This list is not intended to cover absolutely all the tools one brings to bear on solving scientific problems; you may wish to add your own.

1. The Experimental Method
   We discussed this method last lecture.

form an hypothesis	devise an experiment
perform and analyze experiment	interpret results of experiment
refine hypothesis, devise further experiments	develop theories, synthesizing several results

In what sense is the experimental method a tool?
   This entire approach to understanding nature is a way of operating;
it channels our thoughts in particular directions.
  When all you have is a hammer, everything looks like a nail.

2. Apparatus
Excludes experimental samples themselves:
  the latter are the elements of nature that we are studying, not the equipment.
General-purpose vs. special-purpose apparatus:
• General-purpose apparatus provide for numerous experiments.
• Special-purpose apparatus provides for one or a few experiments.

Example from protein crystallography:

• General-purpose: X-ray generator, monochromator, goniostat, detector
• Special-purpose: laser for initiating chemical change; high-pressure cell.

Must we understand the internals of our apparatus in order to use it?
Not necessarily, but it helps, especially with special-purpose equipment.
Sociological difference between physicists and biologists:

1. physicists tend to be "at home" with their apparatus, having designed it themselves;
2. biologists tend to treat their apparatus as black boxes.
3. chemists are intermediate between these extremes.
   
   
3. Mathematics
The language of science, as we said last lecture.
Almost any scientific endeavor uses arithmetic and statistics.
Many use much more sophisticated branches of mathematics--
    Fourier analysis, group theory, partial differential equations, fractals, . . .
Statistics: multiple observations, significance levels
   provides tool to assess correlations among variables.
Recurrent danger: biasing the results toward the model:
  Example from protein crystallography: structure refinement
It can take some very sophisticated tools to escape this problem!
 
4. Computers
We limped along without them until fifty years ago.
[Speed, Flexibility](palmtop,2000) > [Speed, Flexibility](mainframe,1966)

Survey of scientific applications, based on history:

repetitive high-speed arithmetic	FORmula TRANslation
instrument control	word processing
record-keeping ("electronic notebooks")	graphics: representation and analysis
simulation (in silico experiments)	algorithmic algebra (Mathematica, etc.)
communications	access to information repositories (see below)

Dangers of using computers in science

• they can make it easier to get results without understanding
• can invest bogus ideas with undeserved air of authority
  
  
5. Information Repositories
If I had written this lecture seven yours ago I would have headed this "libraries".
Now: libraries, Internet, publicly available databases
How to make the most of these?
• Gee-whiz factor goes up the more modern the repository is.
• It takes some practice to learn how to ask the right questions.
• Some of the Websites help you do that, though.


6. Intuition
This is usually developed from experience: previous similar phenomena; patterns
 
7. Peer Interactions
Simple: face-to-face conversations, phone calls, e-mail
More organized: bulletin boards, Web, previewing manuscripts,
   scientific meetings, scientific societies
true peer review of manuscripts and proposals
How do these help the science you're doing?

generates new ideas	pokes holes in your bad ideas
puts your experiments in a wider context	helps you find procedural tricks
source of free or near-free software, equipment, etc.	starts or maintains funding