Although molecular systematists may use the terminology of cladism, claiming that the reconstruction of phylogenetic relationships is based on shared derived states , the latter is not the case. Rather, molecular systematics is based on the assumption, first clearly articulated by Zuckerkandl and Pauling , that degree of overall similarity reflects degree of relatedness. This assumption derives from interpreting molecular similarity between taxa in the context of a Darwinian model of continual and gradual change. Review of the (...) history of molecular systematics and its claims in the context of molecular biology reveals that there is no basis for the “molecular assumption.”. (shrink)

: Where there are cases of underdetermination in scientific controversies, such as the case of the molecular clock, scientists may direct the course and terms of dispute by playing off the multidimensional framework of theory evaluation. This is because assessment strategies themselves are underdetermined. Within the framework of assessment, there are a variety of trade-offs between different strategies as well as shifting emphases as specific strategies are given more or less weight in assessment situations. When a strategy is underdetermined, (...) scientists can change the dynamics of a controversy by making assessments using different combinations of evaluation strategies and/or weighting whatever strategies are in play in different ways. Following an underdetermination strategy does not end or resolve a scientific dispute. Consequently, manipulating underdetermination is a feature of controversy dynamics and not controversy closure. (shrink)

The molecular clock hypothesis remains controversial more than a quarter of a century after it was first proposed. A variety of approaches have been applied to testing the molecular clock in mammals. In many of these studies apparent refutation of the molecular clock has based on false assumptions about the pattern of mammalian evolution. With a few exceptions there now appears to be little evidence for variation in the rate of molecular evolution among mammalian lineages, although (...) comparison of more genes and proteins among a greater variety of mammalian orders is needed before a definitive conclusion can be reached on the issue. (shrink)

Recent controversy about the use of the vertebrate fossil record for external calibration of molecular clocks centers on two issues, the number of dates used for calibration and the reliability of the fossil calibration date. Viewing matters from a palaeontological perspective, we propose three qualitative, phylogenetic criteria that can be used within a comparative framework for the selection of well-constrained calibration dates from the vertebrate fossil record. On the basis of these criteria, we identify three highly suitable new (...) fossil calibration dates for molecular clock estimates: the lungfish–tetrapod split (between 419 and 408 Ma), the bird–crocodile split (between 251 and 243 Ma), and the alligator–caiman split (between 71 and 66 Ma). Together with our previously suggested bird–lizard split (between 252 and 257 Ma), these four fossil dates span a range of very different ages. They are, in our opinion, more suitable for molecular clock calibration than the traditionally used mammal–bird split, which is less well constrained. We plea for closer interactions between paleontologists and molecular biologists in studying the timescale of vertebrate evolution. BioEssays 27:1069–1075, 2005. © 2005 Wiley Periodicals, Inc. (shrink)

Through a case study of the controversies surrounding the molecular clock, this paper examines the role of visual representation in the dynamics of scientific controversies. Representations of the molecular clock themselves became objects of controversy and so were not a means for closure. Instead visual representations of the molecular clock became tools for the further articulation of an ongoing controversy.

The discoveries, advancements and continuing controversies in the field of molecular evolution are reviewed. Topics summarized are (1) the evolution of the genetic code, (2) gene evolution including the demonstration of homology, estimation of sequence divergence, phylogenetic trees, the molecular clock and the origin of genes and gene families by various genetic mechanisms, and (3) eukaryotic genome evolution, including the highly repeated satellite sequences, the interspersed and potentially mobile repeated sequences and the unique sequence fraction of the genome.

Based on genetic and biochemical advances on the molecular mechanism of circadian rhythms, a computational model for the mammalian circadian clock is used to examine the dynamical bases of circadian‐clock‐related physiological disorders in humans. Entrainment by the light–dark cycle with a phase advance or a phase delay is associated with the Familial advanced sleep phase syndrome (FASPS) or the Delayed sleep phase syndrome (DSPS), respectively. Lack of entrainment corresponding to the occurrence of quasiperiodic oscillations with or without phase jump (...) can be associated with the non‐24 h sleep–wake syndrome. In the close vicinity of the entrainment domain, the model uncovers the possibility of infradian oscillations of very long period. Perturbation in the form of chronic jet lag, as used in mice, prevents entrainment of the circadian clock and results in chaotic or quasiperiodic oscillations. It is important to clarify the conditions for entrainment and for its failure because dysfunctions of the circadian clock may lead to physiological disorders, which pertain not only to the sleep–wake cycle but also to mood and cancer. BioEssays 30:590–600, 2008. © 2008 Wiley Periodicals, Inc. (shrink)

Circalunar clocks, which allow organisms to time reproduction to lunar phase, have been experimentally proven but are still not understood at the molecular level. Currently, a new generation of researchers with new tools is setting out to fill this gap. Our essay provides an overview of classic experiments on circalunar clocks. From the unpublished work of the late D. Neumann we also present a novel phase response curve for a circalunar clock. These experiments highlight avenues for (...) class='Hi'>molecular work and call for rigor in setting up and analyzing the logistically complex experiments on circalunar clocks. Re‐evaluating classic experiments, we propose that (1) circalunar clocks in different organisms will have divergent mechanisms and physiological bases, (2) they may have properties very different from the well‐studied circadian clocks and (3) they may have close mechanistic and molecular relations to seasonal rhythms and diapause. (shrink)

This chapter contains section titled: The Neutral Theory of Molecular Evolution The Molecular Clock The Neutral Null Model Controversy in Molecular Evolution Acknowledgment References Further Reading.

This paper focuses on the consolidation of Molecular Evolution, a field originating in the 1960s at the interface of molecular biology, biochemistry, evolutionary biology, biophysics and studies on the origin of life and exobiology. The claim is made that Molecular Evolution became a discipline by integrating different sorts of scientific traditions: experimental, theoretical and comparative. The author critically incorporates Timothy Lenoir’s treatment of disciplines , as well as ideas developed by Stephen Toulmin on the same subject. On (...) their account disciplines are spaces where the social and epistemic dimensions of science are deeply and complexly interwoven. However, a more detailed account of discipline formation and the dynamics of an emerging disciplinary field is lacking in their analysis. The present essay suggests focusing on the role of scientific concepts in the double configuration of disciplines: the social/political and the epistemic order. In the case of Molecular Evolution the concepts of molecular clock and informational molecules played a central role, both in differentiating molecular from classical evolutionists, and in promoting communication between the different sorts of traditions integrated in Molecular Evolution. The paper finishes with a reflection on the historicity of disciplines, and the historicity of our concepts of disciplines. (shrink)

Ether-drift experiments using opposed masers are examined from the point of view that, if molecules contain indigenous radiation, a maser beam might be idealized as a stream of light clocks. According to a recently developed theory of the light clock, in which relativistic Doppler frequencies are developed from a classical ether model augmented by the Fitzgerald contraction, no effect from ether drift is expected, so that the null result of the experiments is in accord with this version of the (...) ether theory. (shrink)

During the early 1960s, Morris Goodman used a variety of immunological tests to demonstrate the very close genetic relationships among humans, chimpanzees, and gorillas. Molecular anthropologists often point to this early research as a critical step in establishing their new specialty. Based on his molecular results, Goodman challenged the widely accepted taxonomie classification that separated humans from chimpanzees and gorillas in two separate families. His claim that chimpanzees and gorillas should join humans in family Hominidae sparked a well-known (...) conflict with George Gaylord Simpson, Ernst Mayr, and other prominent evolutionary biologists. Less well known, but equally significant, were a series of disagreements between Goodman and other prominent molecular evolutionists concerning both methodological and theoretical issues. These included qualitative versus quantitative data, the role of natural selection, rates of evolution, and the reality of molecular clocks. These controversies continued throughout Goodman's career, even as he moved from immunological techniques to protein and DNA sequence analysis. This episode highlights the diversity of methods used by molecular evolutionists and the conflicting conclusions drawn from the data that these methods generated. (shrink)

Period homeostasis is the defining characteristic of a biological clock. Strict period homeostasis is found for the ultradian clocks of eukaryotic microbes. In addition to being temperature-compensated, the period of these rhythms is unaffected by differences in nutrient composition or changes in other environmental variables. The best-studied examples of ultradian clocks are those of the ciliates Paramecium tetraurelia and Tetrahymena sp. and of the fission yeast, Schizosaccharomyces pombe. In these single cell eukaryotes, up to seven different parameters display (...) ultradian rhythmicity with the same, species- and strain-specific period. In fission yeast, the molecular genetic analysis of ultradian clock mechanisms has begun with the systematic analysis of mutants in identified candidate genes. More than 40 “clock mutants” have already been identified, most of them affected in components of major regulatory and signalling pathways. These results indicate a high degree of complexity for a eukaryotic clock mechanism. BioEssays 22:16–22, 2000. ©2000 John Wiley & Sons, Inc. (shrink)

In the advertising discourse of human genetic database projects, of genetic ancestry tracing companies, and in popular books on anthropological genetics, what I refer to as the anthropological gene and genome appear as documents of human history, by far surpassing the written record and oral history in scope and accuracy as archives of our past. How did macromolecules become "documents of human evolutionary history"? Historically, molecular anthropology, a term introduced by Emile Zuckerkandl in 1962 to characterize the study of (...) primate phylogeny and human evolution on the molecular level, asserted its claim to the privilege of interpretation regarding hominoid, hominid, and human phylogeny and evolution vis-à-vis other historical sciences such as evolutionary biology, physical anthropology, and paleoanthropology. This process will be discussed on the basis of three key conferences on primate classification and evolution that brought together exponents of the respective fields and that were held in approximately ten-years intervals between the early 1960s and the 1980s. I show how the anthropological gene and genome gained their status as the most fundamental, clean, and direct records of historical information, and how the prioritizing of these epistemic objects was part of a complex involving the objectivity of numbers, logic, and mathematics, the objectivity of machines and instruments, and the objectivity seen to reside in the epistemic objects themselves. (shrink)

This article offers three contrasting cases of the use of neutrality and drift in molecular evolution. In the first, neutrality is assumed as a simplest case for modeling. In the second and third, concepts of drift and neutrality are developed within the context of population genetics testing and the development and application of the molecular clock.

A circadian clock, with physiological characteristics similar to those of eukaryotes, functions in the photosynthetic prokaryote, cyanobacteria. The molecular mechanism of this clock has been efficiently dissected using a luciferase reporter gene that reports the status of the clock. A circadian clock gene cluster, kaiABC, has been cloned via rhythm mutants of cyanobacterium, Synechococcus, and many clock mutations mapped to the three kai genes. Although kai genes do not share any homology with clock genes so far identified in eukaryotes, (...) analysis of their expression suggests that a negative feedback control of kaiC expression by KaiC generates the circadian oscillation and that KaiA functions as a positive factor to sustain this oscillation. BioEssays 22:10–15, 2000. ©2000 John Wiley & Sons, Inc. (shrink)

Daily rhythms are a ubiquitous feature of living systems. Generally, these rhythms are not just passive consequences of cyclic fluctuations in the environment, but instead originate within the organism. In mammals, including humans, the master pacemaker controlling 24‐hour rhythms is localized in the suprachiasmatic nuclei of the hypothalamus. This circadian clock is responsible for the temporal organization of a wide variety of functions, ranging from sleep and food intake, to physiological measures such as body temperature, heart rate and hormone release. (...) The retinal circadian clock was the first extra‐SCN circadian oscillator to be discovered in mammals and several studies have now demonstrated that many of the physiological, cellular and molecular rhythms that are present within the retina are under the control of a retinal circadian clock, or more likely a network of hierarchically organized circadian clocks that are present within this tissue. BioEssays 30:624–633, 2008. © 2008 Wiley Periodicals, Inc. (shrink)

Thanks to genetic and biochemical advances on the molecular mechanism of circadian rhythms in Drosophila, theoretical models closely related to experimental observations can be considered for the regulatory mechanism of the circadian clock in this organism. Modeling is based on the autoregulatory negative feedback exerted by a complex between PER and TIM proteins on the expression of per and tim genes. The model predicts the occurrence of sustained circadian oscillations in continuous darkness. When incorporating light‐induced TIM degradation, the model (...) accounts for damping of oscillations in constant light, entrainment of the rhythm by light‐dark cycles of varying period or photoperiod, and phase shifting by light pulses. The model further provides a molecular dynamical explanation for the permanent or transient suppression of circadian rhythmicity triggered in a variety of organisms by a critical pulse of light. Finally, the model shows that to produce a robust rhythm the various clock genes must be expressed at the appropriate levels since sustained oscillations only occur in a precise range of parameter values. BioEssays 22:84–93, 2000. ©2000 John Wiley & Sons, Inc. (shrink)

Mutations that disrupt biological rhythms have existed in microbial and metazoan eukaryotes for some time. They have recently begun to be studied with increasing intensity, both in terms of phenotypic effects of the relevant genetic variants, and with regard to molecular isolation and analysis of the genes defined by two of the ‘clock mutations’. These genetic loci, called period (per) in Drosophila and frequency (frq) in Neurospora, influence not only the basic characteristics of circadian rhythmicity, but also temperature compensation (...) of such daily cycle durations, ‘re‐setting’ of the rhythms' phases, and (for the per mutants) behavioral oscillations associated with much shorter than circadian periodicities. Molecular cloning of Drosophila's per gene, accompanied crucially by the locus's identification in germ‐line transformants, has led to information on its expression ‐ temporally, spatially, and in regard to heterogeneity of mRNA types. Nucleotide‐sequencing analyses of genomic DNA (and/or cDNA) from normal and mutated per alleles have (1) led to the suggestion that this clock gene encodes a family of proteoglycans (which was further indicated by application of antibody reagents obtained by manipulation of one of the gene's exons); and (2) shown that the three types of per mutations ‐ which shorten or lengthen rhythm periodicities or appear to eliminate them ‐ are associated with interesting amino‐acid substitutions or a stop codon, respectively. Analogous molecular findings are awaited from Neurospora, whose frq gene has very recently been cloned and definitively identified, in part via transformation experiments. (shrink)

Most organisms display oscillations of approximately 24 hours in their physiology. In higher organisms, these circadian oscillations in biochemical and physiological processes ultimately control complex behavioral rhythms that allow an organism to thrive in its natural habitat. Daily and seasonal light cycles are mainly responsible for keeping the circadian system properly aligned with the environment. The molecular mechanisms responsible for the control of the circadian clock have been explored in a number of systems. Interestingly, the circadian oscillations that are (...) responsive to environmental stimuli are present very early during development. This review focuses on the advantages of using the zebrafish to study the development of the vertebrate circadian system and light‐dependent signaling to the clock. BioEssays 24:419–426, 2002. © 2002 Wiley Periodicals, Inc. (shrink)

In order to tell the story of Man and understand our emergence better, we can readily follow on from Heinz Tobien, though we do not need to go back so far in time - just a few million years.Clearly, our fundamental origin is animal. Thus it is easy to understand that in the great genealogy (known as phylogeny), there was one vital (geological) moment when our line was forever detached from the animal “kingdom.” The evidence of palaeontology, like that of (...) molecular biology, today locates this point - which is, by definition, the very point of origin of our family, the hominids - in Eastern Africa around 8 million years ago. In order to state this, palaeontology rests on two sets of results. All the most ancient hominids, without exception, are East African, and the oldest of all goes back more than 7 million years. Through the study of various characteristics of the cells of contemporary primates, having arranged them in an order of increasing complexity and having hypothesized that this contemporary complexity may be a reflection of that which developed through time, molecular biology has, on the basis of palaeontological dating, calibrated this transformation and its different stages and constructed what is called a molecular clock. In this way, it has arrived at two conclusions. The primates closest to Man are by far the great African apes (chimpanzees, gorillas), and the “distance” that separates us - in other words the degree of difference that exists between them and us - situates the divergence of our two branches at just over 7 million years. (shrink)

In this paper, I discuss several temporal aspects of paleontology from a philosophical perspective. I begin by presenting the general problem of “taming” deep time to make it comprehensible at a human scale, starting with the traditional geologic time scale: an event-based, relative time scale consisting of a hierarchy of chronological units. Not only does the relative timescale provide a basis for reconstructing many of the general features of the history of life, but it is also consonant with the cognitive (...) processes humans use to think about time. Absolute dating of rocks, fossils, and evolutionary events (such as branching events on the tree of life) can be accomplished through the use of radiometric dating, chronological signals extractable from fossil growth patterns, and the “molecular clock.” Sometimes these different methods of absolute dating, which start from largely independent assumptions and evidentiary bases, converge in their temporal estimates, resulting in a consilience of inductions. At other times they fail to agree, either because fossils and molecules are giving temporal information about different aspects of nature and should not be expected to agree, or because of flawed assumptions that give rise to an inaccurate estimate. I argue that in general, despite the fact that it can be difficult to integrate disparate kinds of evidence, the principle of total evidence should be applied to the dating of evolutionary events. As a historical science, paleontology studies past events we cannot observe directly. This raises questions of epistemic access, meaning that due to the fragmentary nature of the fossil record we may find ourselves without access to the relevant traces to adjudicate between rival hypotheses about the past. The problems and prospects of epistemic access are explored through a case study of the reconstruction of the colors of dinosaurs. The paper closes with a reflection on the Darwin- Lyell metaphor of the fossil record as a highly fragmentary history book, and a call for a reconsideration of the book metaphor in favor of a systems view of the geologic and fossil records. (shrink)

Molecular methods have revolutionised virtually every area of biology, and metazoan phylogenetics is no exception: molecular phylogenies, molecular clocks, comparative phylogenomics, and developmental genetics have generated a plethora of molecular data spanning numerous taxa and collectively transformed our understanding of the evolutionary history of animals, often corroborating but at times opposing results of more traditional approaches. Moreover, the diversity of methods and models within molecular phylogenetics has resulted in significant disagreement among molecular phylogenies (...) as well as between these and earlier phylogenies. How should this broad and multifaceted problem be tackled? I argue that the answer lies in integrating evidence to infer the best evolutionary scenario. I begin with an overview of recent development in early metazoan phylogenetics, followed by a discussion of key conceptual issues in phylogenetics revolving around phylogenetic evidence, theory, methodology, and interrelations thereof. I then argue that the integration of different kinds of evidence is necessary for arriving at the best evolutionary scenario rather than merely the best-fitting cladogram. Finally, I discuss the prospects of this view in stimulating interdisciplinary cross-talk in early metazoan research and beyond, and challenges that need to be overcome. (shrink)

The timing of the origin of flowering plants (Angiosperm) is hotly debated. It has been suggested that the disagreement between the fossil record of angiosperm origin strongly conflicts with the origin estimates generated by molecular clocks. I argue that this conflict reveals lessons about whether or under what conditions scientific disagreement is likely to bear fruit. Specifically, I point to issues of evidence quality and social epistemic structures which deserve more attention in understanding the productivity of disagreement.

A recent study(1) of sequence data from many different proteins has suggested that contemporary prokaryotes and eukaryotes may have shared a common ancestor as recently as 2 billion years ago (the molecular clock). Strong evidence from the geological record, however, indicates that oxygen‐producing microorganisms, perhaps similar to modern cyanobacteria, existed 3.5 billion years ago. The fossil evidence, therefore, suggests that any common ancestor of prokaryotes and eukaryotes must have existed at least 1.5 billion years earlier than suggested by the (...) molecular clock evidence. The discrepancy between molecular and geological evidence for the age of modern cells is considered here, as are aspects of gene descent in the tree of life that might help to account for it. (shrink)

The early evolution of metazoans is a major focus of biological attention, but is the historical record revealed in the Cambrian “explosion” an accurate reflection of original events? The key questions concern the nature of the earliest animals and when they originated. One widely-mooted suggestion is that planktotrophic larvae, typified by the annelidan trochophore and echinoid pluteus, existed long before the metazoan radiations evident in the Cambrian fossil record. This idea could be consistent for recent evidence of divergence times, based (...) on molecular “clocks,” of phyla appearing well before the Cambrian. Now a surprising new discovery of eggs with blastomeres and embryos with well-defined anatomy from the Cambrian (c.530 Myr ago) of China and Siberia promises to extend the arena of debate. In one case a convincing ontogeny can be traced from eggs to adult tube-dwelling cnidarians. In the other example a possible protostome, unhatched and wrapped around the egg, shows segmentation and possibly nascent sclerites. In both, these cases development is direct, i.e., there is no evidence for any planktotrophic larval stage. The implications for our perceptions of both the Cambrian ‘explosion’ and metazoan phylogeny could be considerable. BioEssays 20:676–682, 1998.© 1998 John Wiley & Sons Inc. (shrink)

The genetic equidistance result shows that different species are approximately equidistant to a simpler outgroup in protein sequence similarity, as first reported by Margoliash in 1963. This result, together with those of Zuckerkandl and Pauling in 1962 inspired the molecular clock and in turn the neutral theory of evolution. Here it is shown that the clock/neutral theory had from the beginning overlooked another characteristic of the equidistance result, the overlap feature, which shows a large number of overlapped mutant amino (...) acid positions where any pair of any three species is different provided that the species concerned differ from one another in complexity as a result of macroevolution. In contrast, when simple organisms of similar complexity and short evolutionary divergence are compared, there are only a small number of overlaps largely consistent with chance or the neutral theory. The full reality of the equidistance result strongly supports the Maximum Genetic Diversity hypothesis, a more complete account of hereditary changes. (shrink)

Advances in technology have increased our knowledge of the processes that effect genomic changes and of the roles of RNA networks in biocommunication, functionality, and evolution of genomes. Natural genetic engineering and genomic inscription occur at all levels of life: cell cycles, development, and evolution. This has implications for phylogenetic studies and for biogeography, particularly given the general acceptance of using molecular clocks as arbiters between vicariance and dispersal explanations in biogeography. Léon Croizat’s development of panbiogeography and his (...) explanation for the distribution patterns of organisms are based on concepts of dispersal, differential form-making, and ancestor that differ from concepts of descent used broadly in phylogenetic and biogeographic studies. Croizat’s differential form-making is consistent with the extensive roles ascribed to RNAs in development and evolution and recent discoveries of genome studies. Evolutionary-developmental biology (evo-devo), including epigenetics, and the role of RNAs should be incorporated into biogeography. (shrink)

The discovery of traces of a blood meal in the abdomen of a 50‐million‐year‐old mosquito reminds us of the insights that the chemistry of fossils can provide. Ancient DNA is the best known fossil molecule. It is less well known that new fossil targets and a growing database of ancient gene sequences are paralleled by discoveries on other classes of organic molecules. New analytical tools, such as the synchrotron, reveal traces of the original composition of arthropod cuticles that are more (...) than 400 my old. Pigments such as melanin are readily fossilized, surviving virtually unaltered for ∼200 my. Other biomarkers provide evidence of microbial processes in ancient sediments, and have been used to reveal the presence of demosponges, for example, more than 635 mya, long before their spicules appear in the fossil record. Ancient biomolecules are a powerful complement to fossil remains in revealing the history of life. (shrink)

Language evolution has long been researched. I will review a number of broad, emerging research directions which arguably have the potential to contribute to our understanding of language evolution. Emerging topics in genomics and neurolinguistics are explored, and human-specific levels of braincase globularity – and the broader process of self-domestication within which globularity seems capable of being encapsulated – will be argued to be the central pillars of any satisfactory and interdisciplinary model of language evolution.

Rejuvenation of cells by reprogramming toward the pluripotent state raises increasing attention. In fact, generation of induced pluripotent stem cells (iPSCs) completely reverses age‐associated molecular features, including elongation of telomeres, resetting of epigenetic clocks and age‐associated transcriptomic changes, and even evasion of replicative senescence. However, reprogramming into iPSCs also entails complete de‐differentiation with loss of cellular identity, as well as the risk of teratoma formation in anti‐ageing treatment paradigms. Recent studies indicate that partial reprogramming by limited exposure to (...) reprogramming factors can reset epigenetic ageing clocks while maintaining cellular identity. So far, there is no commonly accepted definition of partial reprogramming, which is alternatively called interrupted reprogramming, and it remains to be elucidated how the process can be controlled and if it resembles a stable intermediate state. In this review, we discuss if the rejuvenation program can be uncoupled from the pluripotency program or if ageing and cell fate determination are inextricably linked. Alternative rejuvenation approaches with reprogramming into a pluripotent state, partial reprogramming, transdifferentiation, and the possibility of selective resetting of cellular clocks are also discussed. (shrink)

The marine ecosystem is governed by a multitude of environmental cycles, all of which are linked to the periodical recurrence of the sun or the moon. In accordance with these cycles, marine species exhibit a variety of biological rhythms, ranging from circadian and circatidal rhythms to circalunar and seasonal rhythms. However, our current molecular understanding of biological rhythms and clocks is largely restricted to solar‐controlled circadian and seasonal rhythms in land model species. Here, we discuss the first (...) class='Hi'>molecular data emerging for circalunar and circatidal rhythms and present selected species suitable for further molecular analyses. We argue that a re‐focus on marine species will be crucial to understand the principles, interactions and evolution of rhythms that govern a broad range of eukaryotes, including ourselves. (shrink)

Extending a normal 24 hours day by four hours is unexpectedly highly disruptive to daily rhythms in gene expression in the blood. Using a paradigm in which human subjects were exposed to a 28 hours day, Archer and colleagues show how this sleep‐altering forced desynchrony protocol caused complex disruption to daily rhythms in distinct groups of genes. Such perturbations in the temporal organisation of the blood transcriptome arise quickly, and point to the fragile nature of coordinated genomic activity. Chronic disruption (...) of the daily and circadian rhythms in sleep compromise health and well‐being and this study reveals potential new molecular targets to combat the disruptive effects of shift work and jetlag. (shrink)

In higher eukaryotes, circadian behaviour patterns have been dissected at the molecular level in Drosophila and, more recently, in the mouse. Considerable progress has been made in identifying some of the molecular components of the clock in the fly, where two genes, period (per) and timeless (tim), are essential for behavioural rhythmicity. The PER and TIM proteins show circadian cycles in abundance, and are part of a negative feedback loop with their own mRNAs. Within the pacemaker neurons, the (...) PER and TIM products are believed to form a complex which allows them to translocate to the nucleus, but how they repress their own transcription is unclear. TIM is rapidly degraded by light, a feature which permits a compelling molecular description of both behavioural light entrainment and phase responses to light pulses. The regulation of per and tim is altered in different Drosophila tissues, however, and comparative analyses of the two genes outside the Diptera reveals further unusual patterns of tissue‐specific regulation. Evolution appears to have modified the way in which the two genes are utilised to generate circadian phenotypes. More recently, the cloning of mouse clock genes, including putative per homologues, opens up exciting possibilities for mammalian molecular chronobiology. (shrink)

The information-hierarchical approach is used to analyze the evolutionary developed organization of mankind. This organization is shown to be hierarchical, from molecular hierarchical levels to the religious ones. Time cycles of each level operation are included in the greater cycle of the next level according to the specific schemes defined by the common information principle of natural system development. Time cycles of levels have duration of 1 second, 6 seconds, 42 seconds, 24 hours, 11 days, 1 years, 33 year, (...) 1,000 years, 3,000 years or 6,000 years and all together make up the mankind clock that is similar to the formerly ascertained biosphere clock. The cycles of duration from 1 second to 33 years form the human biological clock, so the information-hierarchical organization of cell metabolism manifests itself as the key mechanism of the clock. The new scientific field has been characterized. It is the management of sustainable development of the states as evolutionary developed systems with the use of information relationships of their functioning. In the case of Christianity adoption by any large ethnos the next 1,000-year cycle of the Christianity-Judaism system will start. (shrink)

The functions of sleep are still unknown, but are probably related to cellular and molecular aspects of neural function. To better understand the benefits that sleep may bring at the cellular level, recent studies have employed Drosophila melanogaster as a model system and shown that fruit flies share the fundamental features of mammalian sleep. As in mammals, sleep in Drosophila is characterized by increased arousal threshold and by changes in brain electrical activity. Fly sleep is homeostatically regulated independent of (...) the circadian clock, is modulated by stimulants and hypnotics, and is affected by age. Also, fly sleep is associated with changes in brain gene expression similar to those observed in mammals. While Drosophila neurobiology is sufficiently complex to permit meaningful generalizations to mammals and humans, Drosophila genetics is simple enough to allow a rapid mutagenesis screening. An ongoing mutagenesis study has screened ∼5000 mutant Drosophila lines and found that sleep amount, sleep pattern, and the homeostatic regulation of sleep are highly conserved phenotypes in flies. So far, this study has identified 10 short sleeper lines and 4 lines that show no sleep rebound after sleep deprivation. Ultimately, the characterization of these lines should help identifying crucial cellular pathways involved in the regulatory mechanisms of sleep and its functional consequences. BioEssays 25:940–949, 2003. © 2003 Wiley Periodicals, Inc. (shrink)

In higher eukaryotes, circadian behaviour patterns have been dissected at the molecular level in Drosophila and, more recently, in the mouse. Considerable progress has been made in identifying some of the molecular components of the clock in the fly, where two genes, period (per) and timeless (tim), are essential for behavioural rhythmicity. The PER and TIM proteins show circadian cycles in abundance, and are part of a negative feedback loop with their own mRNAs. Within the pacemaker neurons, the (...) PER and TIM products are believed to form a complex which allows them to translocate to the nucleus, but how they repress their own transcription is unclear. TIM is rapidly degraded by light, a feature which permits a compelling molecular description of both behavioural light entrainment and phase responses to light pulses. The regulation of per and tim is altered in different Drosophila tissues, however, and comparative analyses of the two genes outside the Diptera reveals further unusual patterns of tissue‐specific regulation. Evolution appears to have modified the way in which the two genes are utilised to generate circadian phenotypes. More recently, the cloning of mouse clock genes, including putative per homologues, opens up exciting possibilities for mammalian molecular chronobiology. (shrink)

A wide range of biological processes, in all eukaryotes and in some prokaryotes, are controlled by rhythms with a period close to 24 hours. The circadian oscillator, which is responsible for generating these rhythms, is controlled by light signals that maintain its synchrony with the environmental day/night cycle. Higher plants exhibit many circadian rhythms, including rhythms in the transcription of specific genes. Molecular tools derived from such clock‐controlled genes have led to the identification of several circadian rhythm mutants in (...) the genetic model, Arabidopsis thaliana. The extensive understanding of photoperception in this species will make it a powerful system with which to investigate the light regulation of circadian rhythms. We compare Arabidopsis rhythms to the results from other systems, and discuss these data with respect to the current phototransduction models. (shrink)

Humanity's creative role within the living pattern of nature. Explores important scientific discoveries that reveal the self-organizing intelligence at the heart of nature. Examines the idea of a living cosmos from its roots in the earliest cultures, to its eclipse during the Scientific Revolution, to its return today. Reveals ways to reengage our creative partnership with nature and collaborate with nature's intelligence. For millennia the world was seen as a creative, interconnected web of life, constantly growing, developing, and restoring itself. (...) But with the arrival of the Scientific Revolution in the 16th and 17th centuries, the world was viewed as a lifeless, clock-like mechanism, bound by the laws of classical physics. Intelligence was a trait ascribed solely to human beings, and thus humanity was viewed as superior to and separate from nature. Today new scientific discoveries are reviving the ancient philosophy of a living, interconnected cosmos, and humanity is learning from and collaborating with nature's intelligence in new, life-enhancing ways, from ecological design to biomimicry. Drawing upon the most important scientific discoveries of recent times, David Fideler explores the self-organizing intelligence at the heart of nature and humanity's place in the cosmic pattern. He examines the ancient vision of the living cosmos from its roots in the "world soul" of the Greeks and the alchemical tradition, to its eclipse during the Scientific Revolution, to its return today. He explains how the mechanistic worldview led to humanity's profound sense of alienation, for if the universe only functioned as a machine, there was no longer any room for genuine creativity or spontaneity. He shows how this isn't the case and how, even at the molecular level, natural systems engage in self-organization, self-preservation, and creative problem solving, mirroring the ancient idea of a creative intelligence that exists deep within the heart of nature. Revealing new connections between science, religion, and culture, Fideler explores how to reengage our creative partnership with nature and new ways to collaborate with nature's intelligence. (shrink)

Circadian rhythms in the sleep/wake cycle, along with a range of physiological measures, are severely disrupted in individuals with major depressive disorder (MDD). Moreover, several central circadian genes have been implicated as potential genetic factors underlying the illness through candidate gene studies and some genome wide association studies. However, investigations into the molecular underpinnings of circadian disturbances in the human brain have been quite challenging. In their recent publication, Li and colleagues have used a novel approach to determine the (...) rhythmic patterns of circadian gene expression in several regions of the human brain, and how these patterns are disrupted in MDD. Their findings demonstrate that in healthy subjects, several brain regions outside the suprachiasmatic nucleus (the master clock) exhibit diurnal gene expression patterns that are disrupted in the brains of MDD subjects. These findings will provide the foundation for future studies of gene‐specific drug targets, and biomarkers for the disease. (shrink)

Previous research has reported that ethical values of business students are lower than those of their peers in other majors. The purpose of this study was to investigate whether a self-selection bias with respect to ethical values exists among students enrolled as business majors when compared with students planning to enter the engineering profession. Engineering students are exposed to a similar technical orientation in academic curricula and also supply the market for managers.A survey instrument was administered to 195 students enrolled (...) in undergraduate business and engineering programs and a graduate business program. The research instrument measured how business and engineering students perceive their own ethical beliefs and actions and how they perceived the ethical beliefs and actions of their peers. (shrink)

This paper proposes an abstract mathematical frame for describing some features of biological time. The key point is that usual physical (linear) representation of time is insufficient, in our view, for the understanding key phenomena of life, such as rhythms, both physical (circadian, seasonal …) and properly biological (heart beating, respiration, metabolic …). In particular, the role of biological rhythms do not seem to have any counterpart in mathematical formalization of physical clocks, which are based on frequencies along the (...) usual (possibly thermodynamical, thus oriented) time. We then suggest a functional representation of biological time by a 2-dimensional manifold as a mathematical frame for accommodating autonomous biological rhythms. The “visual” representation of rhythms so obtained, in particular heart beatings, will provide, by a few examples, hints towards possible applications of our approach to the understanding of interspecific differences or intraspecific pathologies. The 3- dimensional embedding space, needed for purely mathematical reasons, allows to introduce a suitable extra-dimension for “representation time”, with a cognitive significance. (shrink)

O artigo traz resultados de uma investigação de mestrado que teve por objetivo pesquisar as concepções de um grupo de professores a respeito das funções que os mesmos exercem frente à sociedade contemporânea. Partiu-se da premissa de que suas concepções guardam relação com suas práticas educativas e pedagógicas. Trata-se de uma pesquisa desenvolvida na perspectiva qualitativa, com cinquenta e um professores que atuam em seis escolas estaduais da cidade de Ponta Grossa-PR. Elegeu-se como aporte teórico autores que tratam da formação (...) de professores e da profissão docente, como Freire, Imbernón, Ens e Behrens, Tozetto, Sacristán e Tedesco. Os dados foram coletados por meio de questionários, categorizados e analisados seguindo os pressupostos na Análise de Conteúdo. Três categorias foram configuradas a partir de significantes presentes nas respostas dos professores participantes: Categoria I – Professor como um sujeito transformador: educação em uma forma ampla, Categoria II – Professor como profissional do conhecimento, e Categoria III – Professor enquanto sujeito que desempenha vários papéis sociais. Essas categorias nos possibilitaram inferir que as concepções dos professores em relação ao seu papel na sociedade contemporânea vão além da função social da escola, pois centram-se primeiramente na figura de um profissional transformador do mundo; seguida da noção de profissional do conhecimento e, por fim, da ideia de um profissional que desempenha vários papéis sociais. A pesquisa também apontou uma necessária redefinição da profissão docente para que os professores assumam novas competências profissionais na contemporaneidade. Palavras-chave: Profissão docente. Função dos professores. Sociedade contemporânea. Concepções. (shrink)

The rapidly changing field of genetics affects society through advances in health-care and through implications of genetic research. This study addresses the impacts of new genetic discoveries and technologies on different segments of today's society. The book begins with a chapter on genetic complexity, and subsequent chapters discuss moral and ethical questions arising from today's genetics from the perspectives of health care professionals, the media, the general public, special interest groups and commercial interests.