Tag Archives: University

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.

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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

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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.

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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.

The crisis of Academia between DIY culture, Science advances and Welfare cuts.

If I were to fully analyze the phenomenon of the crisis of the Academia, I would end up consuming every single megabit available for the contents of this site. Such a wide problem could be dissected under several points of view and, for the scopes of this blog, directing the readers to the main aspects I have found will be enough.

To understand the crisis of academia, we should consider two questions. The first is what a student would ask himself before planning his post- school life: wich kind of educational path should I choose to gain the best formation for the work I want to do? And the second question could be made by any entrepreneur who’s designing a business plan based on innovation: where should I find the best developers for a new product? Fifteen years ago, the answer for both questions would have definitely been “University”. Nowadays, things have changed, and this is a good definition of what we call “the crisis of Academia”. In this month, I will try to deepen this in my insights here. Basically, I have found three main reason explaining why universities are facing a crisis.

First reason. Alternatives are quite good anyways. God bless DIY.

We must consider that the alternatives to academia, at the age of the Internet, are getting more and more effective. Many computer scientists gain more information and practice from web and sharing than from universities, and many amazing things are not developed in the labs anymore. Computer Science is obviously the best example we can make. For instance, one could choose to become a database admin leaning on his own forces and obtain a certification that will be surely considered in the labor market. In fact, also the role of majors in this should be better investigated. In many fields of knowledge, from computer science to arts, the mentality of “you gotta make it in this world alone” is rapidly spreading.

Second reason. Universities are failing to be up-to-date.

For a biologist, the most experienced phenomenon it’s definitely the difficulty of universities to keep up with Science advances. If you look at this from an Italian university like I do, it tends to be dramatic. Considering that my university, the Sapienza University of Rome, is the best ranked university for science teaching in Italy, the fact that biology teaching and academic offer haven’t change in the last 10 years, it’s quite explicative. The major progresses in theoretical, computational, synthetic and genomic research have been ignored. For someone who needs to achieve a good formation, the best idea is to supplement what your professors will teach you. No one can actually say that you don’t need to study biology to get a good job in the field, but if you want to be competitive, you must consider to supplement what you learned. University is very often what a mathematician could define as a “necessary but not sufficient condition” to get a good professional profile.

Third reason. Funding cut and war on public education.

In times of crisis, where I consider “crisis” just a buzzword made to justify the shameful welfare cuts that many european governments are actuating, the aspect of the decrease of funds for academia cannot be ignored. We could consider this both as a reason of the crisis of academia and a consequence. The cuts of funds in the universities is mostly verified in two big ambits. It occurs widely in latin- european countries, such as Spain, Portugal and Italy, as a part of the general decrease in investment on welfare triggered by international constraints, but it is also present in Anglo-Saxon countries. In both UK and United States, the rising of the fees for students is really sizable and represents a big problem in terms of social segregation. The cuts and the tightening of the access conditions, and the general pauperization of academic resources cause many students to choose alternative formation.

Anyways, seeing it from a different point, we should consider that one of the best analyzed and most important processes that are going on is that governments are steadily devolving decision power on many aspects of our society to majors and private groups. This theory has been very well explained by Noam Chomsky in an article he wrote two years ago. Basically, governments are losing the control of crucial sides of our society including education. Citizens are more and more in the condition of facing Major directly, bypassing the government intermediation. This could explain the efforts made by private groups to invest and drive the advanced education. The optics of the companies is therefore to choose the best educational system for their own interests. And this system, it may not always be the university.

We can conclude with an optimistic and “evolutionary” consideration. The word “crisis” derive from a greek word (that I don’t even dare to write) indicating both “destruction” and “innovation”. Crisis is a disruptive event that can threaten the same existence of a system, but it also represents a big push for a change. In an evolutionary perspective, we can say that this crisis causes a major pressure on university system that it will be urged to evolve. And the open access courses we can find on coursera or iTunes U, provided by the most prestigious universities are probably a good sign of innovation.