science funding


With 50 Million Users, Is Academia.edu Speeding Up Science?

Today we follow up with Richard Price, the founder and CEO of the most popular social sharing site for the academic sector, Academia.edu. When we talked to Richard almost five years ago, the site had 1.5 million users, mostly academics sharing their own papers so that their peers had access without any paywalls. Today the site boasts over 50 million users and serves as a laboratory for the future of academic publishing.

It’s not hard to understand the site's phenomenal growth. Weathering the hit back by Elsevier and other prestige publishing houses, Academia.edu has been able to open up access to millions of scholarly papers which otherwise would not have been accessible. And the papers are not only available to academics. Anyone can get an account for free. Richard recently found a farmer from Sub-Saharan Africa downloading a paper on water conservation.

In addition, many users now choose to publish on the site rather than with an established journal. An emeritus professor at Berkeley told Richard this:

“If I publish in a journal, it takes two years to come out and seventeen people read the paper. If I upload to Academia, I get 100 views in the first week."

It's a success story in terms of uptake by the scholarly sector, but what does this success mean to Richard and the company, and to its users and the future of publishing?

So far revenue sources are limited. Experiments with a premium service have had mixed results with users pushing back and arguing that "open access to scholarship should be a human right, not a business model." How will the site, which requires huge infrastructure, sustain itself?

Richard said before that the site could speed up science. Has it?

Join us behind the scenes with the mastermind of Academia.edu.

A Republican Staffer on the Gottlieb Hearing

This week at a Senate hearing Scott Gottlieb defended his nomination to be FDA commisioner.  Last night at happy hour we caught up with a Republican staffer who was willing to be candid in exchange for remaining unnamed.

 

Staffer:  Oh, yeah, the Gottlieb nomination.  Sweet little thing.  The nomination, I mean.  Seems like the hearing was weeks ago with this whole “nuclear” warfare going on in the Senate over Gorsuch.  

Mendelspod:  The Republicans looked pretty pleased with Gottlieb, as did some of the Democrats.

Proposed NIH Cuts, Undermining GINA, and Game Changing Drugs: March 2017 with Nathan and Laura

The largest cut to NIH budget ever, rolling back genetic non-discriminatory law—the bad news continues to roll from Washington. But there was great news this month as well.

Both Nathan and Laura are fuming about HR 1313, or a Republican bill to roll back GINA protections. Laura points out that the proposed law builds on an exemption in GINA for wellness programs—a category difficult to define. And Nathan reminds us that families and children could be hurt by the new bill. Theral asks since when did privacy become partisan? GINA passed in ’08 with a vote of 95-0 in the Senate, 414-1 in the House (Ron Paul playing the weirdo there), and it was signed by George Bush.

Then on to some “game changing” drugs for multiple sclerosis and eczema and a successful gene therapy trial for severe sickle cell anemia. Not only are there new therapies, drug manufacturers seem to be getting the message on pricing.

Art in the Lab (Falling in Love with Bacteria)

Today’s guest makes time to create beauty in the lab. Memo Berkmen is a bacterial artist along with being a staff scientist at New England Bio Labs. He and his colleague, Maria Penil, were the winners of the American Society for Microbiology’s agar art contest in 2015. Their felicitous relationship with the unseen, often unnoticed, world of ancient organisms fills us with wonder and inspiration.

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Bacteria art by Memo Berkmen, Maria Penil

Democracy and Science Have Tea at the White House

The wheels on his navy blue Toyota Prius could be heard squeeling as Science wound down the parking structure in Bethesda.  Yes, it's true, Science's parking spot involved two stories and some undwinding to get out on the open road.  Today Mr. Science was headed to the White House for tea with Ms. Democracy.

As it happens, on this particular day, our Mr. Science is a religious man.  One doesn't know how it happened.  It just happened.

Flint Whistleblower Says Today's Science Is to Blame for Its Own Lack of Public Trust

Marc Edwards is telling a different story than the one most of us have been reading and hearing lately. But then he’s used to it.

Marc was the engineer from Virginia Tech who was called one day in September, 2015, by a resident of Flint, Michigan. A Ms Lee Ann Walters wanted Marc to check out her water. When Marc and his team got to Flint they uncovered super high levels of lead in the potable water, with over 100,000 people exposed to high lead levels and 12,000 people with lead poisoning. You know the rest.

But you may not know that a very similar story to Flint played out in the nation’s capital in 2003. A Washington DC water crisis led to a hearing in which Congress found that the CDC had released “scientifically indefensible” reports on the water.

Marc Edwards exposed those reports and lost a contract with the EPA over it.

Aghast at the world of academic science which he says is "gamed by a system of quantitative incentives" and at government agencies who often overlook the truth, Marc now takes aim at the whole system of science. Last year he co-authored a report Academic Research in the 21st Century: Maintaining Scientific Integrity in a Climate of Perverse Incentives and Hypercompetition. The report warns of a tipping point where science “itself becomes inherently corrupt and public trust is lost, risking a new dark age."

The integrity of science has been a major theme here on the program, so while Marc is not a biomedical researcher, his experience in exposing bad science resonates within our own life science community.

In line after quotable line (“The idea of science as a public good is getting lost. In science our product is truth, and our brand is trust. The greatest proportion of truth seekers are not going into science as opposed to other human endeavors."), Marc fillets today’s scientists in government and academia, arguing that the system of science is skewed towards quantitative markers rather than quality: the pressure to publish more papers each year, citations, how much funding, etc.

Marc thinks things have gone so wrong that the war on science today (and yes, he does think there is a war on science), is more the fault of the scientists than any political movement. Somewhat with irony, but more with sadness, he says:

“The Flint water crisis was so bad it restored my faith in politicians. I mean that’s how screwed up it was. The politicians behaved themselves really well. The people who have been indicted are the scientists and engineers."

In-Situ Sequencing, CRISPR Patents, and Racist Milk Drinkers: February 2017 with Nathan and Laura

Commentators Nathan Pearson and Laura Hercher join us to look back on February’s genomics headlines.

Beginning this time with science, Nathan says we should be expecting great things from new in-situ sequencing. Laura found it encouraging that the National Academy of Sciences shifted to be more in support of genome editing. Theral asks what life forms are left to sequence for the Earth BioGenome Project?

Then it’s back to politics. Are the departure of Liz Mansfield from the FDA and Matt Might from the White House the beginning of a brain drain from government agencies in the new administration? We finish with some stories about racism that might fit under the heading “family genomics and black history month."

Scientists vs Trump: January 2017 with Nathan and Laura

As we look back at January’s headlines with our two regular commentators, Nathan and Laura, the question becomes: How much should we ignore the fire raging across America to focus on the science?

Speaking of Trump's new immigration order and the very real threat of a "brain drain," Nathan tells of his own personal time doing research in Iran, commending scientists there and the many Iranian scientists here. But he says Iran has already announced they're going to retaliate.

“We might think more about field work scientists who will be worried about retaliation, about being a target of anti-American violence in the field,” says Nathan. "This gets real for people.”

Laura says “the United States has always been the place to come. If we don’t choose to be that place, someone else will. Someone else will be the leader of the scientific world which has been as important to the development of this nation as being leader of the free world.”

We do get to some science, the first human-pig chimera.

And to some cool new sequencing tools. Or just how cool are they? Illumina announced a new line of instruments this month, but what they didn’t say might be the loudest announcement of all. They didn’t mention anything about nanopore sequencing.

When Long Reads are Double the Price of Short Reads, Short Reads Are Dead, Says Evan Eichler

Each year at this time, sequencing tools leader, Illumina, generates another round of sequencing buzz in the industry, this year by announcing the $100 genome is around the corner with their latest boxes. But more and more, people are asking just what they will get with that $100. Indeed, what do they get today with a $1,500 genome?

Illumina sells short read sequencing technology which is unable to characterize much of the human genome, particularly complex regions which are responsible for many of the known and unknown diseases.

Today’s guest has made his career studying structural variation of the genome. He’s done it with the rapidly improving long read sequencing technology, mostly on instruments produced by Pacific Biosciences. He says researchers have been seduced by the ability to sequence thousands and tens of thousands of genomes as opposed to understanding five or ten genomes really well.

Evan Eichler is a professor of genomics at the University of Washington and first made his name known back with the original Human Genome Project. In the final days of the project, he was brought into the NIH to analyze the genome for structural variation repeats. Neither the private Venter enterprise nor the public attempt had the ability to see them at the time, and with what Evan calls his “young, stupid naivety," he waded into the project. He was able to compare data from the two groups without getting too caught up in the politics and ended up making an important contribution to the final output. Today Evan has established himself so well in the structural variation space that it is said no project into structural variation can be conceived without him.

“Work that we have done over the past couple years has shown that if you apply a new sequencing technology like long reads, you basically uncover 90% of the structural variation that is missed by short read sequencing technology.”

That’s a big number.

“That is a big number,” says Evan, “so the question is, how important are structural variations? That’s open to debate.”

Evan says there is data which shows that structural variant level changes are likely to be more impactful than those of single nucleotide variants (SNVs). He compares SNVs to little tremors and structural changes to earthquakes when it comes to regulating the genome.

As with his mentor, Jim Lupski, (featured on the program here), Evan is adamant that we must stop using short read technology and aligning to a reference genome. Rather, he says, we must get to the place where we are doing de novo assembly of each genome. We can do that in the research setting now, but we must do that clinically as well.

“If we’re still aligning sequences to a reference genome, and that’s our only way for understanding genetic variation ten years from now, clinically we’ve failed. What we need to think about is how to do this right, and that means understanding all the variation from stem to stern in these genomes."

Hank Greely on “The End of Sex" and Other Stuff

Each year at this time we bring on a guest who is somewhat out of the way of our normal lineup, for example, a science fiction writer or a philosopher. Today Theral interviews a law professor who loves to philosophize and write about the impact of biotechnology on our lives now and in the near future. His newest book out this year, “The End of Sex and the Future of Human Reproduction,” is another comprehensive and provocative example of what has made Stanford’s Hank Greely such an in-demand speaker both to scientist and non-scientist audiences alike.

“My prediction in the book is that in twenty to forty years, most people with good healthcare will conceive their children in a lab using stem cell derived eggs--and sometimes sperm—and then do whole genome sequencing preimplantation genetic diagnosis and pick the embryo they want,” says Hank at the outset of today’s extended interview.

Whereas sci-fi writers and the mainstream press often play into what Hank calls "our need for scary bedtime stories," he seeks to understand and elucidate the actual--and less dramatic--"muddling through" of new technologies into our lives.

In addition to discussing the book, we talk with Hank about his relationship to his colleague scientists at Stanford, what he thinks is the breakthrough technology of 2016, and the future of the FDA in the era of Trump.



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