Week Four: Design driven biology

Fall 2015 | Rebecca Van Sciver | Fine Arts C'17


This week we discussed the complex world of microbes and their implications in design driven biology. Design driven biology is the subsection of biological design concerning the deliberate manipulation of living organisms, crossing the boundary between biology and chemistry into the realm of aesthetics. 



Students beginning to build their DNA sequence.

Students beginning to build their DNA sequence.

Our exploration of synthetic biology can be better understood if we denote two categories: the chemical and the biological. The chemical refers to things like atoms, solutions, and molecules--things that don’t have living character but are the building block components of life. The biological refers to things that are actually living. Synthetic biology is a critique of the intersection between the chemical and the biological, and challenges the boundary between making and manipulating life. 

To review: Something is living if it uses energy, has a metabolism, evolves or changes, responds to its environment, is complex, has DNA etc. The simplest form of life is the cell, with DNA as its most basic unit. So if we want to manipulate life, we would have to therefore manipulate DNA. This brings up an interesting question. When is life really "created"? Is childbirth creation of life or just the growing of life that already existed in ovum? Usually when we design life what we are really doing is manipulating life that already exists, or is in the middle of living. We bring an intention to something that is already living, and as long as we have this intention, we are manipulating life. It is important to note that implicit manipulations aren’t considered design, simply consequences, secondary to intention. To be considered design, the manipulation must be intentional, with a desired end in mind.

To truly be creating life, we have to start from scratch, and design something without a history using elements we understand. So in design driven biology, what we are really achieving, is creating lifelike artifacts, not life itself. We can work with building parts like chemicals, atoms, and molecules to make a lifelike system, or we can manipulate an existing design that nature has created for us. For example, in lab this week, making a plasmid and inserting it into a bacterium is not making life but manipulating it. 

Many artists and scientists have explored this topic, some of those discussed in class were Craig Venter and Daniel Gibson. They have worked on projects synthesizing bacterial genomes and making artificial cells. The key take away is that we are working with DNA because it's the common language that living things utilize, so we can use it to program our own functions.



We can use the DNA manipulation discussed above to play with microbes, an object of design that can be manipulated for many different intentions. But why are microbes so important? Why are they at the core of synthetic biology? The are important because bacteria are old ancestors that pioneered the technologies that we use to live today. Mitochondria used to be bacteria, and they make ATP, the core source of energy for all life on earth. Microbes are also important because they are so influential in making our psychology, behavior, development, and neurological functions. In fact, we are microbes, and microbes are us. We cannot think about our own existence without thinking about microbes because without them we would die. This brings about some interesting questions. Do we think about microbes from a moral standpoint? We tend to think of microbes as negative, harmful pathogens or germs. But microbes are in everything, and many of them are positive if not vital for other forms of life.

Microbes don't live independently but in colonies and groups that form a microbiome (a collection of cohabitating microorganisms colonizing an environment).

Microbes don't live independently but in colonies and groups that form a microbiome (a collection of cohabitating microorganisms colonizing an environment).

Microbes don't live independently but in colonies and groups that form a microbiome, a collection of cohabitating microorganisms colonizing an environment. Note the difference between the word "colonize" and the word "inhabit". "Colonize" sounds negative, like the pathogen language. "Inhabit" shows understanding of the beneficial relationship between microbes and others. In a way we use microbes as machines, in which input becomes output. Machines are the manifestation of human sophistication, and by calling bacteria machines, we are changing the scale; we are making them into our own tools which is a new relationship structure. Note that we have titled this week's lab violacein “factory". We exploit their existing machinery and regulate their gene expression to make the protein products we desire. But on a more basic level, we use bacteria as a an artistic medium. Microbes are an unusual medium because they change, evolve, transform, and die. We can regulate and condition them but we cannot truly control them.



Many scientists have combined their understanding of microbes and their understanding of aesthetics to create design driven biological artifacts. Eduardo Kac realized that we would write language into DNA, and wrote a bible verse inside a bacteria. Because DNA stores information and can be replicated cheaply, there is a possibility of using it as communication or code. Researches have also experimented with water marking, in which they add some language to their organism's DNA to be able to identify it as theirs. 

But where do we draw the line between art, science, and ethics? We lack control of this medium, so is using it unethical or potentially dangerous? It it wrong to use something as a means to an end that we rely on to live?

It's tempting to ignore the moral issues and focus on the design and product possibilities instead. Which is what we've seen so far. One designer came up with a milk bottle full of probiotics that uses the resultant color of fecal matter to diagnose possible diseases. This marks a shift, where we are now putting design into an application context. We are creating products that you or your kids or whoever consumes. It's not just the design of DNA that becomes important but how we communicate and deliver the product-- it's the entire package. We also see design probes, which move beyond concepts to embody some fiction but are functioning and exhibited. These are not in the form of objects, but blueprints for a large concept (like the microbial home concept). We start to look at the aesthetic considerations, and even social ones. Josh Kline makes a statement about fedex workers in his portraiture through the bacteria on the objects they carry.

We will have to think about all these concepts when we design projects of our own in the next few weeks.




Violacein sequence.

Violacein sequence.

So far, we have played with chemicals, but haven’t deliberately manipulated any living organisms. This week, however, we will use our understanding of microbes and design driven biology in lab to introduce a new DNA sequence in the form of a plasmid to a bacteria, with the goal of creating a certain output. This is a great example of design driven biology. 

There are a few scientific considerations we will have to keep in mind when designing our pathway. It's important to note that the order of our genes in the plasmid, gene dosing or the number of copies of each gene, and the location of the promoter sequence(s), which is/are currently unknown, could all influence violacein production

So in class today, each lab group selected a design sequence to create. The most popular sequences were those that included extra of gene vio-D. This is because there is a place in our pathway where it forks, to create either violacein (our desired product) or creates a black pigment that we do not want. So by dosing the cell with extra vio-D, the idea is that we are encouraging the cell product to follow the pathway we desire. The other issue is where the promoter lies. If we want the most vio-D, we should place our gene closer to the promoter, but no one yet knows where in the gene sequence it is. Hence our trial and error experimentation. 

It is also possible that we discover even more products of varying colors, which we may see after our plasmid have been inserted to E. Coli and plated in petri dishes.