Cold Spring Harbor lab’s Michael C. Schatz wrote
“The Next 20 Years of Genome Research” with a view of the future and a set of recommendations for the newborns and alike.
Children born this summer will grow up in a drastically different world than the childhoods of the current graduating class or those from twenty years ago. The class of 2035 will have unprecedented access to information, quantitative techniques, and biotechnologies that will be used to manipulate biological systems in currently unimaginable detail. While the foundations of biology will continue to be observation, experimentation, and interpretation, the technologies and approaches used will become ever more powerful and quantitative. More so than ever, we need to revise the curriculum to integrate computational and quantitative analysis as early as possible into their training so they are ready for the world ahead .
My recommendation to the class of 2035 is to embrace the integration of fields that is forming modern biology. To be competitive, you will need to establish a broad interdisciplinary foundation of math and sciences as well as strong communication skills. One of the most important skills you can develop early is computer programming. While sequencing technologies and other instrumentation will come and go over the next 20 years, biology will only continue to grow its dependency on computational analysis. And much like learning to speak a new language is often easier the younger you begin, learning to speak to a computer seems to follow a similar path. But I also encourage you to experiment with the wet side of biology as early as possible as well, since this will help you to appreciate the data you work with and put you in a position to run your own experiments end to end. Indeed, the most profound advances often occur at the intersection of new biotechnology and new quantitative analysis, when you can be the first to generate a novel data type that is used to unravel a mystery of how the world operates. Finally, always remember to keep focused on the most important problems that you can hope to address.
Thankfully our newborns did plenty of experiment on the ‘wet’ side of biology by wetting their beds.
Here is how the future will be delivered to you, according to Michael Schatz -
Over the next twenty years, though, our power for doing so will greatly improve building on the pioneering work of ENCODE , the Roadmap Epigenomics Project , and similar projects that are starting to provide detailed annotations as to the roles and evolution of sequences all throughout the genome.
Readers may note that ENCODE has been thoroughly discredited and ‘Roadmap Epigenomics Project’ is being led by Manolis Kellis, who was accused of fraud and scientific misconduct for his earlier work by Berkeley mathematician Lior Pachter.
An inconvenient request
One of the great things about conferences is that there is time to chat in person with distant friends and collaborators. Last July, at the ISMB conference in Berlin, I found myself doing just that during one of the coffee breaks. Suddenly, Manolis Kellis approached me and asked to talk in private. The reason for his interruption: he came to request that I remove an arXiv post of mine, namely Comment on Evidence of Abundant and Purifying Selection in Humans for Recently Acquired Regulatory Functions, a response to a paper by Ward and Kellis. Why? He pointed out that my arXiv post was ranking highly on Google. This was inconvenient for him, he explained, while insisting that it was wrong of me to post a criticism of his work on a forum where he could not directly respond. He suggested that it would be best to work out any issues I might have with his paper offline. Unfortunately, there was the inconvenient truth that arXiv postings cannot be removed. Unlike some journals, where, say, a supplement can be revised while having the original removed (see the figure switching of Feizi et al.), arXiv preprints are permanent.
My initial confusion quickly turned to anger. After all, my arXiv comment had been rejected from Science where I had submitted it as a technical comment on the Ward-Kellis paper. I had then put it on the arXiv as a last resort measure to at least have some record of my concerns publicly accessible. How is this wrong? Can one not critique the work of Manolis Kellis?
Speaking of futuristic forecasts, readers may also take a look at the following one written by NIH Director Francis Collins in 1999 -
A HYPOTHETICAL CASE IN 2010
General visions of gene-based medicine in the future are useful, but many health care providers are probably still puzzled by how it will affect the daily practice of medicine in a primary care setting. A hypothetical clinical encounter in 2010 is described here.
John, a 23-year-old college graduate, is referred to his physician because a serum cholesterol level of 255 mg per deciliter was detected in the course of a medical examination required for employment. He is in good health but has smoked one pack of cigarettes per day for six years. Aided by an interactive computer program that takes John’s family history, his physician notes that there is a strong paternal history of myocardial infarction and that John’s father died at the age of 48 years.
To obtain more precise information about his risks of contracting coronary artery disease and other illnesses in the future, John agrees to consider a battery of genetic tests that are available in 2010. After working through an interactive computer program that explains the benefits and risks of such tests, John agrees (and signs informed consent) to undergo 15 genetic tests that provide risk information for illnesses for which preventive strategies are available. He decides against an additional 10 tests involving disorders for which no clinically validated preventive interventions are yet available.
John’s subsequent counseling session with the physician and a genetic nurse specialist focuses on the conditions for which his risk differs substantially (by a factor of more than two) from that of the general population. Like most patients, John is interested in both his relative risk and his absolute risk.
John is pleased to learn that genetic testing does not always give bad news his risks of contracting prostate cancer and Alzheimer’s disease are reduced, because he carries low-risk variants of the several genes known in 2010 to contribute to these illnesses. But John is sobered by the evidence of his increased risks of contracting coronary artery disease, colon cancer, and lung cancer. Confronted with the reality of his own genetic data, he arrives at that crucial teachable moment when a lifelong change in health-related behavior, focused on reducing specific risks, is possible. And there is much to offer. By 2010, the field of pharmacogenomics has blossomed, and a prophylactic drug regimen based on the knowledge of John’s personal genetic data can be precisely prescribed to reduce his cholesterol level and the risk of coronary artery disease to normal levels. His risk of colon cancer can be addressed by beginning a program of annual colonoscopy at the age of 45, which in his situation is a very cost-effective way to avoid colon cancer. His substantial risk of contracting lung cancer provides the key motivation for him to join a support group of persons at genetically high risk for serious complications of smoking, and he successfully kicks the habit.
Readers know how that story turned out. The personalized genomics company ‘23 and Me’ was banned by FDA from giving medical advice in 2013. Lior Pachter wrote “23andme genotypes are all wrong”, but later changed the title to “Multiple testing an issue for 23andme” with a note that the previous title was technically correct.