Scientific Reproduction

Philosophy of Science: Horror Vacui and reproduction

Science bases itself on our everyday observations. It began when people started wondering about the significance of their observations. Aristotle was wondering why the stone fell down when he dropped it from midair. He therefore developed a hypothesis about the essences in all things, which explained that the stone was moving towards its natural place - that the stone had a teleos (Ancient Greek: purpose, aim). Nowadays we laugh at that type of explanations but the essence of science still stands: explaining our observations.

Theories and hypotheses have virtues, which a good scientist should comply with: e.g. to follow the rules of good reasoning, being coherent and explaining a phenomenon. To accept a hypothesis or theory one needs to show that it satisfies all demands - and then it needs to be tested by an objective scientist. This is called the demand of reproduction, which can be exemplified by the old story about Horror Vacui, a theory that could not be reproduced.

Horror vacui is a principle used in pre-newtonian physics, which means “fear of the empty space”. It dates back to Aristotle, who believed that vacuum could not exist in nature. For him it seemed like a logical impossibility. Even Galileo Galilei thought that the nature feared the empty space. It changed with his student Evangelista Torricelli, who discovered the pressure of the atmospheric air. He found that the explanation is not that nature fears empty space but that the atmospheric pressure can hold a column of water - and that it can create a vacuum.

A hypothesis or theory must always have implications that can be empirically tested for it to be of any use. The problem with horror vacui was that it could not be tested. There was nothing to observe and therefore, it seemed, nothing to test.

We have made it our obligation to follow the virtue of scientific reproduction. It is fundamental for the scientific method and is integrated in the scientific community.

Confirmation and Bacto-Aid

In our project we tried to follow several other iGEM teams’ protocols and methods for our work. We had trouble with following UCLA’s protocols for producing spider silk. At first we believed we had falsified their method – we certainly believed that we could not corroborate their hypotheses. In the end of the project we found that the things that had gone wrong was not really related to their protocols, but the components we had used in the work. The enzyme we used were of a different type than the one used by UCLA and our streptavidin beads had run past its expiration date.

This is a great example of there not being a final falsification – there was clearly something wrong with our auxiliary hypotheses. The auxiliary hypotheses were also the first place we started looking when the results did not arrive as planned – so having an overview of them helped us find that the mistakes perhaps were with them and not UCLA’s protocols. We also found a mistake in our preliminary purification of PHB. The hypochlorite we used at the first had been stored wrong and the purification became visibly better when we used a different hypochlorite.

Scientific reproduction

Besides using UCLA’s protocols, we also used their BioBricks: BBa_K1763002, BBa_K1763003, BBa_K1763004, BBa_K1763009, BBa_K1763010, BBa_K1763011 and BBa_K176301 for producing the spider silk. We also used existing BioBricks in the production of PHB: BBa_K1149051, BBa_K1682020 and BBa_K93400011. More information of the BioBricks can be found here.

Using existing BioBricks helps other iGEM teams in the coming years, because they will know that the BioBricks have been used more than one time.