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  • 1
    Language: English
    In: Philosophy and Theory in Biology, 12/04/2014, Vol.6(20160405)
    Description: Both popular and scientific definitions of life must account for the possibility of the sub-optimal operation of some function. Identifying the function in question and the criteria for optimality will be necessary steps in crafting a definition that is both intuitive and rigorous. I lay out a rule of thumb—the proper activity criterion—and a three-part typology of binary, range, and preference for understanding definitions of life. The resolution of “optimal” function within a scientific framework presents the central challenge to creating a successful definition of life. A brief history of definitions of life and explanations of biological function is presented to demonstrate the value of the typology. After analyzing three controversial cases—viruses, mules, and stars—I present three possible options for resolution: vitalism, reductionism, and instrumentalism. Only by confronting the consequences of each can we come to consensus about what is necessary and desirable from a common definition.
    Keywords: Biology;
    ISSN: Philosophy and Theory in Biology
    E-ISSN: 1949-0739
    Source: CrossRef
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  • 2
    In: Evolution, August 2014, Vol.68(8), pp.2441-2451
    Description: Evolutionary biology has a complex relationship with ideas of chance, purpose, and progress. Probability plays a subtle role; strikingly, founding figures in statistics were motivated by evolutionary questions. The findings of evolutionary biology have been used both in support of narratives of progress, and in their deconstruction. Likewise, professional biologists bring to their scientific work a set of preconceptions about chance and progress, grounded in their philosophical, religious, and/or political views. From the religious side, questions of purpose are ever‐present. We explore this interplay in five broad categories: chance, progress, intelligence, eugenics, and the evolution of religious practices, each the subject of a semester long symposium. The intellectual influence of evolutionary biology has had a broad societal impact in these areas. Based on our experience, we draw attention to a number of relevant facts that, while accepted by experts in their respective fields, may be unfamiliar outside them. We list common areas of miscommunication, including specific examples and discussing causes: sometimes semantics and sometimes more substantive knowledge barriers. We also make recommendations for those attempting similar dialogue.
    Keywords: Determinism ; Epistemology ; Interdisciplinarity ; Nature Of Science ; Personhood ; Religion ; Teleology
    ISSN: 0014-3820
    E-ISSN: 1558-5646
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  • 3
    Language: English
    In: Current Microbiology, 2004, Vol.48(6), pp.438-440
    Description: Broad variation among anoxygenic reaction centers makes it essential to consider a wide variety when considering the origins of photosynthesis. The photosynthetic core antenna domain in the gene pshA from Heliophilum fasciatum was sequenced doubling the number of core sequences available from heliobacteria. The sequence shares a pattern of hydrophobicity and histidine residues with the core antenna domain of pshA from Heliobacillus mobilis . Sequence identity between the two pshA sequences was 68%, indicating heliobacterial reaction centers show similar diversity to photosystem I throughout cyanobacteria and plastids. Thus, the diversity of anoxygenic phototrophic reaction centers may be greater than previously thought.
    Keywords: Plastids ; Photosynthesis ; Photosystem I ; Microbiology ; Species Diversity ; Genetic Diversity ; Phylogenetics ; Plastids ; Photosynthesis ; Histidine ; Nucleotide Sequence ; Photosystem I ; Hydrophobicity ; Diversity ; Reaction Centers ; Heliobacteria ; Heliobacillus Mobilis ; Photosynthesis, Electron Transport and Related Phenomena ; Productivity ; Psha Gene;
    ISSN: 0343-8651
    E-ISSN: 1432-0991
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  • 4
    Language: English
    In: Journal of Molecular Evolution, 2005, Vol.60(2), pp.153-163
    Description: Phototrophy, the conversion of light to biochemical energy, occurs throughout the Bacteria and plants, however, debate continues over how different phototrophic mechanisms and the bacteria that contain them are related. There are two types of phototrophic mechanisms in the Bacteria: reaction center type 1 (RC1) has core and core antenna domains that are parts of a single polypeptide, whereas reaction center type 2 (RC2) is composed of short core proteins without antenna domains. In cyanobacteria, RC2 is associated with separate core antenna proteins that are homologous to the core antenna domains of RC1. We reconstructed evolutionary relationships among phototrophic mechanisms based on a phylogeny of core antenna domains/proteins. Core antenna domains of 46 polypeptides were aligned, including the RC1 core proteins of heliobacteria, green sulfur bacteria, and photosystem I (PSI) of cyanobacteria and plastids, plus core antenna proteins of photosystem II (PSII) from cyanobacteria and plastids. Maximum likelihood, parsimony, and neighbor joining methods all supported a single phylogeny in which PSII core antenna proteins (PsbC, PsbB) arose within the cyanobacteria from duplications of the RC1-associated core antenna domains and accessory antenna proteins (IsiA, PcbA, PcbC) arose from duplications of PsbB. The data indicate an evolutionary history of RC1 in which an initially homodimeric reaction center was vertically transmitted to green sulfur bacteria, heliobacteria, and an ancestor of cyanobacteria. A heterodimeric RC1 (=PSI) then arose within the cyanobacterial lineage. In this scenario, the current diversity of core antenna domains/proteins is explained without a need to invoke horizontal transfer.
    Keywords: Cyanobacteria ; Green sulfur bacteria ; Heliobacteria ; Phylogeny ; Photosystem I ; Photosystem II ; Reaction center 1 ; Reaction center 2
    ISSN: 0022-2844
    E-ISSN: 1432-1432
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  • 5
    Language: English
    In: Astrobiology, 6(5), 735-813. New Rochelle, NY: Mary Ann Liebert, Inc (2006).
    Description: Peer reviewed
    Keywords: Physical, Chemical, Mathematical & Earth Sciences :: Earth Sciences & Physical Geography ; Physique, Chimie, Mathématiques & Sciences De La Terre :: Sciences De La Terre & Géographie Physique ; Physical, Chemical, Mathematical & Earth Sciences :: Multidisciplinary, General & Others ; Physique, Chimie, Mathématiques & Sciences De La Terre :: Multidisciplinaire, Général & Autres
    Source: ORBi (Open Repository and Bibliography), University of Liège
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