Transcript Mechanism - Blogs - University of Kent

What’s all this fuss about
mechanisms?
Phyllis McKay
University of Kent
Our approach to mechanisms and
the philosophy of causality
From science to metaphysics: our
case studies
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5.
We aim to study scientific use of mechanisms to
work out what mechanisms are, and what they
do. We aim for both depth and breadth:
Physics: gravitational wave emission
Biochemistry: protein synthesis
Evolutionary biology: natural selection
Psychology: theory of mind mechanism
Economics: perhaps the transmission
mechanism
Protein synthesis
Natural selection
Experimental work on protein
synthesis
• The use of various technologies to investigate
microstructure.
– ‘Fifty years have passed since the discovery of the structure of
DNA. This event … expanded understanding of all events in the
pathway from DNA to protein. … In many instances determining
structure has uncovered intricate details of their biological
function.’ (Whitford p310.)
• Bare discovery of the chemicals present – or absent.
– Eg Zamecnik and Hoagaland’s work in 40s and 50s.
• Manipulation experiments.
– eg Crick and Brenner’s work in 1961.
• Replicated, but not repeated extensively.
Franklin’s X-ray diffraction
photograph of DNA
Confirmation of the existence of
replication forks
Experimental work on natural
selection
• Artificial selection experiments, including
extensive repetition of the same trial:
– Eg Clayton and Roberton’s 1957 work on Drosophila.
• How-possibly constructions using simulations:
– Eg Ridley on the eye; Bell on metabolism.
• Manipulation experiments:
– Eg extensive work on clutch size in birds.
• Not uninterested in structure.
• Unexpected, non-replicable results common.
Conclusions on mechanisms to
date
One important aim of science to use mechanisms
in decompositional causal explanation to explain,
in detail how a lower-level mechanism produces
a higher-level phenomenon. They are
characteristically:
1. Hierarchically nested
2. Functionally individuated
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In terms of the phenomenon produced and explained.
3. Real
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Entities that exist in the world that produce
phenomena for the most part independently of how we
describe them or of whether we even observe them.
Note that independence comes in degrees: consider
social and psychological mechanisms.
4.
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Local
Broadly nearby in space and time
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Protein synthesis happens in the cell where proteins are
produced.
Natural selection happens in the population which undergoes
evolutionary change.
Psychological mechanisms involving content-bearing states may
be a problem.
Indexed to the phenomenon produced
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Emission of gravitational waves versus social mechanisms.
Note decompositional not etiological explanation
NOT
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a claim about intrinsicality imported from metaphysics
a locality claim imported from physics.
5.
Modular
• Might mean different things
• One phenomenon one mechanism – implausible.
• One mechanism one phenomenon – implausible.
• One section of the mechanism can be changed with no
significant change to the rest of the mechanism.
• Comes in degrees.
• Possibly relative to a level of description in a
mechanistic hierarchy. May be modular under a narrow
range of conditions only.
• Required for success in this kind of scientific
understanding and explanation.
• Allows sections of mechanisms to be isolated and understood to
a certain extent in isolation from the other sections of the
mechanism.
Philosophical questions about
mechanisms
Methodology of science
• Explanation – how does mechanistic explanation
work, and what are the similarities and differences
in different disciplines?
• Beyond explanation – how, if at all, are
mechanisms involved in prediction and control?
• Causal inference – how do mechanisms add to
dependency relations in causal inference?
• Modularity and decomposition – how are we to
understand it? Are associated practices
analogous? For example, what is the relation
between diagrams and DAGs?
Metaphysics of science
• Causation: How are mechanisms related to
causation? Notice source of counterexamples to
theories of causation.
– Scientists see mechanistic explanation as causal
explanation. Odd if there is no relation between
mechanism and causation
– Link to causal inference.
• Active versus passive metaphysics
• Want answers to these questions that cohere with
the answers to the methodological questions.
What scientists say about their work
• ‘The main purpose of evolutionary biology is to provide a
rational explanation for the extraordinarily complex and
intricate organization of living things. To explain means to
identify a mechanism that causes evolution and to
demonstrate the consequences of its operation.’ (Bell 1997
and 2008 p1, emphasis added.)
• ‘Uncovering the cellular mechanisms resulting in
sequential transfer of information from DNA (our genes)
to RNA and then to protein represents one of major
achievements of biochemistry in the 20th century.’
(Whitford p247, emphasis added.)
Metaphysics of science
• Causation: How are mechanisms related to
causation? Notice source of counterexamples to
theories of causation.
– Scientists see mechanistic explanation as causal
explanation. Odd if there is no relation between
mechanism and causation
– Link to causal inference.
• Active versus passive metaphysics
• Want answers to these questions that cohere with
the answers to the methodological questions.
Machamer, Darden and Craver
Two senses of Explanation
1.
Epistemic: a human practice, aimed at increasing
understanding of the world. Often involves the passing
of information between people. Highly sensitive to the
cognitive abilities and background knowledge of those
improving, receiving and giving the information.
Description of mechanism does the explaining.
2. Physical: mechanisms produce or are responsible for
their phenomena. Independent of whether human beings
understand or even observe them. Mechanism itself
does the explaining.
The distinction is made in the literature (explicitly in Craver
2007). Not always carefully maintained.
MDC claim
• Machamer, Darden and Craver: ‘Mechanisms are entities and
activities organized such that they are productive of regular
changes from start or set-up to finish or termination conditions.’
(p3.)
• Entities: they list ‘cell membrane, vesicles, microtubules,
molecules, and ions.’ (p8.)
• Activities: they list ‘biosynthesis, transport, depolarization,
insertion, storage, recycling, priming, diffusion, and
modulation.’ (p8.) They add both that ‘Activities are the
producers of change,’ (p3) and that, ‘Activities are types of
causes.’ (p6.)
• Activity-Entity Dualism: They say that activities and entities
are ontologically on a par. They argue against both
substantivalists, who would reduce activity talk to talk of
entities and their properties, and process ontologists, who would
reduce entity talk to talk only of activities.
MDC issues
• The activity-entity dualism.
– Activities crucial to their conception of causation in mechanisms,
and to many other features of mechanisms.
– Activities give you the intelligibility crucial for epistemic
explanation. Note (p3) ‘Productive continuities are what make the
connections between stages intelligible.’
• Regularity:
– ‘Mechanisms are regular in that they work always or for the most
part in the same way under the same conditions. The regularity is
exhibited in the typical way that the mechanism runs from
beginning to end; what makes it regular is the productive
continuity between stages.’ (p3)
– Sometimes regularity can be described by a law, sometimes not.
– NOT mean produces phenomenon more than 50% or anything so
crude.
MDC issues
• Productive continuity
• Functional individuation:
– Note only partial.
– MDC say the function of a mechanism is its role in a higher-level
mechanism.
– Potential topping-out problem
• Change:
– homeostatic mechanisms exist to keep a system in a stable state.
• Set up and termination conditions:
– Epistemic: features of a description of a mechanism, maybe not of
the mechanism itself.
• Bottoming-out:
– Also looks epistemic.
Extra comparative stuff
Protein synthesis and natural
selection: a fair comparison
• Mechanisms and their sub-mechanisms are partially
individuated in terms of their functions.
– Protein synthesis is the mechanism for decoding DNA to produce
proteins.
– Natural selection is the mechanism for adaptation.
• Components in protein synthesis (objects, their structures,
and sub-mechanisms) are also partially functionally
individuated.
• For natural selection to be a decompositional mechanism
and yield the same kind of explanation of its phenomenon
we are looking for functionally individuated components –
NOT barely physically similar components.
Function and explanation in protein
synthesis
• ‘In addition to the promoter-like elements, the Xenopus
intergenic spacer contains repetitive short sequences, the
60/81 bp elements, that are clustered in tandem (Fig. 9.10)
and which stimulate transcription when placed at a variable
distance from the promoter and when placed in either
orientation… . They are thus analogous in their activity,
but perhaps not in their mechanism, to the enhancers of
RNA polymerase II …’ (Adams et al. p361.)
• The obsession with structure in protein synthesis exists
because in this field, structure is most often a good guide
to function.
– Note aminoacyl-tRNA synthetases example of an exception.
Protein synthesis and natural
selection: a fair comparison
• Mechanisms and their sub-mechanisms are partially
individuated in terms of their functions.
– Protein synthesis is the mechanism for decoding DNA to produce
proteins.
– Natural selection is the mechanism for adaptation.
• Components in protein synthesis (objects, their structures,
and sub-mechanisms) are also partially functionally
individuated.
• For natural selection to be a decompositional mechanism
and yield the same kind of explanation of its phenomenon
we are looking for functionally individuated components –
NOT barely physically similar components.
The components of natural selection
are also functionally individuated
• First division: directional selection, stabilizing selection,
disruptive selection.
• Second division in directional selection: sorting,
recombination, both sorting and recombination.
• Third division in recombination: structure of DNA and
morphogenesis crucial. Consider gene linkage, epistasis
and pleiotropy.
• Dozens of well-understood sub-mechanisms in the field.
• Population structure the kind of structure functionally
relevant in this field.
• At its lowest levels, evolutionary biology collides with
biochemistry in, for example, meiosis or autoselection.