Culture and sociobiology

Sociobiological concepts are easily misapplied to human behavior because the latter is culturally as well as biologically organized. Because biological and cultural evolution are two linked but conceptually distinct processes, sociobiology is more readily applied to the evolution of cultural capacity than to contemporary cultural behavior. The extent to which the latter is consistent with sociobiological expectation must be determined empirically, although there are theoretical grounds for predicting a limited degree of concordance . [sociobiology, culture, evolution, reductionism, biosocial anthropology]     

奥德姆的生态思想是整体论吗?

奥德姆的生态思想是妥协的整体论,有还原论的一面。把生态系统看作是功能性整体、承认生态系统各层次的涌现属性属于整体论,把生态关系简化为能量关系、把生态系统看作是物理系统的分析方法则是还原论的。这种矛盾的生态思想决定了其方法论的先天不足:生态模型的内在逻辑关系没有理顺;较少考虑生态系统的进化;生态研究方法的排它性等。但是,它并不妨碍奥德姆的生态思想在夯实生态学的本体论基础、促进理论生态学和生态工程学的形成、协调生态整体论与还原论分歧、奠定生态系统服务功能研究基础等方面发挥重要作用。要超越生态整体论与还原论,繁荣发展生态复杂性理论也许是最好的选择。     

Systems biology,emergence and antireductionism

This study explores the conceptual history of systems biology and its impact on philosophical and scientific conceptions of reductionism, antireductionism and emergence. Development of systems biology at the beginning of 21st century transformed biological science. Systems biology is a new holistic approach or strategy how to research biological organisms, developed through three phases. The first phase was completed when molecular biology transformed into systems molecular biology. Prior to the second phase, convergence between applied general systems theory and nonlinear dynamics took place, hence allowing the formation of systems mathematical biology. The second phase happened when systems molecular biology and systems mathematical biology, together, were applied for analysis of biological data. Finally, after successful application in science, medicine and biotechnology, the process of the formation of modern systems biology was completed.Systems and molecular reductionist views on organisms were completely opposed to each other. Implications of systems and molecular biology on reductionist–antireductionist debate were quite different. The analysis of reductionism, antireductionism and emergence issues, in the era of systems biology, revealed the hierarchy between methodological, epistemological and ontological antireductionism. Primarily, methodological antireductionism followed from the systems biology. Only after, epistemological and ontological antireductionism could be supported.     

Economics, Biology, and Naturalism: Three Problems Concerning the Question of Individuality

The paper examines the ramifications of naturalism with regard to the question of individuality in economics and biology. Economic theory has to deal with whether households, firms, and states are individuals or are mere entities such as clubs, networks, and coalitions. Biological theory has to deal with the same question with regard to cells, organisms, family packs, and colonies. To wit, the question of individuality in both disciplines involves three separate problems: the metaphysical, phenomenist, and ontological. The metaphysical problem is concerned with purposeful action: Is the firm or organism exclusively the product of efficient causality (optimization) or is it motivated by final causality (purposefulness)? The phenomenist problem is interested in the substantiality of essences: Is the firm's or organism's scheme of institutions/traits deep or is it extraneous to identity? The ontological problem is related to the issue of reductionism: Is the behavior of lower-level organization governed by a pre-constituted entities or is it context-sensitive? The paper finds that theoretical differences run along the naturalist/anti-naturalist divide rather than along disciplinary specialization. Also, the paper finds that it is not inconsistent for the same theorist to be naturalist with regard to one problem and anti-naturalist with respect to the other two problems.     

Resolving the Anti-Antievolutionism Dilemma: A Brief for Relational Evolutionary Thinking in Anthropology

ABSTRACT   Anthropologists often disagree about whether, or in what ways, anthropology is "evolutionary." Anthropologists defending accounts of primate or human biological development and evolution that conflict with mainstream "neo-Darwinian" thinking have sometimes been called "creationists" or have been accused of being "antiscience." As a result, many cultural anthropologists struggle with an "anti-antievolutionism" dilemma: they are more comfortable opposing the critics of evolutionary biology, broadly conceived, than they are defending mainstream evolutionary views with which they disagree. Evolutionary theory, however, comes in many forms. Relational evolutionary approaches such as Developmental Systems Theory, niche construction, and autopoiesis–natural drift augment mainstream evolutionary thinking in ways that should prove attractive to many anthropologists who wish to affirm evolution but are dissatisfied with current "neo-Darwinian" hegemony. Relational evolutionary thinking moves evolutionary discussion away from reductionism and sterile nature–nurture debates and promises to enable fresh approaches to a range of problems across the subfields of anthropology. [Keywords: evolutionary anthropology, Developmental Systems Theory, niche construction, autopoeisis, natural drift]     

Conditions for a theoretical biology: is biology truly an autonomous science?

In a line of a previous paper, the conditions for a theoretical biology were discussed and it was pointed out that the primary condition is that biology is an autonomous science. This statement is connected to the problem of reductionism. A discussion of the autonomy of biology shows that reductionism cannot be maintained, although particularly in physiology often physics and mathematics are used. Development, organization and evolution of biological systems are typical areas of autonomous biological researches and of autonomous theoretical developments. A sort of reduction to history seems today a nonsensical attempt to reduce the area of free theoretical biological activity.     

The sociological critique of evolutionary psychology: Beyond mass modularity

This paper addresses evolutionary psychology's (EP's) mass modularity account of human intelligence. First, EP is located within 'naturalization of society' discourses. Secondly, the nature and weakness of mass modularity theory is examined. In the third part of the paper, the genetic reductionism of EP is challenged with reference to developmental systems theory (DST). However, in the fourth part, the danger of importing one biological theory to defuse the colonial ambitions of another is highlighted through an examination of sociological systems theory and its relationship with biological systems theory. Nevertheless, DST has stimulated valuable insights in theoretical sociology/anthropology. Modularity is also common in computer models of intelligence as algorithmic computation. EP draws parallels with computer modelling to claim confirmation of its own account. The fifth part of this article challenges the validity of this parallel, drawing upon Harry Collins's sociology of what humans and computers can do. Collins's work highlights the non-modular cultural 'rules' that today's computers cannot follow. In the light of these theoretical and empirical developments I conclude that contemporary sociology offers a valuable and systematic counter to discourses of genetic reductionism and the discourses of technological determination upon which they are parasitic.     

On emergence, agency, and organization

Ultimately we will only understand biological agency when we have developed a theory of the organization of biological processes, and science is still a long way from attaining that goal. It may be possible nonetheless to develop a list of necessary conditions for the emergence of minimal biological agency. The authors offer a model of molecular autonomous agents which meets the five minimal physical conditions that are necessary (and, we believe, conjointly sufficient) for applying agential language in biology: autocatalytic reproduction; work cycles; boundaries for reproducing individuals; self-propagating work and constraint construction; and choice and action that have evolved to respond to food or poison. When combined with the arguments from preadaptation and multiple realizability, the existence of these agents is sufficient to establish ontological emergence as against what one might call Weinbergian reductionism. Minimal biological agents are emphatically not conscious agents, and accepting their existence does not commit one to any robust theory of human agency. Nor is there anything mystical, dualistic, or non-empirical about the emergence of agency in the biosphere. Hence the emergence of molecular autonomous agents, and indeed ontological emergence in general, is not a negation of or limitation on careful biological study but simply one of its implications.     

Molecular biology, darwinism and nomogenesis

The theory of nomogenesis put forward by L. S. Berg in 1922 is discussed. It is shown that side by side with some erroneous anti-darwinian ideas the theory contains a series of important suggestions which anticipate the further development of the synthetic theory of evolution. Berg has foreseen the development of molecular biology. Thus he was the fore-teller of our branch of science. The theory of nomogenesis emphasized the limitations of natural selection which determine the directionality of evolution. Berg treated the speciation as a kind of phase transition. Even the most conscientious critics of Berg have misrepresented the real sense of his works. It is totally groundless to treat nomogenesis as an idealistic of Lamarkian theory. Berg was superior to his critics. However the enthusiasm about nomogenesis in our time shows the inability to separate "the grains from weeds".     

Chemical Ecology and Biomolecular Evolution

The belief in the Darwinian theory of evolution appeared to be shaken when one tried to interpret statements of molecular biology in it. As a consequence there arose a theory of non-Darwinian neutral evolution. The supporters of this theory believe that under natural conditions no factors exist which can distinguish and select organisms on their internal (molecular) structure. In the opinion of these neutralists natural selection cannot in principle control the molecular constitution of organisms. Contrary to the viewpoint of the critics of neutralism it is impossible to admit that nucleic acids, proteins and other biomolecules can evolve without the participation of natural selection. This controversy in contemporary theoretical biology can be solved by integrating the conceptions of molecular ecology with Darwinian theory. Molecular ecology acknowledges the interactions of organisms by means of chemical substances synthesized by them. Such chemical ecological factors play a leading part in the selective stages of biomolecular evolution. These diverse chemical ecological interrelations take place intensively when living beings interact with parasitic microbes.     

Foundations of the new phylogenetics

Evolutionary idea is the core of the modern biology. Due to this, phylogenetics dealing with historical reconstructions in biology takes a priority position among biological disciplines. The second half of the 20th century witnessed growth of a great interest to phylogenetic reconstructions at macrotaxonomic level which replaced microevolutionary studies dominating during the 30s-60s. This meant shift from population thinking to phylogenetic one but it was not revival of the classical phylogenetics; rather, a new approach emerged that was baptized The New Phylogenetics. It arose as a result of merging of three disciplines which were developing independently during 60s-70s, namely cladistics, numerical phyletics, and molecular phylogenetics (now basically genophyletics). Thus, the new phylogenetics could be defined as a branch of evolutionary biology aimed at elaboration of "parsimonious" cladistic hypotheses by means of numerical methods on the basis of mostly molecular data. Classical phylogenetics, as a historical predecessor of the new one, emerged on the basis of the naturphilosophical worldview which included a superorganismal idea of biota. Accordingly to that view, historical development (the phylogeny) was thought an analogy of individual one (the ontogeny) so its most basical features were progressive parallel developments of "parts" (taxa), supplemented with Darwinian concept of monophyly. Two predominating traditions were diverged within classical phylogenetics according to a particular interpretation of relation between these concepts. One of them (Cope, Severtzow) belittled monophyly and paid most attention to progressive parallel developments of morphological traits. Such an attitude turned this kind of phylogenetics to be rather the semogenetics dealing primarily with evolution of structures and not of taxa. Another tradition (Haeckel) considered both monophyletic and parallel origins of taxa jointly: in the middle of 20th century it was split into phylistics (Rasnitsyn's term; close to Simpsonian evolutionary taxonomy) belonging rather to the classical realm, and Hennigian cladistics that pays attention to origin of monophyletic taxa exclusively. In early of the 20th century, microevolutionary doctrine became predominating in evolutionary studies. Its core is the population thinking accompanied by the phenetic one based on equation of kinship to overall similarity. They were connected to positivist philosophy and hence were characterized by reductionism at both ontological and epistemological levels. It led to fall of classical phylogenetics but created the prerequisites for the new phylogenetics which also appeared to be full of reductionism. The new rise of phylogenetic (rather than tree) thinking during the last third of the 20th century was caused by lost of explanatory power of population one and by development of the new worldview and new epistemological premises. That new worldview is based on the synergetic (Prigoginian) model of development of non-equilibrium systems: evolution of the biota, a part of which is phylogeny, is considered as such a development. At epistemological level, the principal premise appeared to be fall of positivism which was replaced by post-positivism argumentation schemes. Input of cladistics into new phylogenetics is twofold. On the one hand, it reduced phylogeny to cladistic history lacking any adaptivist interpretation and presuming minimal evolution model. From this it followed reduction of kinship relation to sister-group relation lacking any reference to real time scale and to ancestor-descendant relation. On the other hand, cladistics elaborated methodology of phylogenetic reconstructions based on the synapomorphy principle, the outgroup concept became its part. The both inputs served as premises of incorporation of both numerical techniques and molecular data into phylogenetic reconstruction. Numerical phyletics provided the new phylogenetics with easily manipulated algorithms of cladogram construing and thus made phylogenetic reconstructions operational and repetitive. The above phenetic formula "kinship = similarity" appeared to be a keystone for development of the genophyletics. Within numerical phyletics, a lot of computer programs were elaborated which allow to manipulate with evolutionary scenario during phylogenetic reconstructions. They make it possible to reconstruct both clado- and semogeneses based on the same formalized methods. Multiplicity of numerical approaches indicates that, just as in the case of numerical phenetics, choice of adequate method(s) should be based on biologically sound theory. The main input of genophyletics (= molecular phylogenetics) into the new phylogenetics was due to completely new factology which makes it possible to compare directly such far distant taxa as prokaryotes and higher eukaryotes. Genophyletics is based on the theory of neutral evolution borrowed from microevolutionary theory and on the molecular clock hypothesis which is now considered largely inadequate. The future developments of genophyletics will be aimed at clarification of such fundamental (and "classical" by origin) problems as application of character and homology concepts to molecular structures. The new phylogenetics itself is differentiated into several schools caused basically by diversity of various approaches existing within each of its "roots". Cladistics makes new phylogenetics splitted into evolutionary and parsimonious ontological viewpoints. Numerical phyletics divides it into statistical and (again) parsimonious methodologies. Molecular phylogenetics is opposite by its factological basis to morphological one. The new phylogenetics has significance impact onto the "newest" systematics. From one side, it gives ontological status back to macrotaxa they have lost due to "new" systematics based on population thinking. From another side, it rejects some basical principles of classical phylogenetic (originally Linnean) taxonomy such as recognitions of fixed taxonomic ranks designated by respective terms and definition of taxic names not by the diagnostic characters but by reference to the ancestor. The latter makes the PhyloCode overburdened ideologically and the "newest" systematics self-controversial, as concept of ancestor has been acknowledged non-operational from the very beginning of cladistics. Relation between classical and new phylogenetics is twofold. At the one hand, general phylogenetic hypothesis (in its classical sense) can be treated as a combination of cladogenetic and semogenetic reconstructions. Such a consideration is bound to pay close attention to the uncertainty relation principle which, in case of the phylogenetics, means that the general phylogenetic hypothesis cannot be more certain than any of initial cladogenetic or semogenetic hypotheses. From this standpoint, the new phylogenetics makes it possible to reconstruct phylogeny following epistemological principle "from simple to complex". It elaborates a kind of null hypotheses about evolutionary history which are more easy to test as compared to classical hypotheses. Afterward, such hypotheses are possible to be completed toward the classical, more content-wise ones by adding anagenetic information to the cladogenetic one. At another hand, reconstructions elaborated within the new phylogenetics could be considered as specific null hypotheses about both clado- and semogeneses. They are to be tested subsequently by mean of various models, including those borrowed from "classical" morphology. The future development of the new phylogenetics is supposed to be connected with getting out of plethora of reductionism inherited by it from population thinking and specification of object domain of the phylogenetics. As the latter is a part of an evolutionary theory, its future developments will be adjusted with the latter. Lately predominating neodarwinism is now being replaced by the epigenetic evolutionary theory to which phylistics (one of the modern versions of classical phylogenetics) seems to be more correspondent.     

Do Organisms Exist?

What is the status of organisms in modern evolutionary biology?I argue that this is a question which centers on the questionof reduction, and towards a complete answer, I pursue issuesthrough three different senses of the term: ontological, methodological,and epistemological. The first sense refers to the ultimatestatus of the entities of the organic world, and in this senseI argue that organisms have no special status. The second senserefers to the question of organization, and I argue that inthe light of modern evolutionary biology organisms do have adistinctive "design-like" organization. The third sense refersto the relationship between theories, in particular to whetherthe theories of the biological sciences can be shown to be logicalconsequences of the theories of the physical sciences. I arguethat such reduction may be possible in principle but difficultin practice. However, from the perspective of the working scientist,this hardly matters. In conclusion, I argue that in some respectsorganisms are not distinctive and in other respects they are.Certainly biologists need not worry for the autonomy of theirsubject.     

How MAP kinase modules function as robust,yet adaptable,circuits

Genetic and biochemical studies have revealed that the diversity of cell types and developmental patterns evident within the animal kingdom is generated by a handful of conserved, core modules. Core biological modules must be robust, able to maintain functionality despite perturbations, and yet sufficiently adaptable for random mutations to generate phenotypic variation during evolution. Understanding how robust, adaptable modules have influenced the evolution of eukaryotes will inform both evolutionary and synthetic biology. One such system is the MAP kinase module, which consists of a 3-tiered kinase circuit configuration that has been evolutionarily conserved from yeast to man. MAP kinase signal transduction pathways are used across eukaryotic phyla to drive biological functions that are crucial for life. Here we ask the fundamental question, why do MAPK modules follow a conserved 3-tiered topology rather than some other number? Using computational simulations, we identify a fundamental 2-tiered circuit topology that can be readily reconfigured by feedback loops and scaffolds to generate diverse signal outputs. When this 2-kinase circuit is connected to proximal input kinases, a 3-tiered modular configuration is created that is both robust and adaptable, providing a biological circuit that can regulate multiple phenotypes and maintain functionality in an uncertain world. We propose that the 3-tiered signal transduction module has been conserved through positive selection, because it facilitated the generation of phenotypic variation during eukaryotic evolution.     

Metabolic complexity in the RNA world and implications for the origin of protein synthesis

Summary A model is presented for the evolution of metabolism and protein synthesis in a primitive, acellular RNA world. It has been argued previously that the ability to perform metabolic functions logically must have preceded the evolution of a message-dependent protein synthetic machinery and that considerable metabolic complexity was achieved by ribo-organisms (i.e., organisms in which both genome and enzymes are comprised of RNA). The model proposed here offers a mechanism to account for the gradual development of sophisticated metabolic activities by ribo-organisms and explains how such metabolic complexity would lead subsequently to the synthesis of genetically encoded polypeptides. RNA structures ancestral to modern ribosomes, here termed metabolosomes, are proposed to have functioned as organizing centers that coordinated, using base-pairing interactions, the order and nature of adaptor-mounted substrate/catalyst interactions in primitive metabolic pathways. In this way an ancient genetic code for metabolism is envisaged to have predated the specialized modern genetic code for protein synthesis. Thus, encoded amino acids initially would have been used, in conjunction with other encoded metabolites, as building blocks for biosynthetic pathways, a role that they retain in the metabolism of contemporary organisms. At a later stage the encoded amino acids would have been condensed together on similar RNA metabolosome structures to form the first genetically determined, and therefore biologically meaningful, polypeptides. On the basis of codon distributions in the modern genetic code it is argued that the first proteins to have been synthesized and used by ribo-organisms were predominantly hydrophobic and likely to have performed membrane-related functions (such as forming simple pore structures), activities essential for the evolution of membrane-enclosed cells.     

Looking for rules in a world of exceptions: reflections on evidence-based practice

After more than a decade, evidence-based medicine (EBM) is well established as an important influence in health care. EBM has engendered a wide range of responses from near-evangelical fervor to angered rejection, with supporters convinced of its scientific superiority and detractors of its needless reductionism. EBM is not a philosophical doctrine, and its originators and proponents have, for the most part, ignored critics and foresworn theorizing. However, EBM claims to be a normative guide to being a better physician. The theoretical, practical, and philosophical dimensions of EBM are intimately intertwined. This essay is a sustained reflection on the issues raised by EBM as experienced by a clinician/teacher who has tried to apply the tenets of EBM in clinical care and teaching over the past decade, and who has sought to expand the borders of EBM from a philosophical point of view.     

On the Neurobiology of Truth

The concept of truth arises from puzzling over distinctions between the real and the apparent, while the origin of these distinctions lies in the neurobiology of mammalian cerebral lateralization, that is, in the evolution of brains that can address the world both indicatively and subjunctively; brains that represent the world both categorically and hypothetically. After some 2,500 years of thinking about it, the Western philosophical tradition has come up with three major theories of truth: correspondence, coherence, and pragmatist. Traditional philosophy has nevertheless failed to arbitrate much among these views; certainly no clear winner has emerged. I argue, however, that contemporary neuroscience provides adequate theoretical grounds for a unified theory of truth. More specifically, I contend that the correspondence, the coherence, and the pragmatic utility of symbols are each biological features of our neurophysiological information processing systems—that is to say, our brains. On my view, the traditional trifurcation of philosophical accounts of the predicate, “is true”, stems from a trifurcation of focus on the information latent in sensory, motor, and somatosensory cortices of the human brain.     

Ins and Outs of Systems Biology vis-à-vis Molecular Biology: Continuation or Clear Cut?

The comprehension of living organisms in all their complexity poses a major challenge to the biological sciences. Recently, systems biology has been proposed as a new candidate in the development of such a comprehension. The main objective of this paper is to address what systems biology is and how it is practised. To this end, the basic tools of a systems biological approach are explored and illustrated. In addition, it is questioned whether systems biology ‘revolutionizes’ molecular biology and ‘transcends’ its assumed reductionism. The strength of this claim appears to depend on how molecular and systems biology are characterised and on how reductionism is interpreted. Doing credit to molecular biology and to methodological reductionism, it is argued that the distinction between molecular and systems biology is gradual rather than sharp. As such, the classical challenge in biology to manage, interpret and integrate biological data into functional wholes is further intensified by systems biology’s use of modelling and bioinformatics, and by its scale enlargement.     

Rejuvenating old fluorophores with new chemistry

The field of organic chemistry began with 19th century scientists identifying and then expanding upon synthetic dye molecules for textiles. In the 20th century, dye chemistry continued with the aim of developing photographic sensitizers and laser dyes. Now, in the 21st century, the rapid evolution of biological imaging techniques provides a new driving force for dye chemistry. Of the extant collection of synthetic fluorescent dyes for biological imaging, two classes reign supreme: rhodamines and cyanines. Here, we provide an overview of recent examples where modern chemistry is used to build these old-but-venerable classes of optically responsive molecules. These new synthetic methods access new fluorophores, which then enable sophisticated imaging experiments leading to new biological insights.     

From geochemistry and biochemistry to prebiotic evolution...we necessarily enter into Gánti's fluid automata

The present study is just an overview of the opening of the geochemical stage for the appearance of life. But that opening would not have been sufficient for the intellectual discovery of the origin of life! The excellent works and many commendable efforts that advance this explanation have not shown the fundamental elements that participate in the theoretical frame of biological evolution. The latter imply the existence of evolutionary transitions and the production of new levels of organization. In this brief analysis we do not intend to introduce the audience to the philosophy of biology. But we do expect to provide a modest overview, in which the geochemical chemolithoautotrophic opening of the stage should be seen, at most, as the initial metabolism that enabled organic compounds to follow the road where a chemical fluid machinery was thus able to undertake the more "sublime" course of organic biological evolution. We think that Tibor Gánti's chemoton is the most significant contribution to theoretical biology, and the only course now available to comprehend the unit of evolution problem without the structuralist and functionalist conflict prevalent in theoretical biology. In our opinion Gánti's chemoton theory travels to the "locus" where evolutionary theory dares to extend itself to entities at many levels of structural organization, beyond the gene or the group above. Therefore, in this and subsequent papers on the prebiotic conditions for the eventual appearance of the genetic code, we explore the formation and the presence of metal sulfide minerals, from the assembly of metal sulfide clusters through the precipitation of nanocrystals and the further reactions resulting in bulk metal sulfide phases. We endeavor to characterize pristine reactions and the modern surfaces, utilizing traditional surface science techniques and computational methods. Moreover, mechanistic details of the overall oxidation of metal sulfide minerals are set forth. We hope that this paper will lead our audience to accept that in a chemically oscillating system the chemoton is a model fluid state automaton capable of growth and self-reproduction. This is not simply a matter of transmitting a pattern, as in inorganic crystals; such self-reproduction must be more complex than crystal growth. Indeed that is what Gánti's theoretical and abstract model offers to us all: we finally have a philosophy of evolutionary units in theoretical biology.     

Farm Animal Production: Changing Agriculture in a Changing Culture

Western attitudes toward animals have undergone a gradual evolution during recent centuries, driven by the scientific recognition that humans and many other species share a common anatomical template, a common phylogenetic ancestry, and certain similarities in their social and emotional lives. This evolving view has been accompanied by a heightened popular respect for animals, which has caused increasing opposition to the relatively utilitarian treatment of animals in modern farming. Western culture also tends to venerate the pastoralist image of humans caring diligently for animals, and North Americans tend to venerate the agrarian life-style of farm families living in harmony with domestic animals and the land. These positive images, which have traditionally lent legitimacy to animal agriculture, have been diminished by changes in production methods during recent decades. The resulting debate between critics and defenders of modern animal production has led to widespread confusion and concern about how animal agriculture affects animal welfare, human health, the environment, and world food security. To resolve this situation will require research to create an accurate understanding of the diverse effects of modern animal agriculture, together with measures to harmonize agricultural practices with changing public values.