A New Aspect to the Origin and Evolution of Eukaryotes

One of the most important omissions in recent evolutionary theory concerns how eukaryotes could emerge and evolve. According to the currently accepted views, the first eukaryotic cell possessed a nucleus, an endomembrane system, and a cytoskeleton but had an inefficient prokaryotic-like metabolism. In contrast, one of the most ancient eukaryotes, the metamonada Giardia lamblia, was found to have formerly possessed mitochondria. In sharp contrast with the traditional views, this paper suggests, based on the energetic aspect of genome organization, that the emergence of eukaryotes was promoted by the establishment of an efficient energy-converting organelle, such as the mitochondrion. Mitochondria were acquired by the endosymbiosis of ancient α-purple photosynthetic Gram-negative eubacteria that reorganized the prokaryotic metabolism of the archaebacterial-like ancestral host cells. The presence of an ATP pool in the cytoplasm provided by this cell organelle allowed a major increase in genome size. This evolutionary change, the remarkable increase both in genome size and complexity, explains the origin of the eukaryotic cell itself. The loss of cell wall and the appearance of multicellularity can also be explained by the acquisition of mitochondria. All bacteria use chemiosmotic mechanisms to harness energy; therefore the periplasm bounded by the cell wall is an essential part of prokaryotic cells. Following the establishment of mitochondria, the original plasma membrane-bound metabolism of prokaryotes, as well as the funcion of the periplasm providing a compartment for the formation of different ion gradients, has been transferred into the inner mitochondrial membrane and intermembrane space. After the loss of the essential function of periplasm, the bacterial cell wall could also be lost, which enabled the naked cells to establish direct connections among themselves. The relatively late emergence of mitochondria may be the reason why multicellularity evolved so slowly. Received: 29 May 1997 / Accepted: 9 October 1997     

A Novel Theory on the Origin of the Genetic Code: A GNC-SNS Hypothesis

We have previously proposed an SNS hypothesis on the origin of the genetic code (Ikehara and Yoshida 1998). The hypothesis predicts that the universal genetic code originated from the SNS code composed of 16 codons and 10 amino acids (S and N mean G or C and either of four bases, respectively). But, it must have been very difficult to create the SNS code at one stroke in the beginning. Therefore, we searched for a simpler code than the SNS code, which could still encode water-soluble globular proteins with appropriate three-dimensional structures at a high probability using four conditions for globular protein formation (hydropathy, α-helix, β-sheet, and β-turn formations). Four amino acids (Gly [G], Ala [A], Asp [D], and Val [V]) encoded by the GNC code satisfied the four structural conditions well, but other codes in rows and columns in the universal genetic code table do not, except for the GNG code, a slightly modified form of the GNC code. Three three-amino acid systems ([D], Leu and Tyr; [D], Tyr and Met; Glu, Pro and Ile) also satisfied the above four conditions. But, some amino acids in the three systems are far more complex than those encoded by the GNC code. In addition, the amino acids in the three-amino acid systems are scattered in the universal genetic code table. Thus, we concluded that the universal genetic code originated not from a three-amino acid system but from a four-amino acid system, the GNC code encoding [GADV]-proteins, as the most primitive genetic code. Received: 11 June 2001 / Accepted: 11 October 2001     

The Origin of Cladocera (Crustacea,Branchiopoda): A New Understanding of an Old Hypothesis

Comparative analysis of the ontogeny of representatives of two sister taxa (Cladocera and Cyclestherida) showed that the paedomorphic morphology of cladocerans (the small number of thoracic segments and segments of branches of antennae II, and the reduction of the carapace) was caused by the cessation of development of the somatic structures at early larval stages of ontogeny. It is demonstrated that this stop is not associated with the accelerated development of the reproductive system (progenesis), since it takes place long prior to the beginning of reproduction. In accordance with this fact, the past hypotheses that cladocerans evolved from the reproducing larvae of the ancestral form or that they are early maturing metanauplii should be recognized as erroneous. Cyclestheria. The origin of Cladocera from a Cyclestheria-like ancestor should be regarded as neotenic, taking into consideration the extended interpretation of this term.     

Organic Aerosols and the Origin of Life: An Hypothesis

Recent experimental work has verified the prediction that marine aerosols could have an exterior film of amphiphiles; palmitic, stearic and oleic acids were predominant. Thermodynamic analysis has revealed that such aerosols are energetically capable of asymmetric division. In a prebiotic terrestrial environment, one of the products of such aerosol fission would have been bacterially sized (microns), the other would have been virally sized (tens of nanometers). Plausible avenues for chemical differentiation between the two particles are discussed, and the probabilities for the transition from geochemistry to biochemistry updated in light of recent palaeo fossil studies.     

Evolution of The Vertebrate Pineal Gland: The Aanat Hypothesis

The defining feature of the pineal gland is the capacity to function as a melatonin factory that operates on a ∼24 h schedule, reflecting the unique synthetic capacities of the pinealocyte. Melatonin synthesis is typically elevated at night and serves to provide the organism with a signal of nighttime. Melatonin levels can be viewed as hands of the clock. Issues relating to the evolutionary events leading up to the immergence of this system have not received significant attention. When did melatonin synthesis appear in the evolutionary line leading to vertebrates? When did a distinct pineal gland first appear? What were the forces driving this evolutionary trend? As more knowledge has grown about the pinealocyte and the relationship it has to retinal photoreceptors, it has become possible to generate a plausible hypothesis to explain how the pineal gland and the melatonin rhythm evolved. At the heart of the hypothesis is the melatonin rhythm enzyme arylalkylamine N-acetyltransferase (AANAT). The advances supporting the hypothesis will be reviewed here and expanded beyond the original foundation; the hypothesis and its implications will be addressed.     

An Alternative Hypothesis For The Origin of the Name Blackfoot

Abstract

Recent ethnographic work with Cree informants supports the hypothesis that the original Cree. term for “Blackfoot” Indians referred to animal (perhaps horse’s) hooves rather than to artificially blackened feet or moccasins.     

Microsatellite Evolution: Testing the Ascertainment Bias Hypothesis

Previous studies suggest the median allele length of microsatellites is longest in the species from which the markers were derived, suggesting that an ascertainment bias was operating. We have examined whether the size distribution of microsatellite alleles between sheep and cattle is source dependent using a set of 472 microsatellites that can be amplified in both species. For those markers that were polymorphic in both species we report a significantly greater number of markers (P < 0.001) with longer median allele sizes in sheep, regardless of microsatellite origin. This finding suggests that any ascertainment bias operating during microsatellite selection is only a minor contributor to the variation observed. Received: 6 January 1997 / Accepted: 19 May 1997     

The Acoustic Habitat Hypothesis: An Ecoacoustics Perspective on Species Habitat Selection

Sound is an inherent component of the environment that provides conditions and information necessary for many animal activities. Soniferous species require specific acoustic and physical conditions suitable for their signals to be transmitted, received, and effectively interpreted to successfully identify and utilize resources in their environment and interact with conspecifics and other heterospecific organisms. We propose the Acoustic Habitat Hypothesis to explain how the acoustic environment influences habitat selection of sound-dependent species. We postulate that sound-dependent species select and occupy habitats with unique acoustic characteristics that are essential to their functional needs and conducive to the threshold of sound frequency they produce and detect. These acoustic habitats are based on the composition of biophony, geophony, and technophony in the soundscape and on the biosemiotics mechanisms described in the eco-field hypothesis. The Acoustic Habitat Hypothesis initiates questions of habitat selection that go beyond the physical attributes of the environment by applying ecoacoustics theory. We outline the theoretical basis of the Acoustic Habitat Hypothesis and provide examples from the literature to support its assumptions. The concept of acoustic habitats has been documented in the literature for many years but here, we accurately and extensively define acoustic habitat and we put this concept into a unified theory. We also include perspectives on how the Acoustic Habitat Hypothesis can stimulate a paradigm shift in conservation strategies for threatened and endangered species.     

On Bacterial Origin of Mitochondria in Eukaryotes in the Light of Current Ideas of Evolution of the Organic World

The hypothesis of bacterial origin of mitochondria, which existed until the end of the 20th century, has been confirmed on the basis of the current concepts of organic world evolution in the open sea hydrosphere and original data on the entry of bacteria (prokaryotes) in the cells of eukaryotes and their transformation into the mitochondrial mechanism of aerobic energy metabolism. This hypothesis can now be considered as a factually substantiated theory. The process of endocytosis of bacteria in the tissues of eukaryotes, which began at the onset of transition of the anaerobic state of open sea hydrosphere and land atmosphere (Early Proterozoic), is considered as the beginning of symbiotic mode of life of organisms of the Proterozoic and Postproterozoic organic world.     

The Evolutionary Origin of Somatic Cells under the Dirty Work Hypothesis

Reproductive division of labor is a hallmark of multicellular organisms. However, the evolutionary pressures that give rise to delineated germ and somatic cells remain unclear. Here we propose a hypothesis that the mutagenic consequences associated with performing metabolic work favor such differentiation. We present evidence in support of this hypothesis gathered using a computational form of experimental evolution. Our digital organisms begin each experiment as undifferentiated multicellular individuals, and can evolve computational functions that improve their rate of reproduction. When such functions are associated with moderate mutagenic effects, we observe the evolution of reproductive division of labor within our multicellular organisms. Specifically, a fraction of the cells remove themselves from consideration as propagules for multicellular offspring, while simultaneously performing a disproportionately large amount of mutagenic work, and are thus classified as soma. As a consequence, other cells are able to take on the role of germ, remaining quiescent and thus protecting their genetic information. We analyze the lineages of multicellular organisms that successfully differentiate and discover that they display unforeseen evolutionary trajectories: cells first exhibit developmental patterns that concentrate metabolic work into a subset of germ cells (which we call “pseudo-somatic cells”) and later evolve to eliminate the reproductive potential of these cells and thus convert them to actual soma. We also demonstrate that the evolution of somatic cells enables phenotypic strategies that are otherwise not easily accessible to undifferentiated organisms, though expression of these new phenotypic traits typically includes negative side effects such as aging.     

Hypothesis: Origin of Life in Deep-Reaching Tectonic Faults

The worldwide discussion on the origin of life encounters difficulties when it comes to estimate the conditions of the early earth and to define plausible environments for the development of the first complex organic molecules. Until now, the role of the earth's crust has been more or less ignored. In our opinion, deep-reaching open, interconnected tectonic fault systems may provide possible reaction habitats ranging from nano- to centimetre and even larger dimensions for the formation of prebiotic molecules. In addition to the presence of all necessary raw materials including phosphate, as well as variable pressure and temperature conditions, we suggest that supercritical CO2 as a nonpolar solvent could have played an important role. A hypothetical model for the origin of life is proposed which will be used to design crucial experiments for the model's verification. Because all proposed processes could still occur in tectonic faults at the present time, it may be possible to detect and analyse the formation of prebiotic molecules in order to assess the validity of the proposed hypothesis.     

Phenotypic Evolution: A Reaction Norm Perspective

By Carl D. Schlichting and Massimo Pigliucci. Sunderland, MA: Sinauer. 1998. 387 pp. ISBN 0-87893-799-4. $38.95 (paper).     

Origin and Evolution of the Brain

Modern biology has not yet come to terms with the presence of many organic codes in Nature, despite the fact that we can prove their existence. As a result, it has not yet accepted the idea that the great events of macroevolution were associated with the origin of new organic codes, despite the fact that this is the most parsimonious and logical explanation of those events. This is probably due to the fact that the existence of organic codes in all fundamental processes of life, and in all major transitions in the history of life, has enormous theoretical implications. It requires nothing less than a new theoretical framework, and that kind of change is inevitably slow. There are too many facts to reconsider, too many bits of history to weave together in a new mosaic. But this is what science is about, and the purpose of the present paper is to show that it can be done. More precisely, it is shown that the whole natural history of the brain can be revisited in the light of the organic codes. What is described here is only a bird’s-eye view of brain macroevolution, but it is hoped that the extraordinary potential of the organic codes can nevertheless come through. The paper contains also another message. The organic codes prove that life is based on semiosis, and are in fact the components of organic semiosis, the first and the most diffused form of semiosis on Earth, but not the only one. It will be shown that the evolution of the brain was accompanied by the development of two new types of sign processes. More precisely, it gave origin first to interpretive semiosis, mostly in vertebrates, and then to cultural semiosis, in our species.     

The Recognition Signal Hypothesis for the Adaptive Evolution of Religion

Recent research on the evolution of religion has focused on whether religion is an unselected by-product of evolutionary processes or if it is instead an adaptation by natural selection. Adaptive hypotheses for religion include direct fitness benefits from improved health and indirect fitness benefits mediated by costly signals and/or cultural group selection. Herein, I propose that religious denominations achieve indirect fitness gains for members through the use of ecologically arbitrary beliefs, rituals, and moral rules that function as recognition markers of cultural inheritance analogous to kin and species recognition of genetic inheritance in biology. This recognition signal hypotheses could act in concert with either costly signaling or cultural group selection to produce evolutionarily altruistic behaviors within denominations. Using a cultural phylogenetic analysis, I show that a large set of religious behaviors among extant Christian denominations supports the prediction of the recognition signal hypothesis that characters change more frequently near historical schisms. By incorporating demographic data into the model, I show that more-distinctive denominations, as measured through dissimilar characteristics, appear to be protected from intrusion by nonmembers in mixed-denomination households, and that they may be experiencing greater biological growth of their populations even in the present day.