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PubMed2001

Evolutionary internalized regularities.

Roger Shepard's proposals and supporting experiments concerning evolutionary internalized regularities have been very influential in the study of vision and in other areas of psychology and cognitive science. This paper examines issues concerning the need, nature, explanatory role, and justification for postulating such internalized constraints. In particular, I seek further clarification from Shepard on how best to understand his claim that principles of kinematic geometry underlie phenomena of motion perception. My primary focus is on the ecological validity of Shepard's kinematic constraint in the context of ordinary motion perception. First, I explore the analogy Shepard draws between internalized circadian rhythms and the supposed internalization of kinematic geometry. Next, questions are raised about how to interpret and justify applying results from his own and others' experimental studies of apparent motion to more everyday cases of motion perception in richer environments. Finally, some difficulties with Shepard's account of the evolutionary development of his kinematic constraint are considered.

Biological Evolution↗
PubMed2002

Facial expression of pain: an evolutionary account.

This paper proposes that human expression of pain in the presence or absence of caregivers, and the detection of pain by observers, arises from evolved propensities. The function of pain is to demand attention and prioritise escape, recovery, and healing; where others can help achieve these goals, effective communication of pain is required. Evidence is reviewed of a distinct and specific facial expression of pain from infancy to old age, consistent across stimuli, and recognizable as pain by observers. Voluntary control over amplitude is incomplete, and observers can better detect pain that the individual attempts to suppress rather than amplify or simulate. In many clinical and experimental settings, the facial expression of pain is incorporated with verbal and nonverbal vocal activity, posture, and movement in an overall category of pain behaviour. This is assumed by clinicians to be under operant control of social contingencies such as sympathy, caregiving, and practical help; thus, strong facial expression is presumed to constitute and attempt to manipulate these contingencies by amplification of the normal expression. Operant formulations support skepticism about the presence or extent of pain, judgments of malingering, and sometimes the withholding of caregiving and help. To the extent that pain expression is influenced by environmental contingencies, however, "amplification" could equally plausibly constitute the release of suppression according to evolved contingent propensities that guide behaviour. Pain has been largely neglected in the evolutionary literature and the literature on expression of emotion, but an evolutionary account can generate improved assessment of pain and reactions to it.

Adaptation, Physiological↗
PubMed2004

Religion's evolutionary landscape: counterintuition, commitment, compassion, communion.

Religion is not an evolutionary adaptation per se, but a recurring cultural by-product of the complex evolutionary landscape that sets cognitive, emotional, and material conditions for ordinary human interactions. Religion exploits only ordinary cognitive processes to passionately display costly devotion to counterintuitive worlds governed by supernatural agents. The conceptual foundations of religion are intuitively given by task-specific panhuman cognitive domains, including folkmechanics, folkbiology, and folkpsychology. Core religious beliefs minimally violate ordinary notions about how the world is, with all of its inescapable problems, thus enabling people to imagine minimally impossible supernatural worlds that solve existential problems, including death and deception. Here the focus is on folkpsychology and agency. A key feature of the supernatural agent concepts common to all religions is the triggering of an "Innate Releasing Mechanism," or "agency detector," whose proper (naturally selected) domain encompasses animate objects relevant to hominid survival--such as predators, protectors, and prey--but which actually extends to moving dots on computer screens, voices in wind, and faces on clouds. Folkpsychology also crucially involves metarepresentation, which makes deception possible and threatens any social order. However, these same metacognitive capacities provide the hope and promise of open-ended solutions through representations of counterfactual supernatural worlds that cannot be logically or empirically verified or falsified. Because religious beliefs cannot be deductively or inductively validated, validation occurs only by ritually addressing the very emotions motivating religion. Cross-cultural experimental evidence encourages these claims.

Anxiety↗
PubMed2005

From monkey-like action recognition to human language: an evolutionary framework for neurolinguistics.

The article analyzes the neural and functional grounding of language skills as well as their emergence in hominid evolution, hypothesizing stages leading from abilities known to exist in monkeys and apes and presumed to exist in our hominid ancestors right through to modern spoken and signed languages. The starting point is the observation that both premotor area F5 in monkeys and Broca's area in humans contain a "mirror system" active for both execution and observation of manual actions, and that F5 and Broca's area are homologous brain regions. This grounded the mirror system hypothesis of Rizzolatti and Arbib (1998) which offers the mirror system for grasping as a key neural "missing link" between the abilities of our nonhuman ancestors of 20 million years ago and modern human language, with manual gestures rather than a system for vocal communication providing the initial seed for this evolutionary process. The present article, however, goes "beyond the mirror" to offer hypotheses on evolutionary changes within and outside the mirror systems which may have occurred to equip Homo sapiens with a language-ready brain. Crucial to the early stages of this progression is the mirror system for grasping and its extension to permit imitation. Imitation is seen as evolving via a so-called simple system such as that found in chimpanzees (which allows imitation of complex "object-oriented" sequences but only as the result of extensive practice) to a so-called complex system found in humans (which allows rapid imitation even of complex sequences, under appropriate conditions) which supports pantomime. This is hypothesized to have provided the substrate for the development of protosign, a combinatorially open repertoire of manual gestures, which then provides the scaffolding for the emergence of protospeech (which thus owes little to nonhuman vocalizations), with protosign and protospeech then developing in an expanding spiral. It is argued that these stages involve biological evolution of both brain and body. By contrast, it is argued that the progression from protosign and protospeech to languages with full-blown syntax and compositional semantics was a historical phenomenon in the development of Homo sapiens, involving few if any further biological changes.

Animal Communication↗
PubMed1988

Location on the evolutionary tree of influenza H3 haemagglutinin genes of Japanese strains isolated during 1985-6 season.

The nucleotide sequences of the haemagglutinin (HA) genes of influenza A (H3N2) isolates from the 1985-6 season in Japan along with those of several viruses isolated between 1982-5 from other countries were analyzed to determine the origin of the 1985-6 Japanese strains. The HA genes of these viruses consisted of 1762 nucleotides and had a three-nucleotide deletion downstream from the stop codon when compared to the sequences of earlier Hong Kong H3N2 viruses. An evolutionary tree of the HA genes of these viruses was drawn using the A/Bangkok/1/79 sequence as the starting point. Eight strains isolated from Asian and Pacific regions including Japan in the 1985-6 season (one in May) had the HA genes located closely on the evolutionary tree but away from those of the isolates in North America and Europe during the 1984-5 season, and a common ancestry for these viruses was suggested.

Amino Acid Sequence↗
PubMed1989

Evolutionary remodeling in a visual system through extensive changes in the synaptic connectivity of homologous neurons.

The cellular mechanisms by which nervous systems evolve to match evolutionary changes occurring in the rest of the body remain largely unexplored. In a distal visual neuropil of a previously unexamined ancient dipteran family, Stratiomyidae, homologues of all of the periodic neurons known already from more recent Diptera can be recognized, occupying the same locations within the unit structure. This points to extreme developmental stasis for more than 200 million years, conserving both cell identity and position. The arborizations that some neurons make also have remained conservative, but others show marked differences between families in both size and branching patterns. At the electron-microscopical level, extensive differences in synaptic connectivity are found, some sufficient to radically redefine the systems roles of particular neurons. The findings bear out an earlier prediction that changes in the connectivity matrix linking conserved neurons may have been a major factor in implementing evolutionary change in the nervous system.

Animals↗
PubMed2005

Biological sensitivity to context: I. An evolutionary-developmental theory of the origins and functions of stress reactivity.

Biological reactivity to psychological stressors comprises a complex, integrated, and highly conserved repertoire of central neural and peripheral neuroendocrine responses designed to prepare the organism for challenge or threat. Developmental experience plays a role, along with heritable, polygenic variation, in calibrating the response dynamics of these systems, with early adversity biasing their combined effects toward a profile of heightened or prolonged reactivity. Conventional views of such high reactivity suggest that it is an atavistic and pathogenic legacy of an evolutionary past in which threats to survival were more prevalent and severe. Recent evidence, however, indicates that (a) stress reactivity is not a unitary process, but rather incorporates counterregulatory circuits serving to modify or temper physiological arousal, and (b) the effects of high reactivity phenotypes on psychiatric and biomedical outcomes are bivalent, rather than univalent, in character, exerting both risk-augmenting and risk-protective effects in a context-dependent manner. These observations suggest that heightened stress reactivity may reflect, not simply exaggerated arousal under challenge, but rather an increased biological sensitivity to context, with potential for negative health effects under conditions of adversity and positive effects under conditions of support and protection. From an evolutionary perspective, the developmental plasticity of the stress response systems, along with their structured, context-dependent effects, suggests that these systems may constitute conditional adaptations: evolved psychobiological mechanisms that monitor specific features of childhood environments as a basis for calibrating the development of stress response systems to adaptively match those environments. Taken together, these theoretical perspectives generate a novel hypothesis: that there is a curvilinear, U-shaped relation between early exposures to adversity and the development of stress-reactive profiles, with high reactivity phenotypes disproportionately emerging within both highly stressful and highly protected early social environments.

Environment↗
PubMed2005

Biological sensitivity to context: II. Empirical explorations of an evolutionary-developmental theory.

In two studies comprising 249 children and their families, the authors utilized secondary, exploratory data analyses to examine Boyce and Ellis' (this issue) evolutionary-developmental theory of biological sensitivity to context. The theory proposes that individual differences in stress reactivity constitute variation in susceptibility to environmental influence, both positive and negative, and that early childhood exposures to either highly protective or acutely stressful environments result in heightened reactivity. In Study 1, 127 3- to 5-year old children were concurrently assessed on levels of support/adversity in home and preschool environments and on cardiovascular reactivity to laboratory challenges. In Study 2, 122 children were prospectively assessed on familial stress in both infancy and preschool and on autonomic and adrenocortical reactivity to laboratory challenges at age 7. In both studies, a disproportionate number of children in supportive, low stress environments displayed high autonomic reactivity. Conversely, in Study 2, a relatively high proportion of children in very stressful environments showed evidence of heightened sympathetic and adrenocortical reactivity. Consistent with the evolutionary-developmental theory, the exploratory analyses also generated the testable hypothesis that relations between levels of childhood support/adversity and the magnitude of stress reactivity are curvilinear, with children from moderately stressful environments displaying the lowest reactivity levels in both studies.

Biological Evolution↗
PubMed2003

Formation of dermal skeletal and dental tissues in fish: a comparative and evolutionary approach.

Osteichthyan and chondrichthyan fish present an astonishing diversity of skeletal and dental tissues that are often difficult to classify into the standard textbook categories of bone, cartilage, dentine and enamel. To address the question of how the tissues of the dermal skeleton evolved from the ancestral situation and gave rise to the diversity actually encountered, we review previous data on the development of a number of dermal skeletal elements (odontodes, teeth and dermal denticles, cranial dermal bones, postcranial dermal plates and scutes, elasmoid and ganoid scales, and fin rays). A comparison of developmental stages at the tissue level usually allows us to identify skeletogenic cell populations as either odontogenic or osteogenic on the basis of the place of formation of their dermal papillae and of the way of deposition of their tissues. Our studies support the evolutionary affinities (1) between odontodes, teeth and denticles, (2) between the ganoid scales of polypterids and the elasmoid scales of teleosts, and (3) to a lesser degree between the different bony elements. There is now ample evidence to ascertain that the tissues of the elasmoid scale are derived from dental and not from bony tissues. This review demonstrates the advantage that can be taken from developmental studies, at the tissue level, to infer evolutionary relationships within the dermal skeleton in chondrichthyans and osteichthyans.

Animals↗
PubMed2004

Surface plasmon resonance: theoretical evolutionary design optimization for a model analyte sensitive absorbing-layer system.

Surface plasmon resonance (SPR) has been widely used in a Kretschmann configuration to study optical thickness changes of layers on a Au surface in response to an analyte. The method has been popularized and optimized for protein layers, but has also been used in the same format for other layers without further optimization including those absorbing at the incident wavelength. In this paper, we examine whether SPR remains the "best"attenuated reflectivity format for absorbing overlayers. Experimental data from the SPR response of a copper phthalocyanine film to nitrogen dioxide are used as an input example for a design process using an evolutionary algorithm. The data showed a trend toward thinner gold layer systems ( approximately 25 nm gave an contrast-enhancement of 42.9% compared with approximately 50-nm Au) or Au-free solutions including a layer with low refractive index. From the evolutionary design predictions, further modification could be tested based on available materials and "redundant layers" could be eliminated from the final selection. By inclusion of the external optics, a design could be selected to accommodate poor precision (+/-0.5 degrees ) in the incident angle and a possible multilayer solution was shown using Teflon AF 1600, with refractive index approximately 1.3. The predicted NO(2) response showed an improvement compared with the classical SPR configuration, and the incident angle chosen by the SGA for the interrogation of these layers was close to a stationary point in the absolute response curve, thus offering very good tolerance to automatic position referencing to the reflectivity minimum.

Equipment Design↗
PubMed1975

Properties of chicken skeletal muscle pyruvate kinase and a proposal for its evolutionary relationship to the other avian and mammalian isozymes.

Pyruvate kinase (EC 2.7.1.40) was isolated and purified from chicken and turkey breast muscle with a purification procedure very similar to that used for the bovine skeletal muscle isozyme (Cardenas, J., Dyson, R., and strandholm, J. (1973), J. Biol. Chem. 248,6931). A study of the chemical and physical properties of the chicken enzyme revealed that it is a tetramer of four apparently identical subunits, closely resembling in this and most other respects the mamalian type 7 isozyme. The properties of these two enzymes are similar enough to permit subunits of chicken type M pyruvate kinase to combine with subunits of mammalian type L (one of the three mammalian isozymes) to form interspecies tetrameric hybrid isozymes in relative quantities that do not differ makedly from those formed when both the M and L isozymes are of mammalian origin. The similarity between the mammalian and avian type M pyruvates kinases suggests a close evolutionary relationship. Further comparisons among the three mammalian and two avian isozymes of pyruvate kinase are consistent with a common evolutionary origin, perhaps from an ancestral form of the type K isozyme, which is the only pyruvate kinase identified in mammalian and avian embryos.

Amino Acids↗
PubMed1998

Consequence of the removal of evolutionary conserved disulfide bridges on the structure and function of charybdotoxin and evidence that particular cysteine spacings govern specific disulfide bond formation.

Scorpion toxins are miniglobular proteins containing a common structural motif formed by an alpha-helix on one face, an antiparallel beta-sheet on the opposite face, and three disulfide bonds making up most of its internal volume. We have investigated the role of these evolutionary conserved bonds by replacing each couple of bridged cysteine residues of the scorpion charybdotoxin by a pair of nonbridging L-alpha-aminobutyric acid (Aba) residues. Three analogues were obtained by solid-phase synthesis, Chab I, Chab II, and Chab III, containing the Aba residues in positions 7 and 28, 13 and 33, 17 and 35, respectively. Circular dichroism analysis showed that the purified Chab II acquired a conformation similar to that of charybdotoxin, while the Chab I and Chab III possess decreased nativelike characteristics. All analogues block single high-conductance Ca(2+)-activated K+ channels from rat skeletal muscle inserted into planar lipid bilayers, but with different potencies. Chab II is the most active analogue (KD = 8.0 x 10(-8) M), with a 9-fold lower affinity as compared to native charybdotoxin. Chab I and Chab III have, respectively, 180- and 580-fold lower affinity. Therefore, the removal of evolutionary conserved disulfide bridges does not prevent the toxin to adopt a functional and presumably nativelike structure. However, removal of one disulfide bond affects the yields of formation of correct pairing between the remaining cysteine residues, and only Chab I preserves the ability to form the native disulfide pairings with high efficiency. This is the only analogue to preserve particular spacings of three and one residue between the cysteines, which have been described to thermodynamically disfavor disulfide bond formation between the cysteines [Zhang R., and Snyder, G. H. (1989) J. Biol. Chem. 264, 18472-18479]. Therefore, we conclude that the position of the cysteine residues in the sequence of charybdotoxin, by disfavoring specific pairings and favoring others, may govern selective formation of specific disulfide bonds, thus, explaining the efficient folding properties of Chab I and of native charybdotoxin. The structural properties of the Chab analogues and the discovered role of the cysteine spacings have interesting implications in protein design and engineering.

Amino Acid Sequence↗
PubMedDate not supplied

Global optimization of Lennard-Jones clusters by a parallel fast annealing evolutionary algorithm.

A parallel fast annealing evolutionary algorithm (PFAEA) was presented and applied to optimize Lennard-Jones (LJ) clusters. All the lowest known minima up to LJ(116) with both icosahedral and nonicosahedral structure, including the truncated octahedron of LJ(38), central fcc tetrahedron of LJ(98), the Marks' decahedron of LJ(75)(-)(77), and LJ(102)(-)(104), were located successfully by the unbiased algorithm. PFAEA is a parallel version of fast annealing evolutionary algorithm (FAEA) that combines the aspect of population in genetic algorithm and annealing algorithm with a very fast annealing schedule. A master-slave paradigm is used to parallelize FAEA to improve the efficiency. The performance of PFAEA is studied, and the scaling of execution time with the cluster size is approximately cubic, which is important for larger scale energy minimization systems.

Journal Article↗
PubMedDate not supplied

Evolutionary-algorithm-based strategy for computer-assisted structure elucidation.

An evolutionary algorithm (EA) using a graph-based data structure to explore the molecular constitution space is presented. The EA implementation proves to be a promising alternative to deterministic approaches to the problem of computer-assisted structure elucidation (CASE). While not relying on any external database, the EA-guided CASE program SENECA is able to find correct solutions within calculation times comparable to that of other CASE expert systems. The implementation presented here significantly expands the size limit of constitutional optimization problems treatable with evolutionary algorithms by introducing novel efficient graph-based genetic operators. The new EA-based search strategy is discussed including the underlying data structures, component design, parameter optimization, and evolution process control. Typical structure elucidation examples are given to demonstrate the algorithm's performance.

Journal Article↗
PubMedDate not supplied

Induction of decision trees via evolutionary programming.

Decision trees have been used extensively in cheminformatics for modeling various biochemical endpoints including receptor-ligand binding, ADME properties, environmental impact, and toxicity. The traditional approach to inducing decision trees based upon a given training set of data involves recursive partitioning which selects partitioning variables and their values in a greedy manner to optimize a given measure of purity. This methodology has numerous benefits including classifier interpretability and the capability of modeling nonlinear relationships. The greedy nature of induction, however, may fail to elucidate underlying relationships between the data and endpoints. Using evolutionary programming, decision trees are induced which are significantly more accurate than trees induced by recursive partitioning. Furthermore, when assessed on previously unseen data in a 10-fold cross-validated manner, evolutionary programming induced trees exhibit a significantly higher accuracy on previously unseen data. This methodology is compared to single-tree and multiple-tree recursive partitioning in two domains (aerobic biodegradability and hepatotoxicity) and shown to produce less complex classifiers with average increases in predictive accuracy of 5-10% over the traditional method.

Biological Evolution↗
PubMed1997

Evolutionary relationships among proteins probed by an iterative neighborhood cluster analysis (INCA). Alignment of bacteriorhodopsins with the yeast sequence YRO2.

PURPOSE: Searching the existing databases for homologous sequences is essential to understanding a protein's structure and function. For a query sequence, its nearest neighbors can be identified by BLAST (basic local alignment search tool). However, a single query sequence is sufficient to define the entire neighborhood of related sequences, and multiple BLAST queries are needed. We describe here a program which permits automated and iterative BLAST analysis of an entire neighborhood of sequences and apply this to search for homologs of the bacteriorhodopsins outside the archaea phylum. METHODS: We have developed a Java program, 'Iterative Neighborhood Cluster Analysis' (INCA), which performs iterative BLAST searches, beginning with a single starter sequence, and proceeding with any other sequence achieving a predefined minimum alignment score. This results in a cluster of sequences where each sequence is related to at least one other sequence by the cutoff score, additional lists of more distantly related sequences for each member of cluster. RESULTS: Bacteriorhodopsins had not been previously aligned with any other protein family with scores indicative of probable homology. Using INCA, we identified a probable homolog in yeast, YRO2_YEAST, also containing seven putative transmembrane domains. A finding of probable homology was supported by additional alignment strategies. CONCLUSIONS: INCA is a useful tool to assess complete protein neighborhoods. With an increasing database, INCA can serve to detect the emergence of evolutionary links between even the most distantly related protein families. Identifying a homolog of the bacteriorhodopsins in yeast illustrates this approach but at the same time highlights the vast evolutionary distances between polytopic membrane proteins, such as the bacteriorhodopsins.

Amino Acid Sequence↗
PubMed2002

Adaptation, punctuation and information: a rate-distortion approach to non-cognitive 'learning plateaus' in evolutionary process.

We extend recent information-theoretic phase transition approaches to evolutionary and cognitive process via the Rate Distortion and Joint Asymptotic Equipartition Theorems, in the circumstance of interaction with a highly structured environment. This suggests that learning plateaus in cognitive systems and punctuated equilibria in evolutionary process are formally analogous, even though evolution is not cognitive. Extending arguments by Adami et al. (2000), we argue that 'adaptation' is the process by which a distorted genetic image of a coherently structured environment is imposed upon a species.

Adaptation, Biological↗
PubMed2002

Evolutionary significance of chromosome changes in northeastern Asiatic red-backed voles inferred with the aid of intron 1 sequences of the G6pd gene.

To evaluate the evolutionary significance of karyotypic characters in red-backed voles (Rodentia, Arvicolinae, genera Clethrionomys and Eothenomys) from northeastern Asia, we constructed phylogenetic trees based on intron 1 sequences (ca. 580 bp) of the X-linked gene G6pd. Phylogenetic trees, constructed using neighbor-joining and maximum-likelihood methods, revealed two major clades in red-backed voles corresponding to the glareolus- and the rufocanus-cytotypes defined by a reciprocal translocation between chromosomes 1 and 9 based on G-band patterns. If confirmed, two types of X chromosome, acrocentric X and subtelocentric X, which have often been claimed to be traits of evolutionary and taxonomic significance, should be considered as examples of homoplasy because they occur sporadically in members of both rufocanus- and glareolus-cytotypes in red-backed voles.

Animals↗