science funding


Preprints and the Future of Science Publishing with Jason Hoyt, PeerJ

A renewed effort has been underway by leading biologists this year to persuade their colleagues to preprint. This is the posting of a paper to an open access server before peer review and publication. The proponents argue that preprinting will be good for science because discoveries will be made available sooner. The peer review process can take several months, and by preprinting, a biologist doesn’t have to wait to get their work out there and begin interacting with the community.

It’s a powerful argument, and one that has been embraced by the discipline of physics for some time. However, only a small fraction of biologists have been willing to jump on board, according to today’s guest, Jason Hoyt. He anticipates that about 5,000 biology papers will be preprinted this year out of a total of 1.5 million.

As co-founder and CEO of the open access publisher, PeerJ, Jason advocates for preprinting. He and his co-founder, Peter Binfield, launched PeerJ Preprints back in 2013, one of the first preprint servers online. At that time, the two co-authored a blog in Scientific American (Who Killed the PrePrint and Could It Make A Return) explaining that historically preprints were the way science was done (though it wasn’t called that). They point out that it's only been in the last 50 years that the peer review process has come to dominate the publication of biological discoveries.

So why are so few biologists making use of preprint servers today? Jason replies that “it’s still early days” for the online servers.

“There’s some good questions being raised about what influence funders or tenure committees could have to encourage preprints," he says. "I don’t think a lot of biologists are educated yet as to what a preprint is, and what the benefits of it are. And that just takes time. It took 300 years for peer reviewed literature to get where it is today. And we’ve been going three years with preprints."

Like the popular open access journal, PLOS (Public Library of Science), PeerJ charges biologists to publish (with a somewhat different business model) and makes their publications freely available for the public to read. But unlikePLOS, PeerJ offers a preprint server at no cost to biologists who use it. Jason anticipates that preprinting will shake up the traditional peer review process. That in the future peer review will be done and paid for separately from publication.

“Publishing—the different components of it—are becoming commoditized already. It’s conceivable that in 10 or twenty years [science publishing] is completely commoditized. Meaning that we preprint first and then we pay for peer review, somehow—maybe the funders do it—and then it’s published separately. . . Maybe there will be an aggregation service that will help people run through this all themselves.”

We finish the interview with Jason’s thoughts on SciHub and questions of copyright.

Human Genome Turns 15: Mike Hunkapiller

We’re all familiar with the announcement in the year 2000 by US President, Bill Clinton, and the UK’s Prime Minister, Tony Blair, that scientists had completed the first draft of the human genome. It was a big deal. But the actual publications didn’t happen until the next year, February of 2001. Which means that this February is the fifteenth anniversary of the publication of the first human genome. For our commemorative show we’re joined by Mike Hunkapiller, the CEO of Pacific Biosciences.

Mike and his team at PacBio are coming off a great year. Their stock is up. Their long read sequencing technology is used for over a thousand scientific publications. And last year they launched a new better, faster, cheaper instrument, the Sequel, which are sold out through the first half of this year. PacBio is cool again.

How much were tool makers in the driving seat of the genomic revolution? And how much further can sequencing improve? Before asking Mike this, we explore some of his memories of those wild days when sequencing the human genome got presidents and prime ministers on the phone with their speech writers.

January 2016: Landergate, Grail, and Cancer Moonshot

“It being the month of Hypeuary, go hither through break in yonder wall called LanderGate, and thou wilt be on route to reach the Grail. Drink from this to find your Cure, and Death shall haunt you even more.” -Pithy Monton

Today we do something a little different. We’re joined by two commentators to look back over the past month’s headlines. Laura Hercher is a genetic counselor on the faculty at Sarah Lawrence College. She’s also a regular contributor to the DNAExchange blog. Nathan Pearson is the Senior Director of Scientific Engagement and Public Outreach at the New York Genome Center.

Framingham for the Modern Era: Josie Briggs on the Precision Medicine Initiative

Josie Briggs is Director of the National Center for Complementary and Integrative Health (NCCIH) at the NIH. She is also currently serving as interim director of the president’s new Precision Medicine Initiative (PMI).

What has happened since the president announced the initiative, what is the proposed timeline going forward, and how much money will there be for the project ongoing?

Josie answers these questions and more in today’s show, comparing the PMI to the well known Framingham Heart Study, probably the nation’s greatest longitudinal study to date. As with the Framingham study, the NIH is hoping that the PMI will engage the general public in biomedical research.

“Having the interest of the public in clinical research, and having people sign up and be engaged and say that they want to be a part of this is, to me, a very important component. In some disease areas, it’s striking how few people participate in clinical research. This is — and the president’s enthusiasm is part of it — this is a way for there to be broader engagement in clinical research,” says Josie.

Does the Reproducibility Project in Cancer Biology Offer a Model for a New Kind of Science Auditing?

Here on the show, we’ve talked about the lack of reproducibility for much of biological research. We’ve bandied around various percentages--is it 50% or up to 90% that can't be replicated? And we’ve poked around various issues that may be causing such poor science.

Nicole Perfito is the manager of the Reproducibility Project: Cancer Biology, an effort between Science Exchange and the Center for Open Science. The goal of this project is to take nearly forty “high impact” papers in the field of cancer and try to replicate them.

The team has reproduced several studies already. What are the main issues that are coming up? How helpful are the original authors being? And are there some low hanging fruit which might lead to dramatic improvements to research if adopted?

The project is still underway, but already Nicole and her team have some interesting hunches.

Brian Kennedy and Aubrey de Grey on their Converging Approaches to Aging Research

Last week we attended the 2015 Rejuvenation Biotechnology Conference where we heard about the latest developments in aging research.

We were fortunate enough to sit down with two of the major figures in the field of aging research, Aubrey de Grey, CSO of the SENS Research Foundation and Brian Kennedy, CEO of the Buck Institute for Research on Aging. Brian and Aubrey have gone about their work in different ways but say that their approaches are now converging as the momentum behind aging research increases.

How do the two see the field since Calico and Human Longevity emerged? What developments in the past year stand out to them? Join us for an exclusive interview with two of the aging field’s visionary leaders.

Ivan Oransky on Today's Retraction Boom

When science journalist Ivan Oransky co-founded Retraction Watch, a blog with the express purpose of making scientific retractions more public, he didn’t think he would be posting much.

“Adam Marcus, my co-founder, was quoted as saying, ‘yeah, we figured we’d post periodically, our mothers would read it, they’d be very happy, nobody would read it other than them.’ Obviously that hasn’t been the case,” says Oransky in this first of a series of podcasts on scientific integrity.

Now putting out almost a post a day and funded in party by a grant from the MacArthur Foundation, the blog has revealed - and no doubt helped drive - a boom in retractions the last few years.

What is leading to so much bad research, and just how is Oransky’s blog keeping scientists honest?

Oranksy points to science career pressures and financial incentives as part of the problem. He also explores the issue of cell line authentication, a particular quality concern in cancer research.

We couldn't resist the chance to pull this veteran journalist into our recent debate over whether the genomics revolution is delivering on its promise.   

And finally, Oransky was at the now infamous woman's luncheon in South Korea last month when a nobel laureate, Tim Hunt, blew the crowd away . . .  and not with brilliance.

 

The Genomics Grinch

One of the handy tools a journalist can use is a sharp pin.  It’s quite helpful when encountering over inflated balloons, such as the politican’s ego,  a financial bubble, or the hype around going to war.   When the pin is used at the right time, and on the right target, there is no question that the resulting “pop” is heard by everyone.  



New to Mendelspod?

We advance life science research, connecting people and ideas.
Register here to receive our newsletter.

or skip signup