Was Darwin a creationist?

Throughout the Origin of Species, Darwin contrasts his theory of natural selection with the theory that God independently created each species. This makes it seem as though the Origin offers a scientific alternative to a theological worldview. A few months after the Origin appeared, however, the eminent anatomist Richard Owen published a review that pointed out the theological assumptions of Darwin's theory. Owen worked in the tradition of rational morphology, within which one might suggest that evolution occurs by processes that are continuous with those by which life arises from matter; in contrast, Darwin rested his account of life's origins on the notion that God created one or a few life forms upon which natural selection could act. Owen argued that Darwin's reliance on God to explain the origins of life makes his version of evolution no less supernatural than the special creationist that Darwin criticizes: although Darwin limits God to one or a few acts of creation, he still relies upon God to explain life's existence.     

Mother's little helpers: What we know (and don't know) about cooperative infant care in callitrichines

Since Darwin ( 1859 ), scientists have been puzzled by how behaviors that impose fitness costs on helpers while benefiting their competitors could evolve through natural selection. Hamilton's ( 1964 ) theory of inclusive fitness provided an explanation by showing how cooperative behaviors could be adaptive if directed at closely related kin. Recent studies, however, have begun to question whether kin selection is sufficient to explain cooperative behavior in some species (Bergmüller, Johnstone, Russell, & Bshary, 2007 ). Many researchers have instead emphasized the importance of direct fitness benefits for helpers in the evolution of cooperative breeding systems. Furthermore, individuals can vary in who, when, and how much they help, and the factors that affect this variation are poorly understood (Cockburn, 1998 ; Heinsohn, 2004 ). Cooperative breeders thus provide excellent models for the study of evolutionary theories of cooperation and conflict (Cant, 2012 ).     

Lifespan Extension Via Dietary Restriction: Time to Reconsider the Evolutionary Mechanisms?

Dietary restriction (DR) is the most consistent environmental manipulation to extend lifespan. Originally thought to be caused by a reduction in caloric intake, recent evidence suggests that macronutrient intake underpins the effect of DR. The prevailing evolutionary explanations for the DR response are conceptualized under the caloric restriction paradigm, necessitating reconsideration of how or whether these evolutionary explanations fit this macronutrient perspective. In the authors’ opinion, none of the current evolutionary explanations of DR adequately explain the intricacies of observed results; instead a context-dependent combination of these theories is suggested which is likely to reflect reality. In reviewing the field, it is proposed that the ability to track the destination of different macronutrients within the body will be key to establishing the relative roles of the competing theories. Understanding the evolution of the DR response and its ecological relevance is critical to understanding variation in DR responses and their relevance outside laboratory environments.     

DIVERSIONARY DISPLAY

.The theories which have been advanced to explain the origin of the various forms of distraction display are considered and found to be inadequate. It is suggested that distraction displays have arisen through the "displacement" of components from other behaviour contexts, particularly threat and epigamic display, which have become ritualized into new behaviour-patterns with survival value.     

Darwin’s two theories, 1844 and 1859

Darwin’s first two, relatively complete, explicit articulations of his theorizing on evolution were his Essay of 1844 and On the Origin of Species published in 1859. A comparative analysis concludes that they espoused radically different theories despite exhibiting a continuity of strategy, much common structure and the same key idea. Both were theories of evolution by means of natural selection. In 1844, organic adaptation was confined to occasional intervals initiated and controlled by de-stabilization events. The modified descendants rebalanced the particular “plant and animal forms … unsettled by some alteration in their circumstances.” But by 1859, organic adaptation occurred continuously, potentially modifying the descendants of all organisms. Even natural selection, the persistent core of Darwin’s theorizing, does not prove to be a significant basis for theory similarity. Consequently, Darwin’s Origin theory cannot reasonably be considered as a mature version of the Essay. It is not a modification based on adjustments, further justifications and the integration of a Principle of Divergence. The Origin announced a new “scientific paradigm” while the Essay did little more than seemingly misconfigure the operation of a novel mechanism to extend varieties beyond their accepted bounds, and into the realm of possible new species. Two other collections of Darwin’s theorizing are briefly considered: his extensive notes of the late 1830s and his contributions to the famous meeting of 1 July 1858. For very different reasons, neither constitutes a challenge to the basis for this comparative study. It is concluded that, in addition to the much-debated social pressures, an unacknowledged further reason why Darwin did not publish his theorizing until 1859, could have been down to his perceptive technical judgement: wisely, he held back from rushing to publish demonstrably flawed theorizing.     

Multiple Explanations in Darwinian Evolutionary Theory

Variational evolutionary theory as advocated by Darwin is not a single theory, but a bundle of related but independent theories, namely: (a) variational evolution; (b) gradualism rather than large leaps; (c) processes of phyletic evolution and of speciation; (d) causes for the formation of varying individuals in populations and for the action of selective agents; and (e) all organisms evolved from a common ancestor. The first four are nomological-deductive explanations and the fifth is historical-narrative. Therefore evolutionary theory must be divided into nomological and historical theories which are both testable against objective empirical observations. To be scientific, historical evolutionary theories must be based on well corroborated nomological theories, both evolutionary and functional. Nomological and general historical evolutionary theories are well tested and must be considered as strongly corroborated scientific theories. Opponents of evolutionary theory are concerned only with historical evolutionary theories, having little interest in nomological theory. Yet given a well corroborated nomological evolutionary theory, historical evolutionary theories follow automatically. If understood correctly, both forms of evolutionary theories stand on their own as corroborated scientific theories and should not be labeled as facts.     

Evolutionary remnants as widely accessible evidence for evolution: the structure of the argument for application to evolution education

Evolution education, in both schools and informal education, often focuses on natural selection and the fit of organisms through natural selection to their environment and way of life. Examples of evidence that evolution has occurred are therefore often limited to a modest number of classic but exotic cases, with little attention to how one might apply principles to more familiar organisms. Many of these classic examples are examples of adaptation; adaptation to local environments is, however, an outcome that could in principle also be explained by supernatural creation or design. A frequent result is the perception among the public is that examples of evolution are rare, and that the existence of well-adapted organisms may just as easily be explained metaphysically. We argue that among categories of evidence of evolution accessible to non-specialists in any environment, the most compelling evidence of common ancestry consists of remnants of evolutionary history evident in homologous features, particularly when those homologies are related to lack of fit of organisms to their way of life (“vestiges”) or to better fit that involves complicated combinations of parts usually assigned other functions (“contrivances”). Darwin emphasized the critical nature of this argument from imperfections, and it has been part of traditional catalogs of “evidence for evolution” for more than a century. Yet while remnants of history are widely used as a category of evidence for evolution, their utility in education of comparative anatomy to document body parts passed on through descent is underemphasized in evolution education at all levels. We explore the use of evolutionary remnants to document common ancestry and evidence for evolution, for application to evolution education.     

Darwin and Mendel: who was the pioneer of genetics?

Although Mendel is now widely recognized as the founder of genetics, historical studies have shown that he did not in fact propose the modern concept of paired characters linked to genes, nor did he formulate the two "Mendelian laws" in the form now given. Furthermore, Mendel was accused of falsifying his data, and Mendelism has been met with scepticism because of its failure to provide scientific explanation for evolution, to furnish a basis for the process of genetic assimilation and to explain the inheritance of acquired characters, graft hybridization and many other facts. Darwin was the first to clearly describe almost all genetical phenomena of fundamental importance, and was the first to present a developmental theory of heredity--Pangenesis, which not only greatly influenced many subsequent theories of inheritance, particularly those of de Vries, Galton, Brooks and Weismann, but also tied all aspects of variation, heredity and development together, provided a mechanism for most of the observable facts, and is supported by increasing evidence. It has also been indicated that Darwin's influence on Mendel, primarily from The Origin, is evident. The word "gene" was derived from "pangen", itself a derivative of "Pangenesis" which Darwin had coined. It seems that Darwin should have been regarded as the pioneer, if not of transmissional genetics, of developmental genetics and molecular genetics.     

The evolution of cultural adaptations: Fijian food taboos protect against dangerous marine toxins

The application of evolutionary theory to understanding the origins of our species'' capacities for social learning has generated key insights into cultural evolution. By focusing on how our psychology has evolved to adaptively extract beliefs and practices by observing others, theorists have hypothesized how social learning can, over generations, give rise to culturally evolved adaptations. While much field research documents the subtle ways in which culturally transmitted beliefs and practices adapt people to their local environments, and much experimental work reveals the predicted patterns of social learning, little research connects real-world adaptive cultural traits to the patterns of transmission predicted by these theories. Addressing this gap, we show how food taboos for pregnant and lactating women in Fiji selectively target the most toxic marine species, effectively reducing a woman''s chances of fish poisoning by 30 per cent during pregnancy and 60 per cent during breastfeeding. We further analyse how these taboos are transmitted, showing support for cultural evolutionary models that combine familial transmission with selective learning from locally prestigious individuals. In addition, we explore how particular aspects of human cognitive processes increase the frequency of some non-adaptive taboos. This case demonstrates how evolutionary theory can be deployed to explain both adaptive and non-adaptive behavioural patterns.     

The dauer hypothesis and the evolution of parasitism: 20 years on and still going strong

How any complex trait has evolved is a fascinating question, yet the evolution of parasitism among the nematodes is arguably one of the most arresting. How did free-living nematodes cross that seemingly insurmountable evolutionary chasm between soil dwelling and survival inside another organism? Which of the many finely honed responses to the varied and harsh environments of free-living nematodes provided the material upon which natural selection could act? Although several complementary theories explain this phenomenon, I will focus on the dauer hypothesis. The dauer hypothesis posits that the arrested third-stage dauer larvae of free-living nematodes such as Caenorhabditis elegans are, due to their many physiological similarities with infective third-stage larvae of parasitic nematodes, a pre-adaptation to parasitism. If so, then a logical extension of this hypothesis is that the molecular pathways which control entry into and recovery from dauer formation by free-living nematodes in response to environmental cues have been co-opted to control the processes of infective larval arrest and activation in parasitic nematodes. The molecular machinery that controls dauer entry and exit is present in a wide range of parasitic nematodes. However, the developmental outputs of the different pathways are both conserved and divergent, not only between populations of C. elegans or between C. elegans and parasitic nematodes but also between different species of parasitic nematodes. Thus the picture that emerges is more nuanced than originally predicted and may provide insights into the evolution of such an interesting and complex trait.     

How mutualisms arise in phytoplankton communities: building eco‐evolutionary principles for aquatic microbes

Extensive sampling and metagenomics analyses of plankton communities across all aquatic environments are beginning to provide insights into the ecology of microbial communities. In particular, the importance of metabolic exchanges that provide a foundation for ecological interactions between microorganisms has emerged as a key factor in forging such communities. Here we show how both studies of environmental samples and physiological experimentation in the laboratory with defined microbial co‐cultures are being used to decipher the metabolic and molecular underpinnings of such exchanges. In addition, we explain how metabolic modelling may be used to conduct investigations in reverse, deducing novel molecular exchanges from analysis of large‐scale data sets, which can identify persistently co‐occurring species. Finally, we consider how knowledge of microbial community ecology can be built into evolutionary theories tailored to these species’ unique lifestyles. We propose a novel model for the evolution of metabolic auxotrophy in microorganisms that arises as a result of symbiosis, termed the Foraging‐to‐Farming hypothesis. The model has testable predictions, fits several known examples of mutualism in the aquatic world, and sheds light on how interactions, which cement dependencies within communities of microorganisms, might be initiated.     

The ecological rationality of helping others: Potential helpers integrate cues of recipients' need and willingness to sacrifice

Why do humans help others? Many theories focus on dimensions like kinship or reciprocity. On their surface, these theories seem unable to explain help directed at fleeting strangers. In response to this puzzle, researchers have proposed that the mind has ecologically rational systems for providing aid. These systems respond to cues that predicted adaptive behavior during human evolution, regardless of whether such cues continue to be predictive in modern environments. In three studies, we test for two cues that might predict whether a potential benefactor will help a potential recipient: the need of the recipient and the extent to which the recipient is willing to sacrifice for the benefactor. Both cues, in ancestral environments, have the potential to predict whether a long-term relationship might be established. Consistent with past research, we find that both cues matter: Needy people and people willing to sacrifice are helped more. However, the cues are not merely additive: In some cases, the cue of need is ignored and only willingness to sacrifice is used. We discuss these results in terms of recent evolutionary theories of emotions.     

Ancient asexual scandals

Asexual organisms that are descended from ancient asexual lineages defy current thinking on the evolution of sexual reproduction; theoreticians have been anxious to explain away their existence. However, a number of groups of organisms, from ferns to rotifers, have been suggested to be anciently asexual, and favourable evidence is being accumulated. Furthermore, new techniques for assessing claims of ancient asexuality have been proposed. Although ancient asexuals challenge current theories of sex, understanding how they manage to persist will help to explain why most organisms are sexual.     

A biological cosmos of parallel universes: Does protein structural plasticity facilitate evolution?

While Darwin pictured organismal evolution as "descent with modification" more than 150 years ago, a detailed reconstruction of the basic evolutionary transitions at the molecular level is only emerging now. In particular, the evolution of today's protein structures and their concurrent functions has remained largely mysterious, as the destruction of these structures by mutation seems far easier than their construction. While the accumulation of genomic and structural data has indicated that proteins are related via common ancestors, naturally occurring protein structures are often considered to be evolutionarily robust, thus leaving open the question of how protein structures can be remodelled while selective pressure forces them to function. New information on the proteome, however, increasingly explains the nature of local and global conformational diversity in protein evolution, which allows the acquisition of novel functions via molecular transition forms containing ancestral and novel structures in dynamic equilibrium. Such structural plasticity may permit the evolution of new protein folds and help account for both the origins of new biological functions and the nature of molecular defects.     

Pan-genome study of Thermococcales reveals extensive genetic diversity and genetic evidence of thermophilic adaption

Thermococcales has a strong adaptability to extreme environments, which is of profound interest in explaining how complex life forms emerge on earth. However, their gene composition, thermal stability and evolution in hyperthermal environments are still little known. Here, we characterized the pan-genome architecture of 30 Thermococcales species to gain insight into their genetic properties, evolutionary patterns and specific metabolisms adapted to niches. We revealed an open pan-genome of Thermococcales comprising 6070 gene families that tend to increase with the availability of additional genomes. The genome contents of Thermococcales were flexible, with a series of genes experienced gene duplication, progressive divergence, or gene gain and loss events exhibiting distinct functional features. These archaea had concise types of heat shock proteins, such as HSP20, HSP60 and prefoldin, which were constrained by strong purifying selection that governed their conservative evolution. Furthermore, purifying selection forced genes involved in enzyme, motility, secretion system, defence system and chaperones to differ in functional constraints and their disparity in the rate of evolution may be related to adaptation to specific niche. These results deepened our understanding of genetic diversity and adaptation patterns of Thermococcales, and provided valuable research models for studying the metabolic traits of early life forms.     

Two neo-Darwinisms

There are two extant theories of evolution, each of which deserves the honourific "neo-Darwinism": Modern Synthesis Replicator theory and a theory I shall call Developmental Darwinism. The principal difference concerns the canonical unit of biological organization. Modern Synthesis replicator theory explains the process of evolution by appeal to the activities of genes or replicators. Developmental Darwinism explains the process of evolution by appeal to the capacities of organisms. In particular, it is the plasticity of organisms, manifested most distinctly during development, that causes adaptive evolution. Despite the fact that each, in its own way, traces its origin to the theory outlined by Darwin, they are radically different. The objectives of this essay are twofold: to underscore the differences between these theories, and to argue that Developmental Darwinism, though nascent, is a viable alternative to Modern Synthesis replicator theory.     

生命之树与进化模式:导言

One and half centuries ago, Charles Darwin (1859) presented overwhelming evidence and argued that all life on the earth shared common descent, and "from so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved". Ernst Haeckel (1886) and several of his contemporaries attempted to trace the pattern of descent among all extant and extinct forms in what Darwin referred to as "the great Tree of Life". Ever since then, systematists and evolutionary biologists have been exploring morphological, cytogenetic, chemical, developmental and molecular characters, and actively developing theories and methods to infer phylogenetic relationships among organisms from these characters. This endeavor has been especially stimulated by the rise of molecular biology and the emergence of computer science over the past 50 years. At the beginning of the 21st century, we are presented with an unprecedented opportunity to reconstruct the entire Tree of Life, and further, to study evolutionary processes and mechanisms in the context of a robust phylogenetic framework.     

Saltatory transitions are a naturally occurring property of evolving systems

On the basis of paleological evidence, it has been suggested that biological evolution need not necessarily be characterized by gradual change. Rather, evolutionary history may display saltatory periods of rapid speciation alternating with periods of relative quiescence, the whole dynamic being called punctuated equilibria. The empirical evidence that has been presented in support of this hypothesis has been the object of a vigorous dispute. Mathematical investigations of complex models of biological evolution that contain random elements have demonstrated that these systems can display saltatory behavior. In this paper we address a more abstract question: can saltations occur in the evolution of very simple, deterministic mathematical systems that function in a constant environment? The answer appears to be yes. Saltations appear as a natural dynamical behavior in the evolution of simplistic information processing networks. We stress that these networks do not constitute a model of biological evolution. However, the appearance of saltations in such simple systems suggests that their appearance in a process as complex as biological evolution is not surprising.     

Under the influence of Malthus's law of population growth: Darwin eschews the statistical techniques of Aldolphe Quetelet

Charles Darwin, James Clerk Maxwell, and Francis Galton were all aware, by various means, of Aldolphe Quetelet’s pioneering work in statistics. Darwin, Maxwell, and Galton all had reason to be interested in Quetelet’s work: they were all working on some instance of how large-scale regularities emerge from individual events that vary from one another; all were rejecting the divine interventionistic theories of their contemporaries; and Quetelet’s techniques provided them with a way forward. Maxwell and Galton all explicitly endorse Quetelet’s techniques in their work; Darwin does not incorporate any of the statistical ideas of Quetelet, although natural selection post-twentieth century synthesis has. Why not Darwin? My answer is that by the time Darwin encountered Malthus’s law of excess reproduction he had all he needed to answer about large scale regularities in extinctions, speciation, and adaptation. He didn’t need Quetelet.     

Evolvability,population benefit,and the evolution of programmed aging in mammals

Programmed aging theories contend that evolved biological mechanisms purposely limit internally determined lifespans in mammals and are ultimately responsible for most instances of highly age-related diseases and conditions. Until recently, the existence of programmed aging mechanisms was considered theoretically impossible because it directly conflicted with Darwin’s survival-of-the-fittest evolutionary mechanics concept as widely taught and generally understood. However, subsequent discoveries, especially in genetics, have exposed issues with some details of Darwin’s theory that affect the mechanics of the evolution process and strongly suggest that programmed aging mechanisms in humans and other mammals can and did evolve, and more generally, that a trait that benefits a population can evolve even if, like senescence, it is adverse to individual members of the population. Evolvability theories contend that organisms can possess evolved design characteristics (traits) that affect their ability to evolve, and further, that a trait that increases a population’s ability to evolve (increases evolvability) can be acquired and retained even if it is adverse in traditional individual fitness terms. Programmed aging theories based on evolvability contend that internally limiting lifespan in a species-specific manner creates an evolvability advantage that results in the evolution and retention of senescence. This issue is critical to medical research because the different theories lead to dramatically different concepts regarding the nature of biological mechanisms behind highly age-related diseases and conditions.