From 2012.igem.org

Latest revision as of 20:14, 26 October 2012

Would you be my chassis?

Introducing Xenopus as a new chassis in the iGEM contest requires a few epistemological investigation. The term “chassis” refers to a specific kind of model organisms which are bound to the specific ways of experimenting developed in synthetic biology. Examples through history have shown that the organisms used for conducting the experimentation often influence deeply the theories and projects inferred. As the term “chassis” is at the center of our study, it is important to remind why Xenopus is an interesting model organism, and to what extent the term chassis is epistemologically relevant when referring to vertebrates.

Xenopus as a model organism

In experimental biology the choice of the right organism is a crucial beginning of research, this has been widely repeated, so was saying Claude Bernard, father of experimental medicine, and confirmed on the matter by many historian and philosophers of biology, such as Lederman and Burian [1]. Though the choice the organism studied is often a matter of contingent circumstances (and it was indeed the case for our research), it often has an undeniable impact on the development of a research. As R. Burian explains, “most biologists realize that the choice of an organism can greatly affect the outcome of well-defined experiments and can thus have a major impact on the valuation of biological theory” [2], thus some model organisms, like Drosophila melanogaster and Escherichia coli accomplished their role with great success, while others, like “Hieracium, Oenothera and Ascaris […] led investigators astray” [3]. The history of Drosophila melanogaster is quite interesting in that matter, as the fly studied by Thomas H. Morgan had a huge impact on the practices and problems of genetics [4], the simplicity of its genome favoring the theory of the central dogma, one gene, one protein, one feature, and the projects of mapping genomes. As genetic modifications had huge impacts on Drosophila melanogaster’s phenotype, we put in the genome an explanatory power that neglected important aspects of the complexity of genetic regulation and organisms’ environment. However it was a fertile way to limit this complexity which would have been ungraspable at the first try.

Synthetic biology brought a new word when referring to model organism: the term “chassis”. Though this term may surprise when first heard (one spontaneously think of mechanics rather than biology) it is quite coherent with the project of synthetic biology: making biology easier to engineer. The epistemology of synthetic biology is not a descriptive one but a pragmatic or a technological one. We have to produce knowledge by building and standardizing our construction, to make it possible to work in a large scale. As synthetic biology introduces new terms, it is important to analyze them in order to get clearly what they mean, and try to establish whether they are necessary or not. Recalling the Occam’s razor, maybe it is no use and sometimes misguiding to multiply entities when there is no need. We will first remind what is understood by the term model organism, and justify why Xenopus is a very interesting model organism. We will analyze the term chassis in order to emphasize the epistemological differences that can be made between a chassis and a model organism, and therefore wonder if Xenopus matches those characteristics.

R. Burian [5] suggested four characteristics defining what a good model organism is: a) the organism should be useful to realize a certain objective of research, b) easy to manipulate regarding the topic of the research, c) there should exist a large amount of experimental resources coming with the organism such as genomic data, and d) the organism should represent a class of organism with a specific interest. Though the practical usefulness of a model organism is mainly the large amount of data gathered around it, it is important for biology to have many different model organisms, representing different nods in the phylogenetic tree and remembering us that contrary to what François Jacob once said, what is true for Escherichia coli isn’t necessary true for the elephant. As seen with the foreword, frogs have been by the past a quite useful organism for biology, for reasons different from those invoked before and on which we will develop in another part of our reflection. The old martyr of experimental physiology [6] has been progressively replaced by the now favorites model organisms of molecular biology and experimental medicine, which are the fly Drosophila melanogaster, the bacteria Escherichia coli, the plant Arabidopsis thaliana and the mouse Mus musculus (these are the most popular).

However batrachians in the name of Xenopus tropicalis are still widely use and might come back in the limelight. In 2010 Xenopus tropicalis’ genome was fully sequenced [7] and the frog is entering the realm of postgenomic model organisms. This frog is slowly replacing its counterpart Xenopus laevis presenting interesting features for various kinds of research. Xenopus laevis was widely used as a model organism in developmental biology, cell biology, toxicology and neurology since the 1950s, being a particularly attractive model because of its easy handling, and the size of its embryo, visible by naked eye. Without being a mammal, this vertebrate is evolutionary close enough with human to give us expandable results [8]. However, Xenopus laevis is a tetraploid and has a quite slow rate of reproduction, reaching its sexual maturity around one or two years, whereas Xenopus tropicalis is a diploid reproducing twice as fast [9] which makes it a more practical model, especially for genetics and for an iGEM project. Though the size of the egg is a bit smaller (< 1mm), it still is visible by naked eye and quite easy to microinject.

Xenopus as a chassis?

Thus Xenopus tropicalis clearly fits the characteristics defining a good model organism. A large amount of data exists on it as its genome has been sequenced, a large variety of studies are already done on Xenopus tropicalis and it is known to be easy to manipulate (characteristics b), c) and d)). If we keep an eye on Burian’s criteria, being a chassis is a specific mode of the first one: being useful to realize a specific objective of research. As a chassis is a specific kind of a model organism, directed toward a specific use, we have to investigate more closely what it is expected from a chassis to get the interest of bringing Xenopus in the realm of engineering. Xenopus is not only interesting for fundamental research, indeed it is an important vertebrate for medical and environmental purposes, like gene therapy [10], drug discovery and environmental risk assessment (it is used this way by the Watchfrog company).

Synthetic biology introduced the term “chassis” as a new way to refer to an organism. The metaphor is quite suggestive, in French the term appeared in the end of XVIIth century in joinery and is today more specifically known when talking about cars: the chassis is the rigid structure on which the various elements constituting the vehicle are fixed. This definition of a chassis can be kept and slightly developed when talking about living things: in synthetic biology, the term chassis primarily concerned bacteria, and specifically Escherichia coli. A chassis is meant to receive designed devices composed of standardized parts realizing specific functions.

Thus a chassis is meant to become a living tool, such as a biosensor (giving us reliable results concerning the state of an environment), a biological factory (producing materials of values, like drugs or fuel) and a cleaning machine doing bioremediation. Even when used for more fundamental purposes (exchanging information, counting), the interest of chassis is to be the container of any application that we can imagine being possibly implemented in it. As the parts implemented in the chassis aimed to be standardized and as the chassis is aimed to be inserted in an industrial system of production, the chassis has to fit some criteria of technological artifacts, as safety, efficiency, reliability and profitability [11]. These are, according to M. Bunge, the epistemological principles driving technology.

These principles of technology applied to living beings make some of us feel uncomfortable, especially when it starts dealing with animals. Not that we are absolutely against animal experimentation, but we are not sure that chassis is a term epistemologically relevant concerning animal biotechnology. After all modifying genomes in order to change the properties of a living being did exist before synthetic biology. Rationally designing animals is not new; mice have been deeply modified in order to serve science since the “construction” of OncoMouse in the mid-80s and these operations lead to intricate controversies on patent laws [12]. Engineering a synthetic, orthogonal hormone as a communication device certainly provides an interesting tool to do research on Xenopus and maybe helps reducing the number of tadpoles needed to test drugs and cosmetics in biotechnological companies. But we have to make it clear that Xenopus is not a tool, it is an animal, an organism on which we are doing tests.

This statement implies some epistemological differences, a tool or an instrument is a well known artifact that gives an output corresponding with the input. We are not interested on what is happening inside it. Chassis gives us the idea of a framework which had no other meaning or end but supporting man-made objects. A chassis is nothing by itself, has no end in itself, it is something that has to be built on. It is not interesting as we already know it because we built it in a particular purpose. There is no adaptation, no research to do on an already existing chassis as everything is already designed to be functional. Hence we believe that this term might be misguiding.

The chassis is an ideal of something like the minimal cell with the minimal genome designed to sustain living properties. By forcing the idea, one might include E. coli, B. subtilis or some other very well-known bacteria, though some may doubt that this the metaphor is totally relevant. But it seems quite inappropriate for more complex forms of life which development and organization are so far from our understanding. For this epistemological reason (and others we will develop latter) we prefer keeping the term model organism against the chassis idea. In our sense it provides a better idea to our work and don’t deny the complexity of life properties. A model organism is an organism we are trying to know, it is a being that helps us increasing our knowledge about nature and about us [13]. The term chassis creates some epistemological and ethical confusion, what is the tool, synthetic biology’s products or the beings modified by synthetic biology?

We discovered with great interest on the eve of the wiki freeze the philosophical work of Pablo Rodrigo Grassi and the FreiGEM 2012 team. They did a quite interesting and accurate epistemological analysis of the concept of “living machine” as a core concept of synthetic biology. We deliver here the personal conclusion of P.R. Grassi:

“While I am indeed sympathetic to the practical work of synthetic biologists, I need to object to its underlying epistemology. One can still heal diseases, produce biofuel, build biosensors and so forth, without using analogical expressions like ‘living machines’, saying that we only understand life when we construct it and arbitrarily determine what belongs to life and what does not. The notion of life as a machine is not self-evident and it would be negligent to persist in it without further revision.”[14]

We believe that the chassis metaphor is quite concerned by this conclusion. We invite the reader interested in an analytical approach of the “living machine” metaphor from the points of view of philosophies of language, of biology and of technology to have a closer look to FreiGEM report .

In last resort, one could say that chassis is a specific term of synthetic biology, a reference for the community principally used like a brand or a slogan. Nothing to make fuss about, and scientist are well aware of what is a tool, what is an organism and so on. However, when this is put in regard with reflections of the non-innocence of metaphors, we may prefer keeping the old terms such as model organism, which do not completely blot living beings out of our representations.

But before arguing against the use of the term chassis especially when referring to animals, we have to spend some time on the theories of animal ethics and the various aims of animal biotechnologies .