintenance of adaptations are different processes. Third, both the Baldwin and parental effects are probably a transient state in an evolutionary cycle connecting initial phenotypic retention of adaptive changes and their eventual genetic determination and, thus, the origin of adaptation and evolutionary change.

Evolution of maternal effects: past and present.

It has been said that many original ideas reflect a convergence of related thought that coalesces into a unified representation of what many have been thinking. This is certainly true for the subfield of maternal effects evolution. The study of maternal effects has a long history. The first two

A CATALOG OF BROAD ABSORPTION LINE QUASARS IN SLOAN DIGITAL SKY SURVEY DATA RELEASE 5

We present a catalog of 5039 broad absorption line (BAL) quasars (QSOs) in the Sloan Digital Sky Survey (SDSS) Data Release 5 (DR5) QSO catalog that have absorption troughs covering a continuous velocity range >= 2000 km/s. We have fit ultraviolet (UV) continua and line emission in each case, enabling us to report common diagnostics of BAL strengths and velocities in the range -25,000 to 0 km/s for SiIV $\lambda$1400, CIV $\lambda$1549, AlIII $\lambda$1857, and MgII $\lambda$2799. We calculate these diagnostics using the spectrum listed in the DR5 QSO catalog, and also for spectra from additional SDSS observing epochs when available. In cases where BAL QSOs have been observed with Chandra or XMM-Newton, we report the X-ray monochromatic luminosities of these sources. We confirm and extend previous findings that BAL QSOs are more strongly reddened in the rest-frame UV than non-BAL QSOs and that BAL QSOs are relatively X-ray weak compared to non-BAL QSOs. The observed BAL fraction is dependent on the spectral signal-to-noise (S/N); for higher-S/N sources, we find an observed BAL fraction of approximately 15%. BAL QSOs show a similar Baldwin effect as for non-BAL QSOs, in that their CIV emission equivalent widths decrease with increasing continuum luminosity. However, BAL QSOs have weaker CIV emission in general than do non-BAL QSOs. Sources with higher UV luminosities are more likely to have higher-velocity outflows, and the BAL outflow velocity and UV absorption strength are correlated with relative X-ray weakness. These results are in qualitative agreement with models that depend on strong X-ray absorption to shield the outflow from over-ionization and enable radiative acceleration....

Consciousness, social heredity, and development: The evolutionary thought of James Mark Baldwin.

James Mark Baldwin is one of the most important and least known early American scientific psychologists. Drawing inspiration from Charles Darwin and other evolutionists of the period, Baldwin developed a biosocial theory of psychological development that influenced both Jean Piaget and Lev S. Vygotsky; and he proposed a mechanism relating learned adaptations in the individual to phylogenesis (frequently termed the "Baldwin effect") that is of considerable interest to those currently modeling processes of learning and evolution. After a brief introduction to Baldwin's career, this article describes the intellectual context within which his evolutionary thinking developed. Three of his most important contributions are then discussed: his theory of individual adaptation or learning, his concept of "social heredity," and his articulation of the "Baldwin effect." The article concludes with a brief evaluation of the contemporary importance of Baldwin's ideas.

Simulation of the evolution of autonomous adaptive agents

A model of evolving populations of self-learning agents is studied, and the interaction between learning and evolution is analyzed. Each agent is equipped with a neural network (NN) adaptive critic design for behavioral adaptation. The model is investigated by an example of a simple agent-broker that predicts stock price changes and uses these predictions for choosing strategies. Three variants of the model are compared, which include either learning and evolution, or only evolution, or only learning. It is shown that the model may exhibit the Baldwin effect; i.e., initially acquired adaptive policy of agents becomes inheritable during evolution. The behavior of the model agents is compared with the searching behavior of simple animals.