The physics of symbols: bridging the epistemic cut

Evolution requires the genotype–phenotype distinction, a primeval epistemic cut that separates energy-degenerate, rate-independent genetic symbols from the rate-dependent dynamics of construction that they control. This symbol–matter or subject–object distinction occurs at all higher levels where symbols are related to a referent by an arbitrary code. The converse of control is measurement in which a rate-dependent dynamical state is coded into quiescent symbols. Non-integrable constraints are one necessary condition for bridging the epistemic cut by measurement, control, and coding. Additional properties of heteropolymer constraints are necessary for biological evolution.     

Neolithic urban primacy: The case against the invention of agriculture

It is proposed that sowing seed preceded agriculture by many millenia and that the invention of sowing is independent of the Neolithic Revolution. The advantages of using permanent seed stores as the source of seed grain is much more difficult to perceive and it is upon this accident that full-scale agriculture waited. Jacobs' (1969) model of cities before agriculture is the explanation of permanent seed bins for purely economic reasons. It is the role of bin permanence in switching the selective mechanism towards cultivars that explains the precipitous events c. 8000 B.C. Once cultivars are developed, true large-scale agriculture becomes an obvious advantage but not until the cultivars are there. Jacobs' model seeks to put hunters and traders into a positive loop that alone produces the city. This could not be so for there is not enough food at appropriate points in the model; but if casual sowing can be invoked as a long-standing precursor, then the extra forcing function allows the vital transition to genetic continuity in the harvested grain.     

Fritz Jahr: the invention of bioethics and beyond

Since the discovery of his work in 1997, Fritz Jahr (1895-1953) has slowly become recognized as the author of the term and concept of bioethics. Jahr's ideas on bioethics were partly different from those shaped by Van Rensselaer Potter in the 1970s and, therefore, might be helpful for the further reform and broadening of modern bioethics. In this article, the authors elucidate ideas from lesser-known works by Jahr, especially those considering animal protection and teaching.     

The interpretations of fox possession: Illness as metaphor

Although fox possession is a rare phenomenon in contemporary Japan, it is a matter of concern in psychiatry and in folk healing. The case study presented here deals with the social process of role transformation, from client to shaman, as a way of self healing. The discussion then assumes that fox possession renders multiple interpretations and argues that it is, in fact, a metaphorical representation in much the same way that biomedical interpretation is. The argument also proposes that an etiological (causal) understanding of fox possession is less productive than a metaphorical one.     

The rational design of biological complexity: a deceptive metaphor

Biologists often claim that they follow a rational design strategy when their research is based on molecular knowledge of biological systems. This claim implies that their knowledge of the innumerable causal connections present in biological systems is sufficient to allow them to deduce and predict the outcome of their experimental interventions. The design metaphor is shown to originate in human intentionality and in the anthropomorphic fallacy of interpreting objects, events, and the behavior of all living organisms in terms of goals and purposes. Instead of presenting rational design as an effective research strategy, it would be preferable to acknowledge that advances in biomedicine are nearly always derived from empirical observations based on trial and error experimentation. The claim that rational design is an effective research strategy was tested in the case of current attempts to develop synthetic vaccines, in particular against human immunodeficiency virus. It was concluded that in this field of biomedicine, trial and error experimentation is more likely to succeed than a rational design approach. Current developments in systems biology may give us eventually a better understanding of the immune system and this may enable us in the future to develop improved vaccines.     

The evolution of biogeochemistry: revisited

Biogeochemistry - The evolution of biogeochemistry, retraces the important historical steps in part, covered by Gorham (Biogeochemistry 13:199–239, 1991) in the 18–19th...     

The stromatoporoid animal revisited: Building the skeleton

Modern coralline sponges secrete a skeleton by means of a basal pinacoderm, intracellularly, or inside the soft tissue on an organic matrix The examination of terminal growth surfaces of stromatoporoids indicates that soft tissue in laminate and amalgamate forms occupied the upper galleries and that the skeletal elements were secreted within the soft tissue on an organic matrix. The stromatoporellids and clathrodictyids secreted the skeleton in modules that are homologous to the chambers of a sphinctozoan. In stromatoporellids the module was bounded by a floor that formed the upper layer of the tripatite lamina below and a roof that became the lower layer of the next lamina; it further included the intervening pillars. In clathrodictyids the module had only a roof and pillars, and the laminae are single layers. other stromatoporoids may have secreted their skeletons at the base of the soft tissue and had minimal occupation of the skeleton. *** Stromatoporoid, sphinctozoa, sclerospongiae, sponge, paleobiology.     

The hunters and the hunted revisited

The dietary niches of extinct animals, including hominids and predators, may be constrained using stable carbon isotope ratios in fossil tooth enamel.(13)C/(12)C ratios of many of the primates abundant in the faunal assemblages of Members 1 and 2 at Swartkrans, including cercopithecoids and Australopithecus (Paranthropus) robustus, and a range of other possible prey species, have been reported previously. Resulting suggestions of a mixed, or omnivorous, diet for A. robustus raise questions about niche overlap with coeval, larger brained Homo. Here we present(13)C/(12)C data from Homo and several large predators including Panthera pardus, Dinofelis sp., Megantereon cultridens and Chasmoporthetes nitidula in Member 1, and P. pardus and P. leo in Member 2, in order to compare the two hominid species and to determine likely predators of the various primates and other macrovertebrates. Results for three Homo cf. ergaster individuals are indistinguishable from those of A. robustus, showing that proportions of C(3)- and C(4)-based foods in their diets did not differ. P. pardus, Megantereon and Crocuta are shown to be likely predators of the hominids and Papio baboons in Member 1, while the Dinofelis individual concentrated on prey which consumed C(4)grasses. The hunting hyaenid C. nitidula preyed on either mixed feeders or on a range of animals across the spectrum of C(3)and C(4)variation. The data from Members 1 and 2 confirm a shift in leopard diets towards animals that consumed C(4)grasses.     

Life, self-reproduction and information: beyond the machine metaphor

The problem of representing information in automation models of self-replication is considered. It is shown that, unlike in the natural reproduction process, in a computable model the reproduced entities do not contain all the information necessary for guiding the process. Current theoretical understanding of life and its replication, based on such models, is argued to be essentially inadequate. The solution to this problem is claimed to require recognition of the theoretical fact that information in living systems is different from that subsumed under the category of "knowledge", which is representable as computer programs or triggers of state transitions. A discussion of fundamentals of a new theory of information and its relationship to replication models is given and a new direction of further developments of biological theories is envisioned.