From 1998-2009 I functioned primarily as an individual scientific researcher using computers to study the evolutionary origins of the central dogma of molecular biology. This work continues through a focus to explore alternatives to the "alphabet" of 20 amino acids with which genetic material evolved to encode proteins, early in our planet's history. Current projects include chemical library construction and analysis, Ramachandran plots for oligopeptides composed of xeno amino acids, and 3D printing xeno amino acids.
Since 2009 I have directed increasing effort towards supporting and developing team-based academic projects and programs fcoused on wider questions of astrobiology andabiogenesis
Abiogenesis: Evolutionary chemical informatics, specifically generating and analyzing amino acid structures beyond those known to biology.
Synthetic biology: Creating informatics tools to collate and analyze the mushrooming world of non-coded amino acids that experimentalists ("wet lab" researchers) have already incorporated into protein synthesis.
Broader active interests are the evolution of fundamental biochemistry, astrobiology, abiogenesis and biosignatures.
INDS core courses, FYE101
BIOL770: Amino Acid Alphabet Evolution
Mayer-Bacon, Christopher, Freeland, Stephen. (2021). A broader context for understanding amino acid alphabet optimality. 520 110661 Journal of Theoretical Biology.
Boring, Emily, Stump, JB, Freeland, Stephen. (2020). Rethinking Abiogenesis: Part 1, Continuity of Life through Time.. 1. 72 Perspectives on Science \& Christian Faith.
Jarzynski, Mark, Engel, Donald, Freeland, Stephen, Boot, Lee R., Murnane, Mark, Lindvig, Katrine, Hillersdal, Line, Earle, David. (2020). Extending CoNavigator into a Collaborative Digital Space. Companion of the 2020 ACM International Conference on Supporting Group Work 127-013 New York, NY: Association for Computing Machinery.
Ilardo, Melissa, Bose, Rudrarup, Meringer, Markus, Rasulev, Bakhtiyor, Grefenstette, Natalie, Stephenson, James, Freeland, Stephen, Gillams, Richard J., Butch, Christopher J., Cleaves, H James. (2019). Adaptive properties of the genetically encoded amino acid alphabet are inherited from its subsets. 1. 9 1--9 Scientific reports.
Ilardo, Melissa, Meringer, Markus, Freeland, Stephen, Rasulev, Bakhtiyor, Cleaves, II, H James. (2015). Extraordinarily adaptive properties of the genetically encoded amino acids. 1. 5 1--6 Scientific reports.
Ilardo, Melissa A., Freeland, Stephen. (2014). Testing for adaptive signatures of amino acid alphabet evolution using chemistry space. 1. 5 1--9 Journal of Systems Chemistry.
Meringer, Markus, Cleaves, H James., Freeland, Stephen. (2013). Beyond terrestrial biology: Charting the chemical universe of $\alpha$-amino acid structures. 11. 53 2851--2862 Journal of chemical information and modeling.
Stephenson, James D., Freeland, Stephen. (2013). Unearthing the root of amino acid similarity. 4. 77 159--169 Journal of molecular evolution.
Philip, Gayle K., Freeland, Stephen. (2011). Did evolution select a nonrandom “alphabet” of amino acids?. 3. 11 235--240 Astrobiology.
Freeland, Stephen. (2009). “Terrestrial” amino acids and their evolution. 1 43--75 Amino Acids, Peptides and Proteins in Organic Chemistry: Origins and Synthesis of Amino Acids.
Lu, Yi, Freeland, Stephen. (2008). A quantitative investigation of the chemical space surrounding amino acid alphabet formation. 2. 250 349--361 Journal of theoretical biology.
Freeland, Stephen. (2008). Could an intelligent alien predict earth’s biochemistry?. 280 Biochemistry and Fine-Tuning.
Barrow, John D., Morris, Simon Conway., Freeland, Stephen, Harper, Jr, Charles L. (2008). Fitness of the cosmos for life. Biochemistry and fine tuning. Cambridge U. Press.
Lu, Yi, Freeland, Stephen. (2006). On the evolution of the standard amino-acid alphabet. 1. 7 1--6 Genome biology.
Lu, Yi, Freeland, Stephen. (2006). Testing the potential for computational chemistry to quantify biophysical properties of the non-proteinaceous amino acids. 4. 6 606--624 Astrobiology.
Zhu, Wen, Freeland, Stephen. (2006). The standard genetic code enhances adaptive evolution of proteins. 1. 239 63--70 Journal of theoretical biology.
Wu, Gang, Wolf, Julie B., Ibrahim, Ameer F., Vadasz, Stephanie, Gunasinghe, Muditha, Freeland, Stephen. (2006). Simplified gene synthesis: a one-step approach to PCR-based gene construction. 3. 124 496--503 Journal of biotechnology.
Knight, Rob D., Freeland, Stephen, Landweber, Laura F. (2004). Adaptive evolution of the genetic code. The genetic code and the origin of life 201--220 Springer.
Freeland, Stephen, Hurst, Laurence D. (2004). Evolution encoded. 4. 290 84--91 Scientific American.
Freeland, Stephen, Wu, Tao, Keulmann, Nick. (2003). The case for an error minimizing standard genetic code. 4. 33 457--477 Origins of Life and Evolution of the Biosphere.
Freeland, Stephen. (2003). Three fundamentals of the biological genetic algorithm. Genetic programming theory and practice 303--311 Springer.
Freeland, Stephen. (2002). The Darwinian genetic code: an adaptation for adapting?. 2. 3 113--127 Genetic Programming and Evolvable Machines.
Knight, Robin D., Freeland, Stephen, Landweber, Laura F. (2001). Rewiring the keyboard: evolvability of the genetic code. 1. 2 49--58 Nature Reviews Genetics.
Freeland, Stephen, Knight, Robin D., Landweber, Laura F. (1999). Do proteins predate DNA?. 5440. 286 690--692 Science.
Knight, Robin D., Freeland, Stephen, Landweber, Laura F. (1999). Selection, history and chemistry: the three faces of the genetic code. 6. 24 241--247 Trends in biochemical sciences.
Freeland, Stephen, Hurst, Laurence D. (1998). The genetic code is one in a million. 3. 47 238--248 Journal of molecular evolution.
Freeland, Stephen, McCABE, BRIDGET K. (1997). Fitness compensation and the evolution of selfish cytoplasmic elements. 4. 78 391--402 Heredity.