And it’s only August. A special issue of Interface Focus on New trends in evolutionary biology: biological, philosophical and social science perspectives, organized by Denis Noble, Nancy Cartwright, Patrick Bateson, John Dupré and Kevin Laland is now available.
The Royal Society journal is “devoted to a particular subject at the interface of the physical and life sciences.” Some of the articles in this edition are open access.
As can be noted from the listed principles, current evolutionary theory is predominantly oriented towards a genetic explanation of variation, and, except for some minor semantic modifications, this has not changed over the past seven or eight decades. Whatever lip service is paid to taking into account other factors than those traditionally accepted, we find that the theory, as presented in extant writings, concentrates on a limited set of evolutionary explananda, excluding the majority of those mentioned among the explanatory goals above. The theory performs well with regard to the issues it concentrates on, providing testable and abundantly confirmed predictions on the dynamics of genetic variation in evolving populations, on the gradual variation and adaptation of phenotypic traits, and on certain genetic features of speciation. If the explanation would stop here, no controversy would exist. But it has become habitual in evolutionary biology to take population genetics as the privileged type of explanation of all evolutionary phenomena, thereby negating the fact that, on the one hand, not all of its predictions can be confirmed under all circumstances, and, on the other hand, a wealth of evolutionary phenomena remains excluded. For instance, the theory largely avoids the question of how the complex organizations of organismal structure, physiology, development or behaviour—whose variation it describes—actually arise in evolution, and it also provides no adequate means for including factors that are not part of the population genetic framework, such as developmental, systems theoretical, ecological or cultural influences.
Criticisms of the shortcomings of the MS framework have a long history. One of them concerns the profoundly gradualist conception the MS has inherited from the Darwinian account of evolution. Darwin saw slight, incremental and accumulating variation as the essential prerequisite without which ‘my theory would absolutely break down.’  a position already characterized by Huxley in 1901  as an ‘unnecessary difficulty.’ Subsequently, the perceived necessity of a slow and continuous flux of variation seemed to have been supported by innumerable studies that demonstrate corresponding behaviours of character variation in natural populations or under artificial selection regimes. The notion of slight successive variation was further reinforced by the molecular conception of genetic variation. When mutation of individual genes or even smaller entities of DNA is taken as the predominant source of variation, it seemed inevitable that phenotypic modifications should be small, because larger changes were deemed to be disruptive and unlikely to produce adaptive outcomes. The supposed randomness of genetic variation further contributed to this view. Today, all of these cherished opinions have to be revised, not least in the light of genomics, which evokes a distinctly non-gradualist picture . In addition, it is necessary to realize that all models of gradual variation are based on empirical measurements of precisely this kind of change and to the exclusion of other forms of variation. If cases of gradual variation are chosen and quantified, and theoretical models are derived from them, it should not be unexpected that it is gradual variation that will be explained.
A friend wonders whether the message could be any more blunt and still get into print: The Modern Synthesis (neo-Darwinism) does not account for the origin of complex features but only for their rise and fall in frequency once they do exist. Or, as Michael Behe puts it in Edge of Evolution (p. 164), “The big question, however, is not, ‘Who will survive, the more fit or the less fit?’ The big question is, ‘How do organisms become more fit?’ ”
If greater fitness is explained by the addition, slow or sudden, of complex new mechanisms, how do we account for that enormous increase in information? Beyond insisting—as some Darwinians do—well, we know that Darwinian evolution is capable of all that because, after all, it happens! Which is the equivalent of saying we know that Magic evolution is capable of all that because, after all, it happens! Whatever that approach is, it is not science.
Suzan Mazur’s new book, Paradigm Shifters is a helpful introduction to new ways of thinking about evolution, as is the Third Way of Evolution site. Mazur is one of the only science writers around who has been reporting on and helping us understand the controversy – as opposed to hiding it or, now and then, explaining it away.
Also from the paper,
A rising number of publications argue for a major revision or even a replacement of the standard theory of evolution [2–14], indicating that this cannot be dismissed as a minority view but rather is a widespread feeling among scientists and philosophers alike.
Indeed, a growing number of challenges to the classical model of evolution have emerged over the past few years, such as from evolutionary developmental biology , epigenetics , physiology , genomics , ecology , plasticity research , population genetics , regulatory evolution , network approaches , novelty research , behavioural biology , microbiology  and systems biology , further supported by arguments from the cultural  and social sciences , as well as by philosophical treatments [28–31]. None of these contentions are unscientific, all rest firmly on evolutionary principles and all are backed by substantial empirical evidence. More.
The Darwin lobby can’t just run all of these people out of town at once without attracting attention…
This shift from “everything is settled” to “we don´t know” is a key step. In lay terms, the Darwinism rammed down the school system by Darwin lobbies and their science writer cronies is out of date. One needn’t agree or disagree with it. If we want to study evolution at all, we must replace it.
See also: Darwinism: Replacement or extension?
NPR: Turkey to stop teaching evolution this fall