Wednesday, January 13, 2010

Thinking about Mechanisms (Part 1): Introduction to Mechanisms

This post is part of my series on the work of philosopher Carl Craver. For an index, see here.

Craver specialises in fleshing out the nature and status of neuroscientific explanations. His particular interest is in mechanistic explanations. This is also one of my own core research interests.

Today, I am going to take a look at an article that Craver published with Peter Machamer and Lindley Darden (two other philosophers of science). He is not the lead author on this piece but it is an important introduction to some of the themes in his work. The full reference for the article is as follows:
Machamer, Darden and Craver, "Thinking About Mechanisms" (2000) 67 Philosophy of Science 1-25
Those of you with a subscription, can access it via JSTOR.

Mechanistic Explanations are...
Mechanistic explanations are commonplace in science. In particular, in molecular biology and neurobiology. Yet there has been a paucity of serious philosophical analysis on the nature of mechanistic explanations. The authors try to provide this analysis.

To follow them, we need to first look at the types of questions mechanistic explanations are supposed to answer. Mechanisms are usually proposed in answer to questions about how something comes about or how something happens. Here are two questions that cry out for mechanistic answers:
  1. How are signals passed from neuron to neuron?
  2. How does DNA replicate?
Examples of mechanistic explanations will help to ground the more philosophical analysis that follows, so we will look at rough answers to each of these questions (we do not need detailed versions now, just general outlines).

The answer to the first of these questions runs along the following lines: neurotransmitter molecules are released by the presynaptic neuron into the synaptic cleft (gap between neurons), these neurotransmitters bind to receptor-proteins on the post-synaptic neuron, this depolarises the post-synaptic neuron which can either inhibit or promote further signaling. The image below illustrates this mechanism.

The answer to the second question runs along the following lines: the DNA double helix is unwound by a helicase enzyme, the charged nitrogenous bases (which make up the structure of DNA) are thus exposed and complementary nitrogenous bases bond to them with the help of additional enzymes. After a couple more stages (apologies for the ambiguity), the DNA molecule is replicated. The image below provides an illustration of this.

To reiterate, more detailed accounts of these two mechanisms will be presented later.

A More Formal Look at Mechanisms
With these examples in tow, we can begin to take a more formal look at mechanisms. The authors provide the following definition:
Mechanisms are entities and activities organised such that they are productive of regular changes from start or set-up to finish or termination.
That's about as dry and non-commital as definitions come, but it does contain two important concepts:
  1. Activities: these are producers of change. In the neurotransmission example, the activities are "diffusion", "binding", "depolarisation" etc.
  2. Entities: these are the things that engage in activities. In the neurotransmission example, the entities are neurotransmitter molecules, neurons, receptor proteins, ion-gated channels etc. To participate in an activity, an entity must have certain properties, e.g. geometric structure or charge.
This approach to mechanisms is deliberately dualistic in that it does not prioritise either activities or entities. Some ontologists do this. For example, substantivalists try to reduce all activities to entities and their transitions; while process theorists try to reduce entities to activities. It important to see that neither dominates: they are interdependent.

Functions are also central to mechanistic explanations. The most oft-cited example is the heart. It is said that the function of the heart is to pump blood. The authors argue that this description of function is wrong because it reduces a function to a property possessed by an entity (the heart "has" the property of blood-pumping).

A better definition (again, a little dry) would be the following:
A function is a role played by both entities and activities in a mechanism.
On this definition, the correct description of the heart's function would be:
The heart has the function of pumping blood and thereby delivering oxygen and nutrients to the rest of the body.
Okay, that's it for now. The next part will take a more detailed look at the mechanism for chemical neurotransmission and see how the formal analysis applies to it.

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