Week Three: Synthetic Biology
Fall 2015 | Wing Dyana So | Visual Studies C'16
Synthetic biology is the engineering of living cells to do something useful. This process was made possible thanks to the advancement of technology and breakthrough science research on DNA, which has enhanced our understanding of the fundamental ‘machinery’ that operates within all living species -- from bacteria to human -- on a cellular level.
Synthetic biology created and added another language to talk about and understand life. Improved scientific knowledge about genes and microbiological processes brings us to a present day, where it is more important now than ever before, to understand the relationship between how life works, and what we can (and should) do about this knowledge.
For designers, literacy in synthetic biology has much potential in not only expanding and critically qualifying this emerging field and practice, but also bringing such products, concepts, and ideas consciously into society.
This week, our class defined synthetic biology, and how it configured within the design discourse through discussion and hands-on practice. On Monday, we walked through synthetic biology’s timeline of development, and touched upon the ethics of the practice with the help of Alexandra Daisy Ginsberg’s chapter on “Design as the Machines Come to Life” in Synthetic Aesthetics. By the end of Wednesday's class, everyone in class put a sequence of bacterial DNA together.
Synthetic Biology and Design: Bio-Building
Our class organized our understanding of synthetic biology into three categories: genes, model organisms, and standardization.
Deoxyribonucleic acid, or DNA, is the fundamental, biological ‘data’ that makes up all life on Earth. It is found within cells, specifically within the nucleus of eukaryotic cells (prokaryotic cells do not have a nucleus). Visually, DNA is a double-stranded helix comprised of nucleotides, and its unwinding and re-winding makes them functional in transferring its information for replication or gene expression. This information comes in the form of the aforementioned nucleotides, a specific ‘alphabet’ of A, T, C and G (U is introduced when RNA gets involved in the transcription phase of gene expression).
This data of DNA contains many meanings. Certain parts of this code stand for genes, or specific traits of an organism. We can see some of these genes through the phenotype expressed the outside of an organism, such as eye color or the average plant height of Mendel’s pea plants.
Upon learning about DNA and realizing the extensive library of genetic information that’s there, technological advancements like DNA sequencing, has led to the development of a formal archive of specific genetic sequences attributed to specific traits. This database is significant to synthetic biologists because it is the basis of what they use to synthesize products out of this universal genetic language.
To make the DNA database practical, synthetic biologists adopted the engineering principle of ‘standardization’ to define a comprehensible and reusable ‘toolkit’ to simplify the DNA construction process. Genes were standardized into carriers called ‘bio-bricks’, which are pieced together to construct a DNA sequence, initiated by a 'prefix' and ending with a 'suffix'. This standardization model was built from the logic of computer programming, and it is essentially like building comprehensive sentences in formal linguistics -- using one's understanding of grammatical structure and parts of speech to develop coherent sentences.
The chart on the right, taken from the "Fundamentals of Synthetic Biology" chapter in The Synthetic Biology Toolkit by BioBuilder, highlights the three "most crucial and well-established techniques" (9) used by synthetic biologists:
- DNA sequencing technology - Using chain-termination chemistry technology to determine the nucleotide patterns within a long DNA strand. This method was developed by Dr. Frederick Sanger and Dr. Walter Gilbert in 1977.
- Polymerase Chain Reaction (PCR) - Using primers, polymerases, free nucleotides, buffers, and heating and cooling to copy DNA and a provided genetic template from another researcher to synthesize a large DNA sequence. This lab-based method was founded in 1983 by Dr. Kary Mullis.
- Recombinant DNA (rDNA) with restriction enzymes and ligase - Using restriction enzymes and ligase as 'DNA scissors and glue' that precisely cut specific DNA sequences from the whole DNA strand, and correctly insert these 'cut pieces' into another organism's genetic sequence. This technique was developed in the 1970s by Dr. Paul Berg, Dr. Stanley Cohen, and Dr. Herbert Boyer.
As scientists continue to add the growing DNA database of genes, the technology used to extract and replicate DNA also continues to improve. Now, there are labs word-wide with DNA printers that can 'print' a desired DNA sequence based from a proposed 'bio-brick' sequence construction. Technological advancements and the use of programming logic to construct DNA is what allowed our class to dive right into this practice on our own through Synbiota's "Violacein Factory".
However, note that just because a standardization model has made DNA construction more practical, easier, and accessible beyond the realm of professional scientists, it does not mean that any arbitrary ordering of bio-bricks will yield an piece of DNA that has the functions desired by the user. Recalling the metaphor of sentence construction, there is a particular grammar to DNA sequences. Synthesizing those that achieve desired outcome -- a core principle driving the design practice particularly -- requires the host organism be able to take in the designed DNA sequence into itself. This integration will determine and assess whether a synthesize DNA performs according to specification.
Altering the DNA of another organism to implement a synthesized DNA is not to be taken lightly, and therefore, is a reason why model organism are used to further the development and refinement of synthetic biology. Model organisms, like the bacteria (E.coli), yeast, and algae, are lifeforms which science have studied extensively enough to predict and anticipate its behaviors. The database for these organisms' genes, as well as the population of these organisms themselves, are bountiful.
Rightfully so, ethics should not be overlooked when it comes to synthetic biology. Synthetic biology works directly with life at its fundamental level, from the genetically modified food we consume to the biodiversity in our planet. Human modification and artificial selection of genes may have been going on since the beginnings of agriculture, but with synthetic biology, the extent of human interference, modification, manipulation, alteration, and intentional selection of natural and artificial genes is very much a part of our daily reality now. Put simply, synthetic biology falls into a duel-use dilemma -- the very usefulness and benefits of its technology, is also inversely capable of great harm.
Our class considers what it means for designers to gain the literacy of synthetic biology themselves through discussion and A.D. Ginsberg's chapter on "Design as the Machines Come to Life." Ginsberg distinguishes that, whereas synthetic biologists are specialists with their fluent and thorough literacy of biology and chemistry, designers are generalists that have the potential to become social critics and pubic intellectuals that can readily apply critical design concepts and practice -- such as those derived from Anthony Dunn and Flora Rab's 'a/b Manifesto' -- through their ideas and products.
"Designers should continue doing what they do best, which is to address...the sensible, human, and beautiful production of things in the world." -- Paola Antonelli, Senior Design Curator at the Museum of Modern Art (MoMA)
Through Synbiota's Violacein Factory, our class was able to start designing and assembling the violacein metabolic pathway using Rapid DNA Prototyping (RDP) technology. Though we have not gone further than that step, what is to follow is the successful verification of our designed assembly through gel electrophoresis, and its transformation within E. Coli.
Violacein is a natural, purple pigment emitted by a type of soil-based bacteria found in the tropics. One of the bacterium known to produce violacein, and is the most studied to date, is Chromobacterium violaceum. In nature, violacein is typically produced in response to stressful conditions, such as in response to changes in pH which indicate the presence of predators like protozoans.
Violacein is believed to have potential, anti-biotic and anti-cancer properties because of its ability to kill off parasites, and much work is currently being done by synthetic biologists to enhance violacein's fermentation fields. Currently, one gram of violacein costs $356,000 per gram (excluding tax).
The image on the left is a physical sample of C. violaceum taken on the day of our lab, to reference.
THE VIOLACEIN METABOLIC PATHWAY
The violacein metabolic pathway, also called the biosynthesis of violacein, that leads to this purple coloration, begins with the amino acid tryptophan (as shown in the diagram below). It takes five biochemical reactions to convert tryptophan to violacein, but getting there requires a combination of five different enzymes (VioA, VioB, VioC, VioD, and Vio E). While these enzymes are known, their order with which to place genes on a plasmid to transfer within the model organism, E. Coli, to get optimal violacein production is not. Knowing this gene sequence order is crucial for knowing how to produce the most optimal amount of violacein.
THE GENOMIKON KIT: VIOLACEIN FACTORY
The difficulty to produce violacein, and the mystery of the enzyme order is what brings us to the lab objective of the Violacein Factory.
As an 'open project', this lab is open-source and all data is accessible to the public. The Genomikon Kit is meant to offer an opportunity for one to try their hands at producing violacein, with the hopes that they could find a way to optimize its growth.
Thus far, the following is known from past experiments with this kit on E. Coli:
- Omitting VioC turns bacteria colonies dark green that also blacken over time [2009, iGEM Cambridge University].
- Omitting VioD results in navy blue colonies [Genomikon Team].
DESIGNING AND TESTING OUR OWN DNA SEQUENCE
Because this may not be the optimal order for maximum violacein production, the Violacein Factory offers the following three suggestions to optimize violacein production in lab:
- Gene Dosing
- Reorder Genes
- Change Experimental Condtitions
CONNECTING BACK TO THE THEME OF ENERGY: violacein
Protein production requires energy. Recall that the metabolic pathway of violacein is an energy-intensive process, meaning that energy is used when the purple hue is emitted by the bacteria.
Despite the lack of prey presence, there is a rich purple hue within the sample petri dish in the lab because violacein is within a sugar-rich environment that is actually controlled and ideal for violacein production. This means that even in utopian conditions, violacein would still be produced.