Realism representational

A step closer toward realism is taken by off-lattice models in which the backbone is specified in some detail, while side chains, if they are represented at all, are taken to be single, unified spheres [44-50]. One indication that this approach is too simplistic was given in [51], which proved that for a backbone representation in which only Ca carbons were modeled, no contact potential could stabilize the native conformation of a single protein against its nonnative ( decoy ) conformations. However, Irback and co-workers were able to fold real protein sequences, albeit short ones, using a detailed backbone representation, with coarse-grained side chains modeled as spheres [49, 52-54]. 

See Bas Van Frassen, "Interpretation in Science and the Arts," paper given at CCACC Conference, "Realism and Representation," Rutgers University, November 1012, 1989. 

Metaphysical realism is the view that assumes a position similar to the external observer watching the waterfall and the painting about it. On the one hand, there is the world. On the other hand, there are our representations and descriptions of it. These may be thoughts, sentences, mental pictures - for our purposes it does not matter. The world is independent of the representations. It would have existed and would have had the same characteristics even if no representations had ever been prepared. A representation is true if it matches the segment of the world it is a representation of. Whether a representation is true is completely independent of what its maker believes about it. It is also independent of the techniques the maker of the representation uses to check how good the representation is, i. e. it is independent of the verification procedures. The verification procedures are useful, but they are linked to truth only contingently. So truth is one thing, verification is another. 

Despite these early developments, models with explicit representations of viruses have not yet been widely applied or tested in natural marine systems. The major question that needs to be addressed is, do we need to account for the impact of viruses in pelagic N-cycle models and if so, at what level of realism Do viruses need to be explicitly modeled or can their effects be parameterized as a component of the generic death terms that we already have in our models ... 

So what good, then, what special value, does chemistry offer contemporary philosophy of science Typically philosophical problems, even problems in philosophy of science, are not confined to a particular science. For general problems—problems about representation, inference, discovery, explanation, realism, intertheoretic and interdisciplinary relations, and so on—what is needed are scientific illustrations that go to the heart of the matter without requiring specialized technical knowledge of the reader. The science needed for most philosophy is familiar, not esoteric, right in the middle of things, mature and diverse enough to illustrate a variety of fundamental issues. Almost uniquely, chemistry fits the description. 

The next stage of realism beyond a lattice model is a continuum bead model, where atoms are grouped together into beads, and the beads are allowed to move continuously in space. Typically, one bead represents a single amino acid in a protein. All-atom representations of biomolecules constitute a further level of sophistication. In this final section of our review we investigate the potential energy surfaces of a continuum bead heteropolymer and a tetrapeptide modeled by an all atom potential. Disconnectivity graphs immediately provide a visual distinction between frustrated and unfrustrated systems in both cases. 

Numerous simulations with implicit solvent have been reported over the last decades with increasing levels of realism [5]. Many of these simulations involve peptides and small proteins over time scales that could not be reached easily with explicit solvent representations [6-8]. There are many fewer cases where implicit solvent simulations were used to study larger biomolecules and biomolecular complexes [9,10]. Such simulations have remained rare for the following reasons ... 

The motives for transparency views such as the foregoing are multifarious. Sometimes the motive is to make room for direct realist theories of perception — theories according to which we are aware of external things and not merely goings-on in our own minds. Sometimes the motive is to make the world safe for materialism — if we are not aware of intrinsic features of our experiences, then we cannot claim that experiences have features that no brain state could have. And sometimes the motive is to pave the way for a representationalist or intentionalist view of experience — a view according to which the character of experience is exhausted by its representational or propositional content. Intentionalism itself may be desired either for its own sake or as a means to the ends of direct realism or materialism. I shall not be concerned with these larger issues here, but shall concentrate on transparency in its own right. 

What seems to be peculiar for chemistry is the priority of entity-realism over theory-realism long before an appropriate theoretical representation was developed chemists denoted their scientific objects as radicals. To put it in other words the discovery of triphenylmethyl has not been the result of theory-driven activities. 

The gas-solid interaetion laws explored in the numerous simulation studies of physisorption vary eonsiderably in their complexity and level of realism. One starts from the simplest case, which is that of the hard wall, which can be planar, either as a free surface or as the boundaries of a slit pore. Of course, other geometries such as the straight-walled cylindrical pore can be studied. These systems are, of course, not very realistic, but they are very valuable in helping one understand the effect of confinement on the properties of a fluid without the complications of an attractive interaction at the wall. In fact, the hard wall idea can be extended by the addition of an attractive square well next to the hard wall that gives a relatively simple representation of the adsorption process as it might be observed in real systems. Still, both the hard wall and the hard wall plus square well models yield only the basic principles of adsorption, and one must go to more realistic representations if comparisons with experimental data are the goal. 

Representational displays are pictorial or symbolic displays. Examples are video images, graphs and maps. These displays may be static or dynamic. Size of display, size of elements displayed, realism, resolution, color, and rate of change affect performance. Symbols are a form of representational display. Chapter 32 discussed them. 

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