Issues in the philosophy of neuroscience include:

• Explanation: What are the phenomena to be explained in neuroscience? What constitutes an adequate neuroscientific explanation? Is it different from the kinds of explanations accepted in physics, chemistry, or elsewhere in biology? What is the difference, for example, between explaining the behavior of the brain in terms of "dynamical systems" and in understanding it by localizing functions and describing neural mechanisms?
  
  
• Theory Structure and Theory Building: What is/are the structure(s) of neuroscientific theories? How are neuroscientific theories represented? How does the structure and representation of a theory guide scientific practices, e.g., experimental design and theory building? What sorts of strategies are likely to be fruitful in building neuroscientific theories? Should one expect or work toward a unified theory of neuroscience?
  
  
• Levels: What is meant by the suggestion that theories in neuroscience span multiple levels of organization? Are these levels of size, theory, explanation, organization, or science? What is the relationship between these different kinds of levels? What does it mean to say that lower-level mechanisms "implement," "realize," or "provide the substrate for" higher level phenomena? If all higher-level phenomena are realized in lower-level mechanisms, does this threaten the existence or causal efficacy of higher-level phenomena?
  
  
• Integrating Fields: How are the results from different subfields of neuroscience integrated together into a single theoretical framework? Is there a privileged field in neuroscience (e.g., molecular biology or computational neuroscience) that is most likely to construct the deepest or most explanatorily fruitful theories? Can or ought one study higher levels of organization in the central nervous system independently of work done by fields attending to other levels of organization?
  
  
• Reduction and Emergence: What would be involved in reducing some mental phenomenon to, e.g., neurophysiological or molecular phenomena? Is this the same thing that one means when one speaks of reducing, e.g. lightening to electrical discharge or gasses to populations of molecules? Does the idea of emergence (as popularized by, e.g., Roger Sperry) make any sense? Is emergence consistent with reduction? How is reduction related to mechanistic explanation? Are higher level phenomena multiply realized by lower level realizers? What are the implications of multiple realization for different formulations of reductionism?
  
  
• Laws, Causality, and Mechanisms: Are there laws of neuroscience? If so, are they interestingly different from the laws found in physics or elsewhere in biology? What is a neural mechanism? How is a mechanistic understanding different from, e.g., dynamical systems? To what extent can the brain be understood mechanistically? What are the reliable strategies or methods for discovering the causal structure of the nervous system? Is it explanatory to identify "neural correlates" of psychological functions? What more is required beyond correlation?
  
  
• Localization of Function: Given individual variability and developmental plasticity, what does it mean to say that a given function localizes to a particular region? What is a function? What is a location? Can parts of the brain be defined without reference to the functions that they perform? Are the functions of the brain multiply realized in the wet-ware of the nervous system? Should functions be understood as adaptations, or as something else (e.g., as merely a capacity in a system)? Is localization an unjustified dogma of neuroscience, built into its techniques and practices, or is there good evidence that cognitive functions can be localized?
  
  
• Computation and Simulation: To what extent can computer simulations play the role of experimental systems in our investigation of the brain? How can simulations teach us something new about the brain and its function? What is the difference between simulation and explanation? To what extent must useful simulations be biologically plausible?
  
  
• Taxonomy and Concept Formation: How are psychological functions to be individuated? Does the existence of two distinct and dissociable mechanisms force the conclusion that there are two distinct functions being performed? What is the inferential relationship between performance in an experimental task (e.g., sorting cards or rhyming nonsense syllables) and component psychological functions? By virtue of what criteria should one distinguish different psychiatric disorders from one another?
  
  
• Evidence and Experimentation: What types of evidence are relevant to evaluating theories in neuroscience? What are the assumptions involved in the use of a given technique (e.g., lesion methods or imaging studies)? What are the strengths and weaknesses of different techniques? How can the results from one technique influence the interpretation of results collected with others? How are new experimental techniques introduced and justified? Under what conditions can introspection legitimately be used as evidence? To what extent (and under what conditions) can reliable inferences be drawn about brain structure based on evidence from single cases? To what extent (and under what conditions) can reliable data be generated by averaging across different subjects? What is an acceptable signal-to-noise ratio in PET and MRI studies? How ought one to proceed with the meta-analysis of different PET and MRI studies?
  
  
• Animal Experimentation and Experimental Models: How does one infer from the psychological and physiological traits in animal models to the psychological and physiological traits in other species? What makes for a good experimental model? To what extent do animal breeding and cloning practices affect the ability to draw inferences based on experimental organisms? How can results obtained in isolated experimental preparations (individual receptors or neurons, hippocampal slices, or decerebrate organisms) be applied back to the intact systems from which they were drawn? How are new experimental models introduced and justified? And how do they change over time in the course of a research program?
  
  
• Theoretical Neuroscience: Is the brain a computer? Does it process information or represent features of the world? Is such description mere metaphor, or does it make a substantive empirical claim about the brain's organization? What evidence can help to assess that claim? How are we to make sense of reference to "information," "representation," and "coding" in neuroscientific theories? To what extent must the explanation of mental phenomena be located within the organism? Must explanations necessarily appeal to features of an organism's natural and social environment?
  
  
• Philosophical Psychopathology: Given the putative explanatory and therapeutic successes of the neurosciences, what is mental about mental disorder? And in what sense are people with mental disorders disordered? Can natural selection help to distinguish mental disorder from proper mental function? What criteria and principles should guide taxonomic classification in works such as the Diagnostic and Statistical Manual (DSM)? To what extent are specific mental disorders natural kinds?