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Recommended books:

 

Sean B. Carroll

The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution. 2006. W. W. Norton
  Kenneth R. Miller

Finding Darwin’s God, A Scientist’s Search for Common Ground Between God and Evolution.  1999.  Harper Collins.

 
Carl Zimmer
At the Water’s Edge, Macroevolution and the Transformation of Life.  1998.  Simon and Schuster, Inc.
  Sean B. Carroll Endless Forms Most Beautiful : The New Science of Evo Devo.  2005.  W.W. Norton.
  Andrew H. Knoll Life on a Young Planet, The First Three Billion Years of Evolution on Earth.  2003.  Princeton University Press.

 

Recommended websites:

HHMI Holiday Lectures On Science, "Evolution: Constant Change and Common Threads"

Phil Gingerich: Research on the Origin and Early Evolution of Whales (Cetacea)

Paleomap Project

Radiometric Dating

Natural History Magazine, November 2005: Darwin & Evolution
(go to: online extras, website archive, Nov. 2005 Darwin and Evolution)

Evolutionary Biology at the University of Wisconsin-Madison

Was Darwin Wrong? (National Geographic Magazine)

Understanding Evolution (The University of California Museum of Paleontology)

The Clergy Letter Project

National Center for Science Education: Statements from Religious Organizations

Evolution Resources (Kenneth R. Miller)

The Great Story