Category Archives: Biology

Messages in the Building Blocks of Life

Craig Venter 1, one of the leading names in genomics research, announced last week that he and his team have created a new single celled organism with what they think could be close to the minimum number of genes to sustain life and reproduce. They did this by “simply” (there was nothing simple about it) removing genes one at a time from a bacteria with an already small genome until they reached the bare minimum to function.   Gene manipulation is of course nothing new, but Venter and his team are reaching closer to something new.

To be clear, Venter and his team are not creating life – they are not growing anything from scratch.  Rather than are taking existing life, and over generations, deliberately manipulating it.  The application of this research, many, many, many years from now, would hopefully be that organisms like this one could be manipulated for manufacturing purposes.  Imagine a bacteria that could consume and metabolize CO2, and produce some kind of fuel like methane as a waste product.  Or vaccines.  Or any of a million other chemical compounds.  This becomes almost the biological equivalent of nanobots out of science fiction.  Imagine if these bacteria could be programmed, through their DNA, to both create the raw materials for a project, and to join those materials into a usable construction.  Bacteria that metabolizes a pollutant, and produces a high strength polymer, and then can collaboratively bind that polymer into usable structures and shapes 2.  By producing the smallest genome possible, Venter hopes to provide a base platform for others to build on in order to maximize the applications of this type of bacterial manufacturing.    Imagine the impacts on human spaceflight alone – instead of bringing raw materials, crews could bring blank bacteria (or algae, or any other simple, rapidly growing organism) with a database of genes to plug in based on the needs of the mission.

While the practical applications of the bacteria get my science fiction writer mind whirling, it’s something else that got my rhetorical gears turning.  One of the things that Venter and his team figured out how to do years ago is what’s called watermarking the genomes.  Basically, it’s signing the genome directly in the code structure of the genome itself.  In this case, they watermarked the DNA of this stripped-down bacteria with the name of the J. Craig Venter Institute.  Other genomic creations by Venter have been signed with the names of the important people on the project, inspirational quotes, and even a website address where people who manage to crack the code can let the Venter Institute know that they cracked the code.  Early versions of the DNA watermarks followed a very simple code: every codon (group of three base pairs, of which there are 20), represents a letter of the alphabet – with obviously six letters not represented.  Venter and his team have created a much more complicated code, which represents all of the letters, numbers, and punctuation for several languages.  

For the direct purposes of Venter’s needs, these watermarks serve several purposes.  First, they obviously sign and take credit for the genome.  But second, they also prove to Venter, and anyone vetting their results, that this is, in fact, synthetic DNA, and not just some kind of natural contaminant or naturally occurring DNA.

This represents and entirely new medium of communication, one with its own affordances and constraints.  For now, the medium is based on existing textual languages, most likely for simplicity sake.  But much as computer programming has developed its own languages (binary being the most basic), what other language forms could be constructed using base pair matchups?  Aside from the language itself, imagine the ability for confidentiality by using this type of communication.  Bacteria would be remarkably easy to conceal.  Then again, in order to eliminate the possibility of contamination of the message being delivered, the bacteria need to be carefully controlled, and kept alive.  Transportation takes time, and bacteria grow and change over time.  But why stop at bacteria?Could we encode messages into our own DNA?  Or our children’s?  How might the impact of genetic mutations interfere with these types of messages encoded into DNA?  And what about ownership after that mutation occurs?  Does the owning creator, the signatory of the DNA, still own the bacteria once it has mutated? Not to mention the sophisticated equipment it takes to both produce and decode these messages.  And the messages have to be produced and encoded into the genome in such a way that they don’t interfere with the rest of the functional DNA.  This is a complicated medium to work with, but already, people have started thinking about how it is to be used.  In addition to the name of his institute and the creators of a previous genome, Venter included some inspirational quotes into the watermarks.  Why?   Because “we were criticized for not trying to say something more profound than just signing the work.”  Already, people are recognizing that with a change of this magnitude, it’s not enough to simply take credit.  If you’re going to use a medium so difficult and expensive, you had better be saying something profound.  

What applications for DNA watermarks could you think of?  Are there ethical considerations that we should be thinking about?