Sequencing 100,000 Asian genomes for tailor-made healthcare - Straits Times, Singapore

NTU to host project database; aim is to reduce bias of medicine towards Westerners - Lin Yangchen

Not too far in the future, you may be able to receive tailor-made medical treatment for your body, increasing your chances of survival and recovery from serious illnesses.

This is one of the aims of an initiative to sequence the genomes of 100,000 Asians over the next three to four years. The move will try to reduce the bias of modern medicine towards Western populations.

An earlier project in 2009 stimulated interest in Asian genetics when it surveyed specific genetic variations across 1,928 people in South-east and East Asia.

Now, Singapore's Nanyang Technological University (NTU) will host the database for the ambitious new project, which was announced by the non-profit multinational consortium, GenomeAsia 100K, in February.

NTU president Bertil Andersson noted that almost all current personal genomics efforts focus on Western populations. He said: "The new consortium will benefit the Asian population as it sheds light on the genetic fabric of Asians."

ACCOUNTABILITY

Singapore has very high standards in finance and corporate law.

NTU'S PROFESSOR STEPHAN SCHUSTER, on the partners of GenomeAsia 100K choosing NTU to host their database because of Singapore's reputation for accountability.

Asia has more than four billion people, making up more than half of the world's population.

The project aims to cover at least 40 countries across Asia, and all major ethnic groups on the continent.

Combined with data such as people's living environment and health status, the exercise will make it possible to better understand and treat diseases in Asians, said venture capital firm Emerge Ventures. The Singapore firm supports the consortium's meetings, and helps it find potential partners and philanthropic donors.

The consortium's scientific chairman, NTU's Professor Stephan Schuster, said: "There is a massive bias in medical research; Europeans have been developing drugs for Europeans without asking how compatible these pharmaceuticals are for the rest of the world."

He explained the benefits of customising medical treatment to individual patients, an approach known as precision medicine.

For example, he said, the debilitating effect of chemotherapy on cancer patients makes it important to administer the right drug to minimise suffering and maximise the chances of recovery.

GenomeAsia 100K comes after a similar initiative - the 100,000 Genomes Project - was launched in 2012 by the British government-owned company Genomics England.

The partners of GenomeAsia 100K chose NTU to host their database because of Singapore's reputation for accountability, said Prof Schuster. He said: "Singapore has very high standards in finance and corporate law. We were given the trust and confidence from the other Asian countries." He stressed that the consortium will abide by the United States' Genetic Information Nondiscrimination Act of 2008, which prohibits the use of genetic data in health insurance and employment.

When data enters the database, it will be accessible only to the consortium members for an initial period of 18 to 36 months for analysis, after which it will be made available in anonymised form to the scientific community at large, he added.

To date, 50,000 DNA samples have been collected through blood or saliva samples from a network of clinics across Asia with the help of two of the consortium's founding members, genomics companies Macrogen in South Korea and MedGenome in India.

Macrogen's chairman, Professor Jeong Sun Seo, said: "As the consortium is envisioned to be independent of any government's interest, there is greater scope for comprehensive coverage of the peoples of Asia."

Mr Mahesh Pratapneni, chief executive of Emerge Ventures and exective chairman of GenomeAsia 100K, added: "The consortium is expected to contribute towards better global healthcare outcomes by channelling the collective capabilities of the leading industry players in the region."

The consortium is in talks with potential academic and industry partners in Singapore, Malaysia and Thailand, and is looking for more partners and philanthropic sources to make up the US$150 million (S$200 million) total funding it says it needs.

Prof Schuster pointed out that any concerns about ethnicity issues are unfounded. He said: "Some people are apprehensive that if you unravel differences in ethnicity, you make some people a lesser man and others a better man.

"But it's not true. It gives people pride in their identity, and also it gives them their history."

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!  

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.

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.

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.

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.

Denial: Self Deception, False Beliefs, and the Origins of the Human Mind by Ajit Varki - Book Review

A Great question but an unconvincing answer!

In this book Ajit Varki addresses a very critical and important question that would strike any one looking at human evolution - how come our species is the only one that attained self consciousness? Why didn't any other species cross the barrier? The dinosaurs did get plenty of time - even by cosmological standards, 200 million years is a decent time period.

Most probably I would not have read this book, except that I happened to meet Ajit Varki at a conference recently. (Btw, the conference was 'From Bones to Genomes' at Sitges close to Barcelona - a fantastic conference with speakers like Matt Ridley, Svante Paabo, Chris Stringer etc - making it a veritable heaven for those interested in Evolution, Genetics and Population history). His book was also mentioned in some side discussions and that prompted me to download the kindle version (talk about the benefits of technology!) and take a stab at it.

However the approach of the book was rather surprising. Ajit had decided on the answer upfront - that humans were able to cross the 'intelligence barrier' by being able to deny the inevitability of death. To make it clearer, according to Ajit the barrier that prevents any species from attaining self consciousness is that it will not have the neuronal connections or capabilities to handle the fact that death is inevitable. Only the human brain developed in such a way that both self consciousness and death denial ability developed together at some time (only once) in our past and that was the turning point. The book is then one long argument (in the author's words) to try to convince himself and the reader that the argument is correct. (lot of cherry picking!) Ajit acknowledges that there is no clear evidence to prove his thesis and also acknowledges that it is not falsifiable but does try to be as fair as possible in outlining that. He still gets carried away with his theory and even attempts to compare the situation with that of Darwin's Evolution theory in the late 19th century. But he ignores that Darwin did not start with a conclusion - he had discovered a large number of facts that led him to a conclusion which is not the case here.

The book is an interesting read and the author is a very knowledgable person that makes the narrative fun. But I have to say that his answer to an all-important question is possible but not probable.