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September 2017 with Nathan and Laura: Venter Blunder, RNAi Returns, and Monthly Science Moments

To honor Laura's pentametric thirst,

We write the summary today in verse.

 

Was it a quake that had no epicenter,

That silly paper out by J. Craig Venter?

 

And after years of silencing the market

Has RNAi at last knocked out its target?

 

Then Nathan gives to yuppies devil's choice.

Which one libs: gluten dough or GMOs?

 

Know Then Thyself: Kari Stefansson, deCODE genetics

Kari Stefansson is a name well known in the field of human genetics. His founding of deCODE genetics in his native Iceland in 1996 took our field into a new frontier with the unique opportunity to work with not only a homogenous population but also to integrate with a large centralized healthcare database. It also surfaced a huge ethical debate about genomic privacy.

We’re very happy to welcome Kari to the program for the first time to talk about his vision for deCODE now that the company has been bought by Amgen. The company has continued to publish papers revealing major findings of rare variants associated with common diseases. Just last month Kari and deCODE published a paper in the NEJM with the discovery of a gene called ASGR1. The gene lowers the risk of heart disease by a substantial 34%.

Kari is passionate about discovery for the sake of discovery.

“All life on earth is rooted in information that lies in the simple code of As and Gs and Cs and Ts of DNA,” he reminds us. “Some of our discoveries are knowledge for the sake of knowledge. It is man studying man.”

But he also points out that as soon as they made the discovery of the ASGR1 heart-protective gene, researchers at Amgen went to work immediately on a drug discovery program. And, he says, he knows that many other pharma companies have already begun similar programs.

deCODE is perhaps best known though for their project to create a genomic database unlike any in the world. And for the ethical issues this has brought up. Last year deCODE announced that they had sequenced enough individuals to impute the genomes for the entire population of Iceland. This could lead to a new kind of preventative healthcare system that would be a model for other countries everywhere. It’s also left Kari and his colleagues scratching their heads over whether, for example, they have a social obligation to find out who in Iceland carries the dangerous BRCA mutations.

He shares some dramatic statistics that reveal their dilemma:

"Women who carry this mutation have 86% probability of developing a lethal cancer. They have 72% probability of developing breast cancer. They have a life expectancy that is twelve years shorter than non-carriers. They are three times more likely to die before the age of 70 than the non-carriers. And most of this risk could be mitigated by preventative surgery, for example.”

The interview goes well over our typical target of 20 minutes. But Kari is a deliberate thinker and an eloquent speaker. Enjoy.

Going Beyond the $1,000 Genome with Mark Gerstein

Though recent guests at Mendelspod say we're not quite to the $1,000 genome, we're close enough to use that benchmark in genomics discussions. But what are we getting for that almost $1,000?

Mark Gerstein is the co-director of the Yale Computational Biology and Bioinformatics program where he focuses on better annotation of the human genome and better ways to mine big genomics data. He has played a big role in some of the large genomics initiatives since the first human genome project, including ENCODE and the 1,000 Genomes Project.

“I’m very enthusiastic, of course, about the thousand dollar genome, but I don’t think that a true human genome has arrived for a thousand dollars,” Mark says at the outset of today’s interview. "The great excitement of next generation sequencing—which is deserved—has also obscured that there are a lot of very deep technical questions in terms of really assembling the tricky parts of the genome and really being able to conceptualize the more complex bits of human genetic variation that need to be tackled.”

So what are those tricky remaining parts? Mark shares his interest into the importance of structural variation, and says there is much more to learn from the overlooked non-coding portion of the genome. He’s particularly interested in pseudogenes.

We took some audience questions for Mark which lead us into a discussion of how best to query and mine big genomics data. As with several other leading bioinformaticians on the show, Mark agrees that privacy is the big issue for genomics and for society at large.

Ethical Issues around Editing Human Germline for the Future. Today It's about Plants and Animals, Says NYU's Art Caplan

 Art Caplan is a prodigious writer on the topic of medical ethics. How prodigious? How about thirty-two books and over 700 peer reviewed papers on ethical conundrums ranging from organ donation to end of life care.

He spends about half his time as a public figure, engaging the lay audience, for example, through op-eds like his recent piece for the Washington Post arguing that doctors who oppose vaccination should lose their license. The other half of his time he spends developing materials meant for an academic audience.

In today’s interview, Art begins by saying that ethical issues around the genome editing of plants and animals are much more pressing today than the current furor over human germline editing. That we can leave to our grandchildren, he says. What we must pay more attention to now is the introduction of genetically engineered mosquitos into the ecosystem.

Well versed in all of the major ethical issues which have surfaced here at Mendelspod, including the rise of prenatal diagnostics and abortions and the evolution of privacy, Art is pro science and technology, yet still sees himself like a “biblical prophet."

Just what is the role of a bioethicist? Is it possible to slow down science and technology?

 

A Revolution in Data Gathering: John Wilbanks

Podcast brought to you by: Assay Depot - the world's largest cloud-based marketplace for research services. With Assay Depot, you can easily find the perfect research service provider and manage your project from anywhere in the world.

Guest:

John Wilbanks, Senior Fellow , The Kauffman Foundation Bio and Contact Info

Listen (7:31) Disconnect between informed consent and digital technology

Listen (9:26) Consent to Research Project

Listen (5:59) Who will be the early volunteers to share their data?

Listen (11:46) Access2Research petition at White House-now what?

Listen (3:59) Can you describe the nature of the legal threats you've received?

Listen (3:33) Would you donate your child's data to research?

Listen (4:23) Data gathering undergoing a revolution

"I like making it easier to share things," says John Wilbanks, a senior fellow at the Kauffman Foundation. Also a member of the Board of Directors for Sage Bionetworks, Wilbanks has been involved in numerous projects having to do with opening up important content and data. Now he runs the Consent to Research Project where he is designing systems that allow people to donate their research to data. Wilbanks discusses the disconnect that is emerging between informed consent and the realities of the digital revolution. In this comprehensive interview he talks about the Access2Research petition he recently spearheaded to extend the NIH's open access policy to the other federal agencies.

Why does John like making it easier to share things? Hear about his past and find out his thoughts on data gathering in the future.

Listen to Wilbanks' TED talk

A 'Revolution in Science' with Joseph Jackson

Podcast brought to you by: Assay Depot - the world's largest cloud-based marketplace for research services. With Assay Depot, you can easily find the perfect research service provider and manage your project from anywhere in the world.

Guest:

Joseph Jackson, StartUp Science Bio and Contact Info

Chapters (Move marker to advance)

0:50 StartUp Science Event

2:41 What do you mean by a revolution in science?

6:45 Orthodox economics doesn't account for the impact of technology

25:33 What does privacy mean today?

39:06 "I believe it's attainable to eliminate aging in the next 50 years."

46:53 What is the most influential book you've read?

Joseph Jackson is is a leader in the open science movement. He organizes the yearly Open Science Summit and most recently he's a founding member of StartUp Science, a new event and business plan competition that took place June 15, 16th here in Silicon Valley.

Joseph believes there's an organizational revolution going on in science. Not shy of being a futurist, Joseph says that it's possible to eliminate aging in the next 50 years.



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