Causality, randomness, intelligibility, and the epistemology of the cell

Because the basic unit of biology is the cell, biological knowledge is rooted in the epistemology of the cell, and because life is the salient characteristic of the cell, its epistemology must be centered on its livingness, not its constituent components. The organization and regulation of these components in the pursuit of life constitute the fundamental nature of the cell. Thus, regulation sits at the heart of biological knowledge of the cell and the extraordinary complexity of this regulation conditions the kind of knowledge that can be obtained, in particular, the representation and intelligibility of that knowledge. This paper is essentially split into two parts. The first part discusses the inadequacy of everyday intelligibility and intuition in science and the consequent need for scientific theories to be expressed mathematically without appeal to commonsense categories of understanding, such as causality. Having set the backdrop, the second part addresses biological knowledge. It briefly reviews modern scientific epistemology from a general perspective and then turns to the epistemology of the cell. In analogy with a multi-faceted factory, the cell utilizes a highly parallel distributed control system to maintain its organization and regulate its dynamical operation in the face of both internal and external changes. Hence, scientific knowledge is constituted by the mathematics of stochastic dynamical systems, which model the overall relational structure of the cell and how these structures evolve over time, stochasticity being a consequence of the need to ignore a large number of factors while modeling relatively few in an extremely complex environment.     

Parallelism,parsimony, and the phytogeny of the lemuridae

In spite of the increasing popularity of cladistic methods in studies of primate systematics, few authors have investigated the effects of parallel evolution when such methods are applied to empirical data. To counter the effects of parallelism, cladistic techniques rely on the principle of evolutionary parsimony. When parsimony procedures are used to reconstruct the phylogeny of the Lemuridae, nine highly parsimonious phylogenies can be deduced. Further choice among these competing hypotheses of relationship is determined by the extent to which one embraces the parsimony principle. The phylogeny obtained by the most rigorous adherence to the parsimony principle is one which is wholly consistent with traditional evolutionary classifications of the Lemuridae. Moderate levels of parallelism can lead to the generation of several plausible, alternative phylogenetic hypotheses; less than 25% of the characters analyzed here need have evolved in parallel, yet they are largely responsible for the ambiguity of the nine different lemurid phylogenies. This suggests that phylogeny reconstructions based entirely on cladistic methods do not provide a suitable basis for the construction of classifications for groups such as the order Primates, where the degree of parallelism is likely to be quite high.     

Content and Concentration of Taurine,Hypotaurine, and Zinc in the Retina,the Hippocampus,and the Dentate Gyrus of the Rat at Various Postnatal Days

Taurine and zinc possess neurotrophic and neuroprotective properties, and they have been demonstrated to interact in the central nervous system (CNS). The aim of this work was to determine taurine, hypotaurine, and zinc levels during postnatal development and any possible significant correlation between them in selective areas of the CNS with differential taurine level regulation and intrinsic capacity to proliferate. Taurine and hypotaurine content (nM/region) and concentration (nM/mg protein) and total zinc levels were determined in the retina, hippocampus, and dentate gyrus of the rat at postnatal days 5, 10, 15, 20, 30, and 50. Taurine and hypotaurine increased during development in the retina without significant correlation between them. In the hippocampus there was a progressive decrease, and in the dentate gyrus there was an initial increase and a posterior decrease of taurine and hypotaurine levels. Correlation between the two amino acids was observed at P10, P15, and P50 for the hippocampus and at P15, P30, and P50 for the dentate gyrus. The variations in total zinc levels followed a biphasic behavior, with an early decrease and later increase. Significant and positive correlation of zinc and taurine was only observed in the hippocampus at P30 and P50 and negative in the dentate gyrus at P30. No significant correlation was obtained for the retina. The maintenance of taurine levels in specific CNS areas does not seem to be related to the availability of the precursor, hypotaurine, which might have a role by itself. There are critical postnatal periods during which there is a preservation of taurine, hypotaurine, or zinc levels. It seems that these requirements could be related to zinc-taurine interactions.     

Solubility, adsorption, and the thermodynamics of the cutoff effect

For many years, the expression "cutoff effect of anesthesia," has been used to denote the failure of the higher alcohols or paraffins to produce anesthesia. As such, it is used to assess the plausibility of specific models, proposed for anesthesia. However, the uses were shown, in many respects, to be problematic. This article augments the notion of the cutoff to fit for all cases in which only some of the molecules in a homologous series are anesthetics. We find that the location of the cutoff points is affected by three free energy quantities: that of the adsorption of the agent to the anesthetic "site" (f(sl,site)), that of the perturbation of the site (f(ll,site)), and that of the evaporation of the agent from its pure condensed phase (Deltamu degrees (evaporation)). This outcome indicates that the cutoff cannot be attributed to a single parameter. In addition, the analyses that attribute the cutoff to the failure of compounds to obey the much-used Meyer-Overton correlation will have to be amended. This article shows that cutoff results can be used to elucidate the structure of a site.     

Phylogenetic circumscription of Saccharomyces, Kluyveromyces and other members of the Saccharomycetaceae, and the proposal of the new genera Lachancea, Nakaseomyces, Naumovia, Vanderwaltozyma and Zygotorulaspora

Genera currently assigned to the Saccharomycetaceae have been defined from phenotype, but this classification does not fully correspond with species groupings determined from phylogenetic analysis of gene sequences. The multigene sequence analysis of Kurtzman and Robnett [FEMS Yeast Res. 3 (2003) 417-432] resolved the family Saccharomycetaceae into 11 well-supported clades. In the present study, the taxonomy of the Saccharomyctaceae is evaluated from the perspective of the multigene sequence analysis, which has resulted in reassignment of some species among currently accepted genera, and the proposal of the following five new genera: Lachancea, Nakaseomyces, Naumovia, Vanderwaltozyma and Zygotorulaspora.     

Bonding, biophilia, biosynergy, and the future of primates in the wild

Human and nonhuman primates bond with one another in countless ways, and the results are varied and vital to the individuals and species involved. The manifesto that is the basis for the collection of essays in which this commentary is included proposes that the "human/nonhuman bonds that arise in primatological research and practice deserve and demand study and research." An essential corollary of this proposal is that the primatologists themselves must be studied. The aim of this essay is to explore the influence of human/nonhuman primate bonding on conservation practice and on the future of primates in the wild. This commentary applies the author's professional experience as a conservation psychologist and his research on the impact of profound interspecies bonds on human worldviews, attitudes, and behavior. It examines two general categories of bonds: those driven by Biophilia (human fascination with life) and those influenced by Biosynergy (mutual enrichment of life). It is the author's premise that biosynergy promotes complex collaborative interspecies bonds that broaden the conservationist's desire to enhance synergy among all organisms in an ecosystem. Conversely, biophilia induces relatively simple unidirectional bonds between humans and other animals that deepen the conservationist's desire to understand and protect certain species. This contrast raises some crucial questions. Do biophilia-driven bonds between conservationists and their favorite primates blind them to the synergistic needs of all species and impair their ability to work for sustained preservation of threatened habitat? Does biosynergy-based human/nature bonding enhance focus on conservation as an ecological science and thus ignore species-specific factors crucial to assure survival of endangered primates? How can both types of bonds be optimally applied to the conservation of wildlife and wilderness?     

Ethology, Natural History, the Life Sciences, and the Problem of Place

Investigators of animal behavior since the eighteenth century have sought to make their work integral to the enterprises of natural history and/or the life sciences. In their efforts to do so, they have frequently based their claims of authority on the advantages offered by the special places where they have conducted their research. The zoo, the laboratory, and the field have been major settings for animal behavior studies. The issue of the relative advantages of these different sites has been a persistent one in the history of animal behavior studies up to and including the work of the ethologists of the twentieth century. This revised version was published online in July 2006 with corrections to the Cover Date.     

Race,class, politics,and the disappearance of work

“When Work Disappears” has shaped research agendas on poverty, racial hierarchy, and urban social and economic dynamics. That is a lot for one article, yet two issues warrant more analysis. They are the ways in which socially defined “race” – rather than or in combination with class – explains the impact of sustained joblessness, and the political behaviours that may emerge in response to work’s disappearance. I point to evidence showing that both race and class have independent associations with the loss of work in poor African-American communities, as well as interactive effects. In the political arena – too often neglected by sociologists studying poverty – sustained, community-wide joblessness or underemployment are associated both with withdrawal from political engagement and with the recent resurgence of right-wing populism. Even after several decades of intensive research, we have more to learn about the interactions of race, class, politics, and the disappearance of work.     

Geology,Oil and Gas Potential,Pipelines, and the Geopolitics of the Caspian Sea Region

The Caspian Sea region contains oil and gas reserves that are comparable to those of other of the world's fossil-fuel-producing regions, excluding the Middle East. We review here the economic, environmental, and complicated geopolitical concerns with respect to exploration and recovery of the region's fossil fuels. These include mud volcanoes, gas hydrates, earthquakes, pollution, rapid changes in sea level, desertification, ownership of resources, and the transportation routes of fossil fuels. Significant advances have been made concerning these problems in the short time since the breakup of the Soviet Union, fueling optimism for the future of the region.-     

Morphological properties of the last primaries,the tail feathers,and the alulae of Accipiter nisus,Columba livia,Falco peregrinus,and Falco tinnunculus

We investigated the mechanical properties (Young's modulus, bending stiffness, barb separation forces) of the tenth primary of the wings, of the alulae and of the middle tail feathers of Falco peregrinus. For comparison, we also investigated the corresponding feathers in pigeons (Columba livia), kestrels (Falco tinnunculus), and sparrowhawks (Accipiter nisus). In all four species, the Young's moduli of the feathers ranged from 5.9 to 8.4 GPa. The feather shafts of F. peregrinus had the largest cross‐sections and the highest specific bending stiffness. When normalized with respect to body mass, the specific bending stiffness of primary number 10 was highest in F. tinnunculus, while that of the alula was highest in A. nisus. In comparison, the specific bending stiffness, measured at the base of the tail feathers and in dorso‐ventral bending direction, was much higher in F. peregrinus than in the other three species. This seems to correlate with the flight styles of the birds: F. tinnunculus hovers and its primaries might therefore withstand large mechanical forces. A. nisus has often to change its flight directions during hunting and perhaps needs its alulae for this maneuvers, and in F. peregrinus, the base of the tail feathers might need a high stiffness during breaking after diving. J. Morphol. 276:33–46, 2015. © 2014 Wiley Periodicals, Inc.     

Suffering, justice, and the politics of becoming

To suffer is to undergo, to bear, to endure. Suffering exists on the underside of agency; it is as important to ethics as agency. The experience of suffering is never entirely captured by the ethical, political, medical and spiritual categories in which it is represented. Perhaps an engagement with suffering can open up hidden connections between these domains. After examining John Caputo and Friedrich Nietzsche comparatively on the relation between suffering and ethics, this essay explores the relation of the politics of becoming to suffering. The politics of becoming is a paradoxical process by which a new cultural identity is drawn into being and yet is irreducible to the energies and motives that spurred its initiators to action. To exemplify and think the politics of becoming is to call into question the sufficiency of existing paradigms of morality. A critical examination of the Rawlsian model of justice brings out, for example, the insufficiency of justice to the politics of becoming. It suggests the need, first, to pursue an ethics of engagement between several parties drawing upon a variety of sources of ethical inspiration and, second, to cultivate ldcritical responsiveness to new social movements that struggle to place new identities onto the cultural register. If the latter movements sometimes modify general understandings of suffering, identity, justice and medical practice they also indicate the role cultural thinkers can play in re-examining periodically established codes of interaction between these domains.A paper presented, with commentaries, as the 1995 Roger Allan Moore Lecture at Harvard Medical School, Center for the Study of Culture and Medicine, May 11, 1995.     

Darwin,Wallace, and Huxley,and Vestiges of the Natural History of Creation

Conclusion Publication of the Vestiges and the rather primitive theory of evolution it expounded thus played a significant role in the careers of Darwin and Wallace. In addition, in spite of his poor opinion of the Vestiges, it presented Huxley with a convenient topic for critical discussion and the opportunity to focus more attention on the subject of evolution. The dynamic interactions among these leading figures of nineteenth-century natural science helped spur the development of more sophisticated models of evolution.Darwin had a proper appreciation of Chambers's contribution to evolutionary thought, although he fully recognized the shortcomings of this work. He understood the importance of allowing fresh ideas about organic change to be ventilated. However, he was primarily concerned with his own theory and viewed all developments in evolutionary biology from this perspective. If he did not give full consideration to Chambers and his book early on, it was due mainly to his feeling that the concepts in the Vestiges were very different from his own; he was therefore reluctant to embrace them as the forerunners of his own theory. As a scholar, he was also troubled by the scientific errors in the book. However, the record demonstrates that he attempted to make amends for any oversight on his part. His generous letter to Chambers's daughter, and his gracious treatment of Chambers during the brief time the latter lived in London, are ample proof of that.The attacks of Huxley, Sedgwick, and other prominent natural historians and geologists at the time, the problems inherent in Chambers's evolutionary theory, and the publication of the Origin, are the major reasons why the Vestiges became a neglected work. Nevertheless, Chambers's contribution will always stand out because, together with those of other late eighteenth- and early nineteenth-century predecessors of Darwin, it laid the foundations of modern evolutionary thought and, more importantly, helped prepare the scientific community for the more fully developed ideas of Darwin and Wallace.     

Molecules, Morphology, Fossils, and the Relationship of Angiosperms and Gnetales

Morphological analyses of seed plant phylogeny agree that Gnetales are the closest living relatives of angiosperms, but some studies indicate that both groups are monophyletic, while others indicate that angiosperms are nested within Gnetales. Molecular analyses of several genes agree that both groups are monophyletic, but differ on whether they are related. Conflicts among morphological trees depend on the interpretation of certain characters; when these are analyzed critically, both groups are found to be monophyletic. Conflicts among molecular trees may reflect the rapid Paleozoic radiation of seed plant lines, aggravated by the long branches leading to extant taxa. Trees in which angiosperms are not related to Gnetales conflict more with the stratigraphic record. Even if molecular data resolve the relationships among living seed plant groups, understanding of the origin of angiosperm organs will require integration of fossil taxa, necessarily using morphology.     

Molecules,fossils, and the origin of tetrapods

Summary Since the discovery of the coelacanth, Latimeria chalumnae, more than 50 years ago, paleontologists and comparative morphologists have debated whether coelacanths or lungfishes, two groups of lobe-finned fishes, are the closest living relatives of land vertebrates (Tetrapoda). Previously, Meyer and Wilson (1990) determined partial DNA sequences from two conservative mitochondrial genes and found support for a close relationship of lungfishes to tetrapods. We present additional DNA sequences from the 12S rRNA mitochondria gene for three species of the two lineages of lungfishes that were not represented in the first study: Protopterus annectens and Protopterus aethiopicus from Africa and Neoceratodus forsteri (kindly provided by B. Hedges and L. Maxson) from Australia. This extended data set tends to group the two lepidosirenid lungfish lineages (Lepidosiren and Protopterus) with Neoceratodus as their sister group. All lungfishes seem to be more closely related to tetrapods than the coelacanth is. This result appears to rule out the possibility that the coelacanth lineage gave rise to land vertebrates. The common ancestor of lungfishes and tetrapods might have possessed multiple morphological traits that are shared by lungfishes and tetrapods [Meyer and Wilson (1990) listed 14 such traits]. Those traits that seem to link Latimeria and tetrapods are arguably due to convergent evolution or reversals and not to common descent. In this way, the molecular tree facilitates an evolutionary interpretation of the morphological differences among the living forms. We recommended that the extinct groups of lobe-finned fishes be placed onto the molecular tree that has lungfishes and not the coelacanth more closely related to tetrapods. The placement of fossils would help to further interpret the sequence of morphological events and innovations associated with the origin of tetrapods but appears to be problematic because the quality of fossils is not always high enough, and differences among paleontologists in the interpretation of the fossils have stood in the way of a consensus opinion for the branching order among lobefinned fishes. Marshall and Schultze (1992) criticized the morphological analysis presented by Meyer and Wilson (1990) and suggest that 13 of the 14 morphological traits that support the sister group relationship of lungfishes and tetrapods are not shared derived characters. Here we present further alternative viewpoints to the ones of Marshall and Schultze (1992) from the paleontological literature. We argue that all available information (paleontological, neontological, and molecular data) and rigorous cladistic methodology should be used when relating fossils and extant taxa in a phylogenetic framework. Offprint requests to: Axel Meyer     

Parasitism,the diversity of life,and paleoparasitology

The parasite-host-environment system is dynamic, with several points of equilibrium. This makes it difficult to trace the thresholds between benefit and damage, and therefore, the definitions of commensalism, mutualism, and symbiosis become worthless. Therefore, the same concept of parasitism may encompass commensalism, mutualism, and symbiosis. Parasitism is essential for life. Life emerged as a consequence of parasitism at the molecular level, and intracellular parasitism created evolutive events that allowed species to diversify. An ecological and evolutive approach to the study of parasitism is presented here. Studies of the origin and evolution of parasitism have new perspectives with the development of molecular paleoparasitology, by which ancient parasite and host genomes can be recovered from disappeared populations. Molecular paleoparasitology points to host-parasite co-evolutive mechanisms of evolution traceable through genome retrospective studies.     

Obcells as Proto-Organisms: Membrane Heredity, Lithophosphorylation, and the Origins of the Genetic Code, the First Cells, and Photosynthesis

I attempt to sketch a unified picture of the origin of living organisms in their genetic, bioenergetic, and structural aspects. Only selection at a higher level than for individual selfish genes could power the cooperative macromolecular coevolution required for evolving the genetic code. The protein synthesis machinery is too complex to have evolved before membranes. Therefore a symbiosis of membranes, replicators, and catalysts probably mediated the origin of the code and the transition from a nucleic acid world of independent molecular replicators to a nucleic acid/protein/lipid world of reproducing organisms. Membranes initially functioned as supramolecular structures to which different replicators attached and were selected as a higher-level reproductive unit: the proto-organism. I discuss the roles of stereochemistry, gene divergence, codon capture, and selection in the code's origin. I argue that proteins were primarily structural not enzymatic and that the first biological membranes consisted of amphipathic peptidyl-tRNAs and prebiotic mixed lipids. The peptidyl-tRNAs functioned as genetically-specified lipid analogues with hydrophobic tails (ancestral signal peptides) and hydrophilic polynucleotide heads. Protoribosomes arose from two cooperating RNAs: peptidyl transferase (large subunit) and mRNA-binder (small subunit). Early proteins had a second key role: coupling energy flow to the phosphorylation of gene and peptide precursors, probably by lithophosphorylation by membrane-anchored kinases scavenging geothermal polyphosphate stocks. These key evolutionary steps probably occurred on the outer surface of an `inside out-cell' or obcell, which evolved an unambiguous hydrophobic code with four prebiotic amino acids and proline, and initiation by isoleucine anticodon CAU; early proteins and nucleozymes were all membrane-attached. To improve replication, translation, and lithophosphorylation, hydrophilic substrate-binding and catalytic domains were later added to signal peptides, yielding a ten-acid doublet code. A primitive proto-ecology of molecular scavenging, parasitism, and predation evolved among obcells. I propose a new theory for the origin of the first cell: fusion of two cup-shaped obcells, or hemicells, to make a protocell with double envelope, internal genome and ribosomes, protocytosol, and periplasm. Only then did water-soluble enzymes, amino acid biosynthesis, and intermediary metabolism evolve in a concentrated autocatalytic internal cytosolic soup, causing 12 new amino acid assignments, termination, and rapid freezing of the 22-acid code. Anticodons were recruited sequentially: GNN, CNN, INN, and *UNN. CO₂ fixation, photoreduction, and lipid synthesis probably evolved in the protocell before photophosphorylation. Signal recognition particles, chaperones, compartmented proteases, and peptidoglycan arose prior to the last common ancestor of life, a complex autotrophic, anaerobic green bacterium. Received: 19 February 2001 / Accepted: 9 April 2001     

Parasites,info-disruption,and the ecology of fear

There is growing interest in the ecological consequences of fear, as evidenced by the numerous studies on the nonconsumptive, trait-mediated effects of predators. Parasitism, however, has yet to be fully integrated into research on the ecology of fear, despite it having direct negative and often lethal effects on hosts and being the most common life history strategy on the planet. This might at least be partly due to the traditional, but untested, assumption that anti-parasite responses are weak relative to anti-predator responses. To test this hypothesis, we quantified the activity and location responses of Bufo americanus tadpoles to one of six chemical cues: water; cercariae of Echinostoma trivolvis, a trematode which infects and can kill amphibians; a snail releasing E. trivolvis cercariae; an uninfected snail; food; or conspecific alarm chemicals signaling predation. There is also literature encouraging research on the context dependency and pollution-induced disruption of fear responses. Consequently, before quantifying responses to the chemical cues, half of the B. americanus were exposed to the herbicide atrazine (201 μg/l for 4 days), a reported inhibitor of fear responses in fish. Tadpoles were attracted to food, were indifferent to an uninfected snail, avoided alarm chemicals, and exhibited avoidance and elevated activity in response to a snail shedding cercariae and cercariae alone. Atrazine had no detectable effects on B. americanus’ responses to the tested cues despite the use of a higher concentration and longer exposure duration than has been repeatedly shown to inhibit chemical cue detection in fish. The magnitude of anti-parasite and anti-predator responses were qualitatively similar, suggesting that the fear of disease and its ecological consequences could be comparable to that of predation. Consequently, we call for a greater integration of parasites into research on the ecology of fear and trait-mediated indirect effects.     

Molecular phylogenetics of squamata: the position of snakes, amphisbaenians, and dibamids, and the root of the squamate tree

Squamate reptiles (snakes, lizards, and amphisbaenians) serve as model systems for evolutionary studies of a variety of morphological and behavioral traits, and phylogeny is crucial to many generalizations derived from such studies. Specifically, the traditional dichotomy between Iguania (anoles, iguanas, chameleons, etc.) and Scleroglossa (skinks, geckos, snakes, etc.) has been correlated with major evolutionary shifts within Squamata. We present a molecular phylogenetic study of 69 squamate species using approximately 4600 (2876 parsimony-informative) base pairs (bp) of DNA sequence data from the nuclear genes RAG-1(approximately 2750 bp) and c-mos(approximately 360 bp) and the mitochondrial ND2 region (approximately 1500 bp), sampling all major clades and most major subclades. Under our hypothesis, species previously placed in Iguania, Anguimorpha, and almost all recognized squamate families form strongly supported monophyletic groups. However, species previously placed in Scleroglossa, Varanoidea, and several other higher taxa do not form monophyletic groups. Iguania, the traditional sister group of Scleroglossa, is actually highly nested within Scleroglossa. This unconventional rooting does not seem to be due to long-branch attraction, base composition biases among taxa, or convergence caused by similar selective forces acting on nonsister taxa. Studies of functional tongue morphology and feeding mode have contrasted the similar states found in Sphenodon(the nearest outgroup to squamates) and Iguania with those of Scleroglossa, but our findings suggest that similar states in Sphenodonand Iguania result from homoplasy. Snakes, amphisbaenians, and dibamid lizards, limbless forms whose phylogenetic positions historically have been impossible to place with confidence, are not grouped together and appear to have evolved this condition independently. Amphisbaenians are the sister group of lacertids, and dibamid lizards diverged early in squamate evolutionary history. Snakes are grouped with iguanians, lacertiforms, and anguimorphs, but are not nested within anguimorphs.     

Observation, objectivity, and the conflict of ideas

The first two terms of this title are clear, representing, respectively, the guiding motto of the Society, and the common thread that unites members with very diverse interests and approaches to the understanding of behavior. Then, the last part of the title is elaborated: the conflict of ideas. This aspect is important both in terms of social values, and in terms of the interests of a scientific society operating in the modern world. Within science, there are forces that weaken genuine scientific discussion, and these need at least to be explicated so that their deleterious effects can be minimized. Finally, it is suggested that although the Society has done well in facilitating oral discussion, there is room for improvement in its readiness to engage in written intellectual conflict.