Why I am not a bioinformatician (only).

Applying for doctoral positions is a full- time activity. A bit frustrating the most of the times, but at least you get to explore the scientific environments in several places in the world. And you may eventually get a job. I am a cell biology master graduated who did a bioinformatics master thesis project, right after a two- years experience in a wetlab working on cancer cachexia. My CV tends to be appealing (sometimes…) to those guys working in a wet- lab that need to supplement their project with some computational research. Actually, the question I am asked the most is whether I am a bioinformatician or not. And this is a very good question.

A matter of education. Italians do it strange.

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In my university, “La Sapienza”, there is no specific bioinformatics coursework. To be a bioinformatician, a student may consider enrolling in a cell or molecular biology master, and to join, right after, a bioinformatics lab for thesis. Everything is learned on the field. This will sound strange, but the mentality of italian university is to provide a very wide and non- specific coursework, in order to let the students grow in their general knowledge and follow their creativity. So, I decided that cell biology and bioinformatics matched really good. This tend to puzzle the people reviewing my profile, because they have no official paper proving my computer skills. And many of them ask me if I am, or I “feel to be” , a bioinformatician. Actually, I can tell with a little confidence but still a big humilty, that my computational skills, and knowledge of algorythms, are comparable to the bioinformatics grads I have met around. In my master thesis I developed a multi- modular python script to fetch and process regulatory sequences on bacterial genomes, in order to find a conserved protein binding motif. Nothing special, but a fairly good bioinformatics project. Don’t take me wrong, I don’t want to disparage bioinformatics masters, I am just saying that I choosed a different path and I am going to explain why I think it may work.

A little step backward. WARNING: some unrequested (but maybe useful) sophistry here.

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Let’s start from a simple point. The word bioinformatics consists of the words biology and informatics, and its definition should sound like “the application of informatics to the study of biological systems“. Fine, but the question I am going to put is: what is informatics? For some reason that I totally ignore, in the Anglo-Saxon countries they tend to replace the word informatics with the more appealing computer science. It is not the same, since the most of the science in information technology is related to math. Informatics has brought us to use computers instead of paper and blackboards, but it was born on blackboards and paper anyways. Informatics is definitely not a matter of computers only. IMHO, the best definition of informatics we can agree is “scientific study of information“. This assumption shifts the problem, because our definition of bioinformatics will become “scientific study of information in biological systems“.

And as we consider that informatics is not made on computers only, we should ask if bioinformatics, the scientific study of information in biology, can actually be made on computers only in its turn.

Not a matter of computers only.

computer-destroying-o

The answer to this question is obviously no, in biology we don’t study how information  is stored and transferred with computers only. Actually, the most of the work is made on the wetlab side, where the information is collected. In silico approaches are very often used to rationalize the information rallied during experiments. This applies to many fields, ranging from genomics and biochemistry up to developmental biology and ecology. Sometimes is possible to model some well- known information scheme to produce theoretical models, as it happens in structural biology but, even in that case, we cannot really get rid of some good ol’ wetlab work. Another point is complexity. Biological systems are organized in nested and communicating complex systems. On one hand, we must admit that computers are very useful in the understanding of biological complexity but, on the other hand, we must consider that the lack of proper theoretical tools limits the range of application of computational methods. Very often, the only tools available to understand the information flow in a biological system are experimental, as systems biology can clearly witness.

The big paradox of bioinformatics

trying-to-remember

We are rapidly ending up in a paradox. If we think to a defining feature of living organisms, sneaking among the several proposed definitions of life, we come to the conclusion that information is that feature. All living systems are defined as such because they can store and transfer information. This makes the same term bioinformatics even pointless, since it’s a matter of fact that all biology is oriented to the study of how information flows in living systems.

Actually, the borders between computational and wetlab research are rapidly blurring, and the match of wet and dry lab methods are mandatory for the great majority of current projects. The answer I tend to give to anyone asking me about my being a bioinformatician is that the point is not me being a bioinformatician, the point is biology being an information science, whereas computational methods and wetlab protocols, databases and Petri dishes, python and pipette live together in a perfect harmony.

The matter is still education.

yes-maam

Ok, fine. But why this dissertation? There is a very important consequence of all this. If you are in science, you will most likely be interested in how the educational systems evolve, and how biology is taught in universities. This is even more relevant in the light of the crisis of academia, that requires a collective effort to improve our educational systems in order to keep them effective and democratic. Given that modern biology requires a productive collaboration between computational, mathematical and theoretical approaches and wetlab, how should we organize them into courseworks? Provided that we strongly need bioinformatics- dedicated masters to prepare people to be fully oriented on the computational side, the question is still if we should improve the teaching of theoretical subjects as base subjects in bachelor degrees. The main approach in this is to assume the computer side as an end point, a specialization to be provided to students with a biology background. Maybe we should consider to improve the teaching of informatics, math and theoretical biology in the first years of university, in the optics to take these subjects as fundamental for any biologist.

Ultimately, I can tell that I am not really devoted to address myself with specific definition. I keep going on, that’s the point. I tried to match cell biology and bioinformatics, and this seems to work, since I am getting good feedbacks to my applications. Obviously, fingers crossed.

PS. If you are asking whether the proper word should be bionformaticist or bioinformatician, please lose yourself in this thread on biostars and let me know. That is exactly the kind of things that bore me to death.

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