Lindley Darden uses cases from the history of biology to 
address questions in philosophy of science, especially reasoning
in discovery. 

Her current research is on reasoning strategies in molecular
biology, especially reasoning in anomaly resolution with a 
focus on purported anomalies for the central dogma of molecular
biology (DNA-->RNA--protein), such as adaptive mutation.

Also she is analyzing the concept of mechanism in molecular biology.


Research proposal
July, 1998
The Discovery of Mechanisms in Molecular Biology
Lindley Darden

Mechanisms are what is discovered in much of science, especially in 
molecular biology.  This work proposes a new analysis of the concept
of a mechanism, which includes the activities of mechanisms, as well  
as their component parts. Types of activities important in molecular  
biology are geometrico-mechanical, e.g. an inducer fitting into a  
groove of a repressor protein and changing its shape; electro- 
chemical, such as covalent bonding between amino acids or hydrogen  
bonding between nuclei acid bases; and energetic, such as active  
consumption of ATP or passive diffusion across a membrane.  When  
mechanisms are proposed, the scientist must specify the activities, as  
well as the components parts, the set-up conditions, a continuous  
transition of steps, and the termination conditions, such as the  
production of a product.



Questions to be addressed are the following: How are mechanisms  
represented?  How are mechanisms discovered, evaluated, and revised?  
What reasoning strategies are sufficient for mechanism discovery, 
evaluation, and revision?  What experimental strategies are used for 
testing hypothesized mechanisms?



The primary case study to be examined is the mechanism of protein 
synthesis represented by the "central dogma" of molecular biology in 
the period from 1953 until about 1970 (plus some anomalies still 
problematic).  The mechanism’s historical development through cycles 
of discovery, evaluation, and revision illustrates the process of 
anomaly-driven mechanism redesign, one of several important reasoning 
processes in contemporary molecular biology.

A paper on the discovery of the mechanism of protein synthesis, 
written with Carl Craver, will appear in 
Studies in the History and Philosophy of 
Biological and Biomedical Sciences. 



This work thus contributes to questions in philosophy of science 
about the nature of theory structure in molecular biology--a set of 
mechanisms-- and the reasoning in scientific change--reasoning 
strategies for discovering, evaluating, and improving mechanisms.