From its inception Darwinian evolutionary biology has been seen as having a problematic relationship of fact and theory. While the forging of the modern evolutionary synthesis resolved most of these issues for biologists, critics continue to argue that natural selection and common descent are “only theories.” Much of the confusion engendered by the “evolution wars” can be clarified by applying the concept of phenomena, inferred from fact, and explained by theories, thus locating where legitimate dissent may still exist. By setting (...) such analysis in the context of research traditions, it is possible to gain further insight into the complex interplay of facts, phenomena, and theories. Two case studies are explored to assess the value of such approaches, one from within evolutionary biology, the Baldwin effect, and one from outside, intelligent design. (shrink)

The launch of a revolutionary new scientific theory represents a rare occasion on which the apparently cumulative development of science might be influenced by particular events. Yet in the case of the Darwinian revolution it is often claimed that the theory of evolution by natural selection would have emerged more or less inevitably, given the scientific and cultural circumstances prevailing in mid-Victorian Britain. This essay challenges that claim by arguing that if Darwin had not been there to write his Origin (...) of Species the subsequent development of biology would have occurred along a line that steadily diverged from the sequence of events we actually experienced. There would certainly have been an evolutionary movement in the late nineteenth century, but there would have been no selection theory to disturb the progressionist assumptions of the time. A totally non-Darwinian evolutionism might not have generated the challenges that led to the emergence of modern genetics in the early twentieth century, resulting in a very different understanding of the relationship between development, heredity, and environment. (shrink)

In this article we argue for an extension of Pere Alberch’s notion of developmental morphospace into the realm of cognition and introduce the notion of cognitive phenotype as a new tool for the evolutionary and developmental study of cognitive abilities.

Evolutionary biology is a field currently animated by much discussion concerning its conceptual foundations. On the one hand, we have supporters of a classical view of evolutionary theory, whose backbone is provided by population genetics and the so-called Modern Synthesis (MS). On the other hand, a number of researchers are calling for an Extended Synthe- sis (ES) that takes seriously both the limitations of the MS (such as its inability to incorporate developmental biology) and recent empirical and theoretical research on (...) issues such as evolvability, modularity, and self-organization. In this article, I engage in an in-depth commentary of an influential paper by population geneticist Michael Lynch, which I take to be the best defense of the MS-population genetics position published so far. I show why I think that Lynch’s arguments are wanting and propose a modification of evolutionary theory that retains but greatly expands on population genetics. (shrink)

If the problem of the origin of life is conceptualized as a process of emergence of biochemistry from proto-biochemistry, which in turn emerged from the organic chemistry and geochemistry of primitive earth, then the resources of the new sciences of complex systems dynamics can provide a more robust conceptual framework within which to explore the possible pathways of chemical complexification leading to living systems and biosemiosis. In such a view the emergence of life, and concomitantly of natural selection and biosemiosis, (...) is the result of deep natural laws (the outlines of which we are only beginning to perceive) and reflects a degree of holism in those systems that led to life. Further, such an approach may lead to the development of a more general theory of biology and of natural organization, one informed by semiotic concepts. (shrink)

The Darwinian concept of natural selection was conceived within a set of Newtonian background assumptions about systems dynamics. Mendelian genetics at first did not sit well with the gradualist assumptions of the Darwinian theory. Eventually, however, Mendelism and Darwinism were fused by reformulating natural selection in statistical terms. This reflected a shift to a more probabilistic set of background assumptions based upon Boltzmannian systems dynamics. Recent developments in molecular genetics and paleontology have put pressure on Darwinism once again. Current work (...) on self-organizing systems may provide a stimulus not only for increased problem solving within the Darwinian tradition, especially with respect to origins of life, developmental genetics, phylogenetic pattern, and energy-flow ecology, but for deeper understanding of the very phenomenon of natural selection itself. Since self-organizational phenomena depend deeply on stochastic processes, self-organizational systems dynamics advance the probability revolution. In our view, natural selection is an emergent phenomenon of physical and chemical selection. These developments suggest that natural selection may be grounded in physical law more deeply than is allowed by advocates of the autonomy of biology, while still making it possible to deny, with autonomists, that evolutionary explanations can be modeled in terms of a deductive relationship between laws and cases. We explore the relationship between, chance, self-organization, and selection as sources of order in biological systems in order to make these points. (shrink)

This paper investigates what molecular biology has done for our understanding of the gene. I base a new account of the gene concept of classical genetics on the classical dogma that gene differences cause phenotypic differences. Although contemporary biologists often think of genes in terms of this concept, molecular biology provides a second way to understand genes. I clarify this second way by articulating a molecular gene concept. This concept unifies our understanding of the molecular basis of a wide variety (...) of phenomena, including the phenomena that classical genetics explains in terms of gene differences causing phenotypic differences. (shrink)

In September 2008, 10 years after the untimely death of Pere Alberch (1954–1998), the 20th Altenberg Workshop in Theoretical Biology gathered a group of Pere’s students, col- laborators, and colleagues (Figure 1) to celebrate his contribu- tions to the origins of EvoDevo. Hosted by the Konrad Lorenz Institute for Evolution and Cognition Research (KLI) outside Vienna, the group met for two days of discussion. The meeting was organized in tandem with a congress held in May 2008 at the Cavanilles Institute (...) for Biodiversity and Evolutionary Biology (ICBiBE) in Valencia, Spain. The talks at the KLI were equal parts: nostalgic remembrance, excitement over new ways of thinking about old problems, and an unrepressed vitriol against the resurgence of reductionist thinking in EvoDevo. Here we highlight some of the key aspects of Pere’s life and work that informed and infused the talks. (shrink)

In recent years, biologists have increasingly been asking whether the ability to evolve — the evolvability — of biological systems, itself evolves, and whether this phenomenon is the result of natural selection or a by-product of other evolutionary processes. The concept of evolvability, and the increasing theoretical and empirical literature that refers to it, may constitute one of several pillars on which an extended evolutionary synthesis will take shape during the next few years, although much work remains to be done (...) on how evolvability comes about. (shrink)

The Modern Synthesis (MS) is the current paradigm in evolutionary biology. It was actually built by expanding on the conceptual foundations laid out by its predecessors, Darwinism and neo-Darwinism. For sometime now there has been talk of a new Extended Evolutionary Synthesis (EES), and this article begins to outline why we may need such an extension, and how it may come about. As philosopher Karl Popper has noticed, the current evolutionary theory is a theory of genes, and we still lack (...) a theory of forms. The field began, in fact, as a theory of forms in Darwin’s days, and the major goal that an EES will aim for is a unification of our theories of genes and of forms. This may be achieved through an organic grafting of novel concepts onto the foundational structure of the MS, particularly evolvability, phenotypic plasticity, epigenetic inheritance, complexity theory, and the theory of evolution in highly dimensional adaptive landscapes. (shrink)

PUNCTUATED cquilibrium has finally obtained an unambiguous and incontrovertiblc majoxity—that is, our theory is now 21 ' years old. We also, with parental pride (and, therefore, potential..

In 1937, just as Dobzhansky published the book that later generations would laud as the foundation of the modern synthesis, the American Naturnlist published a symposium on "supraspecific variation in nature and in classification." Alfred C. Kinsey, who later became one of America's most controversial intellectuals for his study of basic behaviors in another sort of WASP,1 led off the symposium with a summary of his extensive work on a family of gall wasps, the Cynipidae. In his article, Kinsey strongly (...) advocated the central theme of the developing synthesis: Evolution at all scales, particularly macroevolution, could be explained by the genetic mechanisms observed in laboratories and local populations. He first complained that some geneticists and naturalists were still impeding a synthesis with their insistence upon causal separation of levels: "Just as some of the geneticists have insisted that the laboratory genetics may explain the nature and origin of Mendelian races, but not of natural species, so others indicate that the qualities of higher categories must be explained on bases other than those involved in species" (1937, p. 208). He then defended the central postulate. (shrink)

Philosophers now treat the relationship between classical genetics and molecular biology as a paradigm of nonreduction and this example is playing an increasingly prominent role in debates about the reducibility of theories in other sciences. This paper shows that the anti-reductionist consensus about genetics will not withstand serious scrutiny. In addition to defusing the main anti-reductionist objections, this critical analysis uncovers tell-tale signs of a significant reduction in progress. It also identifies philosophical issues relevant to gaining a better understanding of (...) what is now happening in genetics and of what we might expect to happen in other sciences. (shrink)

Philosophers now treat the relationship between classical genetics and molecular biology as a paradigm of nonreduction and this example is playing an increasingly prominent role in debates about the reducibility of theories in other sciences. This paper shows that the anti-reductionist consensus about genetics will not withstand serious scrutiny. In addition to defusing the main anti-reductionist objections, this critical analysis uncovers tell-tale signs of a significant reduction in progress. It also identifies philosophical issues relevant to gaining a better understanding of (...) what is now happening in genetics and of what we might expect to happen in other sciences. (shrink)