Cells are cognitive entities possessing great computational power. DNA serves as a multivalent information storage medium for these computations at various time scales. Information is stored in sequences, epigenetic modifications, and rapidly changing nucleoprotein complexes. Because DNA must operate through complexes formed with other molecules in the cell, genome functions are inherently interactive and involve two-way communication with various cellular compartments. Both coding sequences and repetitive sequences contribute to the hierarchical systemic organization of the genome. By virtue of nucleoprotein complexes, (...) epigenetic modifications, and natural genetic engineering activities, the genome can serve as a read-write storage system. An interactive informatic conceptualization of the genome allows us to understand the functional importance of DNA that does not code for protein or RNA structure, clarifies the essential multidirectional and systemic nature of genomic information transfer, and emphasizes the need to investigate how cellular computation operates in reproduction and evolution. (shrink)

Robustness is a fundamental property of biological systems, observed ubiquitously across species and at different levels of organization from gene regulation to ecosystem. The theory of biological robustness argues that robustness fosters evolv-ability and that together they entail various tradeoffs as well as characteristic architectures and mechanisms. We argue that classes of biological systems have evolved to enhance their robustness by extending their system boundary through a series of symbioses with foreign biological entities . A series of major biological innovations (...) has been achieved by events consistent with this framework: horizontal gene transfer, serial endosymbiosis, oocytes-mediated vertical infection, and host-symbiont mutualism for bacterial flora. Self-extending symbiosis contributes to robustness because symbiotic foreign biological entities can enhance the adaptative capacity of the system against environmental perturbations as well as contribute novel functions. In addition, evolutionary history indicates that the degree of symbiosis achieved has substantially changed from tight integration into the genome to loose integration as bacterial flora . The most dramatic example can be seen in the symbiosis of host immune system and bacterial flora in which substantial function of host defense depends on the proper maintenance of bacterial flora and its adaptive capability. Biological systems following this type of evolutionary path might have attained high levels of functionality, robustness, and evolvability. Thus, robustness, evolution, and self-extending symbiosis may form essential system principles for biology. (shrink)

Developmental systems theory (DST) expands the unit of replication from genes to whole systems of developmental resources, which DST interprets in terms of cycling developmental processes. Expansion seems required by DST's argument against privileging genes in evolutionary and developmental explanations of organic traits. DST and the expanded replicator brook no distinction between biological and cultural evolution. However, by endorsing a single expanded unit of inheritance and leaving the classical molecular notion of gene intact, DST achieves only a nominal reunification of (...) heredity and development. I argue that an alternative conceptualization of inheritance denies the classical opposition of genetics and development while avoiding the singularity inherent in the replicator concept. It also yields a new unit--the reproducer--which genuinely integrates genetic and developmental perspectives. The reproducer concept articulates the non-separability of "genetic" and "developmental" roles in units of heredity, development, and evolution. DST reformulated in terms of reproducers rather than replicators preserves an empirically interesting distinction between cultural and biological evolution. (shrink)

What factors drove the transformation of the cyanobacterial progenitor of plastids (e.g. chloroplasts) from endosymbiont to bona fide organelle? This question lies at the heart of organelle genesis because, whereas intracellular endosymbionts are widespread in both unicellular and multicellular eukaryotes (e.g. rhizobial bacteria, Chlorella cells in ciliates, Buchnera in aphids), only two canonical eukaryotic organelles of endosymbiotic origin are recognized, the plastids of algae and plants and the mitochondrion. Emerging data on (1) the discovery of non‐canonical plastid protein targeting, (2) (...) the recent origin of a cyanobacterial‐derived organelle in the filose amoeba Paulinella chromatophora, and (3) the extraordinarily reduced genomes of psyllid bacterial endosymbionts begin to blur the distinction between endosymbiont and organelle. Here we discuss the use of these terms in light of new data in order to highlight the unique aspects of plastids and mitochondria and underscore their central role in eukaryotic evolution. BioEssays 29:1239–1246, 2007. © 2007 Wiley Periodicals, Inc. (shrink)

A variety of scientific disciplines have set as their task explaining mental activities, recognizing that in some way these activities depend upon our brain. But, until recently, the opportunities to conduct experiments directly on our brains were limited. As a result, research efforts were split between disciplines such as cognitive psychology, linguistics, and artificial intelligence that investigated behavior, while disciplines such as neuroanatomy, neurophysiology, and genetics experimented on the brains of non-human animals. In recent decades these disciplines integrated, and with (...) the advent of techniques for imaging activity in human brains, the term cognitive neuroscience has been applied to the integrated investigations of mind and brain. This book is a philosophical examination of how these disciplines continue in the mission of explaining our mental capacities. (shrink)