The Thermosynthesis Home Page 
Describes and explains a theory that shows how organisms can use or may have used thermal cycling as an energy source, for example in volcanic hot springs, as an evolutionary step towards photosynthesis.
http://www.geocities.com/ResearchTriangle/Node/5345/Farside Research Institute 
The evolution group of the Institute of Molecular BioSciences at Massey University, Palmerston North, New Zealand.
http://imbs.massey.ac.nz/Research/MolEvol/Farside/welcome.htm
How molecular biology opens up a 21st Century view of evolution 
Transcript of chat with biochemist James Shapiro of the University of Chicago on his concept of "natural genetic engineering" at the cellular level.
http://www.iscid.org/james-shapiro-chat.php
Betran's Lab 
Research and publications on the origin of new genes, new functions, and their role in genome evolution, adaptation, and species differences.
http://www3.uta.edu/faculty/betran/
Symmetry-breaking and Molecular Evolution 
Explores the structural relationship between cosmological symmetry-breaking and the form of molecular evolution leading to biological systems on Earth. It thus forms an alternative to historical hypotheses in which the form of biogenesis is believed to be the product of a linked sequence of specific conditions, bridged by stochastic selection processes.
http://www.dhushara.com/book/biocos/symevol.htm
Szostak Laboratory 
Details work exploring the evolution of novel ribozymes (deoxyribo and ribonucleic acid catalysts) from populations of random sequences, attempting to shed light on the origins of biological catalysis.
http://genetics.mgh.harvard.edu/szostakweb/
ExPASy Life Science Directory 
Part of the ExPASy Molecular Biology Server, this extensive list includes almost exclusively pointers to information sources for life scientists with an interest in biological macromolecules.
http://www.expasy.org/links.html
Molecular Phylogenetics and Evolution 
Journal is dedicated to bringing Darwin's dream-to "have fairly true genealogical trees of each great kingdom of Nature"-within grasp. Provides a forum for molecular studies that advance the understanding of phylogeny and evolution.
http://www.elsevier.com/wps/find/journaldescription.cws_home/622921/description