Perfumer and Flavorist: Biological Scent Design
Lucky Peach: Eating For Two
MoMA Design and Violence Project: Synthetic PhiX174 Bacteriophage
The New Inquiry: Osmic Frequencies
The Toast: Gal Science: How Nail Polish Works
LadyBits on PopSci: The Forgotten Woman Who Made Microbiology Possible
Blueprints for the Unknown: Synthetic Biology as Collective Fantasy
Rather than asking if synthetic biology will save the world or destroy it, perhaps it's more useful to start with a much simpler question: does synthetic biology actually exist?
The Toast: Wolabachia, the misandrist bacteria
Symbiosis and the evolution of 100% female societies (in wasps).
Superflux Blog: DNA Stories
What if personalized medicine happens? Thinking about the future of our DNA dreams.
Omni Reboot: Edible Memories
Can you eat a memory? We take a peek into a long-forgotten controversy from the strange annals of biological psychology.
Lucky Peach 13:
Huge for the Holidays
Between "full" and reflexive vomiting — the body's final defensive strategy for overfullness — there is a lot of room for holiday overeating. Full text on PopSci.
In Vitro Meat Cookbook: Essay — Growing the Future of Meat
Advocates of in vitro meat—and perhaps readers of this essay—may see in my criticism a wish to
return to nature, to reverse technological progress and throw us all into a life of agrarian serfdom. But a critique of this particular technology is not the same as arguing against all technology. Seeing criticism of in vitro meat as anti-technology relies on the assumption that technology is only one thing, that it has a singular path, and that in vitro meat is already inevitable. This kind of argument is intended to shut down reasoned debate, closing off discussion of how technologies come into existence and work in the real world in favor of a blind faith that in the future, we will inevitably control
all the variables.
Synthetic Aesthetics: Investigating Synthetic Biology's Designs on Nature: Chapter — The Inside-out Body
We collected microbes from our own skin, rubbing cotton swabs over our hands and in between our toes, in our armpits and inside our noses. Each swab was put into a small jar of organic pasteurized whole milk and warmed overnight. In the morning, the acids produced by the microbes had done their work. We could strain the curds away from the whey, making a series of small cheeses. These cheeses were of course not the aged masterpieces of artisan cheesemakers, but microbial sketches, capturing some of the ecological diversity of different bodies and different body parts, bringing to the foreground the living odors of the body.
Synberc Blog: The Structure of Industrial Revolutions
The Book of Invisible Life: Lactobacillus
Arc 1.3: Afterparty Overdrive: Fun and Games in the Garden
Industrialised biotechnology offers us commoditised biology, simplified and sterilised, hidden in vats pumping out
medicines and fuels. In food and agriculture, biotechnology leaves us with just a handful of species that we then
process into the thousands of products you can find at the supermarket. But food is not just fuel; it’s life, cuisine, and culture. Our bodies aren’t machines; they are complex biological systems, assemblages of human and microbial cells that grow and change. The genomes of the human ecosystem can be read and perhaps even rewritten, but they will still respond to our environment, to our food, to our culture,
in varied and beautiful ways.
Six Parties Symposium on Synthetic Biology Travel Fellowship Essay:
The Crux, Discover Magazine Blogs:
Intellectuals in their self-flattering wish-fulfillment say that knowledge
is power, but the truth is that knowledge further empowers only those who have or
can acquire the power to use it.
De Meyer SE, Briscoe L, Martinez-Hidalgo P, Agapakis C, Estrada de Los Santos P, Seshadri R, Reeve W, Weinstock G, O'Hara G, Howieson J, Hirsch AM. “Symbiotic Burkholderia species show diverse arrangements of nif/fix and nod genes, and lack typical high affinity cytochrome cbb3 oxidase genes.” Molecular Plant Microbe Interactions, 2016.
Angus AA, Agapakis CM, Fong S, Yerrapragada S, Estrada-de los Santos P, Yang P, Song N, Kano S, Caballero-Mellado J, de Faria SM, Dakora FD, Weinstock G, and Hirsch AM. "Plant-Associated Symbiotic Burkholderia Species Lack Hallmark Strategies Required in Mammalian Pathogenesis." PLOS ONE, 2014, 9(1), e83779.
Kaplan D, Maymon M, Agapakis CM, Lee A, Wang A, Prigge BA, Volkogon M, and Hirsch AM. “A Survey of the Microbial Community in the Rhizosphere of Two Dominant Shrubs of the Negev Desert Highlands, Zygophyllum dumosum Boiss. and Atriplex halimus, Using Cultivation-Dependent and -Independent Methods.” American Journal of Botany. 2013, 100(9).
Boyle PM, Burrill DR, Inniss MC, Agapakis CM, Deardon A, DeWerd JG, Gedeon MA, Quinn JY, Paull ML, Raman AM, Theilmann MR, Wang L, Winn JC, Medvedik O, Schellenberg K, Haynes KA, Viel A, Brenner TJ, Church GM, Shah JV, and Silver PA. "A BioBrick Compatible Strategy for Genetic Modification of Plants." Journal of Biological Engineering, 2012, 6:8.
Agapakis CM, Niederholtmeyer H, Noche RR, Lieberman TD, Megason SG, Way JC, and Silver PA.
Towards a Synthetic Chloroplast. PLoS ONE, 2011, 6(4): e18877.
Barstow B, Agapakis CM, Boyle PM, Grandl G, Silver PA, and Wintermute EH. "A synthetic system links FeFe-hydrogenases to essential E. coli sulfur metabolism." Journal of Biological Engineering, 2011, 5:7.
Agapakis CM, Ducat DC, Boyle PM, Wintermute EH, Way JC, and Silver PA.
Insulation of a Synthetic Hydrogen Metabolism Circuit in Bacteria. Journal of Biological Engineering, 2010, 4:3.
*JBE most highly accessed article of 2010
Florez JC, Sjögren M, Agapakis CM, Burtt NP, Almgren P, Lindblad U, Berglund G, Tuomi T, Gaudet D, Daly MJ, Ardlie KG, Hirschhorn JN, Altshuler D, Groop L.
Association testing of common variants in the insulin receptor substrate-1 gene (1RS1) with type 2 diabetes. Diabetologia. 2007, 50(6): 1209-17.
Hines J, Roy M, Cheng H, Agapakis CM, Taylor R, Crews CM.
Myriaporone ¾ structure- activity relationship studies define a pharmacophore targeting eukaryotic protein synthesis. Molecular BioSystems. 2006, 2: 371-9.
Florez JC, Wiltshire S, Agapakis CM, Burtt NP, de Bakker PIW, Almgren P, Boström KB, Tuomi T, Gaudet D, Daly MJ, Hirschhorn JN, McCarthy MI, Altshuler D, Groop L.
High-density haplotype structure and association testing of the insulin-degrading enzyme (IDE) gene with type 2 diabetes in 4,206 people. Diabetes. 2006, 55(1): 128-35.
Florez JC, Agapakis CM, Burtt NP, Sun M, Almgren P, Rastam L, Tuomi T, Gaudet D, Hudson TJ, Daly MJ, Ardlie KG, Hirschhorn JN, Groop L, Altshuler D.
Association Testing of the Protein Tyrosine Phosphatease IB Gene (PTPN1) With Type 2 Diabetes in 7,883 People. Diabetes. 2005, 54(6): 1884-9.
Videlock EJ, Chung VK, Hall JM, Hines J, Agapakis CM, Austin DJ.
Identification of a Molecular Recognition Role for the Activation Loop Phosphotyroside of the Src Tyrosine Kinase. Journal of the American Chemical Society. 2005, 127(6): 1600-1.
Reviews & Viewpoints
Agapakis CM. "Designing Synthetic Biology." ACS Synthetic Biology, 2013, DOI: 10.1021/sb4001068.
Agapakis CM and Tolaas S. "Smelling in Multiple Dimensions." Current Opinion in Chemical Biology (special issue on Aesthetics), 2012, 16(5-6): 569-575.
Agapakis CM, Boyle PM, and Silver PA. "Natural Strategies for the Spatial Optimization of Metabolism in Synthetic Biology." Nature Chemical Biology, 2012, 8(6): 527-535.
Agapakis CM and Silver PA.
Modular Electron Transfer Circuits for Synthetic Biology: Insulation of an Engineered Biohydrogen Pathway. Bioengineered Bugs, 2010, 1:6.
Agapakis CM and Silver PA.
Synthetic Biology: Exploring and Exploiting Biological Modularity Through the Design of Novel Biological Networks. Molecular BioSystems, 2009, 5: 704-13.
Walker, R., Agapakis CM, Watkin E, and Hirsch AM. (2015) Symbiotic nitrogen fixation in legumes: perspectives on the diversity and evolution of nodulation by Rhizobium and Burkholderia species. In: Biological Nitrogen Fixation, Volume 2. F.J. deBrujjn, (ed.). John Wiley & Sons.
Agapakis CM and Tolaas S. (2014) The Inside-Out Body. In A. D. Ginsberg, J. Calvert, P. Schyfter, A. Elfick, and D. Endy (Eds.), Synthetic Aesthetics: Investigating Synthetic Biology's Designs on Nature (pp. 255-266). The MIT Press.