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What the DBT is about

March 10, 2013

The Department of Biotechnology. 

It  is important that we keep in mind that the DBT is part of the Ministry of Science and Technology. Therefore, it is natural that all that we do and try is built on developing a strong foundation and capacity in the Life Sciences. A broad and deep capacity for research in the fundamentals of all of biology ensures that we can grasp new opportunities be they in basic science or it applications.

Today’s possibilities of applications in agriculture, health, energy, biotech all come from yesterday’s investment in basic science. If we are to be truly innovative in applications for our societies, we must develop a culture of fundamental research where we define and work on problems that are truly cutting-edge. Otherwise, we will constantly be borrowing or buying the fruits of basic research done elsewhere. This route, of building on the investment of richer societies in basic research, may be an option if our goal in science is to be a vendor of services, but is a shortsighted option even here. If we are to cater to the legitimate demands of our society, developing our foundations and contributing our share to the world’s intellectual growth, as we interact and collaborate, is the only route.  Future posts will elaborate on DBT’s substantial investments in basic biology in a whole range of ways.

Starting by stressing the importance of investment in basic science is not to say that quality applied-research or applications of science and technology will magically happen. Quite the opposite. A vaccine or a drug against a disease that is relevant to the developing world cannot be bought off the shelf. Neglecting to think and act towards developing and applying technology to sustainable agriculture or new bio-fuels or cheaper drugs, is suicidal.  If the science to embark on such projects is available now, we must embark on them speedily. These adventures are no less exciting and no less exacting than basic science. Indeed, the requirements of taking the route to seeing your research used places extraordinary demands that those of us in blue-sky research environments often do not appreciate. Here too, the DBT has the whole range of exciting programs that future posts will address.  While these posts on the specifics of what we are doing in basic and applied life sciences and biotechnology appear soon, your comments on what aspects of basic and applied-science India should invest and how we should go about it will be much appreciated. 

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12 Comments
  1. Suggestion for basic/applied science research – From a limited experience of toying with the idea of generating novel bioinformatic tools I am convinced that bioinformaticians (is that the right term?) and the experimentalists live in different planets. However, if they can be brought together, driven by mutual need, it can do wonders. There is a lot of data in the public domain which if mined effectively can generate attractive testable hypotheses.
    Can DBT come of with a funding scheme to entice and coax these two groups to work together?

  2. Thanks Amitabha. What do you ( and others) think of the European Bioinformatics Institute (http://www.ebi.ac.uk/) model? Can it be applied here? With Variations?
    Best
    Vijay

    • Thanks Vijay. I will study your suggestion and get back to you soon.

      Regards,

      Amitabha

    • Dear Vijay,
      I now had a chance to look at EBI website. Please do not consider it arrogant but this is still largely a bioinformatics community driven agenda. I have looked at their publications which is largely in the bioinformatics (theory) journals. All the group leaders are bioinformaticians.

      My idea is fundamentally different. As an experimentalist I feel the need of specialized/custom made bioinformatic tools but I cannot excite appropriate colleagues to design those. Similarly, I believe a bioinformatician may like to have his/her predictions tested by an experimentalist but the appropriate colleague may not be available/willing. However, I know that in India we have capable people in both these domains. Somehow if DBT can catalyze a synergy great things can happen. In the absence of an inducement we are well settled in our comfort zones.

      What I propose is that let there be a specific call for proposal for collaborative projects where at least one of the PIs will be an experimentalist and another one will be a bioinformatician. The project may be funded in a different manner as well to maximize the output:

      1. The initial project proposal may be funded for 1-2 year(s) and in this period no consumable expenses will be provided. However, funding for travel and stay in the collaborator’s institute may be provided. The idea is to utilize existing data to generate new hypothesis using existing or novel bioinformatic tools.

      2. There should be a presentation after 1-2 years. If the team can convince the task force that they have generated several testable hypotheses worthy of pursuing further then only DBT will grant fund for the wet lab work.

      3. There should be a clearly stated objective mentioning how the newly generated information will be utilized bioinformatically.

      =========================
      =========================

      Such a program or a variant of this can achieve another objective – a breed of students who will be comfortable with both kinds of approaches. I do not think this tribe exists, at least in a significant enough number. I may be ignorant.

      Amitabha

      P.S. – I will be happy to elaborate, with specific examples, when we meet next time.

      • Seema permalink

        Yes, your way is good but practically speaking, really not good enough. There have been instances where an experimentalist after a long, hard work done by a bioinformatician simply switched this bioinformatician by another one who used the first bioinformatician’s way of doing things by just replacing the softwares and just getting another set of results which were not even validated. Another instance came when the experimentalist in collaboration with a bioinformatician, setup his own laboratory and didn’t keep his promise of validating the bioinformatician’s findings. There should be a mechanism in place if mutual trust and cooperative spirit is to prevail. Unless the collaborators are honest to each other, a huge chunk of funding is never going to work out and all that is left is a half-way result, either in the form of half-done experiment (due to requirement of more time) or as a predictive hypothesis generated by Bioinformatics.

  3. A lowly yet hopeful grad student’s perspective on this wonderful call for ideas:
    I am an aspiring computational/statistical genomicist who really thinks that India (and specially IIT’s) should really invest in bringing people from different areas together. We are in a post modern biological world, where most interesting problems can only be solved if computational scientists will think as biologists, and in turn biologists will have a look at the bigger picture by thinking as a computational scientist. Let me explain this through a small project that I was involved in. A top research lab at Penn is looking at changes in the chromatin landscape with aging of the cell. People have found clear differences in the epigenetic marks in senescent and proliferating cells and have connected it with solid functional changes. This is a great story and a publishable unit. The project did use the expertise of lots of data analysts during the peak calling/mapping phase. However it was not yet computationally interesting. It gets so however if a statistician/computational scientist comes up with an idea of modeling the change in the chromatin landscape via some regression model and seeing the tipping point when there is a sharp change in the landscape (aka the second derivative is also higher), and then associating it with other transcriptome data to generate new testable biological hypotheses.
    There is so much research going on in India focusing on the first problem, and the second problem separately. However I see no reason as to why people with different expertise cannot jointly work on problems.
    While these are the changes at the top, I think real change will happen at the training level. While IIX’s are great and they provide real quality education, I still think that they should allow students to take more electives so that they are exposed to interesting problems in different disciplines. Please have a look at this graduate program in the School of Medicine at Penn (http://www.med.upenn.edu/gcb/index.shtml). People in this program take classes in Gene Expression, Cell Biology, Genetic Principles, Statistical Inference, Bayesian Statistics, Machine Learning and Algorithms. I think encouraging institutes in India, to start programs like these will go a long way in developing the next general of scientists that our dear country desperately needs.

    In case I have not mentioned this before, I am really glad that DBT has opened up, and is actually soliciting views/ideas from real folks !

  4. Speaking of Bioinformatics, how I wish the scientific mindset would grow beyong seeing gel bands specifying DNA and protein in every paper presented in journal club and encourage itself to learn to look at beautiful hypotheses generated by Computational biology tools in the form of molecular models, trajectories generated using molecular dynamics and the likes. I think that every computational biologist who has studied in-depth can understand the gel bands, but not every molecular biologist can understand nor try to understand computational biology, as if it is like billions of blue, blistering barnacles; which it surely is not. An attempt to kindle interest in computational biology is covered in my blog here: http://seemauoh.wordpress.com/. Welcome!

  5. binay panda permalink

    vijay, excellent blog and a great space to share ideas. sorry, i didn’t notice it earlier.

    on bioinfomatics, it’s time that the nation has a concerted view and initiative. due to legacy issues, most folks in india, who practice bioinformatics are from the protein/peptide field and that certainly is important. however, the field has moved beyond proteins/peptides to more high-throughput technology like arrays and sequencing. on the ebi mode, i think its a good model but may not work in its pure form in india. this is purely looking at ebi over the last 10-15yrs and how other inst, especially sanger, has come up in ebi’s vicinity to take up newer and bigger challenges. hence, while keeping the ebi model in picture, we need to have evolution of challenges, technologies and nature of collaborations in mind as well.

    secondly, bioinformatics, can’t be practiced without biology. hence, the proposed large initiatives in bioinformatics must be tied to biology initiatives. in other words, both biologists and computational biologists must be tied with common objectives, goals and outcomes.

    thank you. binay panda

    • Dear Binay and others interested in this topic. We’ve often discussed the problem. Now, given the boundary conditions of people, spaces, resources etc. we need to home in on what is to be done. If we get multiple views and ideas on this ( what and how to do), we can move ahead. There have been ‘committee’ discussions on these matters. However, a global discussion on multiple forums will be of real value
      Cheers
      VijAy

  6. binay panda permalink

    vijay, thank you for your reply. absolutely, getting a global discussion will be of real value. binay

  7. binay panda permalink

    vijay, thank you. it will be a pleasure to add value to such a discussion. i look forward to it. binay

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