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)

Biologists rely heavily on the language of information, coding, and transmission that is commonplace in the field of information theory developed by Claude Shannon, but there is open debate about whether such language is anything more than facile metaphor. Philosophers of biology have argued that when biologists talk about information in genes and in evolution, they are not talking about the sort of information that Shannon’s theory addresses. First, philosophers have suggested that Shannon’s theory is only useful for developing a (...) shallow notion of correlation, the so-called causal sense of information. Second, they typically argue that in genetics and evolutionary biology, information language is used in a semantic sense, whereas semantics are deliberately omitted from Shannon’s theory. Neither critique is well-founded. Here we propose an alternative to the causal and semantic senses of information: a transmission sense of information, in which an object X conveys information if the function of X is to reduce, by virtue of its sequence properties, uncertainty on the part of an agent who observes X. The transmission sense not only captures much of what biologists intend when they talk about information in genes, but also brings Shannon’s theory back to the fore. By taking the viewpoint of a communications engineer and focusing on the decision problem of how information is to be packaged for transport, this approach resolves several problems that have plagued the information concept in biology, and highlights a number of important features of the way that information is encoded, stored, and transmitted as genetic sequence. (shrink)

Familiarity with Charles Darwin's treatise on evolution is essential to every well-educated individual. One of the most important books ever published--and a continuing source of controversy, a century and a half later--this classic of science is reproduced in a facsimile of the critically acclaimed first edition.

The role played by the concept of genetic coding in biology is discussed. I argue that this concept makes a real contribution to solving a specific problem in cell biology. But attempts to make the idea of genetic coding do theoretical work elsewhere in biology, and in philosophy of biology, are probably mistaken. In particular, the concept of genetic coding should not be used (as it often is) to express a distinction between the traits of whole organisms that are coded (...) for in the genes, and the traits that are not. (shrink)

In many species the mutation rate is higher in males than in females, a phenomenon denoted as male mutation bias. This is often observed in animals where males produce many more sperm than females produce eggs, and is thought to result from differences in the number of replication‐associated mutations accumulated in each sex. Thus, studies of male mutation bias have the capacity to reveal information about the replication‐dependent or replication‐independent nature of different mutations. The availability of whole genome sequences for (...) many species, as well as for multiple individuals within a species, has opened the door to studying factors, both sequence‐specific and those acting on the genome globally, that affect differences in mutation rates between males and females. Here, we assess the advantages that genomic sequences provide for studies of male mutation bias and general mutation mechanisms, discuss major challenges left unresolved, and speculate about the direction of future studies. (shrink)

Historians and philosophers of science agree that Darwin had an understanding of species which led to a workable theory of their origins. To Darwin species did not differ essentially from ‘varieties’ within species, but were distinguishable in that they had developed gaps in formerly continuous morphological variation. Similar ideas can be defended today after updating them with modern population genetics. Why then, in the 1930s and 1940s, did Dobzhansky, Mayr and others argue that Darwin failed to understand species and speciation? (...) Mayr and Dobzhansky argued that reproductively isolated species were more distinct and ‘real’ than Darwin had proposed. Believing species to be inherently cohesive, Mayr inferred that speciation normally required geographic isolation, an argument that he believed, incorrectly, Darwin had failed to appreciate. Also, before the sociobiology revolution of the 1960s and 1970s, biologists often argued that traits beneficial to whole populations would spread. Reproductive isolation was thus seen as an adaptive trait to prevent disintegration of species. Finally, molecular genetic markers did not exist, and so a presumed biological function of species, reproductive isolation, seemed to delimit cryptic species better than character-based criteria like Darwin’s. Today, abundant genetic markers are available and widely used to delimit species, for example using assignment tests: genetics has replaced a Darwinian reliance on morphology for detecting gaps between species. In the 150th anniversary of The Origin of Species , we appear to be returning to more Darwinian views on species, and to a fuller appreciation of what Darwin meant. (shrink)

In The Origin of Species (1859) Darwin challenged many of the most deeply-held beliefs of the Western world. Arguing for a material, not divine, origin of species, he showed that new species are achieved by "natural selection." The Origin communicates the enthusiasm of original thinking in an open, descriptive style, and Darwin's emphasis on the value of diversity speaks more strongly now than ever. As well as a stimulating introduction and detailed notes, this edition offers a register of the many (...) writers referred to by Darwin in the text. (shrink)

Commentary on Bergstrom and Rosvall, ‘The transmission sense of information’, Biology and Philosophy. In response to worries that uses of the concept of information in biology are metaphorical or insubstantial, Bergstrom and Rosvall have identified a sense in which DNA transmits information down the generations. Their ‘transmission view of information’ is founded on a claim about DNA’s teleofunction. Bergstrom and Rosvall see their transmission view of information as a rival to semantic accounts. This commentary argues that it is complementary. The (...) idea that DNA is transmitting information down the generations only makes sense if it is carrying a message, that is to say if it has semantic content. (shrink)