Representing Genes, First Workshop 

January 17-19 2003, University of Pittsburgh




Opening Address: The definition of genes is the theory of genetics and vice-versa

Raphael Falk

De Vries’ interpretation of the Faktoren that Mendel selected for demonstrating lawful inheritance, as preformed pangens or ‘unit characters’, introduced a constant tension into genetic theory. Johannsen’s concept of the ‘gene’, rather than settling it, only perpetuated this dialectic tension between genes that “summarize” quantities obtained by manipulation of empirical variables, and genes as constructs, that add certain existence propositions to the empirical relations. Hoping that one day “we may be able to grind them with a mortar in a beaker,” researchers were constrained by following markers of genes in hybridization experiments. Watson-Crick’s model of DNA suggested that the gene could now be characterized straight forwardly, in physico-chemical terms. However the converged molecular notion of the classical gene soon diverged as a result of unexpected empirical findings. The dynamics of the dialectic tension between an abstract, operative concept and a discrete material entity proved its power again when the achievements of molecular research forced conclusions that there is no way to identify, either structurally or functionally, discrete DNA sequences as ‘genes’. Attempts to define genes by forward predictions from the properties of DNA sequences (ironically called “reverse genetics”) only support the notion of genes as epistemologically fundamental generic terms that relate to invariant entities of inheritance and development.



Focus Group A: Hard Cases

Schaffner, Knight, Fogle, Waters, Griffiths

Locate specific ‘hard cases’ for the classical molecular gene concept, such as those described in Fogle (2001). What are the general characteristics that make these ‘hard cases’ and what are some specific examples in genomes? What additional (i.e. additional to the basic concept of the molecular gene) criteria seem to be appealed to for resolution of these cases (resolution meaning a decision about the presence of a certain number of gene and other, non-gene, elements)?


Perhaps also, if time permits, what are some broader domains of research (perhaps defined by classes of ‘hard cases’?) where the discrete gene concept started to become disfavored, neglected in favor of some alternative vocabulary for describing genetic elements?



Focus group B: Genic Nomenclature

Delehanty, Love, Kaplan, Burian, Sirtes, Clough

What are the explicit and implicit conventions for genic nomenclature? What inferences can be drawn from these about the kinds of differences between sequences that are salient for working biologists? How congruent are those salient factors with factors mentioned in current philosophical accounts of the identity conditions for genes and other kinds of sequence? What aspects of nomenclature might constitute variables that could be manipulated in survey questions?



Focus Group C: “Top down” gene concepts

Mitchell, Lennox, Brigandt, Robert, Parker, Moss

Various authors have introduced concepts like Gene P (Moss), the classical Mendelian gene (Waters), a schematic ‘gene role’ to which we can retreat when some current structural specification of the gene becomes problematic (Burian), or the ‘abstractive concept/intervening variable of (Falk, 1986). How do these different proposals relate to one another and is there some common strand that is worth stating in its own right as a broad kind of gene concept? How do the various proposals see the top-down concept(s) as relating to the molecular gene concept(s) proposed by the same and other authors? What testable consequences might these envisaged relationships have?



Focus Group D: Kinds of biologists

Tabery, Schwartz, Love, Griesemer, Stotz, Falk, Larson

What are the plausible groupings we might treat as independent variables - such as affiliation (discipline, societies, preferred loci of publication), research topics, molecular techniques? How might these variables be operationalized?


Focus Group E: ‘Conflation’ of gene concepts

Fogle, Moss, Griesemer, Schwartz, Falk, Tabery

Some authors, notably Moss and Fogle have emphasized that molecular and ‘top down’ gene concepts get conflated. What are the consequences of such conflation supposed to be? How might the claim that such conflations occur be tested? What are some specific phenomena in genomes, in development, or in evolution, descriptions of which might be good materials to use in conducting these tests?




Focus Group F: The informational gene and the genetic program

Lennox, Robert, Knight, Parker, Griffiths, Love

DST theorists and others have claimed that conceiving the gene as an informational entity leads to the backgrounding of other explanatory factors. Evelyn Keller has extensively discussed the shortcomings of the idea of a genetic program (as opposed to a developmental program).  What specific errors might be supposed to flow from one or both of these ideas? How might one empirically distinguish whether someone is using one or both of these ideas? How might the supposed errors that flow from them be operationalised?



Focus Group G: The power of gene-based explanation

Delehanty, Brigandt, Schaffner, Schwartz, Waters, Mitchell

Many authors, Dick Burian in ‘Reconceiving animals...’ and Ken Waters in his posts to the listserv on 01/10, for instance, have mentioned the limits of narrowly gene-based explanations. Whether working biologists recognize these limits is controversial. Brian Hall, in ‘The gene is not dead...’ states strongly that they do, and suggests that it would be valuable to have some social scientists do a survey to see if ‘genetic determinism’ in biology really is just a myth invented by commentators! 


What are these supposed limits to gene-based explanations? How might one go wrong as a scientist if one failed to recognize these limits? Where (research context, research community) might one expect to find such failures and how might one test for their occurrence?


Ken Schaffner and Ken Waters have both emphasized the ‘instrumental primacy’ of genes, meaning something like the unique epistemic role of linear sequences and its handle-like capacity, allowing biologists to ‘grasp’ sequences and also to use them to ‘hold’ and manipulate other objects. Is this intended by these or any other authors as a descriptive thesis? If so, how would its predictions differ from a view that sees biologists as endorsing an ontological primacy of the genes? How might such a difference be tested?



Focus Group H: Kinds of Biologists II

Stotz, Clough, Larson, Sirtes, Burian, Rheinberger

Continuing discussion of what are the plausible groupings we might treat as independent variables - such as affiliation (discipline, societies, preferred loci of publication), research topics, molecular techniques? How might these variables be operationalized?


Focus Group I: ‘Top-Down’ gene concepts II

Falk, Burian, Brigandt, Parker, Sirtes, Clough

How can the possible question #2 (see other document) be altered or supplemented to make the results more relevant to some of the other approaches to the top down gene (Water’s Mendelian gene, Falk’s intervening variable, Burian’s schematic gene concept). Are these concepts appropriately placed in the same ‘family’ as gene P?



Focus Group J: How loose is the contemporary gene concept?

Waters, Knight, Rheinberger, Delehanty, Lennox

Comparing Ken Waters’ account of the molecular gene as a description of current status of the gene concept to the idea that ‘gene’ is a loose term for any sequence that is of interest. Is there still a distinctive status for some (sets of) sequences as genes - those that are the ‘image in the DNA’ of a linear product?  Identify cases to put to a biologists that might discriminate these two hypotheses. 



Focus Group K: Issues arising from Saturday’s discussions

Griesemer, Stotz, Moss, Love, Larson, Griffiths

Reply to the requests for feedback in the document summarizing possible questions we might address that were identified on Saturday.



Focus Group L: Behavior genetics

Tabery, Fogle, Robert, Schaffner, Waters, Mitchell

What are the distinctive features of thought about the gene and/or genetic causation in behavior genetics? How might behavior geneticists (or some subset of them) be used as a group in contrast to some other group to test some thesis about the gene?