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      Volume 30, Issue 1

      February 2005,   pages  1-142

    • Foreword

      Vidyanand Nanjundiah Stuart A Newman Scott F Gilbert

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    • The century beyond the gene

      Evelyn Fox Keller

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      In an increasing number of biological laboratories, the focus of research is shifting from sequence data to the functional meaning of that data. No longer content with structural mappings, there is a renewed interest abroad in what the United States Department of Energy calls, ‘Bringing Genomes to Life’. For many, this means a movement beyond ‘reductionism’ to a ‘systems biology’. The question is, what does this mean?

    • The use of Xenopus oocytes and embryos as a route towards cell replacement

      J B Gurdon

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      When nuclei of somatic cells are transplanted to enucleated eggs of Xenopus, a complete reprogramming of nuclear function can take place. To identify mechanisms of nuclear reprogramming, somatic nuclei can be transplanted to growing meiotic oocytes of Xenopus, and stem cell genes activated without DNA replication. The combination of somatic cell nuclear transfer with morphogen signalling and the community effect may lead towards the possibility of cell replacement therapy. When mechanisms of nuclear reprogramming are understood, it may eventually be possible to directly reprogramme human somatic cell nuclei without the use of eggs.

    • Collateral damage: Spread of repeat-induced point mutation from a duplicated DNA sequence into an adjoining single-copy gene in Neurospora crassa

      Meenal Vyas Durgadas P Kasbekar

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      Repeat-induced point mutation (RIP) is an unusual genome defense mechanism that was discovered in Neurospora crassa. RIP occurs during a sexual cross and induces numerous G : C to A : T mutations in duplicated DNA sequences and also methylates many of the remaining cytosine residues. We measured the susceptibility of the erg-3 gene, present in single copy, to the spread of RIP from duplications of adjoining sequences. Genomic segments of defined length (1, 1.5 or 2 kb) and located at defined distances (0, 0.5, 1 or 2 kb) upstream or downstream of the erg-3 open reading frame (ORF) were amplified by polymerase chain reaction (PCR), and the duplications were created by transformation of the amplified DNA. Crosses were made with the duplication strains and the frequency of erg-3 mutant progeny provided a measure of the spread of RIP from the duplicated segments into the erg-3 gene. Our results suggest that ordinarily RIP-spread does not occur. However, occasionally the mechanism that confines RIP to the duplicated segment seems to fail (frequency 0.1–0.8%) and then RIP can spread across as much as 1 kb of unduplicated DNA. Additionally, the bacterial hph gene appeared to be very susceptible to the spread of RIP-associated cytosine methylation.

    • Stochasticity or the fatal `imperfection' of cloning

      Reiner A Veitia

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      The concept of clone is analysed with the aim of exploring the limits to which a phenotype can be said to be determined geneticaly. First of all, mutations that result from the replication, topological manipulation or lesion of DNA introduce a source of heritable variation in an otherwise identical genetic background. But more important, stochastic effects in many biological processes may superimpose a phenotypic variation which is not encoded in the genome. The source of stochasticity ranges from the random selection of alleles or whole chromosomes to be expressed in small cell populations, to fluctuations in processes such as gene expression, due to limiting amounts of the players involved. The picture emerging is that the term clone is a statistical over-simplification representing a series of individuals having essentially the same genome but capable of exhibiting wide phenotypic variation. Finally, to what extent fluctuations in biological processes, usually thought of as noise, are in fact signal is also discussed.

    • The return of the whole organism

      Patrick Bateson

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      The long trend towards analysis at lower and lower levels is starting to reverse. The new integrative studies must make use of the resources uncovered by molecular biology but should also use the characteristics of whole organisms to measure the outcomes of developmental processes. Two examples are given of how movement between levels of analysis is being used with increasing power and promise. The first is the study of behavioural imprinting in birds where many of the molecular and neural mechanisms involved have been uncovered and are now being integrated to explain the behaviour of the whole animal. The second is the triggering during sensitive periods in early life by environmental events of one of several alternative modes of development leading to different phenotypes. A renewed focus on the whole organism is also starting to change the face of evolutionary biology. The decision-making and adaptability of the organism is recognized an important driver of evolution and is increasingly seen as an alternative to the gene-focused views.

    • Do plants and animals differ in phenotypic plasticity?

      Renee M Borges

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      This paper compares the flexibility in the nexus between phenotype and genotype in plants and animals. These taxa although considered to be fundamentally different are found to be surprisingly similar in the mechanisms used to achieve plasticity. Although non-cognitive behaviour occurs in plants, its range is limited, while morphological and developmental plasticity also occur to a considerable extent in animals. Yet both plants and animals are subject to unique constraints and thus need to find unique solutions to functional problems. A true comparison between the plant and animal phenotype would be a comparison between plants and sessile photo-synthesizing colonial invertebrates. Such comparisons are lacking. However, they would provide important insights into the adaptive significance of plasticity in these groups. It is also suggested that a comparison of inflexible traits in these groups would provide an understanding of the constraints, as well as the costs and benefits, of a plastic versus non-plastic phenotype in plants and animals.

    • Not in their genes: Phenotypic flexibility, behavioural traditions and cultural evolution in wild bonnet macaques

      Anindya Sinha

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      Phenotypic flexibility, or the within-genotype, context-dependent, variation in behaviour expressed by single reproductively mature individuals during their lifetimes, often impart a selective advantage to organisms and profoundly influence their survival and reproduction. Another phenomenon apparently not under direct genetic control is behavioural inheritance whereby higher animals are able to acquire information from the behaviour of others by social learning, and, through their own modified behaviour, transmit such information between individuals and across generations. Behavioural information transfer of this nature thus represents another form of inheritance that operates in many animals in tandem with the more basic genetic system. This paper examines the impact that phenotypic flexibility, behavioural inheritance and socially transmitted cultural traditions may have in shaping the structure and dynamics of a primate society – that of the bonnet macaque (Macaca radiata), a primate species endemic to peninsular India. Three principal issues are considered: the role of phenotypic flexibility in shaping social behaviour, the occurrence of individual behavioural traits leading to the establishment of social traditions, and the appearance of cultural evolution amidst such social traditions. Although more prolonged observations are required, these initial findings suggest that phenotypic plasticity, behavioural inheritance and cultural traditions may be much more widespread among primates than have previously been assumed but may have escaped attention due to a preoccupation with genetic inheritance in zoological thinking.

    • Mechanisms for the environmental regulation of gene expression: Ecological aspects of animal development

      Scott F Gilbert

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      The environment can play a significant role in the production of phenotypes. However, the developmental mechanisms by which the environmental agents effect normal development are just becoming known. At least three paths have been found through which the environment can modify gene activity. The first is the neuroendocrine route. Here, the nervous system monitors the environment and transfers signals to the endocrine system. The endocrine hormones can then alter gene expression. The second route involves environmental factors that change the methylation pattern of genes, thereby altering their transcriptional capabilities. The third route involves the direct induction of gene expression in the host by microbial symbionts. The normal regulation of phenotype production by the environment should be considered a normal component of development and developmental biology.

    • The pre-Mendelian, pre-Darwinian world: Shifting relations between genetic and epigenetic mechanisms in early multicellular evolution

      Stuart A Newman

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      The reliable dependence of many features of contemporary organisms on changes in gene content and activity is tied to the processes of Mendelian inheritance and Darwinian evolution. With regard to morphological characters, however, Mendelian inheritance is the exception rather than the rule, and neo-Darwinian mechanisms in any case do not account for the origination (as opposed to the inherited variation) of such characters. It is proposed, therefore, that multicellular organisms passed through a pre-Mendelian, pre-Darwinian phase, whereby cells, genes and gene products constituted complex systems with context-dependent, self-organizing morphogenetic capabilities. An example is provided of a plausible ‘core’ mechanism for the development of the vertebrate limb that is both inherently pattern forming and morphogenetically plastic. It is suggested that most complex multicellular structures originated from such systems. The notion that genes are privileged determinants of biological characters can only be sustained by neglecting questions of evolutionary origination and the evolution of developmental mechanisms.

    • Can morphogenesis be understood in terms of physical rules?

      Ryuji Takaki

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      Because the morphogenesis of biological systems is not fully understood, researches from various points of view are necessary. The present author has recently made computer simulations with his colleagues to construct branching systems of human organs, such as the lung airway and the liver blood vessels. In the simulations certain rules are assumed to govern bifurcating processes of the systems. These rules are expressed in terms of physical and geometrical concepts, such as minimum energy consumption and uniform filling of branches in the space of organs. Results of computer simulation are quite similar to real structures. However, actual mechanisms of morphogenesis, i.e. effects of genes or proteins, are not considered in these studies. In this article, the present work is discussed in relation to the concept of biological pattern formation by Meinhardt and a recent study by Miura and Shiota on lung growth.

    • Genotype, phenotype and cancer: Role of low penetrance genes and environment in tumour susceptibility

      Ashwin Kotnis Rajiv Sarin Rita Mulherkar

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      Role of heredity and lifestyle in sporadic cancers is well documented. Here we focus on the influence of low penetrance genes and habits, with emphasis on tobacco habit in causing head and neck cancers. Role of such gene-environment interaction can be well studied in individuals with multiple primary cancers. Thus such a biological model may elucidate that cancer causation is not solely due to genetic determinism but also significantly relies on lifestyle of the individual.

    • Emergentism as a default: Cancer as a problem of tissue organization

      Ana M soto Carlos Sonnenschein

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      During the last fifty years the dominant stance in experimental biology has been reductionism. For the most part, research programs were based on the notion that genes were in ‘the driver’s seat’ controlling the developmental program and determining normalcy and disease (genetic reductionism and genetic determinism). Philosophers were the first to realize that the belief that the Mendelian genes were reduced to DNA molecules was questionable. Soon after these pronouncements, experimental data confirmed their misgivings. The optimism of molecular biologists, fueled by early success in tackling relatively simple problems, has now been tempered by the difficulties found when attempting to understand complex biological problems.

      Here, we analyse experimental data that illustrate the shortcomings of this sort of reductionism. We also examine the prevailing paradigm in cancer research, the somatic mutation theory (SMT), the premises of which are:

      1. cancer is derived from a single somatic cell that has accumulated multiple DNA mutations;
      2. the default state of cell proliferation in metazoa is quiescence; and
      3. cancer is a disease of cell proliferation caused by mutations in genes that control proliferation and the cell cycle.

      We challenge the notion that cancer is a cellular problem caused by mutated genes by assessing data gathered both from within the reductionist paradigm and from an alternative view that regards carcinogenesis as a developmental process gone awry. This alternative view, explored under the name of the tissue organization field theory (TOFT), is based on premises that place cancer in a different hierarchical level of complexity from that proposed by the SMT, namely:

      1. carcinogenesis represents a problem of tissue organization comparable to organogenesis, and
      2. proliferation is the default state of all cells.

      We propose that the organicist view, in which the TOFT is based, is a good starting point from which to explore emergent phenomena. However, new theoretical concepts are needed in order to grapple with the apparent circular causality of complex biological phenomena in development and carcinogenesis.

    • Language from a biological perspective

      Mohinish Shukla

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      The faculty of language is unique to the human species. This implies that there are human-specific biological changes that lie at the basis of human language. However, it is not clear what the nature of such changes are, and how they could be shaped by evolution. In this paper, emphasis is laid on describing language in a Chomskyan manner, as a mental object. This serves as a standpoint to speculate about the biological basis of the emergence and evolution of language.

    • Language cannot be reduced to biology: Perspectives from neuro-developmental disorders affecting language learning

      D Vasanta

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      The study of language knowledge guided by a purely biological perspective prioritizes the study of syntax. The essential process of syntax is recursion – the ability to generate an infinite array of expressions from a limited set of elements. Researchers working within the biological perspective argue that this ability is possible only because of an innately specified genetic makeup that is specific to human beings. Such a view of language knowledge may be fully justified in discussions on biolinguistics, and in evolutionary biology. However, it is grossly inadequate in understanding language-learning problems, particularly those experienced by children with neurodevelopmental disorders such as developmental dyslexia, Williams syndrome, specific language impairment and autism spectrum disorders. Specifically, syntax-centered definitions of language knowledge completely ignore certain crucial aspects of language learning and use, namely, that language is embedded in a social context; that the role of envrironmental triggering as a learning mechanism is grossly underestimated; that a considerable extent of visuo-spatial information accompanies speech in day-to-day communication; that the developmental process itself lies at the heart of knowledge acquisition; and that there is a tremendous variation in the orthographic systems associated with different languages. All these (socio-cultural) factors can influence the rate and quality of spoken and written language acquisition resulting in much variation in phenotypes associated with disorders known to have a genetic component. Delineation of such phenotypic variability requires inputs from varied disciplines such as neurobiology, neuropsychology, linguistics and communication disorders. In this paper, I discuss published research that questions cognitive modularity and emphasises the role of the environment for understanding linguistic capabilities of children with neuro-developmental disorders. The discussion pertains to two specific disorders, developmental dyslexia and Williams syndrome.

    • The nature-nurture controversy in its most recent avatar: A response to Shukla and Vasanta

      Prathibha Karanth

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