Courses

• BIO 111 - Molecules, Genes, & Cells (Spr. 08)
• BIO 309 - Genomics, Proteomics, & Systems Biology (Fall 07)
• BIO 111 - Molecules, Genes, & Cells (Spr. 07) Guest Lecture

Research

Synthetic Biology is a blossoming field with plenty of room on the cutting edge for exploratory research. Currently at Davidson College, I am working with professors A. Malcolm Campbell (Biology Dept.) and Laurie Heyer (Math Dept.) and undergraduates involved in independent research to develop computational systems in E. coli, or "living hardware."

Using BioBricks interchangeable parts and the Hin/hix recombination system from Salmonella typhimurium, we have engineered a system where tandem fragments of DNA are rearranged by inversions to generate different permutations. As a proof of concept for DNA computing in vivo, we have developed a DNA representation of the "Burnt Pancake Problem" to be solved by random reversals in vivo (see the Davidson 2006 iGEM Team page for details). Further development of the modified Hin/hix inversion system is underway to tackle the NP-complete Hamiltonian Path problem.

Web Presentations

• Creating Living Hardware Using Synthetic Biology - presented at Florida A&M University, April 2007

International Genetically Engineered Machines Competition (iGEM)

• Davidson/ MO Western 2007 iGEM Team
• Davidson/ MO Western 2006 iGEM Team

Publications

• Haynes KA, Broderick ML, Brown AD, Butner TL, Dickson JO, Harden L, Heard LH, Jessen EL, Malloy KJ, Ogden BJ, Rosemond S, Simpson S, Zwack E, Campbell M, Eckdahl TT, Heyer LJ, Poet JL. (2008) Engineering bacteria to solve the Burnt Pancake Problem. J Biol Eng. 2:8. [Epub ahead of print]
• Haynes, K.A., Broderick, M.L., Brown, A.D., Butner, T.L., Harden, L., Heard, L., Jessen, E., Malloy, K., Ogden, B., Rosemond, S., Simpson, S., Zwack, E., Campbell, A.M., Eckdahl, T., Heyer, L.J., Poet, J. (2007). Computing With Living Hardware. IET Synth. Biol. 1: 44-47.

Teaching

Fields that involve DNA manipulation technology present tremendous opportunities to train future researchers. In addition to investigating synthetic biology in the lab, I have designed an advanced level undergraduate lecture/lab course based upon a Genomics course originated by Dr. A. Malcolm Campbell. Genomics, Proteomics, and Systems Biology uses an inquiry based approach to familiarize students with key concepts in Genomics research and gives students hands-on experience in gene annotation and microarray data analysis. The Fall 2007 students created web pages that summarize their investigations of human genetic diseases.

Teaching Affiliations

• Genomics Consortium for Active Teaching (GCAT)

News

• 6/02/08, MSNBC.com: Living computers solve complex math puzzle, by Bryn Nelson
• 5/30/08, Scientific American: DNA Computer Puts Microbes to Work as Number Crunchers, by Nikhil Swaminathan
• 5/28/08, Discovery News: Bacteria-Run Computer Solves Math Puzzle, by Eric Bland
• 5/23/08, Radio Interview: NPR Science Friday with Ira Flatow, guest Karmella Haynes: Calculating Bacteria: Real Computer Bugs? (Click here to listen)
• 5/23/08, Nanowerk News: Living computer solves Burnt Pancake Problem
• 5/23/08, Technological Innovation (Brazil): "Living Computer" is built with genetically modified bacteria
• 5/22/08, Davidson College News: "Science Friday" and Other Media Plan Stories on "Bio Computer" Research, by Bill Giduz
• 5/21/08, Science Daily: New Meaning For The Term 'Computer Bug': Genetically Altered Bacteria For Data Storage
• 5/21/08, Sott.net: New Meaning For The Term 'Computer Bug': Genetically Altered Bacteria For Data Storage
• 5/21/08, iTnews (Australia): Living computers best left Open Source, researcher says, by Liz Tay
• 5/21/08, Fabrica de bani (Romania): Computer din bacterii
• 5/20/08, Telegraph (UK): Bacteria can be turned into living computers, by Roger Highfield
• 5/21/08, Fabrica de bani (Romania): Computer din bacterii
• 5/20/08, Yahoo News (India): Scientists create 'living computers' by genetically altering E. coli bacteria
• 5/20/08, Gizmag: First living computer used for flipping pancakes
• 5/20/08, e! Science News: Researchers bring new meaning to the term 'computer bug'
• 5/20/08, Physorg.com: Researchers bring new meaning to the term 'computer bug'
• 5/20/08, news.SmasHits.com: Scientists create 'living computers' by genetically altering E. coli bacteria
• 5/20/08, Khabar Express (India): Scientists create 'living computers' by genetically altering E. coli bacteria
• 5/20/08, Daily India (India): Scientists create 'living computers' by genetically altering E. coli bacteria
• 5/20/08, Medical News Today: 'Living Computers' Created Using Genetically Altered Bacteria
• 5/20/08, Daily Science News: Researchers bring new meaning to the term 'computer bug'
• 5/20/08, Shakhty.com (Former USSR): Computer bacteria
• 5/20/08, Top News (India): Scientists create ‘living computers’ by genetically altering E. coli bacteria, by Sahil Nagpal
• 5/20/08, Genome Technology Online: There's Supposed to Be a Bug in the System
• 5/20/08, Lenta (Russia): Computer bacteria
• 5/19/08, Science News: I, Computer: Engineered bacteria become the first living computers, by Patrick Barry
• 5/19/08, Bio-Medicine: Researchers bring new meaning to the term 'computer bug'
• 5/19/08, GEN Genetic Engineering & Biotechnology News: Researchers bring new meaning to the term 'computer bug'
• 5/19/08, FirstScience News: Researchers bring new meaning to the term 'computer bug'
• 12/04/07, Davidson College News: Davidson's Bacterial Computer Win Gold in Synthetic Bio Competition
• 10/2007, Nature: Teacher's Group Brings Genomics Revolution to Minority Colleges (download pdf), by Erika Check
• 5/2007, HHMI Bulletin: Judges Flip for Bacterial Computer (download pdf), by Dennis Meredith
• 11/03/06, Davidson College News: Research Team Scores Big for Bio-Computer..., by Adam Martin

Miscellaneous

• Moving sale - ends June 26th
• Orisha Folklorico @ Davidson College 2008
• My Artwork