Difference between revisions of "Team:Toulouse/Practices"

Genetically Modified Organisms (GMOs) are at the heart of the current debate focusing on their use. Synthetic biology, an emerging science that only now reaches the public, is a field that sets off strong reactions. Used to questions, comments such as “researchers play God by modifying living beings”, and the prevailing societal distrust, we naturally developed a reflexion about the limits to give to our project.

Formerly, the field of biology matched its greek definition: bios meaning life and logos, study, biology was indeed the study of life and living beings. This has changed in the recent years since biology today does not describe life, but rather rebuilds it.

This evolution induced a certain fear in societies marked by an historical creationism springing from monotheistic religions. In these societies, living beings are held to be untouchable, it is thus necessary to comprehensively explain what synthetic biology is, what our project is, as well as what experiments we are conducting in the lab in order to give people who have no background in this field the key elements to start a discussion. Indeed, since most people have a vague or no idea of what synthetic biology covers, they tend to be negatively prejudiced towards the unknown. As scientists, we have to take these fears into consideration and address them as best we can.

But this must be accompanied by a questioning of Science itself. Indeed, Science cannot assume that the regulation of its researches is the lot of scientists only, rather it is its duty to communicate the results of the researches and to have transparency on the experiments conducted. Scientists should be able to acknowledge that they don’t know something rather than lying to the public. Indeed it is often easier to trust someone when the doubts are clearly stated than when everything is allegedly under control but it cannot be verified.

Before we can have any kind of ethical reflexion concerning our project, we asked ourselves how to best define our “work material”, meaning living beings. Indeed, to be able to estimate the possible consequences of our actions, we first have to characterize what we are modifying.

As was said previously, living beings are sacred in our society because they still hold some part of mystery. Christianity having been predominant historically in Western Europe, it still has an influence on people’s minds and a notion that could be assimilated to sin still clings to the modification of organisms.

We can then ask ourselves the following questions: is it possible to have control over organisms, and if yes, to which extent? It actually seems that we do not have the power to control them entirely, we can only act on a few metabolic pathways, a few functions, at the same time.

When discussing the different concepts and approaches of synthetic biology, we have to take into account that ethical reflexions depend on the core values of a society and thus differ from one to the other.

First of all, since we are participating in iGEM, we reflected on its acronym: international Genetically Engineered Machine. Using the word “machine” appears to us as a mechanistic reductionism. A machine is the assembly of known and controllable components, and this term seems to indicate that we assimilate a living being to a completely characterized system responding to physical and chemical laws. But a machine such as a plane can be built from start to finish whereas a living being like a bacterium cannot. Thus it appears that to use the word machine is somewhat misleading, because biology is much more complicated than that.

For the competition, we have to build genetic constructs called Biobricks. The name Biobrick calls to mind the Lego game and this parallel further asks the question of synthetic biology being conceived as an assembly game.

Hence we asked ourselves the extent to which we could consider our experiments commonplace or ordinary.

Our reflexion on these ethical issues led us to realize that the reluctance towards the modification of living organisms could be linked to an anthropocentric vision of the world. Indeed, as long as human actions do not have an impact on man himself, they do not cause much reaction.

Anthropocentrism, which places human beings above everything and particularly above nature, is the utilitarian vision. Naturalists on the contrary believe that nature takes precedence over humans and must be protected from their utilization. For them, humans are not above nature, they are at a level with non-human elements.

Ethics is in close relationship with law, especially when it comes to modifying living organisms.

If we focus on the human being, according to the law, his body does not belong to him, he only has a right of use. This means that he cannot sell, rent or modify his body.

On a closer scale, mammals, and for instance domestic animals like cats, are less obvious but still recognized legal entities. They are granted sensibility, have a status of slave, their master is held responsible for their actions, and the law protects them to a certain extent.

Finally, some organisms are qualified as “res nullus”. This includes for instance bees, bacteria and all other micro-organisms. Nevertheless the loss of a bacterial colony does not affect us emotionally in the same way the loss of a swarm does. Invisible organisms hold less emotional importance in our eyes.

The link we keep with nature is complex and ambivalent. On the one hand, we consider nature as fragile and in need of protection whereas on the other hand we see it as strong enough to provide all the resources we need to survive.

In the previous decades or centuries, our vision of nature was more pragmatic and focused on the fulfilling of our needs. Today we tend to “mummify” it in order to preserve it. This change in attitude brought along a defiance towards everything that aims at modifying nature.

Numerous products synthesized through the modification of microorganisms (reprogrammed bacteria…) are currently of great significance. For example they can be used to synthesize drugs, or produce biofuels…

Modifications can appear on organisms without the intervention of human beings. Microorganisms actually possess diverse means enabling them to evolve in order to adapt to new environments. Among these, we can name horizontal transfer, a phenomenon that happens between bacteria from different lines, from the same species or not. This way, the bacteria that receive the genes develop new characteristics such as resistance to an antibiotic.

These mutations appearing without the intervention of man are accepted by society because they are considered as natural. Synthetic biology reproduces this mechanism while reducing the time normally required for it to appear.

Another ethical issue that was raised by the concept of modifying living organisms was that of intellectual property. If patenting an organism were possible, it would lead us back to the perception of life as a machine, or a chemical factory, with no sense of wonder or admiration. GMOs are new creations in that a genetic modification gives a new strain, but this strain has been obtained from organisms coming from nature. Thus it does not seem moral to reduce life to a trading object.

However, patents on living beings do not patent the organism in itself, rather a specific technique or modification. Therefore the patent does not grant a property right on the biological material.

Does having the power to act on DNA and thus to modify the characteristics of a microorganism change our relationship to nature? Working with living organisms induces all kinds of emotions, be it wonder, curiosity or even fear. Contrary to what one could think, feeling fear as a scientist is essential and should not be overlooked since this is what makes us be more cautious and take a step back to study the implications of our work.

Furthermore bees are the first pollinating species in terms of fruits and vegetables produced thanks to them thus the advantages of protecting them are obvious for global trade.

Being aware of the worrying decrease in bee population and having developed an ethical reflexion since the beginning of this project, we endeavoured to learn more about the causes of this decrease.

It is due primarily to the overuse of pesticides that have proven to act as neurotoxins to bees. However we decided not to act against this threat. Indeed using synthetic biology to solve a problem attributed to a human behaviour did not seem relevant to us. Measures to educate populations to a rational and responsible use of those pesticides would be more appropriate.

Another of the major causes of death for the bees is the parasitic mite Varroa Destructor. The infestation of European bee colonies by this parasite was caused by their contact (wanted or not) with infested asian bees through globalization. Though it is true that the problem first originated with men, today we cannot solve it by changing our behaviour. In this case, synthetic biology could prove to be the solution.

Furthermore we tried to design a system that would be as respectful of the bee’s life cycle and products as possible, hence the circadian regulation and natural molecules.

Finally, we do not aim at completely eradicating the parasite from the environment. In fact, Asian honeybees are capable of identifying the varroa’s presence on themselves and of getting rid of it. Some colonies in Europe seem to start developing behaviours of the same kind. Thus we only wish to slow down the infestation by varroa with our system, to grant honeybees enough time to adapt to the menace and reach a balance with Varroa.

Bacteria have a high growth rate and can spread and mutate quickly. This aspect is all the more frightening as bacteria are microscopic and thus the risk is invisible. When the invisible can have an impact on the visible, fear might arise.

On the other hand it is also crucial to make sure that our molecules do not have a negative impact on the bees.

Early on in the project, we thought about how best to address the biocontainment issue regarding our bacterial system. Thus we have decided to put our bacteria in a small plastic bag. This specific plastic called TPX® is microporous and the size of the pores will not allow the bacteria to pass through. We also chose to place this bag in a solid device, adding yet another barrier between the bacteria and the environment.

During the summer, our lab was in the engineering school INSA wich possesses a safety department with one prevention advisor and several prevention assistants assigned to the laboratories. Their goal is to ensure the well being of the employees regarding safety rules and risk prevention. In our laboratory, the LISBP, safety is supervised by Nathalie Doubrovine who was the one instructing us regarding safety procedures.
As new interns we had to take part in a general training session to learn how to identify the risks and prevent ourselves and our colleagues from harm. We also followed several other trainings that allowed us to use technical apparatus such as autoclave or Nuclear Magnetic Resonance (NMR).
The laboratory safety training requirements of the LISBP are detailed in the Rules and Procedures of the LISBP.

Every new LISBP employee has to attend this training session regardless of its status (researcher, PhD student, intern...). The training is divided into two parts. The first one is a training concerning general prevention in research laboratories. This one is taken individually with the NEO software and the explanations of the prevention assistant. It also informs the employee about the emergency numbers.
The second one is a training about the techniques used during our stay concerning microbiological, chemical and incendiary risks.
We then have a test to make sure that we were understood and aware of the previous presentations.

We used the NMR machine kindly made available to us by the MetaToul platform to analyse our culture supernatant. This is a powerful but very expensive equipment, based on the magnetic resonance of the atoms. Due to this, specific rules have to be respected when working with it.
In order to protect the user, access to the NMR is not allowed for people wearing pacemakers, drug pump systems, staples on soft or hard tissue, and pregnant women.
Secondly, in order to protect the technological material, when entering the room the user should not wear a lab coat, nor have anything in his pockets, especially anything made of metal.

INSA Toulouse is a public school for engineers thus the biosafety guidelines are not specific to our institution; the French national regulations about working conditions and the manipulation of genetically modified organisms are applied.
The regulation on workers' protection against risks resulting from their exposure to pathogenic biological agents (Decree No. 94-352 of 4 May 1994) includes microorganisms, cell cultures and human endoparasites which may cause infections, allergies or toxicity.
This Decree is the French transposition of the Directive 90/679 / EEC and is also transcribed in the Labour Code (Articles L4421-1 R4421-1 to R4427-5.)
The Decree of the 16th July 2007 describes the technical preventive measures that are to be set up in research laboratories (including containment), education, analysis, anatomy and surgical pathology, autopsy rooms, and industrial and agricultural facilities where workers are likely to be exposed to biological pathogens.
The rules of health, safety, and preventive medicine applied in public services in France (and thus in all public facilities working in scientific and technological domains) are set out in the Decree No. 82-453. This decree refers to the Labour Code, Public Health Code and Environmental Code.
The Decree No. 2011-1177 is related to the use of genetically modified organisms.

We used the chemical hood when we had to manipulate dangerous and volatile chemicals. For example, all manipulations dealing with formic and butyric acid were done under such a hood.

The water-bathes were used extensively (transformation, digestion, etc.). However, they can be dangerous because of the exposition to hot or even boiling water. To prevent the burning risk associated with heat, steam and projections, we used special gloves. We made sure to always check that the water-bathes were turned off at the end of the day.

To manipulate into a sterile area and thus avoid external contamination by unwanted microorganisms we used a Biological safety cabinet (FASTER – Ultrasafe). The bench of the BSC was cleaned with ethanol before and after each manipulation. We also cleaned the BSC completely every two weeks.