Thursday, November 12, 2015

The Brain: The Story of You by David Eagleman - A book review

From Incognito to Singularity!

In his earlier illuminating book ‘Incognito’, David Eagleman showed us our hidden selves and challenged us to think about ourselves differently. He continues in that direction in his new book ‘The Brain: The Story of you’ and visualizes the possibilities of the future of the brain  and in fact the future of our species.  The Singularity is a concept popularized by the well known futurist scientist Ray Kurzweil (refer his book ‘The Singularity is Near’ in 2005) where he envisioned a future where we will be able to leave our bodies and live in a digital world by uploading our brains into a computer system. Kurzweil was pretty much vague on the details  but Eagleman in this book shows us how challenging that can be.

With over 100 billion neurons and many trillions of connections among them, the complexity of the brain is unquestionable but understandable. However the fact that  ‘consciousness’ emerges from this is the amazing outcome that leaves us in awe. Kurzweil had argued that ‘consciousness’ is a rather natural outcome of a complex interconnected system, and in books like the ‘The Age of Spiritual machines’ it was assumed that soon computers and robots (and may be the Internet) would develop a consciousness.

But as we understand more about the biological nature of the brain and its learning system, we will start doubting whether an artificial system will ever develop  consciousness on its own. I don’t doubt that when technology is advanced enough we would be able to create a human like (or a human better) intelligence but I don’t  think a machine or AI system can naturally develop  consciousness if its creator (that is us) did not train it to. 

The best parts of David Eagleman’s book are where he explains (a) how the plasticity of the brain and its self learning ability to understand patterns can be leveraged in the future to provide different inputs to the brain (than the normal sensory inputs that we are born with) (b) how many other inputs that we don’t normally recognize influence our brain – a beautiful example is on how our emotions are influenced by the input  to our brain from our facial muscles when we witness an event (c) what will be our future – I leave this for you to read and find out!  

Thursday, August 6, 2015

Interview with ET HealthWorld


INTERVIEW: MedGenome raises Series B to advance the practice of precision medicine in India

MedGenome, a leading provider of genomics research services globally announced $20 million Series B investment from Sequoia Capital on June 22nd 2015.

MedGenome, a leading provider of genomics research services globally announced $20 million Series B investment from Sequoia Capital on June 22nd 2015. Sam Santhosh, CEO MedGenome, speaks to Shahid Akhter on the path that MedGenome is treading now and what lies ahead.

1. What prompted you to genomics and how has been the journey so far?

The completion of the first draft of the human genome by the International Human Genome Project in 2001 originally attracted me to this field. 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. I spent few years in reading and learning about the subject during which 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 now we are at a stage talking about a $1000 genome in two weeks.

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, animal sciences, environmental protection, bio-fuel, and so on. Using the same technologies vertical solutions in these domains could be developed. So I created a services company called SciGenom and MedGenome was incubated as an entity for medical genetics. And we spun it off as a separate company in 2013. So far the growth has been encouraging.
We have a leading position in clinical genomics in India and has set the benchmark for clinical genomics in emerging markets. We have also pioneered genomics-based research in India through our network of collaborators to enhance our understanding of the diseases at the genetic and molecular level. These were possible because of our extreme focus on bringing the latest advancements in technology in the Indian market - be it the advanced NGS lab in Bangalore or the launch of the non-invasive prenatal test for the first time in a facility in India - and success in developing world class bioinformatics pipelines.
2. What was your initial vision for the company? Where do you think you are with the vision?

Initial vision was to create a company in India applying genomics to improve personalized medicine in India and reduce the burden of inherited diseases. Subsequently the vision got enhanced to provide genomic research solutions to pharma once we understood the potential of Indian population to provide better understanding of complex diseases. And this has been very exciting and rewarding experience.

We have the most advanced technologies in our lab, for example the latest Illumina HiSeq 4000 machine addition to our lab; the first in India. We have developed intellectual property through proprietary platforms such as OncoMD, our cancer mutation platform and OncoPept, our immunotherapy solutions supported by our unique bioinformatics pipelines and proprietary databases. We are also the leading clinical genomics company in the country. We have our presence in the US as well through our R&D lab in San Francisco and office in Boston. And the recent Series B funding will allow us to expand our offerings and reach further.
3. How do you find the concept of 'genetic testing' gaining currency in India today? How does this compare with global market?

We have seen good progress on the acceptance of genetic testing. It is a function of awareness and the affordability, both of which have been focus actions for MedGenome as the leader in the market.
What has been very encouraging is the consistency of the prescribers once they see the value of genetic testing in their practice. We work with thousands of doctors every month across hundreds of institutions and the collaborations have been very enlightening.

It is also important to not stop at delivering a report but also support the patient in learning about the specific nature of the genetic condition. Which is where counselling plays an important role.

Globally, genetic testing has gained considerable traction in clinical setting for diagnosis, prevention, treatment and management of a wide variety of diseases with an underlying genetic reason, in light of the recent advances and celebrity endorsements. It is a rapidly expanding segment of the molecular diagnostics market worldwide given the increasing awareness about the value that these tests bring to the healthcare providers.

4. How would you summarize the trends in the molecular diagnostics sector over the past five years?

Genomics has seen rapid advances in the technology of decoding the DNA, triggering a revolution in our ability to understand the genetic and molecular basis of health and disease.

Genomic biomarkers as companion diagnostics are helping the pharma majors to provide more targeted therapies. Oncology has taken a lead in this so far but applications in other disease areas have been looked into. Genomics to enable differential diagnosis in neurological disorders is a good example of this.

Translation of large scale sequencing data into information of clinical utility is gaining importance globally. In the US, many companies have leveraged this opportunity - Foundation medicine is offering comprehensive genomic profiling for tumors, Invitae provides genetic testing across multiple disease areas and Natera has grown on its proprietary non-invasive prenatal tests. Over a million tests in NIPT have been prescribed in the US so far. So an understanding of the need and the acceptance for genetic testing have been encouraging so far.

Predictive medicine, using advances in accurate technologies in medicine, genomics, proteomics, cell biology, imaging etc. and allowing us to predict how, when, and in whom a disease will develop has gained traction in the recent years. This could be a new revolution in human health care where genetic information contained in an individual's genome is interpreted to predict future predisposition to diseases. Many companies have been built and are experiencing growth leveraging this trend, in the US especially.

Lot of work went into advancing the use of genomics in exploratory research and drug discovery in the recent years.
5. Your opinion about the genetic testing market and where does MedGenome stand?

 Genetic testing has clinical applications for diagnostic, predictive, carrier, prenatal & pre-implantation testing, and newborn screening, also playing a vital role in pharmacogenetic testing. It offers distinct advantages because of its ability to facilitate early disease detection with simpler and cost effective treatment and stratification of patients into groups allowing selection of optimal therapy.

It is going to be the standard in the future. A genetic testing report will be an integral part of a physician's decision making process. As far as MedGenome, it is a leader in the clinical genomics market. MedGenome offers more than 100 tests currently across Oncology, cardiology, ophthalmology, neurology and nephrology. We have pioneered the launch of advanced genetic tests in the country - such as the non-invasive prenatal test launched this year. We will be the only company conducting this test in a facility in India.

Outside India, we are focused on providing diagnostic and research solutions only. Our OncoMD, cancer analytics platform, provides valuable clinical parameters to enhance the value of a diagnostic report through an API integration. Our OncoPept, cancer immunotherapy solution, allows identification and prioritization of peptides towards vaccine development by pharma and biotech.

6. What hurdles you have faced since inception?

 One of the first hurdles was on educating the prescribers and the patients on a larger scale about genetic test offerings and the impact it can have on patient's life. We had few who were aware and were early adopters, but to scale and customize the offerings, we needed to generate awareness. Cost of infrastructure was also important. We focused on having the latest technologies in sequencing for India and that required investment. It has allowed us to provide high quality reports with faster turn-around times which is essential for the stakeholders. We also had to develop our IP on population specific variants in Indian patients. Such information allowed us to refine our genomic data interpretation more accurately giving us an edge in the Indian market.
7. What are the challenges you feel the genomics and biotech industries are facing today? Do we need regulations or code of conduct?

 Rising R&D costs is a challenge that is experienced by the biotech companies globally. Regulatory barriers and reimbursement from insurance companies is also having a significant impact on the success of the industry. Genomics, as a discipline, is recently studied as a means to improve R&D efficiency by improved patient stratification for clinical trials, thereby reducing the time and cost required for the trial. Regulatory authorities are also encouraging this as the results from these trials are more targeted and in favour of the needy.
From genetic testing perspective as well, certain factors like regulatory body approval, and reimbursement from insurance companies are crucial. In the western world, insurers have started accepting genomic tests in their formulary as it is expected to reduce the cost of down-the-line treatment. Another challenge is on patient confidentiality and ownership of genomic data. Requirement is to have policies and committees to enforce a check on this as genetic testing grows in the clinical practice.
In India, these tests are yet to be offered at affordable prices. There is also a great need for clinicians who have a good understanding of genomics and its clinical significance. Genetics, as far as I understand, is not widely adopted as part of the medical college curriculum in India.

The patient journey must be well managed so that if a particular condition is identified, the experts are brought in to handle the situation and help the individual. There is a dearth of genetic counsellors who can explain genomics findings to the affected individuals and their families. In addition to this, lack of baseline genomics data of Indian origin and unclear policies on intellectual property rights also pose hindrances to the industry.
8. Where do you see MedGenome 10 years from today?

 We want to be a global leader in genomics-based diagnostics and research. A company working on cutting-edge technologies and where core capabilities and Intellectual property are built.

We have an opportunity to look beyond generics in the Indian health care space and contribute towards drug discovery and exploratory research and gain a prominent role in the global healthcare industry.
9. Any advice you would like to give to budding entrepreneurs?
Science provides huge number of opportunities for budding entreprenuers. I would urge them to look beyond IT and Ecommerce and leverage the revolutionary advances in Genetics, Nanotechnology, Neuroscience and Robotics to develop products and solutions that can make a significant difference to humanity.

Thursday, July 23, 2015

Walking Whales: The journey from land to water in eight million years by Hans Thewissen - Book Review

How Whales originated in India and conquered the Oceans!

Evolution provides countless of amazing stories as we look at how each species evolved.  But story of the whales  (which are mammals) ancestors that went from land to water about 40 to 50 million years ago beats the best of them. And in between for a few million years there were whales (much smaller off course than the ones we see now) that had legs and could walk on land as well as swim in the water!

Hans Thewissen who discovered the first ‘walking whale’ later called Ambulocetus in Pakistan in the early 1990s, tells this fantastic story in great detail. The science behind the discovery and the subsequent journey is meticulously explained and this book will be a great learning experience for any reader. Starting from what makes a whale a whale (it is the tymphanic bone in the ear), to the importance of teeth and the dental formula (just by a tooth an expert can tell you what species it belongs to!) is amazing. Other interesting facts such as the oxygen isotopes in the bones that lets you determine whether the species lived in land or water, makes the book so enjoyable to read.

Perseverance is the key to success and the author’s efforts in India and Pakistan over the last 20 years in searching for and discovering numerous fossils and his focused studies in understand the swimming, feeding, breeding activities of this species underlies that.  The deciphering of  the development of the brain, vision, hearing etc of the Ambulocetus and related species from different fossil fragments makes a large part of the book feels like a detective story. The author’s skill in explaining not only biology and paleontology, but also other domains like geology and plate tectonics is wonderful. I have not read a better explanation of plate tectonics anywhere else! The isolation of the Indian peninsula after it broke away from the Africa about 50 million years ago gave the walking whales an opportunity to evolve in isolation.

Many Indians spent considerable time worshipping their Gods in the Himalayas but instead if they had spent a fraction of that time understanding how the Himalayas were formed, they might be able to appreciate the forces of Nature better. And the story of the Whales and their journey to conquer the oceans should be inspiring to all Indians.

Friday, June 19, 2015

Early bird gets the free sex?

From: Nature - June 11, 2015

Lazy male birds pay a high price

Male songbirds that sleep late risk having their female partners mate with another male.
Mating outside of a monogamous pair in birds normally happens early in the morning. To find out if rising earlier or later would affect reproductive patterns of great tits (Parus major), Timothy Greives of North Dakota State University in Fargo and his co-workers captured male birds in Germany and implanted them with a device that releases melatonin. This hormone is generated mostly at night to set the circadian clock. Male tits that had night-time-like levels of melatonin around the clock began their daily activities on average 10 minutes later than the control group. Their nests also contained more offspring fathered by another male, suggesting that the late-rising males were less able to defend their mates.

Saturday, May 30, 2015

A Well-ordered Thing: Dmitrii Mendeleev And The Shadow Of The Periodic Table - Book Review

The man and the country behind the periodic table!

The periodic table would match any other basic scientific discovery on the impact to science and most of us would have heard of Mendeleev (though we might spell it and pronounce it in many different ways). However compared to many other well known scientists like Newton or Darwin or Einstein, we would be hard pressed to recollect much additional information about Mendeleev. We would also be surprised to hear that he came out of Russia - country hardly known for its scientific prowess in the 19th century. Michael Gordin aims to set that right and shows us a full picture of Mendeleev across his life time and the life and culture of Tsarist Russia at that time period.

The author makes it clear that this is not a traditional biography. His plan is to highlight the dilemmas of a nation at the cross roads of history and the achievements of a polymath from a poor background who nevertheless achieves tremendous success (along with failures). And that makes a fantastic story. How come the Periodic table came from Russia? What were the steps that led Mendeleev on this path? How did the final table evolve? What were the other areas that Mendeleev worked on? What were the challenges that he faced? These are the questions that you will find answers to, in this book. Some of it will seem very relevant to modern times - the play of economics, politics, superstition in science and society seems to apply equally well in the 21st century.

This is a good read for anyone interested in history, culture and science. The story of a gifted individual and a great nation and the impact of fundamental transforrmatory forces on them will be difficult to forget.

Wednesday, February 25, 2015

A Primate's Memoir: A Neuroscientist's Unconventional life among the Baboons by Robert Sapolsky - A Book Review

Exploits of a ‘hippie scientist’ in Africa

This book is supposed to be a study of the baboons in Africa by a neuroscientist. The author ‘joins’ a troop of baboons  in Kenya, gives them various names from the old testament and monitors them closely. Joining is obviously an exaggeration as the author is armed with his jeep and other accessories but more or less camps closely to the troop and tracks the activities of the troop members. The main objective of the study seems to be tracking the stress level of the male members as they pass through the various hierarchical positions in the troop. This is achieved by anesthetizing them occasionally using a blow dart gun and then taking their blood samples. He also observes the social behavior of the members including tracking ‘who is making out with who’.

Only less than 20% of the book cover the baboons while the rest is spent on various adventures of the author in different African countries, in the national parks as well as interactions with the ‘black’ natives. A typical western person’s view of African life is depicted in those descriptions if one can suffer to read through all of it. How much of these are ‘hallucinations’ and what are real is difficult to make out.

I don’t think this book merits as a science book by any standards – since very little of science (forget neuroscience) is covered. Couple of chapters (one in the beginning and one towards the end) are interesting from a view of understanding baboon group behavior. However the author hardly seems to take into account the trauma he must have been imparting on the group by walking around and darting them! He acknowledges that they would run away from him and it was an uphill task for him to get close to them, as time went along. It is a basic rule in science that the process of measuring does affect the metric that you are trying to measure – but in this case the stress level induced by the scientist would dramatically influence whatever he was trying to measure.

Maybe my criticism is unduly harsh considering that the study was done many years back and the book itself was published in 2001. Reading it in 2015, I would be looking at it from a much later perspective. But  still, it will be hard to deny the basic facts that I have highlighted and I would not recommend anyone wasting time with this book.