Spenser Skates: Genome Engineering Day 4

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Transformation Results

Plate Transformation Expected Results Colonies Transformation Efficiency
1 regular M13K07 plasmid Many colonies 200 colonies 40,000 colonies /ug DNA
2 backbone + no ligase No colonies 0 colonies 0 colonies / ug DNA
3 backbone + ligase No colonies 0 colonies 0 colonies / ug DNA
4 backbone + insert + ligase Some colonies 0 colonies 0 colonies / ug
5 backbone + insert + ligase Some colonies 0 colonies 0 colonies / ug

We did not observe any colonies on any plates except the one with the regular M13K07 plasmid. This implies our attempt to place the insert in the M13 plasmid was not successful, which could be due to a number of reasons. One of the steps in creating the insert is the most likely point of failure. It is possible that the restriction enzyme did not cut the plasmid how we expected it to, or that the insert sequences did not stick to the cut ends of the plasmid, or that the reaction did not end up producing a piece of DNA that was properly annealed together, or that the bacterial host rejected the modified plasmid, or that the plasmid was modified to encode a fatal mutation for the M13 bacteriophage, or that one of the reactions destroyed the plasmid's viability, or any combination of these reasons.

Essay 2: Editorial: Meaning of Life in Nature (2007) 447: 1031 - 1032:

  • "it would be a service...to dismiss the idea that life is a precise scientific concept"

Andrew Pollack’s editorial The Meaning of Life in Nature attacks what he views as synthetic biology’s attempt to “create life.” He argues that we should “dismiss the idea that life is a precise scientific concept” because there is such ambiguity over what really constitutes life and the distinction between “living” things and “non-living” things. His overarching point is that the holy grail of synthetic biology: to engineer artificial life, and the impetus that drives it, are not well founded as the formation of life is “gradual, contingent and precarious,” such that no process can truly be said to create life. While synthetic biology is one of the steps towards making biology an engineering discipline so that we are able to create more than describe, the goal of “creating” life is nonetheless still just as awesome in spite of the fact that the progress we make towards the goal is gradual.

Pollack has said that any distinction made about living things is not valid in order to dismiss the claim that synthetic biology is about “creating life.” Pollack concedes that the science is well on its way to creating an artificial cell, but those who are in the field with the purpose of creating their own “Frankenstein” are misguided, as there does not exist a true qualitative difference between working with inert and working with living things. Pollack ultimately wants to say that synthetic biology does not bring that much new to the table in terms of achievable goals, and those who practice synthetic biology and try to draw up criteria for what constitutes life are misguided.

I argue that because a clear line cannot be drawn in synthetic biology between “creating life” and not creating life does not mean certain things cannot qualify as fulfilling the goal of creating life. Scientific achievements do not happen overnight. Rather, the goal of creating artificial life is one that synthetic biology is gradually making its way towards. It is not too much to say the creation of an artificial cell genome from parts is the creation of life.

Refactoring an M13 bacteriophage is one degree of progress towards engineering living systems completely. There is more ambiguity in the creation aspect of creating living systems than whether they should be considered living or not. It is very clear that we are working with living systems and our goals are designed around their manipulation. It is less clear what counts as “creation” of life and what counts as “modification” of life.

Although certain achievements may be seen as different degrees of engineering living things, such as refactoring of a preexisting genome, customizing of a particular genome with parts from other genomes, or creating a new organism from distinct parts, they can all still be considered in a way “creating life.” We are doing something unique with living systems that has not been done before and adding an artificial component to suit our needs. This is in essence creating an artificial and customized organism.

Synthetic biology is called synthetic biology and not, say, synthetic chemistry, for a reason. We are dealing with the attempt to engineer living systems. Although there are different degrees of engineering a living system, such as refactoring a genome versus creating an artificial cell from separate parts, living systems are the subjects in question. It is still a continuum, such that living systems can be broken down into smaller individual parts, such as the genetic material for an organism, the proteins which help it function, etc. Being able to create a particular DNA sequence is not creating life, but integrating an engineered piece of DNA into a preexisting piece of life such that it does something novel is creating a customized version of life to perform some new function.

There is no reason why we cannot come up with a definition for life. Indeed, one may argue that even if a consensus definition does not already exist, there are things that are considered engineering life. While we may disagree on whether refactoring a genome for ease of engineering use should be considered “creating life” we can agree that creating an artificial cell from separate base components is definitely creating life. There is no ambiguity around creating a new species artificially on a cellular level by adding all the chemical components together. Few would disagree that this is creation of new life artificially.

In all, we are attempting to create life in synthetic biology as much as someone in synthetic chemistry is trying to create a particular chemical. While there may be varying degrees of working with living systems and modifying or creating them, we are ultimately manipulating the components and systems of life itself. There is no good reason to become scared away from using the term “creating life” in synthetic biology.