Interview in Future Medicine Magazine

http://www.futuremedicineonline.com/detail_news.php?id=78

‘Genome man’ of India

Sreekanth Ravindran | 10-March-April-2013

Sam Santhosh is the Chief Executive Officer of SciGenom, a genome company based in Kochi, which specialises in DNA sequencing. In an exclusive interview withFuture Medicine, he says that genomics will fuel the next revolution in medicine

By Sreekanth Ravindran

What inspired you to start SciGenom?

The completion of the first draft of the human genome by the International Human Genome Project in 2001 originally attracted me to this field. With my background in software engineering, I was intrigued by the opportunity produced through understanding and leveraging the genomic source code which is the language of life for all living beings. However, I had no connection with biology after high school and so it took a few years of reading and evening classes to get a thorough grasp of the subject. During this period, the DNA sequencing technology went through a revolution by exponentially reducing sequencing cost while increasing processing speed. For example, sequencing the first human genome took 10 years and cost about $3 billion, while, as of now, one can sequence a human genome in two weeks for $5,000.

With the advent of these new technologies called Next Generation Sequencing (NGS), I saw the opportunity of creating a company for genome sequencing and data analysis. Genomics can create dramatic changes in healthcare, agriculture, environmental protection, bio-fuel, and so on. Understanding the ‘language of life’ now is a momentous turning point just as the development of language itself for communication was a major tipping point in the history of our species about 30 to 40 thousand years ago. By deciphering the genome, humanity will be able to move to the next level of evolution.

This belief gave me the inspiration to start SciGenom– the name meaning ‘Science of the Genome’.  Though I have been living in the US for the last 20 years, I felt that with the changing global economic climate, I should start my new company in India and since I am from Kerala, I chose Kochi as the starting location.

How progressive and developed is the Indian genome industry and what are its advantages or shortcomings in comparison with the West?

The Indian genome industry is still in its infancy and has yet to fully develop. At the same time, we have many advantages compared to the West, includinglower manpower cost, strength in information technology and a growing economy which makes us unique. The disadvantages are lack of scientific leadership and research expertise, and unpredictable regulations driven by populist politics. The first can be overcome by attracting Indian NRI scientists back to India and by collaborating with other research institutions in different parts of the world. The second requires time and improvements in education throughout India.

What are the ethical issues preventing genome research companies from going the whole hog?

A critical issue is patient confidentiality and ensuring the individual understands what their genetic results mean. Another dilemma is ownership of genomic data. With advances in genetic testing for disease prediction, a major question arises over what becomes the information and who determines its use.

Tell us about your tie-ups with international companies, agencies and governmental bodies, and your areas of research. Are you faced with any policy bottlenecks?

We have research collaborations with Dr Schuster’s lab in Penn State College, Pennsylvania, and with the University of Toronto in Canada. Our areas of research are in molecular diagnostics, cancer treatment and metagenomics. In molecular diagnostics, our goal is to reduce the cost of genetic tests and make it affordable to all sections of the population. In cancer, we are looking at familial cancer and some forms of cancer that are more prevalent in India and hence have not attracted much attention in the West. In metagenomics, we are exploring the microbial communities in several water sources and soil samples to better understand the effect of bacteria and other microbes on human health and society.

Policy bottlenecks have not significantly affected our operations till date. However, some outdated rules like the restriction on sending human samples abroad as well as lack of regulations in medical diagnostics creates confusion in the field.

Were any of the Indian companies or individuals part of the international human genome project? How much of the research findings have made it to the mainstream medical practices so far and how far is India in making these solutions available to the common man?

India was not part of the original human genome sequencing project. However, CSIR sponsored Human Variome Project starting in 2003mapped variations in1,000 medically important genes across various groups in India.  Currently, India is part of the International Cancer Genome project where scientists from across the world are using sequencing technologies to understand cancer.

Research findings from the human genome project and the cancer genome projects are starting tomake personalised medicine a reality. However, given that such applications are in its infancy,it will be sometime before all the information is fully applied in mainstream practice of medicine. For those interested further on this topic I would urge them to read “The creative destruction of medicine” by DrEric Topol.

Is India lagging behind in streamlining genomic education and research? Do you have any suggestions?

India is definitely lagging behind in genomic education and research. In this regard, I have a few suggestions to make. When it comes to research, we need to follow the US model which has proved to be successful. The Indian government has already done well in the area of funding by providing large number of grants and creating public-private partnership schemes. What we need to do is attract not only NRI scientists to come back but also foreign scientists to set up labs in India and provide them sustained support with grants covering longer periods of time.

In education, we need to develop our own model. With the world’s largest youth population, poor infrastructure, lack of qualified teachers, etc we have significant challenges. One way to solve this gap is by leapfrogging over older models as we did with computers and telecommunications. We need to enable long distance learning, leveraging the internet and modifying the education system so that what the student learns matches the industry requirements. Furthermore, greater emphasis needs to be given to science – I would even recommend having a science track in MBA programmes like they have for Finance, Marketing, HR, IT etc. This will generate more business managers with a proper understanding in science who can lead our country into the next decade.

What are your future plans?

SciGenom will continue to build its current offerings in DNA sequencing, Bioinformatics and Medical Diagnostics. Later this year,we plan to spin off our medical diagnostics division (MedGenome) as a separate company with a CLIA certified central lab in Chennai and satellite labs in all major cities throughoutIndia. We plan to raise about $5M for this expansion.

Do you think India can emerge a leader in the area of genomics with its scientific manpower edge over others? How can we arrest brain-drain and make brain-gain in this field?

It will be difficult for India to take leadership in this field, but we can become a strong player if we play our cards well. At present, we don’t have an edge in scientific manpower– we lack expertise and leadership. However, brain-drain in the short term still works well for us, as we lack the facilities to teach them all, our youngsters can go out and learn in the best labs across the globe. What we need to do is to attract them back,along with already-trained NRI scientists,with advantageousopportunities in India.

We also have to have a realistic understanding of where we stand today. India, at present,has less than 5,000 qualified biology scientists in the whole country.The US, on the other hand, has that number in one of their largeruniversities and they have hundreds of such universities. Their spending on research is also astronomical compared to what we can afford. So we need to be clever in developing a strategy. It will be good for India to understand how smaller countries like South Korea and Singapore are contributing by focusing on a specific area critical to their national interest. For example, Singapore faces a shortage of fresh water – about 70 per centof it comes from Malaysia. Singapore has made it their goal to become self sufficient within the next five years. They aim to do this by achieving 100 per cent reuse of waste water, by using genomic technologies in waste water treatment. Arguably, they can achieve world leadership in that field. India can learn much from these approaches.

Do you think Indian hospital and healthcare chains are at par with their Western counterparts in the field of genomics? Is there a difference in the Indian and Western approach towards this emerging science?

Applying genomics to healthcare is new everywhere in the world. However, the Westis adopting it much faster than us but they also have their own challenges due to the more complex healthcare systems and role played by insurance companies. The problem with our approach is that we lack a clear plan. We have to make a cohesive approach taking into account our genetic heritage, diversity and challenges.

Is the common man in India aware of the real benefits of genomics? Do you think there should be awareness campaigns to generate more interest in this subject?

Even in the West, the common man has yet to become aware of the full benefits of genomics. In India, we definitely need to have awareness campaigns and other schemes for all sections of society to understand and take advantage of this knowledge. For example, farmers can breed better varieties of crops if they understand the genes that affect many of the traits that they are looking for.

The Last Crusade - The epic voyages of Vasco Da Gama' by Nigel Cliff - Book Review

Journey from the end of the world!

Medieval Europe considered Lisbon in Portugal to be the end of the world. Vasco Da Gama's discovery in 1498 of the a direct sea route from Portugal to South India and his epic voyages from Lisbon to Calicut in Kerala, India marked a turning point not only in global commerce but also signaled the start of European colonialism which would convulse the world for the next many centuries. These facts are well known. However Nigel Cliff in this book clearly explains how christian religious fundamentalism also played a major role in motivating this small country of around 1 million people to undertake this fantastic endeavor in the face of high odds, as the final crusade of their centuries old war against Islam. Now it is hard to imagine that it took the English and the Dutch another 200 years to overcome the lead the Portugal established in commerce with the East through this sea route.

Vasco Da Gama is a well known figure in Kerala as well as the rest of India. Growing up in Kerala, the impression I had of Gama was that of a brave but cruel explorer out for adventure, glory and financial gain. A few books and a couple of movies on him that are available in India do not portray anything different. The local christians in Kerala maintain that the Portuguese were 'surprised' to see Christians in India and since the Kerala Christians were following the Persian (Syrian) rituals, the Portuguese fought them and burnt their churches (this did happen, but that was over a 100 years later). But Nigel Cliff paints a much different story. One of the major hopes of the Western World was to find Christian strongholds in the East and use their help in continuing their fight against Islam. Further their world view was so limited at that time (maybe even now to a large extent when you see the Christian right in mid-west US) that they imagined the all non muslims were christians! It is really funny to see Gama and his crew visiting Hindu temples in Calicut and seeing them as crude versions of Christian worship!!

The 'Last Crusade' provides a clear explanation of Gama's motives and actions, and the hatred of Muslims and Islam that led to his antagonistic behavior with the local kingdoms of Kerala who were having centuries of good relationship with Muslims. Not only Muslims, but Christians and Jews as well were enjoying a safe sanctuary in Kerala where complete religious tolerance was practiced. It will need another book to understand how in a place that supported the horrible 'caste' system of Hinduism where a large segment of the population was mentally and physically subjugated, could at the same time welcome all religious faiths from across the word and live with them in perfect harmony. One reason might have been the fact that being a small strip of land in the coastal peninsula, protected by a mountain range on one side and the mighty ocean on the other sides, only refugees or traders could come to Kerala - till the time larger ships and canons starting with Gama could venture in.

Well researched and well narrated, the Last Crusade is a good read. Definitely written from a Western point of view, it hardly covers the Indian (or Kerala) perspective. However that is understandable. But I was disappointed at the lack of maps which should have been rather easy to include. Since a significant part of the book covers the various voyages a few maps (both current and the old) would have given the reader much more enjoyment. Fortunately with wikipedia access it is not a serious problem.

Religion has played a major role in all human civilizations and unfortunately continue to do so today. In spite of generating continuous conflict and inflicting tremendous harm, it is not difficult to imagine it having helped humanity many times in the past in battling and surviving unimaginable odds where maybe only 'faith' was the final weapon. But now with a much better understanding of what we are and how we became us and our place in the Universe, it is high time that we as a species find better solutions. Books like these are good steps in the right direction for understanding our past mistakes.

The Whole Genome Matters!

With the publication of over 30 papers last week from the ENODE project, it has become clear that a large part of the human genome plays a role in our cells. In the last few years, many findings were showing that some of the non coding regions (99% of the genome) were involved in regulating the genes (the 1% coding part of the genome) but nobody expected the ENCODE project's claim that 80% of the genome plays some part - whether this ends up being an exaggeration or not, I think we have a paradigm shift in our understanding of the genome.

The San Francisco Chronicle covered the news in its front page

http://www.sfgate.com/default/article/DNA-Junk-Now-Seen-as-Complex-Switches-3843289.php

The NY Times also gave it good coverage

http://www.nytimes.com/2012/09/06/science/far-from-junk-dna-dark-matter-proves-crucial-to-health.html?_r=0

For a complete technical coverage check out

www.nature.com/encode

Nature has also put a free iPad app in the Apple Store. Check out the video recording - it gives a good overview of the Encode project as well as the results.

What a Plant knows - A field guide to the Senses by Daniel Chavotiz (Book Review)

Plants and Us - the shared genetic heritage between long separated cousins!

We as a species find it very easy to identify with other animals and we are adept at imagining anthropomorphic qualities in them but we seldom feel the same with plants. In this book ‘What a Plant knows’,  Daniel Chamovitz examines how plants see, feel, hear, smell and remember and shows us that the genetics underpinnings are the same as us, though they took a different evolutionary path in the last one billion years.

Starting with Darwin’s contribution in the study of plants (it is amazing  how much a single man has contributed to the field of evolutionary biology), Daniel looks at the different ‘senses’ from a plant’s point of view, the role of the various genes and how they have evolved to create the huge diversity in the plant kingdom that we see today. The best thing about the book is the way Daniel defines the fundamentals of each ‘sense’, how we humans use that sense and how it differs when it comes to the realm of plants.

Maybe not as eloquent as Richard Dawkins or as technically deep as Nick Lane, Daniel Chamovitz brings a different style of science writing that I found fascinating. Explaining the concepts in a very clear and simple manner, while not dumbing it down, Dainiel has done a remarkable job.  Though the book is on plants, I found its coverage of genomics (from the basics to the complex) one of the best that I have seen. (Never seen a better one line definition of ‘Epigenetics’).

We take plants for granted and see them basically as food for us. Though we  acknowledge their greenery, beauty and other contributions to making earth a habitable place, we still never take them as seriously  as we would consider animals or birds. However any one who read this  book will start looking at plants differently. From the carnivorous venus fly trap to the stately oak tree, we will start admiring the innovations that our cousins have come up with using the same genetic code that we share with them.

Don’t miss this book – it will enhance your senses!

Why Nations Fail by Daron Acemoglu- Book Review

Recipe for Success!

We tend to believe that the People and the Land make up the Nation - and hence the ability of the people and the quality of the land whether it is the geography or the availability of natural resources that determines whether a Nation will succeed or fail. But in this well researched book the authors show that it is the nature of the political and economic institutions which a nation creates that determines success or failure.

Authoritarian political institutions and extractive economics institutions are recipes for failure. But why do some countries or even adjacent cities develop them while their neighbors get democracy and inclusive economic institutions? Small initial differences going back hundreds of years which divert nations in different directions, contingent events, calamities, great personalities all explain the destinies of nations.

Covering countries from the West and the East, from Africa to Indonesia, from Australia to Antartica, the authors have a done a great job covering history, politics and economics and providing such insights that the book is a pleasure to read. There have never been a doubt that with free markets and equal opportunity, people from all backgrounds and nationalities can do well. For many decades we have seen immigrants from the world over get to the shores of the United States and do exceedingly well. But it had been difficult to understand why America developed they way it did while neighboring Mexico went down the other way. Or countries like China and India with ancient civilizations and colorful histories ended up being poor nations with millions on impoverished people. And why are they able to now rise back? And which model will succeed? Read the book to find out - you will not regret the effort.

I wish they can make this a compulsory read for all politicians......