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Evolutionary developments beyond Darwinian assumptions

Found a great piece, titled Darwin’s Legacy written by Nathalie Gontier that summarizes neatly the development of ideas that challenge and go beyond the simplistic Darwinian/neo-Darwinian assumptions. However it is not to be read as a complete rejection of Darwinian ideas, rather only to understand its sever shortcomings in describing a lot of new data and empirical scenarios. Following is excerpt from one of its main sections. For references and complete read, kindly click on the above mentioned link:

In its modern Neodarwinian version, evolution by means of natural selection has come to imply that small, genetic variations that are phenotypically displayed by organisms, and that are caused by chromosomal rearrangements and random mutations, are positively selected for in relation to the environment when adaptive. Over time, the natural selection of favourable traits gradually leads to the diversification from the original species up to the point that a new species evolves.

However, what does this mean exactly? What assumptions are made when natural selection is formulated as such? On a meta-level, evolution by means of natural selection, as defined by Neodarwinians, implies the following:

Natural selection is always active: there is always a scarcity of resources which results in a constant struggle and a constant favouring of the fit over the unfit, and species, therefore, also constantly evolve by means of natural selection;
Natural selection occurs slowly and gradually (at a constant rate): mutations are chance events, and the possible selection and transmission of adaptive mutations are confined to the germ line and always require the emergence of a new generation, making evolution a timely event;
Because of the requirement of germ line transmission of novel traits, the origin of new species occurs as a vertical process: species either evolve themselves out of existence by evolving into new ones (anagenesis); or they split off from older species (cladogenesis);
Natural selection occurs at the interface of a phenotype and the environment: in other words, the phenotype is the unit of selection, and evolution by means of natural selection occurs at the level of the environment.

Today, advances in the study of evolution have called many of the above made assumptions into question. The following criticisms can be objected:

(1)
Because genes are the stuff that organisms and ultimately evolution is built upon, population genetics and later molecular genetics have been dominating all theorizing on how evolution by means of natural selection occurs. The exclusive focus on the distribution of genetic traits has resulted in the idea that microevolution (small random genetic changes) suffices to explain macroevolution (the evolution of species). This gene and mutation-centred idea has been put forward to the neglect of the role of the organism, the environment and species.
(2)
Darwin had already recognized that besides adaptive and maladaptive traits, organisms can display neutral traits that appear to have no use in the struggle for existence. He recognized the existence of such neutral traits as a major challenge to his theory. How could these neutral traits have evolved when selection was constantly active? The only answer could be that sometimes selective pressures are loosened and no struggle for existence occurs. Interested in how traits originate and how they migrate within and across populations (how they are distributed over space and time), population geneticists came to realize that not all traits are selected and spread as a consequence of their adaptive values. Genetic drift theory and neutral evolution, first introduced by Wright (1932) and later elaborated upon by Kimura (1968, 1983), explain how the transmission of traits from parents to offspring is mostly the result of random sampling and thus of stochastic processes. Because causation can be attributed to genetic drift, we can call it an evolutionary mechanism just as natural selection is one. And the recognition that several evolutionary mechanisms can be active, requires that we investigate how these mechanisms alternate one another. A further major consequence of the theory of genetic drift is that evolution is not necessarily characterized by an increase in fit between an organism and its environment, and that consequently, evolution is not necessarily progressive.
(3)
When selection pressures are strengthened or loosened, this can tamper with the rate of evolution. It follows that the evolutionary rate, although perhaps gradual, is not constant. The idea of gradualness implies that intermediates need to be found between species. As Darwin already noted, the fossil record often does not show the remains of such intermediates between different species. The fossil record has, therefore, been called incomplete, and the field of palaeontology has been considered useless in helping to prove evolution. Eldredge and Gould (1972) however argued that the gaps in the fossil record need to be taken at face value. That is, the gaps are real and they provide us with an empirical observation that can tell us something about evolution. The authors introduced the theory of punctuated equilibria to explain the rapid occurrence of new species in the fossil record without the apparent presence of intermediates. According to the theory of punctuated equilibria, evolution is characterized by long periods of stasis wherein no permanent evolutionary changes occur, which are punctuated by short periods of rapid change. During these long periods of stasis, new variations can occur (due to random mutations), but drift and the size of a population often make it impossible for these novelties to become fixed. In other word, even when there is variation over long periods of time, speciation will not automatically occur. Microevolutionary processes such as genetic mutations, taken on their own, are incomplete to explain the origin of new species (macroevolution). Rather, the theory of punctuated equilibria suggests that additional explanations need to be sought to explain how speciation occurs. One of these additional explanations is the role of the physical environment. Climate changes or natural barriers between populations (allopatric speciation) can facilitate if not induce speciation. This in turn has strong consequences for how we understand species and the process of speciation, because punctuated equilibria suggests that species are real entities and speciation events are real as well.
(4)
Zooming in on the role of the environment, we can argue that for a long time, the study of the environment was only relevant in so far as it gave the scene where selection and speciation can occur. The environment was considered to be of a purely physical nature, and to be external to the organism. Systems theory and ecological thinking would undo of this assumption by arguing that the environment of an organism is by and large made up of other organisms (Van Valen 1973). Lewontin (2000) would argue that organisms can, to a greater or lesser extent, construct their own environment through a process called niche construction. And organisms can change their phenotypes in relation to a changing environment, a process that is called phenotypic plasticity by West-Eberhard (2003). These theories have significantly blurred the once distinctive barrier between organism and environment.
Epigeneticists and evolutionary developmental biologists (evo–devo) brought to light that the internal milieu of an organism, and non-genetic factors, are highly relevant for the origin and evolution of species (Goodman and Coughlin 2000). During the formation of the Modern Synthesis, a firm line was drawn between ontogeny, the development of the individual from conception until death; phylogeny, the evolution of species; and the external environment, the place where evolution occurred. Today, scientists undo of all these boundaries. Notions of eco–devo or ecological developmental biology (Gilbert 2001), and even eco–evo–devo are introduced from within a systems theoretical perspective. Evolution is understood as a hierarchical process, it occurs at several levels of biological organisation. These organisational levels are determined by both upward and downward causation (Campbell 1974): the parts determine the whole, but the whole also determines the parts in new ways. Biological systems are probably unique in portraying emergent properties.
(5)
The adaptive status of a trait is not fixed, rather it can change. Dependent on environmental changes, adaptive traits can become maladaptive, or neutral traits can become adaptive. The function of a trait is not constant either, since the function of a trait can be put to use in a rather different context than the context in which it evolved; or a non-functional trait can require a function in the course of evolution. The latter are the processes identified as co-optation and exaptation by Gould and Vrba (1982).
(6)
The requirement of germ line transmission of novel traits, together with the resulting emphasis on evolution being vertical, has resulted in the neglect of hybridization, lateral or horizontal gene transfer and symbiogenesis as possible evolutionary mechanisms. Nonetheless, we now know that the latter are indeed mechanisms that can introduce novel traits, and that can even lead to the origin of new species. Symbiogenesis, as an evolutionary mechanism, was first brought to the attention by Constantin Merezhkowsky (1910), and it was later independently rediscovered by Wallin (1927) and Margulis (1970, 1998). It is now widely recognized that the cell organelles present in eukaryotic organisms evolved out of the merging of nucleated cells with different prokaryotes. Margulis further argues that the first nucleated cells also originated as the result of the merging of different prokaryotes. In fact, the field of symbiogenesis today is a fast rising one, with implementations reaching as far as botany, insectology, virology and zoology (Sapp 2003). It now becomes abundantly clear that every organism alive today is the result of symbiogenetic mergers; it undergoes lateral gene transfer through contact with parasites, or through bacterial or viral infections; and it lives, to a great or lesser extent, in symbiosis with other creatures.
(7)
All of the above has resulted in major theoretical re-conceptualisations of evolutionary terminology. What is an ‘organism’, ‘species’, ‘environment’, and ‘evolutionary mechanism’?
Organisms used to be regarded as homogeneous (even sterile), well-demarcated, passive entities that evolved as a whole, in an ever-changing environment that actively selects the adaptive ones. Organisms were unable to change their evolutionary faith. Today, we know that organisms can, to some extent, actively construct both their external environment (via niche construction), as well as internal environment (through immunological processes that allow or block parasites to enter, and that allow to create conditions that are different from the external milieu). Symbiogenetic studies have further made it necessary to consider most if not all organisms as superorganisms, because organisms have a heterogeneous nature: they are made up of different organisms with which they function as an emerging whole. A crucial question then becomes how these different structures are able to combine and function as a whole.
The species concept has also been the subject of serious reconsideration. Adhering to natural selection and acknowledging that it is a gradual and automatic process where intermediates successively follow one after the other, necessitates that one understands ‘species’ as unreal, theoretical constructs that merely facilitate theory-formation. Microevolutionary events occur incessantly and as a consequence populations constantly change. Species are not fixed entities. Indeed, Darwin himself adhered to a nominological species concept, arguing that species’ boundaries are arbitrarily drawn by us humans, because species are non-existent. A consequence of punctuated equilibria and its introduction of macroevolutionary processes is that species are considered real entities that have clear spatial and temporal boundaries. Mayr’s (1942) biological species concept, the concept most associated with the Modern Synthesis, takes the possibility to hybridize and produce fertile offspring as prime criteria to belong to the same species. The symbiogenetic species concept as defined by Margulis and Sagan (2002, p. 94), on the other hand, takes the possibility of lineage crossing as an identifying criteria of different species. Moreover, symbiogenesis implies that just like organisms, species too are not homogenous entities, but rather are formed through the interaction of different species, if not altogether through the incorporation of different gene sets and whole organisms (such as microbes). Finally, the acknowledgement of the existence of species makes it necessary to ask whether species themselves are units of evolution.
The environmental concept has also undergone significant changes through time. Focus has shifted from understanding the environment as a monolithic whole, to recognizing the heterogeneous nature and multi-layeredness of the environment. An environment is dividable into many different habitats, and an environment can include physical forces such as climate change or gravitational forces, and biological elements such as other organisms. The internal milieu of an organism also creates an environment that can be the scene of evolution. As the quintessential location of where evolution by means of natural selection occurs, the environment is the major level of evolution. Recognizing the heterogeneous nature of the environment has, therefore, implied recognizing multilevel evolution.
Finally, the nature of an evolutionary mechanism has been subject to revision. Natural selection has been criticized by physicists for its lack of predictive value. They state that selection cannot provide us with a law of nature. The recognition of different mechanisms has made us realize that mechanisms are not constant forces like physical forces appear to be. Rather, their workings are dependent on a series of conditions. We need to identify those conditions. Mechanisms also not merely provide us with a mode of evolution, they also have consequences for theories on evolutionary rates, and the recognition of different mechanisms has made us contemplate the nature of their interaction: how do different mechanisms work together? Or do they alternate one another? These are just a few of the major questions in need of an answer.
(8)
Finally, since the introduction of natural selection, the application range of evolutionary theory has widened immensely. As a consequence, the following research questions have been raised. What entities can evolve? Where does this evolution occur? How does it occur? Answers to these questions have been sought in the units and levels of selection debate. Today, however, we search not only for the units and levels of selection. We also search for the units, levels and underlying mechanisms of all sorts of evolution (the evolution of life, the brain, culture, …). Darwin saw evolution as something that occurs primarily through natural selection, and this selection occurred at the interface between an organism and an environment. Dawkins (1976, 1982) argued that organisms are mere vehicles. The true units of evolution were the genes. Many evolutionary biologists and philosophers of science have further argued that these genes can be selected at many levels.
One of the consequences of acknowledging evolution as a fact of nature has been that everything in the organic world can only be the result of some kind of evolutionary process. Recognizing the heterogeneous nature of an individual implies that several parts of the individual can evolve faster or slower and by means of different evolutionary mechanisms. In other words, the organism is a unit of evolution itself decomposable into subunits that are also subjected to evolution. This calls out for the recognition of multiple units of evolution. Recognizing the heterogeneous nature of the environment implies that multilevel selection (Maynard Smith and Szathmáry 1995; Okasha 2005) can occur. Recognizing the heterogeneous nature of evolutionary mechanisms again implies that multilevel evolution (rather than merely selection) can occur and that even multi-mechanism evolution can occur: evolution occurs through a combination of different mechanisms (Gontier, this volume).
This has widely expanded the range of natural selection and evolutionary thought. Evolutionary thinking is not merely relevant for biology, or for understanding the evolution of organisms. Group-level behaviours such as culture, or products of biological organisms such as cognition or epistemology, are now considered to be the outcome of evolution. Therefore, they must be explainable by the mechanisms of evolution. Evolutionary biology today is expanded to include evolutionary psychology, evolutionary epistemology, evolutionary anthropology, archaeology, economics, etc.
Categories: Darwin, Non-Darwin, Philosophy

A Third Way by Shapiro

An online article by James A. Shapiro

Excerpt:
The recent reviews in your columns of books by Dennett, Dawkins, and Behe are testimony to the unflagging interest in controversies about evolution. Although such purists as Dennett and Dawkins repeatedly assert that the scientific issues surrounding evolution are basically solved by conventional neo-Darwinism, the ongoing public fascination reveals a deeper wisdom. There are far more unresolved questions than answers about evolutionary processes, and contemporary science continues to provide us with new conceptual possibilities.

Unfortunately, readers of Boston Review may remain unaware of this intellectual ferment because the debate about evolution continues to assume the quality of an abstract and philosophical “dialogue of the deaf” between Creationists and Darwinists. Although our knowledge of the molecular details of biological organization is undergoing a revolutionary expansion, open-minded discussions of the impact of these discoveries are all too rare. The possibility of a non-Darwinian, scientific theory of evolution is virtually never considered. In my comments, then, I propose to sketch some developments in contemporary life science that suggest shortcomings in orthodox evolutionary theory and open the door to very different ways of formulating questions about the evolutionary process. After a discussion of technical advances in our views about genome organization and the mechanisms of genetic change, I will focus on a growing convergence between biology and information science which offers the potential for scientific investigation of possible intelligent cellular action in evolution.

Full text @ Boston Review

His other more scientific publications

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