Can new genetic information and complexity evolve by known biological mechanisms? Yes.
The combination of random mutation plus non-random natural selection leads to the evolution (or creation if you will) of new genetic information and complexity. Random mutation creates genetic variation; natural selection sorts out those genotypes that are best adapted to the environment. Here are some theoretical models on how this might happen, which are based on natural genetic systems:
Christoph Adami, Charles Ofria, and Travis C. Collier 2000. Evolution of biological complexity. Proc. Natl. Acad. Sci. USA, Vol. 97, Issue 9, 4463-4468, April 25, 2000 (link)
Lenski RE, Ofria C, Collier TC, Adami C 1999. Genome complexity, robustness and genetic interactions in digital organisms. Nature 1999 Aug 12;400(6745):661-4 (link)
T. D. Schneider, "Evolution of Biological Information", Nucleic Acids Research, 28(14): 2794-2799, 2000 (link)
Allan Force, Michael Lynch, F. Bryan Pickett, Angel Amores, Yi-lin Yan, and John Postlethwait 1999. Preservation of Duplicate Genes by Complementary, Degenerative Mutations. Genetics, Vol. 151, 1531-1545, April 1999, Copyright © 1999 (link)
Michael Lynch and Allan Force 2000. The Probability of Duplicate Gene Preservation by Subfunctionalization. Genetics, Vol. 154, 459-473, January 2000, Copyright © 2000 (link)
Michael Lynch 2002. Intron evolution as a population-genetic process. Proc. Natl. Acad. Sci. USA, Vol. 99, Issue 9, 6118-6123, April 30, 2002. (Abstract)
Here are two applications of Darwinian evolution to industrial design, using random mutation plus non-random natural selection. The biotech industry uses directed evolution to design new molecules. Engineers use genetic algorithms to design everything from airplane wings to traffic flow patterns. We've empirically seen the underlying genetic mechanisms work in natural biological systems.
Beneficial Mutations:
Michelle M. Riehle, Albert F. Bennett, and Anthony D. Long 2001. Genetic architecture of thermal adaptation in Escherichia coli. Proc. Natl. Acad. Sci. USA, Vol. 98, Issue 2, 525-530 (link)
Olah B, Kiss E, Gyorgypal Z, Borzi J, Cinege G, Csanadi G, Batut J, Kondorosi A, Dusha I. 2001. Mutation in the ntrR gene, a member of the vap gene family, increases the symbiotic efficiency of Sinorhizobium meliloti. Mol Plant Microbe Interact 2001 Jul;14(7):887-94 (link)
Marianne Imhof and Christian Schlötterer 2001. Fitness effects of advantageous mutations in evolving Escherichia coli populations. Proc. Natl. Acad. Sci. USA, Vol. 98, Issue 3, 1113-1117 (link)
J. J. Bull, M. R. Badgett, and H. A. Wichman 2000. Big-Benefit Mutations in a Bacteriophage Inhibited with Heat. Molecular Biology and Evolution 17:942-950 (link).
H. A. Wichman, M. R. Badgett, L. A. Scott, C. M. Boulianne, J. J. Bull 1999. Different Trajectories of Parallel Evolution During Viral Adaptation. Science 285, 422-424 (link).Evolution of genetic information:
Susanna K. Remold and Richard E. Lenski 2001. Contribution of individual random mutations to genotype-by-environment interactions in Escherichia coli. Proc. Natl. Acad. Sci. USA, Vol. 98, Issue 20, 11388-11393, September 25, 2001 (link)
Papadopoulos D, Schneider D, Meier-Eiss J, Arber W, Lenski RE, Blot M 1999. Genomic evolution during a 10,000-generation experiment with bacteria. Proc Natl Acad Sci U S A 1999 Mar 30;96(7):3807-12 (link)
Hall BG, Malik HS. 1998. Determining the evolutionary potential of a gene. Mol Biol Evol 1998 Aug;15(8):1055-1061 (link)
Hall BG. 2001. Predicting Evolutionary Potential. I. Predicting the Evolution of a Lactose-PTS System in Escherichia coli. Mol Biol Evol 2001 Jul;18(7):1389-1400 (link)Speciation:
Vulic M, Lenski RE, Radman M 1999. Mutation, recombination, and incipient speciation of bacteria in the laboratory. Proc Natl Acad Sci U S A 1999 Jun 22;96(13):7348-51 (link)
Back to biological complexity. We're still piecing the parts of the puzzle together. Historical geology tells us that large scale evolutionary change (aka macroevolution) takes long periods of time, millions of years and longer; molecular genetics tells us the same thing (e.g. see 29 Evidences for Macroevolution ). Recent studies suggest that episodes of macroevolution were preceded by episodes of gene, chromosome, or whole genome duplication, which were subsequently followed by the evolution of new regulatory gene functions and pathways. Check out the University of Oregon and Indiana University's EvoDevo website for their NSF-IGERT training grant, Evolution, Development, and Genomics, and the links on their research page, for descriptions of some of the latest research in this area.
A recent book that's accessible to people with some background in biology is...
S Carroll, J Grenier, S Weatherbee 2001. From DNA to Diversity: Molecular genetics and the evolution of animal design. Blackwell Science, 232pp. (link)
The senior author is the president of the Society for Developmental Biology. Here's his website http://www.molbio.wisc.edu/carroll/
http://www.its.caltech.edu/~mirsky/index.htm