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PubMed2002

Social intelligence, innovation, and enhanced brain size in primates.

Despite considerable current interest in the evolution of intelligence, the intuitively appealing notion that brain volume and "intelligence" are linked remains untested. Here, we use ecologically relevant measures of cognitive ability, the reported incidence of behavioral innovation, social learning, and tool use, to show that brain size and cognitive capacity are indeed correlated. A comparative analysis of 533 instances of innovation, 445 observations of social learning, and 607 episodes of tool use established that social learning, innovation, and tool use frequencies are positively correlated with species' relative and absolute "executive" brain volumes, after controlling for phylogeny and research effort. Moreover, innovation and social learning frequencies covary across species, in conflict with the view that there is an evolutionary tradeoff between reliance on individual experience and social cues. These findings provide an empirical link between behavioral innovation, social learning capacities, and brain size in mammals. The ability to learn from others, invent new behaviors, and use tools may have played pivotal roles in primate brain evolution.

Animals↗
PubMed2002

On the evolution of cells.

A theory for the evolution of cellular organization is presented. The model is based on the (data supported) conjecture that the dynamic of horizontal gene transfer (HGT) is primarily determined by the organization of the recipient cell. Aboriginal cell designs are taken to be simple and loosely organized enough that all cellular componentry can be altered and/or displaced through HGT, making HGT the principal driving force in early cellular evolution. Primitive cells did not carry a stable organismal genealogical trace. Primitive cellular evolution is basically communal. The high level of novelty required to evolve cell designs is a product of communal invention, of the universal HGT field, not intralineage variation. It is the community as a whole, the ecosystem, which evolves. The individual cell designs that evolved in this way are nevertheless fundamentally distinct, because the initial conditions in each case are somewhat different. As a cell design becomes more complex and interconnected a critical point is reached where a more integrated cellular organization emerges, and vertically generated novelty can and does assume greater importance. This critical point is called the "Darwinian Threshold" for the reasons given.

Biological Evolution↗
PubMed2000

Testing a biosynthetic theory of the genetic code: fact or artifact?

It has long been conjectured that the canonical genetic code evolved from a simpler primordial form that encoded fewer amino acids [e.g., Crick, F. H. C. (1968) J. Mol. Biol. 38, 367-379]. The most influential form of this idea, "code coevolution" [Wong, J. T.-F. (1975) Proc. Natl. Acad. Sci. USA 72, 1909-1912], proposes that the genetic code coevolved with the invention of biosynthetic pathways for new amino acids. It further proposes that a comparison of modern codon assignments with the conserved metabolic pathways of amino acid biosynthesis can inform us about this history of code expansion. Here we re-examine the biochemical basis of this theory to test the validity of its statistical support. We show that the theory's definition of "precursor-product" amino acid pairs is unjustified biochemically because it requires the energetically unfavorable reversal of steps in extant metabolic pathways to achieve desired relationships. In addition, the theory neglects important biochemical constraints when calculating the probability that chance could assign precursor-product amino acids to contiguous codons. A conservative correction for these errors reveals a surprisingly high 23% probability that apparent patterns within the code are caused purely by chance. Finally, even this figure rests on post hoc assumptions about primordial codon assignments, without which the probability rises to 62% that chance alone could explain the precursor-product pairings found within the code. Thus we conclude that coevolution theory cannot adequately explain the structure of the genetic code.

Codon↗
PubMed1978

Use of T4 RNA ligase to construct model substrates for a ribosomal RNA maturation endonuclease.

RNase M5 of Bacillus subtilis specifically cleaves a 179-nucleotide precursor 5S rRNA to yield mature 5S rRNA (116 nucleotides) and two fragments derived from the termini. Possible recognition elements for RNase M5 within the precursor structure include nucleotide sequences arranged with 2-fold rotational and translational symmetry about the substrate bonds. We have used bacteriophage T4 RNA ligase to construct, from synthetic oligonucleotides and mature or precursor 5S rRNA fragments, test substrates lacking these symmetry elements. The susceptibilities of the artificial substrates to RNase M5 demonstrate that the symmetrically arranged sequences are not used in the RNase M5 interaction with the precursor. Additionally, the synthetic protocols permitted the invention of an acid-soluble assay for RNase M5 and, potentially, other specific endoribonucleases.

Bacillus subtilis↗
PubMed1983

Classes of unitarizable derived functor modules.

For a real semisimple Lie group G, the description of the unitary dual remains an elusive question. One of the difficulties has been the lack of technique for constructing unitary representations. Unitary induction from parabolic subgroups of G yields unitary representations by the very definition of these representations. However, not all unitary irreducible representations of G are obtained by this type of induction. In addition, we need derived functor parabolic induction [ef. Vogan, D. (1981) Representations of Real Reductive Lie Groups (Birkhäuser, Boston)] to describe all irreducible representations of G. For this second type of induction, the obvious analogues from parabolic subgroup induction regarding unitarity are false. In this announcement, we describe a setting where derived functor parabolic induction yields unitary representations of G. These results include proofs of unitarity for some of the representations conjectured to be unitary by Vogan and Zuckerman [(1983) Invent. Math., in press] and also proofs of unitarity for some which lie outside the domain described in those conjectures.

Journal Article↗
PubMed1985

Outlining social physics for modern societies-locating culture, economics, and politics: The Enlightenment reconsidered.

A groundwork is laid for a formulation of the modern human social system as a field continuum. As in a simple material physical field, the independent implied relationships of materials or processes in flux have to be based on local conservations of mass, energy, and momentum. In complex fields, the transport fluctuations of momentum are transformed into action modes (e.g., [unk] pdq = SigmaH(i) = H, a characteristic quantum of action over a characteristic cycle time). In complex living systems, a fourth local conservation of population number, the demographic variable, has to be added as a renormalized variable. Modern man, settled in place via agriculture, urbanized, and engaged largely in trade and war, invents a fifth local conservation-value-in-trade, the economic variable. The potentials that drive these five fluxes are also enumerated. Among the more evident external and internal physical-chemical potentials, the driving potentials include a sheaf of internal potential-like components that represent the command-control system emergent as politics. In toto, culture represents the social solvent with the main processes of economics and politics being driven by a social pressure.

Journal Article↗
PubMed1993

Early evolution of photosynthesis: clues from nitrogenase and chlorophyll iron proteins.

Chlorophyll (Chl) is often viewed as having preceded bacteriochlorophyll (BChl) as the primary photoreceptor pigment in early photosynthetic systems because synthesis of Chl requires one fewer enzymatic reduction than does synthesis of BChl. We have conducted statistical DNA sequence analyses of the two reductases involved in Chl and BChl synthesis, protochlorophyllide reductase and chlorin reductase. Both are three-subunit enzymes in which each subunit from one reductase shares significant amino acid identity with a subunit of the other, indicating that the two enzymes are derived from a common three-subunit ancestral reductase. The "chlorophyll iron protein" subunits, encoded by the bchL and bchX genes in the purple bacterium Rhodobacter capsulatus, also share amino acid sequence identity with the nitrogenase iron protein, encoded by nifH. When nitrogenase iron proteins are used as outgroups, the chlorophyll iron protein tree is rooted on the chlorine reductase lineage. This rooting suggests that the last common ancestor of all extant photosynthetic eubacteria contained BChl, not Chl, in its reaction center, and implies that Chl-containing reaction centers were a late invention unique to the cyanobacteria/chloroplast lineage.

Amino Acid Sequence↗
PubMed1993

On the span of supersymmetric Young tableaux.

De Concini et al. [De Concini, C., Eisenbud, D. & Procesi, C. (1980) Invent. Math. 56, 129-165] have established for classical Young bitableaux the fact that the span of all bitableaux of shape lambda over the rationals includes all bitableaux of all shapes mu > lambda. We extend their result to the more general setting of supersymmetric Young tableaux. Our proof, even in the classical case, has the advantage of providing an explicit combinatorial algorithm for the computation of the coefficients.

Journal Article↗
PubMed1995

Relationship between evolutionary rate and cellular location among the Inv/Spa invasion proteins of Salmonella enterica.

For 21 strains of Salmonella enterica, nucleotide sequences were obtained for three invasion genes, spaO, spaP, and spaQ, of the chromosomal inv/spa complex, the products of which form a protein export system required for entry of the bacteria into nonphagocytic host cells. These genes are present in all eight subspecies of the salmonellae, and homologues occur in a variety of other bacteria, including the enteric pathogens Shigella and Yersinia, in which they are plasmid borne. Evolutionary diversification of the invasion genes among the subspecies of S. enterica has been generally similar in pattern and average rate to that of housekeeping genes. However, the range of variation in evolutionary rate among the invasion genes is unusually large, and there is a relationship between the evolutionary rate and cellular location of the invasion proteins, possibly reflecting diversifying selection on exported proteins in adaptation to variable host factors in extracellular environments. The SpaO protein, which is hypervariable in S. enterica and exhibits only 24% sequence identity with its homologues in Shigella and Yersinia, is secreted. In contrast, the membrane-associated proteins SpaP, SpaQ, and InvA are weakly polymorphic and have > 60% sequence identity with the corresponding proteins of other enteric bacteria. Acquisition of the inv/spa genes may have been a key event in the evolution of the salmonellae as pathogens, following which the invention of flagellar phase shifting facilitated niche expansion to include warm-blooded vertebrates.

Adhesins, Bacterial↗
PubMed1996

New infinite families of exact sums of squares formulas, Jacobi elliptic functions, and Ramanujan's tau function.

In this paper, we give two infinite families of explicit exact formulas that generalize Jacobi's (1829) 4 and 8 squares identities to 4n(2) or 4n(n + 1) squares, respectively, without using cusp forms. Our 24 squares identity leads to a different formula for Ramanujan's tau function tau(n), when n is odd. These results arise in the setting of Jacobi elliptic functions, Jacobi continued fractions, Hankel or Turánian determinants, Fourier series, Lambert series, inclusion/exclusion, Laplace expansion formula for determinants, and Schur functions. We have also obtained many additional infinite families of identities in this same setting that are analogous to the eta-function identities in appendix I of Macdonald's work [Macdonald, I. G. (1972) Invent. Math. 15, 91-143]. A special case of our methods yields a proof of the two conjectured [Kac, V. G. and Wakimoto, M. (1994) in Progress in Mathematics, eds. Brylinski, J.-L., Brylinski, R., Guillemin, V. & Kac, V. (Birkhäuser Boston, Boston, MA), Vol. 123, pp. 415-456] identities involving representing a positive integer by sums of 4n(2) or 4n(n + 1) triangular numbers, respectively. Our 16 and 24 squares identities were originally obtained via multiple basic hypergeometric series, Gustafson's C(l) nonterminating (6)phi(5) summation theorem, and Andrews' basic hypergeometric series proof of Jacobi's 4 and 8 squares identities. We have (elsewhere) applied symmetry and Schur function techniques to this original approach to prove the existence of similar infinite families of sums of squares identities for n(2) or n(n + 1) squares, respectively. Our sums of more than 8 squares identities are not the same as the formulas of Mathews (1895), Glaisher (1907), Ramanujan (1916), Mordell (1917, 1919), Hardy (1918, 1920), Kac and Wakimoto, and many others.

Journal Article↗
PubMed1997

Stepped versus continuous rotatory motors at the molecular scale.

Nature invented molecular rotatory devices such as the flagellar motor and ATP synthase. Photoselection techniques have been frequently used to detect the rotational random walk of proteins but only rarely for the rotational drift of subunits in proteins. Pertinent theories predict an oscillatory behavior of the polarization anisotropy, r, for unidirectional rotational drift, as opposed to a monotonic relaxation of r for bidirectional random walk. The underlying assumption of an angular continuum is questionable for intersubunit rotation in proteins. We developed a theory for stepped rotatory devices. It predicts the damped oscillation of r under unidirectional drift. Damping increases with decreasing number of steps. For only three steps a quasi-monotonic relaxation of r is predicted for both random walk and drift. In photoselection experiments with active F-ATPase we observed the relaxation of r when a spectroscopic probe was attached to the central beta-subunit. This behavior is compatible with the expectation for a three-stepped rotatory device.

Flagella↗
PubMed1998

Locomotion: dealing with friction.

To move on land, in water, or in the air, even at constant speed and at the same level, always requires an expenditure of energy. The resistance to motion that has to be overcome is of many different kinds depending on size, speed, and the characteristics of the medium, and is a fascinating subject in itself. Even more interesting are nature's stratagems and solutions toward minimizing the effort involved in the locomotion of different types of living creatures, and humans' imitations and inventions in an attempt to do at least as well.

Animals↗
PubMed1998

Developmental rescue of Drosophila cephalic defects by the human Otx genes.

The molecular mechanisms of head development are a central question in vertebrate and invertebrate developmental biology. The anteriorly expressed homeobox gene otd in Drosophila and its homolog Otx in mouse are required for the early development of the most anterior part of the body, suggesting that a fundamental genetic program of cephalic development might be conserved between vertebrates and invertebrates. We have examined this hypothesis by introducing the human Otx genes into flies. By inducing expression of the human Otx homologs with a heat shock promoter, we found that both Otx1 and Otx2 functionally complement the cephalic defects of a fly otd mutant through specific activation and inactivation of downstream genes. Combined with previous morphological studies, these results are consistent with the view that a common molecular ground plan of cephalization was invented before the diversification of the protostome and the deuterostome in the course of metazoan evolution.

Amino Acid Sequence↗
PubMed2000

Information theory, atoms in molecules, and molecular similarity.

Using information theory, it is argued that from among possible definitions of what an atom is when it is in a molecule, a particular one merits special attention. Namely, it is the atom defined by the "stockholders partitioning" of a molecule invented by Hirshfeld [(1977) Theor. Chim. Acta 44, 129]. The theoretical tool used is the minimum entropy deficiency principle (minimum missing information principle) of Kullback and Liebler [(1951) Ann. Math. Stat. 22, 79]. A corresponding analysis is given of the problem of assessing similarity between molecules or pieces of molecules.

Journal Article↗
PubMed2005

The euryarchaeota, nature's medium for engineering of single-stranded DNA-binding proteins.

The architecture of single-stranded DNA-binding proteins, which play key roles in DNA metabolism, is based on different combinations of the oligonucleotide/oligosaccharide binding (OB) fold. Whereas the polypeptide serving this function in bacteria contains one OB fold, the eukaryotic functional homolog comprises a complex of three proteins, each harboring at least one OB fold. Here we show that unlike these groups of organisms, the Euryarchaeota has exploited the potential in the OB fold to re-invent single-stranded DNA-binding proteins many times. However, the most common form is a protein with two OB folds and one zinc finger domain. We created several deletion mutants of this protein based on its conserved motifs, and from these structures functional chimeras were synthesized, supporting the hypothesis that gene duplication and recombination could lead to novel functional forms of single-stranded DNA-binding proteins. Biophysical studies showed that the orthologs of the two OB fold/one zinc finger replication protein A in Methanosarcina acetivorans and Methanopyrus kandleri exhibit two binding modes, wrapping and stretching of DNA. However, the ortholog in Ferroplasma acidarmanus possessed only the stretching mode. Most interestingly, a second single-stranded DNA-binding protein, FacRPA2, in this archaeon exhibited the wrapping mode. Domain analysis of this protein, which contains a single OB fold, showed that its architecture is similar to the functional homologs thought to be unique to the Crenarchaeotes. Most unexpectedly, genes coding for similar proteins were found in the genomes of eukaryotes, including humans. Although the diversity shown by archaeal single-stranded DNA-binding proteins is unparalleled, the presence of their simplest form in many organisms across all domains of life is of greater evolutionary consequence.

Amino Acid Motifs↗
PubMed2001

Münchhausen by proxy syndrome in clinical child neuropsychology: a case presenting with neuropsychological symptoms.

Münchhausen by proxy syndrome (MBPS) is a rare but dramatic variant of child abuse. In MBPS adults, mostly the mother, invent, manipulate, or produce the child's illness, and as a consequence the child has to undergo numerous diagnostic or treatment procedures. Typically, valid information about the etiology of the child's illness is withheld by the parents, and reversible symptoms vanish, when the child and the responsible adults are separated. Although valid statistical data about the epidemiology of MBPS are not available, MBPS should be considered more often than normally recognized. Neurological and neuropsychological presentations including developmental delays and learning problems appear to be common among MBPS cases so that clinical child neuropsychologists should be aware of this problem and consider MBPS at least in some of the mysterious cases that come to their attention. The present study describes a case of MBPS in which neurological and neuropsychological symptoms predominate. It presents a MBPS variant that is characterized by developmental delays and learning problems induced by unnecessary isolation at home, hospitalization, and treatment procedures. In the present case MBPS was at first suspected following neuropsychological assessment, since some of the main features of non-authenticity of symptom presentation gave cause for suspecting deceptive behavior on the mother's (and possibly also on the maternal grandmother's) side.

Adult↗
PubMed1998

Roots and routes of Russian neurosurgery (from surgical neurology towards neurological surgery).

Regular and purposeful neurosurgical interventions started at the end of the nineteenth century. Both surgical and neurological roots of the emerging speciality could be traced. The surgical roots of neurosurgery were the invention of anaesthesia, aseptics and antiseptics which made brain operations relatively safe and markedly reduced postoperative mortality. The neurological roots were the improvement of topical diagnosis in neurology and the understanding of the anatomy and physiology of the nervous system. The first operating room at the neurology department of the Russian Military Medical Academy was established in 1897 by the famous Russian neurologist and psychiatrist Vladimir Bekhterev (1857-1927). According to Bekhterev, neurology should become a surgical speciality like gynaecology or opthalmology and "neurologists will take a knife in their hands and do what they should do". Bekhterev's pupil Ludwig Puusepp (1875-1942) became the first full-time Russian neurosurgeon ("surgical neurologist"). He headed the first university course in surgical neurology in the world organised in 1909 at Bekhterev's Psychoneurological Institutte in St. Petersburg and bacame professor of surgical neurology in 1910. The role of neurologist might be illustrated by the development of a sterotactic instrument named "encephalometer" designed by D. Zernov in 1889 and improved by G. Rossolimo in 1907. The idea was to map cerebral structures in degrees of latitude and longitude similar to mapping the terrestrial globe in order to localise the brain lesion and enhance its minimally invasive removal....

History, 19th Century↗
PubMed1998

The patentability of human genes: an ethical debate in the European Community.

The European Parliament rejected in 1995 the European Commission proposal to harmonize legal protection of biotechnological inventions. Although it did not seem initially the most contentious of the many issues involved in the current legal and ethical debate around biomedicine and genetics, patenting is now focusing bioethics in Europe.

Bioethics↗