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Biological robotics

In previous sections, we discussed ethical issues concerning synthetic biology in more or less general terms. However, even if we were able to answer all questions asked there, these would not fulfill our desires. Indeed, there is a lot of uncertainty (remember master Yoda) about the outcome of synthetic biology.

KULeuven iGEM 2008 project

For our project, we have been working on a bacterial drug delivery system, called Dr. Coli. What is special about Dr. Coli, is that it consists of several different subsystems that work together in a very tight network to do some more or less specialized tasks. We would like to refer here to our project page for more details on Dr. Coli.


The input mechanism we use is a dummy for a disease-sensing device. The signal triggering this input is proportional to the signal that comes out of this device, as well in time as in quantity.


Directly coupled to the input device, we placed an output device. Also here, we used a dummy output that replaces the production of peptide drugs, or enzymes that make sure drugs get produced by Dr. Coli. We used Green Fluorescent Protein (GFP) for this, as fluorescence is easily measured in a quantitative way using Fluorescent-activated Cell Sorting (FACS). This technique not only provides data about the location of the mean intensity, it also gives us a distribution of intensities that makes sure we can fit the measurements better in with the whole picture. However, the reactivity of GFP is quite low, as it is a long-living protein. We thus added an LVA-tag to the protein, which makes the GFP faster degrading. This makes our measurements more time-responsive.


Dr. Coli has to be able to overcome background signals from the input, which are not uncommon in biological systems. We obviously do not want these signals to activate different cascades further on in the network of safety mechanisms. We will not go into detail on our filter system here, as the most important thing is its meaning in our model. For those who are interested, we would like to refer to the component pages on our wiki.


The invertimer system is composed of an inverter with a timer in cascade. As long as no input signal is present, the inverter will invert the zero input to a nonzero output. This output is an organic molecule that accumulates in the cell (and can diffuse out of the cell and between cells). When a certain threshold concentration has been reached, the cell death mechanism is activated. Therefore this system can work as a timer.

Cell death

The molecule produced by the timer accumulates more and more, until it reaches a critical concentration, where it can activate a suicide gene. This means that when there is no input signal for a period of time that is long enough for the timer molecule to accumulate, cell death will occur. This is indeed a very easy tool to get rid of Dr. Coli when the patient is cured.


Some diseases cause symptoms of which the severeness can fluctuate in time. This means that the patient can be almost symptomless for a certain period, after which illness reoccurs. At that moment, we want Dr. Coli to reset its timer so that after the reoccurred symptoms have been overcome, the timer starts from zero again. This has been implemented by constructing a reset gene for the timer molecule directly after the filter. This reset gene codes for an enzyme that breaks down the timer molecule. This way, when input signal re-emerges, the timer is reset.


There is, up to now, no possible way to produce Dr. Coli, or to preserve him. Since Dr. Coli is, in absence of input signal, constantly counting towards its own suicide, he will die before he can be given to the patient. This all is a consequence of the filter system. The perfect solution to this problem is to make Dr. Coli remember whether he has come into contact with disease signal or not and passes this memory on to his offspring. Let’s figure out what happens then.

In the beginning, Dr. Coli is produced in a bioreactor in one or the other pharmaceutical plant. As Dr. Coli is made from empty E. coli and plasmids, his memory will be in the 0-state. Dr. Coli is then transported to the pharmacist, who sells it to the doctor, who administrates it to his patient. The patient is ill, so Dr. Coli is activated and makes a drug, but at the same time, his memory is switched to the 1-state. As the patient is, of course, ill for a time that is longer than the generation time of Dr. Coli, the latter will grow.

More and more Dr. Coli accumulates in the gastro-intestinal system, and the patient will feel the healing effects of Dr. Coli. All this offspring will have the same memory state, because the memory consists of a concentration of the memory molecule in the cytoplasm, and when cell division occurs, the resulting concentration (which will be half of the first concentration) is high enough to keep the memory in the correct state and add another half of memory molecule. When there is no more input signal, all cells will die. The patient is cured and Dr. Coli has left the patient. Mission accomplished.