Computational biology: this is how this science aspires to solve some of humanity's great problems
Sounds like something very new, but actually it is not. Computational biology is almost as old as computer science. In fact, Alan Turing, the British mathematician and cryptographer unanimously considered one of the fathers of computer science, used the first computers to develop mathematical models of morphogenesis, which is roughly the biological process that explains how an organism develops a certain form .
Turing worked in this area in the early 1950s, at the dawn of modern computing. This fact reflects that one of the first applications of computing as we know it was, precisely, biology, but the greatest advances that are promoting the alliance between these two disciplines have occurred in the last two decades. And this has caused scientists' expectations to be over the top due to a compelling reason: Computational biology aims to solve some of the biggest problems humanity is facing today.
Computational biology: what it is and how it differs from biological computing
How much their names are alike can cause us to confuse them, but biological computing and computational biology are not the same thing. They do not pursue the same objective, and their scope of work is not the same either.A simple way to understand what these two disciplines are requires viewing computational biology as the science that uses computing tools to help us better understand the most complex biological systems, and biological computing as the branch of computing that studies how we can use elements of a biological nature, such as proteins or DNA molecules, to process and store information.
Both disciplines rely on the alliance established between biology and computer science, but their starting point is very different. That of computational biology is the biological sciences, and that of biological computation is computer science. And from there they turn to the other discipline to propose solutions to their own problems. In this article we are going to investigate computational biology to discover why it is important and what are the problems that could help us to solve in the medium and long term, but if you want to know more about biological computing you can tell us in the comments and we will prepare another article to help us get to know it a little better.
A third discipline with which computational biology is related, and for which reason it is worth knowing, is bioinformatics. Curiously, there is some controversy as to whether it is really necessary to make any kind of distinction between the two. The prestigious journal Nature is one of the publications that considers that computational biology and bioinformatics are essentially the same, and the definition it proposes seems to fit perfectly in both disciplines.
Their names are similar, but biological computing and computational biology are not the same. They do not pursue the same objective, and their scope of work is not the same.
According to Nature, "computational biology and bioinformatics constitute an interdisciplinary field that develops computational procedures to analyze large collections of biological data, such as sequences of the genetic code, cell populations or proteins, with the aim of making predictions and discovering new biology. The computational procedures they use resort to analytical methods, mathematical models, and simulation. ” As you can see, this definition is quite precise and does not make any distinction between the two disciplines.
On the other hand, one of the institutions that defend that computational biology and bioinformatics are largely intertwined, but are not the same, is the American National Institute of Health, known as NIH (National Institute of Health). According to this organization, "bioinformatics uses principles derived from the information sciences to make the enormous, diverse and complex volume of data with which the natural sciences work more comprehensible and useful."
On the other hand, also according to the NIH, "computational biology uses a mathematical and computational approach to answer theoretical and experimental questions in the field of biology." And he concludes by pointing out the following: "Although bioinformatics and computational biology are different, they overlap significantly." As you can see, the distinction that the NIH establishes between these disciplines is not very clear, so it is reasonable that we stay with the idea that they both use computing as a tool for solving complex problems in the field of biology .
Computational biology is not just about biology and informatics
Computational biology, first and foremost, is an interdisciplinary science. As we have seen, it is concerned with developing algorithms and mathematical models that can help us better understand biological systems and the relationships that exist between them. Before going any further, it is important that we understand what a biological system is, so we can define it as a set of organs or structures that work together and in a coordinated way to solve a physiological need for a living being. Our bone system, for example, offers us the structural support that our muscles require and the protection that our internal organs and soft tissues need.
Computational biology can help us better understand biological systems and the relationships that exist between them
The study of these systems is part of the very heart of biology, but this science has a broader scope. And it is also concerned with the behavior of living beings individually, the evolution of species as a whole, the interaction that occurs between them and their relationship with the environment. Fortunately, computing is a very valuable tool that can help us better understand the complexity of all these areas of study, but to use it in this context it is not enough to have a very solid foundation in biology and programming knowledge.
It is also important to be comfortable with statistics, physics, mathematics, biochemistry, genetics, or molecular biology, among other scientific disciplines. And it is very complicated, if not almost impossible, for a person who is dedicated to computational biology to have deep knowledge of all these subjects, which is why biologists, geneticists, mathematicians, doctors, biochemists and engineers often coexist in research teams in informatics, among other professionals, so that together they can face the multidisciplinary approach that a science as ambitious as computational biology requires.
The MareNostrum 4 supercomputer, which is the most powerful in Spain and one of the most advanced in the world, is used, among many other scientific areas, to execute the algorithms that researchers in computational biology develop.
Now, what concrete tools does computing, beyond programming, put on the table to contribute to solving the most complex problems posed by biology? Quite simply, all those that are useful when processing large volumes of data to infer new knowledge, such as big data, machine learning or quantum computing. Biologists currently have tools that allow them to collect much more data than a few decades ago in their study area, so the challenge is posed by the need to process all this information. This explains why the increase in computing capacity that computers have experienced during the last decades has an essential role in computational biology.
The knowledge that these computer tools provide us is not only valuable to better understand the biological systems we have spoken about, but also to create mathematical models and computer simulations capable of predicting the behavior they will have in the future. And this has very interesting applications in fields as diverse as ecology, neuroscience, pharmacology, genetics or oncology, among other scientific branches.
These are some of the problems that computational biology aspires to solve
"Biology is the only science capable of responding to the fundamental problems facing the world, such as the health of human beings or that of the planet itself." This statement by Arvind Gupta, the founder of the biotech and patronage company IndieBio, to the venture capital company NfX fairly well reflects the scope of the life sciences. The latter company argues that three of the areas in which computational biology has the ability to make a difference in the coming years are longevity enhancement therapies, immunotherapy, and applications of the CRISPR gene editing technique.
There are no doubt that there are three areas of study that can have a very positive impact on people's lives, but in reality, this is only a small sample of the scope of computational biology. Another field in which this discipline aspires to achieve very significant advances is computational neuroscience, which deals with the functioning of our brain by analyzing the ability to process information that the structures that make up our nervous system have.
Computational biology branches out in areas such as neuroscience, pharmacology, anatomy or genetics, among others
Another area of study covered by the computational biology umbrella is computational pharmacology. It is responsible for studying the link between the genetic information that a specific organism possesses (this concept is known as a genotype) and the way in which a certain type of disease affects it. It also deals with developing the drugs that are necessary to treat these diseases as effectively as possible.
Computational anatomy, on the other hand, deals with the study of the form that living beings acquire, analyzing all the scales of their morphology, from the largest structures that we can observe with the naked eye to the microscopic ones. One of the most important applications in this field in medicine is that it can help us interpret the information collected by nuclear magnetic resonance equipment more accurately. Many hospitals use these machines to observe the alterations in the tissues that can reveal the presence of cancer cells and other pathologies.
Computational ecology is concerned with finding solutions to the most pressing ecological problems we are facing, such as global warming or climate change.
Another very interesting branch of computational biology is computational genetics, which studies the genetic material of an organism or a species as a whole. It is a concept that in biology is known as the genome. This discipline has already reached very important milestones, such as the Human Genome Project, an international scientific investigation that in April 2003 managed to completely map the human genome in what is the most ambitious international collaboration that has been carried out up to now in the field of biology.
In addition, computational biology applied to cancer treatment is concerned with predicting the mutations that a certain manifestation of this disease will undergo in order to combat them more effectively. To make this possible, the computational biologists working in this area design specific algorithms that carry out these predictions from enormous data collections that they have previously collected thanks to the analysis of the DNA, RNA and other biological structures of the patients who are being studied.
Computational biology applied to cancer treatment is concerned with predicting the mutations that a certain manifestation of this disease will undergo in order to combat them more effectively
As we have just seen, many of the areas of study covered by computational biology aspire to have a beneficial impact on people's health, but this discipline can also help us to take better and better care of our planet. This is precisely the ultimate purpose of computational ecology, a branch of computational biology that is concerned with solving the ecological problems that put our planet in trouble, such as global warming or climate change.
To achieve this, it uses the enormous processing power of today's computers to analyze gigantic collections of data and carry out simulations that can help us better understand the origin of the ecological challenges we face and predict their behavior. Computational biology includes other areas of study beyond those we have just seen, but the ones we have reviewed allow us to get a fairly precise idea of the scope that this scientific discipline currently has.
Computational biology in Spain
Thirteen years ago Professor Alfonso Valencia, from the National Center for Biotechnology-CSIC, published an article in which he analyzed in a quite detailed way the role that computational biology had in Spain at that time, and the panorama until then had not been very flattering. Professor Valencia emphasized in his text the idea that the absence of important initiatives in areas such as genomics, which is in charge of studying the genetic material of biological systems, and proteomics, which tries to better understand the structure and function of proteins, had caused a scientific and technological delay in Spain.
The Computational Biology Group of the National Center for Supercomputing is one of the leading Spanish institutions
Alfonso Valencia also includes in his article several very important projects that, fortunately, were already underway in 2006, which was the year in which he published it, and which aimed to end the disadvantageous situation in which Spain was compared to the leading countries in computational biology. The National Genotyping Center, the Proteomics Institute, the DNA Bank and the National Bioinformatics Institute are some of the institutions that are leading the activity in computational biology in the public sector.
In addition, many of the Spanish universities that offer degrees in the area of biological sciences have introduced bioinformatics into their academic curricula and have made specific master's degrees in computational biology available to their students. The Autonomous University of Madrid, the Polytechnic University of Madrid, the University of Barcelona and the Carlos III Health Institute are some of the Spanish centers that currently provide training in the areas of bioinformatics and computational biology.
In any case, currently one of the leading Spanish institutions in this area is the Computational Biology Group led by Professor Alfonso Valencia within the National Center for Supercomputing, which is located in Barcelona. This group is investigating areas as interesting as predicting the consequences of mutations in the evolution of cancer; epigenomics, which studies how age and exposure to the environment can alter the behavior of genes; cognitive computing, which designs algorithms capable of simulating human thought processes within a computer; and artificial intelligence, among other areas of study.
Images | Egor Kamelev | Ralph W. Lambrecht