This paper has two goals. The first goal is to show that the structuralists’ claims about dependence are more significant to their view than is generally recognized. I argue that these dependence claims play an essential role in the most interesting and plausible characterization of this brand of structuralism. The second goal is to defend a compromise view concerning the dependence relations that obtain between mathematical objects. Two extreme views have tended to dominate the debate, namely the view that all (...) mathematical objects depend on the structures to which they belong and the view that none do. I present counterexamples to each of these extreme views. I defend instead a compromise view according to which the structuralists are right about many kinds of mathematical objects (roughly, the algebraic ones), whereas the anti-structuralists are right about others (in particular, the sets). I end with some remarks about how to understand the crucial notion of dependence, which despite being at the heart of the debate is rarely examined in any detail. (shrink)

This paper takes up the cause of species pluralism. An argument for species pluralism is provided and standard monist objections to pluralism are answered. A new form of species pluralism is developed and shown to be an improvement over previous forms. This paper also offers a general foundation on which to base a pluralistic approach to biological classification.

Species pluralism gives us reason to doubt the existence of the species category. The problem is not that species concepts are chosen according to our interests or that pluralism and the desire for hierarchical classifications are incompatible. The problem is that the various taxa we call 'species' lack a common unifying feature.

We outline three very different concepts of the gene—instrumental, nominal, and postgenomic. The instrumental gene has a critical role in the construction and interpretation of experiments in which the relationship between genotype and phenotype is explored via hybridization between organisms or directly between nucleic acid molecules. It also plays an important theoretical role in the foundations of disciplines such as quantitative genetics and population genetics. The nominal gene is a critical practical tool, allowing stable communication between bioscientists in a wide (...) range of fields grounded in well-defined sequences of nucleotides, but this concept does not embody major theoretical insights into genome structure or function. The post-genomic gene embodies the continuing project of understanding how genome structure supports genome function, but with a deflationary picture of the gene as a structural unit. This final concept of the gene poses a significant challenge to conventional assumptions about the relationship between genome structure and function, and between genotype and phenotype. (shrink)

I argue that there are at least four different ways in which the term ‘function’ is used in connection with the study of living organisms, namely: function as activity, function as biological role, function as biological advantage, and function as selected effect. Notion refers to what an item does by itself; refers to the contribution of an item or activity to a complex activity or capacity of an organism; refers to the value for the organism of an item having a (...) certain character rather than another; refers to the way in which a trait acquired and has maintained its current share in the population. The recognition of a separate notion of function as biological advantage solves the problem of the indeterminate reference situation that has been raised against a counterfactual analysis of function, and emphasizes the importance of counterfactual comparison in the explanatory practice of organismal biology. This reveals a neglected problem in the philosophy of biology, namely that of accounting for the insights provided by counterfactual comparison. (shrink)

In its last round of publications in September 2012, the Encyclopedia Of DNA Elements (ENCODE) assigned a biochemical function to most of the human genome, which was taken up by the media as meaning the end of ‘Junk DNA’. This provoked a heated reaction from evolutionary biologists, who among other things claimed that ENCODE adopted a wrong and much too inclusive notion of function, making its dismissal of junk DNA merely rhetorical. We argue that this criticism rests on misunderstandings concerning (...) the nature of the ENCODE project, the relevant notion of function and the claim that most of our genome is junk. We argue that evolutionary accounts of function presuppose functions as ‘causal roles’, and that selection is but a useful proxy for relevant functions, which might well be unsuitable to biomedical research. Taking a closer look at the discovery process in which ENCODE participates, we argue that ENCODE’s strategy of biochemical signatures successfully identified activities of DNA elements with an eye towards causal roles of interest to biomedical research. We argue that ENCODE’s controversial claim of functionality should be interpreted as saying that 80 % of the genome is engaging in relevant biochemical activities and is very likely to have a causal role in phenomena deemed relevant to biomedical research. Finally, we discuss ambiguities in the meaning of junk DNA and in one of the main arguments raised for its prevalence, and we evaluate the impact of ENCODE’s results on the claim that most of our genome is junk. (shrink)

Over these last few years once again the relationship between biology and information has been debated with great liveliness. The crucial points concern the meaning of the term ‘information’ and whether the so-called “information talk” is really necessary inside biology.I will proceed by first commenting on some points of the debate (§ 2), then showing that a biophysical account of the process from the nucleotide sequences to the correlated amino acid sequences is possible (§ 3). In this way, I will (...) suggest that a satisfying account of that process can be offered without entering the quicksand of information. (shrink)

Analysis of two key ways of characterizing genes—as causes of phenotypic effects and as genomic DNA sequences—has yielded widespread pessimism that they can be united in a coherent gene concept. This raises important questions about the epistemology of genomic research: If analysis of a genome sequence cannot yield information about genes defined both in terms of their products and their DNA sequence, then what could we learn from it? I investigate basic tools of genomic analysis, argue that they do not (...) reflect the application of either gene concept, and clarify how we learn from genomic research. (shrink)

This paper aims to give an impression of how biologists, at the turn of the twentieth century, came to conceptualize and define the hidden entities presumed to govern the process of hereditary transmission. With that, the stage was set for the emergence of genetics as a biological discipline that came to dominate the life sciences of the twentieth century. The annus mirabilis of 1900, with its triple re-appreciation of Gregor Mendel’s work by the botanists Hugo de Vries, Carl Correns, and (...) Erich Tschermak, can be seen as the watershed after which theorizing about heredity and experimentation—selecting pure lines and Mendelian crossing—became tightly connected. As to concepts before this, this paper will analyze Carl von Nägeli’s ‘idioplasm’, Hugo de Vries’s ‘pangenes’, and August Weismann’s ‘germ plasm’. Carl Correns’s Anlagen and Wilhelm Johannsen’s ‘genes’ would replace them in the decade after 1900.Keywords: Idioplasm ; Pangenes ; Germ plasm ; Anlagen ; Gene; Genotype. (shrink)

For at least a century it has been known that multiple factors play a role in the development of complex traits, and yet the notion that there are genes “for” such traits, which traces back to Mendel, is still widespread. In this paper, we illustrate how the Mendelian model has tacitly encouraged the idea that we can explain complexity by reducing it to enumerable genes. By this approach many genes associated with simple as well as complex traits have been identified. (...) But the genetic architecture of biological traits, or how they are made, remains largely unknown. In essence, this reflects the tension between reductionism as the current “modus operandi” of science, and the emerging knowledge of the nature of complex traits. Recent interest in systems biology as a unifying approach indicates a reawakened acceptance of the complexity of complex traits, though the temptation is to replace “gene for” thinking by comparably reductionistic “network for” concepts. Both approaches implicitly mix concepts of variants and invariants in genetics. Even the basic question is unclear: what does one need to know to “understand” the genetic basis of complex traits? New operational ideas about how to deal with biological complexity are needed. (shrink)

In recent years geneticists have witnessed many significant observations which have seriously shaken the traditional concept of the gene. These specifically include the facts that (1) the boundaries of transcriptional units are far from clear; in fact, whole chromosomes if not the whole genome seem to be continuums of genetic transcription, (2) many examples of gene fusion are known, (3) likewise many examples of so-called encrypted genes are known in the organelle genomes of microbial eukaryotes and in prokaryotes, and (4) (...) in addition to the structure of the gene, its functional status can also be inheritable, and, further, (5) epigenetic extra-genomic modes of inheritance, called genetic restoration, seem to be a rather common phenomenon, meaning that organisms can sometimes rewrite their DNA on the basis of RNA messages inherited from generations past. I will briefly review these observations and discuss the difficulties of defining the gene, and then formulate a new view, which is called the relational or systemic concept of the gene. It has to be noted that genes assume their information content characteristics in the Shannonian sense as nucleotide sequences of DNA (or RNA). However, on the basis of this we cannot say anything about their information content in the semantic sense. The semantic information content of genes is context-dependent. Genes namely assume their biochemical characteristics usually only within living cells, their developmental characteristics only within living organisms, and their evolutionary characteristics only within populations of living organisms. (shrink)