Historians of economics are well aware of the non-neutrality of the research methods economists use. Or are they? Sure, we know that also research methods – statistics, experiments, field observation, armchairs, you name it – have their histories. And obviously, that makes them an integral part of how economics developed. However, in this reasoning the research method itself has remained a passive and neutral information producing device. Jan Tinbergen became famous for combining mathematics and statistics in a novel way, in which the resulting econometrics was and is understood as a tool that can be applied by anyone alike. Similarly, Fogel and Engerman applied a whole bunch of empirical methods to the history of slavery, in which their tools might have been inappropriately used or interpreted, but in themselves were have been understood as neutral. Despite being aware that the tools have their own histories, historians of economics have essentially maintained a view of research methods as neutral and passive.
I want to contest this view. Research methods are not neutral tools, but actors that actively shape economists’ view of the social world. The exact same experiment makes Vernon Smith and Richard Thaler see two different social realities, and makes these two economists develop their own theories in diverging ways. It is not just that economists like Smith and Thaler have different economic views, and in particular it is not the case that their views converge because of the laboratory experiment, data collection, or field experiment. Quite the contrary, the experiment actively diverges Smith and Thaler’s economics. Research methods are not neutral and passive tools, but actively manipulating actors who need to be treated as such.
History of Economics Playground Redux 
Isn’t it the argument that a priori theory represents a self-contained, and thereby “neutral” form of argumentation, but that the acts of abstraction and analysis cannot be objective, per Weber’s discussion of the “ideal type” in his 1904 essay “‘Objectivity’ in Social Science and Social Policy”? (I’m not sure if this is what you have in mind, but I’ve been reading Bruce Caldwell on the conflicts with the Historical School, and his discussion of the history of these arguments is very useful).
On Fogel and Engerman’s “Time on the Cross” in particular, and the question of objectivity in inquiry in general, a good collection of essays is Thomas Haskell’s book “Objectivity is Not Neutrality: Explanatory Schemes in History”. I don’t have this in front of me, but apparently Haskell was able to uncover invalid economic presuppositions made by Fogel and Engerman in their analysis. I don’t know if that was the last word, but it may be of use…
Your post is non-controversial in, say, the Philosophy of Science. Thomas Kuhn probably made the issue paramount first (paradigms), but it’s certainly evident before that (e.g. Quine, off the top of my head).
I suspect recent thinkers, e.g. Roy Bhaskar, also share that view. He’s more focused on the reverse, though – the ontology, and how it (hopefully) gives rise to successful methodologies. ‘Tis the only hope, really: that an inappropriate methodology returns useless results, else we would have no way of progressing towards truly useful metholodogies that accurately describe the way the world is. But whatever.
A methodology presupposes certain things – e.g. it involves inplicit assumptions about the world – so any methodological choice is also a (dirty word) ontological choice.
Which is why a variety of methodologies remain valuable (even if only across, rather than within, disciplines). Of what use Sociology, save for its highly refined approach to QDA?
I am not sure that Fogel and Engerman is a good example since it had been the center of a huge controversy at the time of their publication, see Christelle de Rouvray’s Phd Thesis (LSE). Else it has never been ‘neutral’ for anyone but (some of) the cliometric and economic community.
Haskell’s book of essays on objectivity responds to Peter Novick’s magnificent book on the Historical profession, THAT NOBLE DREAM, that historicizes standards of objectivity and neutrality among American historians. Interestingly, of what I can remember of the book, Novick makes no reference to tools, but reflects mostly on the self-image of the historian and the kind of statements she profess.
The politics of objects and space always reminds me of M. Foucault, but then again, almost everything reminds me of Foucault.
Cheers all, but what I’m struggling to unravel are three issues. 1) The objective history does not exist thesis. 2) The non-neutrality of the historian thesis, which roughly says that the historian uses the research methods at his disposal as he pleases. This includes both the more or less accidental mistakes as in Haskell’s objections against Fogel and Engerman, and more explicit use or even bending of history. (Medvedev on Stalin jumps to mind). 3) The non-neutrality of the research method, in that the arrival of a new research method, or new use or application of the research method, makes different scientists look at the same phenomenon in new, but different new ways. Does that make sense? Any (taxonomizing) reading suggestions on 3)?