FDA Releases Proposed Guidances For Next Generation Sequences

Last week the Obama Administration released one of its periodic fact sheets announcing recent actions on the Precision Medicine Initiative (PMI).  The PMI is trying to build tools and gather data to make it easier to target therapies and other medical treatments for specific individuals.

Part of this latest fact sheet is the announcement that the Food and Drug Administration (FDA) is releasing draft guidance on oversight for what’s called next generation sequencing (NGS).  This category of tests measures a much higher number of genetic variants than current sequencing.  The agency believes that these draft guidances – one on standards for analytical validity of NGS tests and another on using evidence from public genome databases to demonstrate the clinical validity of NGS tests – can be sufficiently flexible for a family of tests that is emerging and notably distinct from existing sequencing and related tests.  This is a situation where the agency likely believes that establishing some boundaries for a new testing field can support the development of such tests.

If you’re interested in providing comment on either draft guidance (or both), you will need to submit them by October 6.

Private Email Use For Government Work Not Just A Classification Problem

Remember folks, I am not a lawyer.

On Tuesday the U.S. Court of Appeals for the District of Columbia Circuit ruled on a Freedom of Information Act (FOIA) lawsuit (H/T G. William Thomas) involving the Office of Science and Technology Policy (OSTP) and the Competitive Enterprise Institute (CEI).  The CEI had requested documents under FOIA, and as part of that request sought emails from an email account that OSTP Director John Holdren has from the Woods Hole Research Center (where he served as director prior to becoming OSTP Director).

At first blush you may consider this an overreach, but according to the ruling (page 3), the OSTP had previously shown in a separate FOIA lawsuit involving CEI that Director Holdren had used the Woods Hole account for work related purposes.  The proof was a Vaughn Index produced by OSTP, so the agency had to know that there would be work-related email on the Woods Hole account.  (I have not been able to find the Vaughn index in question, which was complicated immensely by the Court failing to cite the specific case.  The FOIA improvements signed into law earlier this week can’t come fast enough.)

Those who follow the news may find this annoyingly familiar.  While the case currently dominating the news is more involved, and has the extra wrinkle of involving classified material, public officials have been using private email for public business for a while.  Personally, I don’t think it should be permitted in any instance.  (And this kind of nonsense is not limited to federal officials.)

And this is where I might differ with those concerned about fishing expeditions conducted into personal email accounts.  If there had been no evidence to suggest Holdren was using a private account for government business, I would certainly consider it an overreach for CEI to want OSTP to search Holdren’s private email.  In that situation, CEI would need to demonstrate why it felt that documents relevant to its request could be expected on that account and the corresponding search would need to be very targeted.

The case will return to the district court that dismissed the case back in March 2015 for further proceedings.  The OSTP may have other grounds to contest the production of these emails, and there will certainly be a new OSTP Director (perhaps one with an Acting in front) by the time the case is resolved.

50th Anniversary of FOIA Marked By Signing Of Updated Legislation

While it did not come into effect until 1967, this Fourth of July marks the 50th anniversary of the signing of the Freedom of Information Act (FOIA).  The law is how the public can access the records of any federal agency, provided the information does not fall under one of nine categories of exemptions.  A well-intentioned law, the response to FOIA requests can leave something to be desired, with agencies citing exemptions or imposing serious burdens of time and cost on parties requesting information.  An effort to update and reform the legislation has been in the works for several years, and on July 1st, President Obama signed into law the FOIA Improvement Act of 2016.

The bill does not provide new resources for agencies to comply with FOIA requests.  This is unfortunate because the slowness of an agency’s response is a common criticism of FOIA compliance (and could be used to delay or stonewall transparency efforts).  However, the bill does put into law several changes, that if successfully implemented, could make it easier to access government information even if you weren’t the one making a request under FOIA.

The new law puts into law a ‘presumption of openness’ that both the Clinton and Obama Administrations applied to their FOIA responses.  That means agencies would comply with requests unless the information is specifically barred from disclosure by law or that it would present a ‘forseeable harm’ to one of the exemptions in FOIA.  It also limits to 25 years the exemption for documents used for an agency’s ‘deliberative process’ (internal decision making).

The law pushes forward the efforts to digitize FOIA requests and compliance.  It requires the development of a government-wide online portal through the Office of Management and Budget for FOIA requests.  It would also make available online records that have been released in response to FOIA requests, with an emphasis on those records that have been requested multiple times or have otherwise been determined to be subject to frequent requests.

This is unlikely to be the end of public pressure to reform and update FOIA.  Various groups interested in public disclosure of government activity will continue to argue that the public interest should favor disclosure more than it currently does, and the limited resources available for FOIA will continue to make compliance an afterthought for agencies.

The Obama Administration announced additional FOIA actions in connection with the signing.  The Chief FOIA Officers Council outlined in the law (formalizing an existing group) will have its first meeting on July 22, and it will work on identifying the top challenges in complying with the law.  The Department of Justice pilot program on proactively posting FOIA responses online (rather than distributing them just to the requesters) will be reviewed and perhaps expanded.  Guidance on implementing the new FOIA law will be released later this year, along with specifics on a cross-agency goal to improve agency compliance with FOIA requests.

As there is little time left in this Administration, it’s worth considering how either of the presumptive Presidential candidates may approach the new FOIA in their tenure as President.  Given the high-profile instances of each campaign failing to disclose relevant information or act in ways that lack transparency, it seems likely to me that the open government groups aren’t looking to let up in their campaigns to make government decisions and activities more transparent.

Brexit And UK Science And Technology: A Big Leap Into The Unknown And The Uncertain

I’ll concede that my U.K. readers are likely well aware of everything here and certainly better informed.  Feel free to move along.

The June 23 referendum in the U.K. that turned in favor of the nation leaving the E.U. prompted a great deal of uncertainty.  In a poll conducted by Nature pre-referendum, notable majorities of both U.K. researchers and E.U. researchers (not including the U.K.) preferred that the U.K. remain.  While the U.K. remains a member of the E.U. for now, the chance that it is leaving could give pause to a host of potential collaborations.  And perhaps that is the most significant impact of the so-called Brexit on both the U.K. and its European neighbors.

There are two main reasons for this.  First, and what has been most immediately felt (if just anecdotally), is the potential restrictions on the freedom of movement members of the European Union enjoy.  With minimal limitations, nationals of an E.U. state have the right to work in another E.U. state comparable to that of nationals of that country.  Once the U.K. leaves (should it leave), its researchers would be harder to hire in E.U. member states than they are at present, and vice versa.  Additionally, the ability of U.K. students to study in E.U. member states (and vice versa) will likely be affected, even though U.K. universities have been quick to assure students from E.U. member states that they still have a place in their institutions.  Secondly, there are several research programs supported in whole or in part by E.U. agencies that provide funds for researchers and institutes in E.U. member states.  Again, so far only anecdotally, there has been reluctance to include U.K. researchers in future applications for these programs, and their eligibility to participate in these programs once the country leaves the Union would be at best dramatically reduced.

Yes, the U.K. would have additional money post-exit that it could use to cover the shortages in funding for research.  However, according to MP Nicola Blackwood, Chair of the Science and Technology Committee in the House of Commons, the U.K. has won a greater share of E.U. research funds than its contribution.  Given the chaotic state of the country’s political leadership (which may not stabilize once a successor is found for Prime Minister Cameron) and the government’s recent penchant for austerity, I’m skeptical that U.K. research would receive the same amount of research funding that it would have benefited from through the E.U.  MP Blackwood may be as skeptical, as she has called a committee inquiry on the subject that starts on Tuesday.

There is the potential to mitigate the disruptions coming for U.K. research.  The extensive relationships forged between U.K. and E.U. researchers, as well as between U.K. and E.U. policymakers (such as former Scotland and E.U. Chief Scientific Adviser Dame Anne Glover) could help preserve existing relationships and provide avenues by which the U.K. can argue for continued scientific collaboration with the Continent.

The current state of U.K. political leadership is such that it will be some time before a coherent plan for U.K. science emerges.  The two ministers with science in their portfolio, MPs George Freeman (life sciences) and Jo Johnson (universities and science) both supported remaining in the E.U.  What remains to be seen is to what extent the next Prime Minister will retain current ministers.  Should this new Prime Minister be one who supported exiting the E.U., they may not want to retain anyone who supported remaining.  With Jo Johnson also being the brother of Boris Johnson, who just left the race for party leader, that next Prime Minister has an extra reason to not retain him.  (Of course, the race for party leader has been sufficiently Machiavellian that a future PM may wish to keep one Johnson on for some kind of connection to the other.)

With all of this speculation, I think it worth noting that however the consequences of this referendum unfold, science, technology and the funding for them are not likely to be high on the list of concerns for most of the parties involved.  Success or failure in ensuring a healthy research relationship for the E.U. and the U.K. could depend on how well those very concerned about science and technology keep that in mind when making their case to those who aren’t.

Cancer Moonshot Summit Backdrop For Several Administration Announcements

Today was the Cancer Moonshot Summit in Washington, D.C.  Vice President Biden hosted that event, while there were roughly 270 similar events across the country, with approximately 6,000 participants engaged with cancer in some capacity.  The Cancer Moonshot page on Medium has plenty of stories about the various commitments made and efforts in progress to make it easier to share knowledge and questions about cancer.

The White House has released a fact sheet in connection with the Summit summarizing these and other commitments made by public and private sector entities.  I want to highlight some of the government commitments, particularly those I think could be used in other fields.  They include:

  • The National Cancer Institute is developing an API (application programming interface) for clinical trial data hosted on cancer.gov.  This would make it easier for other parties to access, analyze, and re-use this data for a host of different applications.
  • Several cross-agency agreements to utilize the supercomputing resources of the Department of Energy to speed up various research efforts.
  • Efforts at the U.S. Patent and Trademark Office and the Food and Drug Administration to reduce the time required for various regulatory review and other administrative processes.

Of particular note is something the Vice President said concerning clinical trials.  With several institutions failing to report (in a timely fashion, or at all) clinical trial data, the Vice President expressed an interest in following through on the legal penalties for not complying with the law.  National Institutes of Health Director Francis Collins indicated that a final rule was expected soon that should provide additional authority to the agency to crack down on those failing to comply.

More information on the Summit should emerge over the next few days, as information comes in from the other events across the nation.


The Government Wants To Hear From You About AI

Yesterday the Federal Register published a Request for Information (RFI) from the Office of Science and Technology Policy (OSTP).  The RFI is part of the ongoing White House Initiative on the Future of Artificial Intelligence, which includes an ongoing series of workshops (the latest was today in Pittsburgh, and another is scheduled for July 7 in New York City).  The OSTP is asking for comments between now and July 22.

The RFI is open-ended, but the document lists 10 different topics that are of particular interest around artificial intelligence (AI):

(1) The legal and governance implications of AI;
(2) the use of AI for public good;
(3) the safety and control issues for AI;
(4) the social and economic implications of AI;
(5) the most pressing, fundamental questions in AI research, common to most or all scientific fields;
(6) the most important research gaps in AI that must be addressed to advance this field and benefit the public;
(7) the scientific and technical training that will be needed to take advantage of harnessing the potential of AI technology, and the challenges faced by institutions of higher education in retaining faculty and responding to explosive growth in student enrollment in AI-related courses and courses of study;
(8) the specific steps that could be taken by the federal government, research institutes, universities, and philanthropies to encourage multi-disciplinary AI research;
(9) specific training data sets that can accelerate the development of AI and its application; and
(10) the role that “market shaping” approaches such as incentive prizes and Advanced Market Commitments can play in accelerating the development of applications of AI to address societal needs, such as accelerated training for low and moderate income workers (see https://www.usaid.gov/cii/market-shaping-primer).

The main goal of the White House initiative is to identify and pursue opportunities for using AI to support the provision of government services.  So if you can tailor your submissions to account for this, it might boost your chances of getting attention.  Either way, you will have to limit your submissions to 2,000 words or less.  And submit those comments by July 22.

Update Corner: STEM Fastrack; Collections Funding Restored; Collections Underused

Two updates on previously posted stories.

Back in April, the comic strip On the Fastrack had a storyline involving the character Fistula Breech (usually called Fi in the strip) giving a speech to girls about science, technology, engineering and mathematics (STEM) careers.  Starting on June 20th (but only revealing the STEM connection on June 21), that story was revisited.  This time the story line focuses more on how much Fi is *not* interested in making the presentation and how that eventually affects the speech.  I shan’t spoil anything (for all I know, the story will continue tomorrow), but my favorite of this stretch so far is the June 24th strip.

Also in April, I noted that an infrastructure program sponsored by the National Science Foundation (NSF) would have its funding suspended pending a program review.  It’s the program from the Division of Biological Infrastructure that supports biological specimen collections.  Thankfully the NSF decided to continue funding (on an alternate year basis) while the review continues.  Community feedback likely influenced the change of heart, as many researchers and scientific societies described the value of this program to research in their comments to the agency.

It’s a move consistent with this call from the Director of the Smithsonian’s National Museum of Natural History to increase funding for such collections.  Kirk Johnson described the value of historical collections to help track and fight diseases for Smithsonian.com   (H/T The FrogHeart Daily) He went into further detail in an op-ed for The Proceedings of the National Academy of Sciences with colleagues from the museum, the Department of Health and Human Services and Columbia University.  In that piece the authors make the case not just for utilizing existing collections to help with diseases like the Zika virus and the emergence of hanta virus in the 1990s, but to make collections of relevant specimens during disease outbreaks in order to help track the disease and be better prepared for the possibilities of the disease coming back.