What would science look like if it were invented today – part II: knowledge structuring
09.30.09 by Daniel Mietchen
Editor’s Note: This is the second of two parts of a guest post for the Euroscientist, the blog of Euroscience.org. Part I can be found here. FundScience.org cross-posts this article, as well as forthcoming installments, because of our passion to promote open science and collaboration, not only between scientists, but between the scientific community and the public.
Part II: What would knowledge structuring look like if it were invented today
Science is already a wiki if you look at it a certain way. It’s just a highly inefficient one — the incremental edits are made in papers instead of wikispace, and significant effort is expended to recapitulate existing knowledge in a paper in order to support the one to three new assertions made in any one paper. (John Wilbanks)
There are many ways to structure knowledge. One is via coordinated cellular activity in your brain. Others may involve spatial arrangements of sheets of paper or numeric arrangements of digital documents. Here, we will focus on the difference between the latter two, building on a previous outline.
Structuring scientific knowledge online
Let us first consider some practical aspects of organizing scientific knowledge in online environments:
- Newly incoming information can be inserted at any time later, independent of press runs — some call this micropublication. For example, part I of this post has already been “published” on the blog, but its wiki version can still be updated with references that were not available at the time. This may not be relevant for blog posts, but consider it as a proof of principle for writings in general, including scholarly reviews on a topic.
- In sharp contrast to current practice in paper-based scholarly journals, online platforms like public wikis make the whole article openly accessible right form the start. Detailed explanations of keywords and key concepts can be linked from within the article, and the article itself can be put in linked context via a variety of mechanisms, e.g. categories (Wikipedia), Related Articles (Citizendium), or links to other ontological frameworks (like MeSH terms).
- Documents can be edited simultaneously by multiple authors. Google docs have been doing this for years, Etherpad improves on it, and Google Wave (scheduled to be released later this week) is going to have truly realtime simultaneous editing as well; while wikis are currently somewhat limited in this regard.
- Suitably designed schemes for identifying authors, their individual contributions, and versions of the whole document provide for bug tracking, permanent availability of text (or code) snippets, and attribution. For example, Wikibu tells you that at this point, the users RokerHRO, Proxima, Saperaud, 87.122.87.61, and BirgitLachner have been the main contributors to the Aggregatzustand (state of matter) entry in the German Wikipedia, and the individual contributions to the blog post you are reading can be viewed via its version history, embedded here:
These are certainly not all the aspects of online environments relevant to science (for instance, we have left out data management issues) but let us contend with these four for the moment and consider what their combination implies for the structuring of knowledge:
It is technically possible that all researchers currently investigating a given topic could coordinate their efforts by collaboratively creating, editing, and maintaining a central set of interlinked knowledge elements (be these wiki articles, knols, or other structures) that explain what is known about their topic in detail and embed it in a wider context.
As implied by the introductory quote, it is probably fair to say that this could make research on that particular topic (as well as teaching and outreach) much more efficient. Just imagine you had a time slider and could watch the history of research on general relativity, plate tectonics, self-replication, or cell division unfold from the earliest ideas of their earliest proponents (and opponents) onwards up to you, your colleagues, and those with whom you compete for grants. So why don’t we do it?
Structuring scientific knowledge on paper
Traditionally, given the scope of a particular journal, knowledge about specialist terms (which may describe completely non-congruent concepts in different fields), methodologies, notations, mainstream opinions, trends, or major controversies could reasonably be expected to be widespread amongst the audience, which reduced the need to redundantly say and then repeat the same things all over again and again (in cross-disciplinary environments, there is a higher demand for proper disambiguation of the various meanings of a term). Nonetheless, redundancy is still quite visible in journal articles, especially in the introduction, methods, and discussion sections and the abstracts, often in a way characteristic of the authors (such that services like eTBLAST and JANE can make qualified guesses on authors of a particular piece of text, with good results if some of the authors have a lot of papers in the respective database, mainly PubMed, and if they have not changed their individual research scope too often in between).
Of course, there would be side effects: A manuscript well-adapted to the scope of one particular journal is often not very intelligible to someone outside its intended audience, which hampers cross-fertilization with other research fields (we will get back to this below). When using paper as the sole medium of communication there is not much to be done about this limitation. Indeed, we have become so used to it that some do not perceive it as a limitation at all. Similar thoughts apply to manuscript formatting. However, the times when paper alone reigned over scholarly communication have certainly passed, as discussed in part I. The relative merits of paper-based and wiki-based scholarly communication are covered in more detail at a dedicated Wikiversity page.
Cross-field fertilization is crucial with respect to interdisciplinary research projects, digital libraries and multi-journal (or indeed cross-disciplinary) bibliographic search engines (e.g. Google Scholar), since these dramatically increase the likelihood of, say, a biologist stumbling upon a not primarily biological source relevant to her research (think shape quantification or growth curves, for instance). What options do we have to systematically integrate such cross-disciplinary hidden treasures with the traditional intra-disciplinary background knowledge and with new insights resulting from research?
As a sidenote, lack of context is also a consistent feature of most “Facebooks for scientists” — in fact, the whole set of scholarly pages on the web is the appropriate network for researchers but so far it is not optimally connected, particularly because formal scholarly communication has not yet fully hatched from the structures from the paper-based era (see also this nice overview of the current situation). If it had, this would shift the focus away from periodicals (and, in passing, render things like a journal’s scope and Journal Impact Factor superfluous; see part I), which is likely to meet resistance from the publishing establishment. Yet, authors might just act on their needs by moving their “content” to grow in better production and exchange surroundings like the ones discussed here. Without good authors, no established publisher will be able to keep their grip on anyone’s research habits and thinking.
Wikis as an example of public knowledge environments online
Groupware comes to mind in this regard, and wikis in particular (another example would be collaborativey edited mindmaps, like the one embedded above that represents the topics covered by this blog post series): They allow us to aggregate and inter-link diverse sets of knowledge in an online-accessible manner, basically for free. The by now classical example is Wikipedia, and one scientific journal — RNA biology — has already announced that it requires an introductory Wikipedia article for papers it is to publish on RNA families, an idea that recently spurred a debate on the merits of such an initiative and of doing it with Wikipedia where basically anyone can edit any page, regardless of subject matter expertise.
An investigation (video lecture by Bill Wedemeyer here, a brief annotation here) of the quality of a set of science articles in the English Wikipedia is currently being written up for classical paper-style publication but the preliminary results indicate that “[t]here is a subset of reliably helpful science articles on the English Wikipedia for outreach, teacher training, and general science education” (slide shown at 29:35min in the video). However, the distribution of the set of articles was skewed towards the Good Article and Featured Article classes, which constituted only 2% of the English Wikipedia at the time of investigation, and it did not include articles in the humanities (scheduled to come next). Further information on academic studies about Wikipedia is available via these two Wikipedia pages.
The larger Wikipedias have a serious problem with vandalism: take an article of your choice and look in its history page for reverts – most of them will be about changes like this or worse. This is less of an issue with more popular topics for which large numbers of volunteers may be available to correct “spammy” entries but it is probably fair to assume that most researchers value their time too much to spend it on repeatedly correcting such information if it had already been correctly entered once. Other problems with covering scientific topics at Wikipedia include the notability criteria which have to be fulfilled to avoid an article being deleted, and the rejection of “original research” in the sense of not having been peer reviewed before publication. Peer review is indeed an important aspect of scholarly communication, as it paves the way towards the reproducibility that forms one of the foundations of modern science. Yet we know of no compelling reason to believe that it works better before than after publication (doing it beforehand was just a practical decision in times when journal space was measured in paper pages).
Fortunately, the Wikipedias are not the only wikis around, and amongst the more scholarly inclined alternatives, there are even a number of wiki-based journals, though usually with a very narrow scope and/or a low number of articles. On the contrary, Scholarpedia (which has classical peer review and an ISSN and may thus be counted as a wiki journal, too), OpenWetWare, Citizendium and the Wikiversities are cross-disciplinary and structured (and of a size, for the moment) such that vandalism and notability are not really a problem. With minor exceptions, real names are required at the first three, and anybody can contribute to entries about anything, particularly in their fields of expertise. None of these is even close to providing the vast amount of context existing in the English Wikipedia but the difference is much less dramatic if the latter were broken down to scholarly useful content, as discussed above. Out of these four wikis, only OpenWetWare and some Wikiversities (here counted as one) currently allow for original research to be published on their site — in the case of OpenWetWare, this is indeed the main purpose. Furthermore, a number of more specialized scholarly wikis exist (e.g. WikiGenes, the Encyclopedia of Earth, the Encyclopedia of the Cosmos, or the Dispersive PDE Wiki) which can teach us about the usefulness of wikis within specific academic fields.
We will not dwell on any details here, but since new suggestions about combining elements of wiki and scholarly environments keep coming in, e.g. in the form of a Wikipedia journal, we will list a number of features we deem desirable for future scholarly wikis, derived from experience with existing ones. These include, in no particular order:
- Some system of peer review (basically, any wiki allows comments, annotations or formal reviews on talk pages of users or articles but these ratings should be featured more prominently; templates like those visualizing article status at Citizendium may help with that); this may be as simple as disallowing individuals to add information to Citizendium when the only available support is their own non-reviewed research published at OpenWetWare — the real name policy will minimize misuse
- Uploadability of all kinds of media that traditionally (if you can call a habit that barely is a decade old a tradition already) went along with paper-based publications as “supporting online information” (which would be easily integrated in an all-online non-printable article with no sharp space limitations).
- Stable versions for content that has undergone peer review (like the Approved Articles at Citizendium, or the results of the double phase review model at the OA journal ACPD/ACP), along with draft versions for anything else (including improvements to and updates of previous stable versions); like any non-protected page at the Wikipedias, these draft versions can serve as a playground, though a real-name policy would probably make it a more educational one
- Search engines that integrate or otherwise compare favourably with major scholarly search engines on the web (the already mentioned Google Scholar and PubMed as well as, say, the BioText Search Engine that searches Open Access text and images), also in terms of the updating frequency.
- pan-disciplinary scope, with consistent disambiguation of specialist terms (mainly but not fully achieved at Citizendium)
- Separate namespaces for references (already in use at the Dispersive PDE Wiki and the French Wikipedia, in test at Citizendium); as a side line, this would open up ways for new citation metrics, via the What links here function
- Separate namespaces for original research. Encyclopedic endeavours need expert input. This is most likely to be achievable if the encyclopedic activites can be integrated with the experts’ workflow, e.g. via platforms like OpenWetWare.
- Attributability of contributions (automatically realized, though not in the traditional scholarly way, in any wiki with a real name policy like that at Citizendium, via the User contributions function; special arrangements exist at Scholarpedia and WikiGenes; OpenWetWare does allow nicknames but real names prevail; the Wikiversities have basically the same user name policy as the Wikipedias)
- Easy download of selected sets of pages for local archiving or analysis.
- Licenses that allow unrestricted reuse and derivative work if the original source is properly acknowledged (typically CC-by-SA or the older GFDL, both of which have been made compatible now)
- Resource-effective design (see also discussions on the energy use of the internet and individual websites). This overview may also help in working out an ecological footprint scheme applicable to research, as described previously.
- integration with the non-scholarly world (certainly achieved in the Wikipedias and Citizendium), particularly with students (cf. the Eduzendium initiative at Citizendium) and non-English contents
- Automation of the formatting, as already common in non-wiki environments, e.g. with LaTeX templates, for which collaborative editing environments exist too. None of the wikis we know comes close to that, albeit templates are heavily used at the various Wikipedias and, to a lesser extent but in a more consistent manner, at Citizendium; they seem to be rather rarely used on smaller or more specialized wikis. The same applies to references, though automated wikification has already progressed considerably here, despite the lack of wiki export functions at publisher’s sites (or of suitable XML-to-wiki converters for those who provide XML)
- Integration with mind maps (which structure knowledge) and databases (which harbour bits of knowledge that are hard to interpret without a broader context).
One of the most useful templates in use at Citizendium is that for subpages (open the Biology article in a separate window to see what this is about) :
- The article’s main page is a stable version, approved by an author with expertise in that field
- Next comes the Talk tab that leads to the discussion page, as per default in any wiki
- The Draft tab leads to the editable version (this only applies for articles that have already been approved; in others, the main page is editable)
- The Related Articles tab roughly corresponds to “see also” in the Wikipedias but is more usefully structured for navigation and somewhat replaces the categories which are heavily used in Wikipedia but only to a limited extent at Citizendium
It is interesting to see that these and other individual subpages largely complement existing social networking tools and have thus the potential to replace them (or to be replaced by them), at least for scholarly purposes:
- The Bibliography subpage is a context-based alternative to CiteULike, Zotero, BibSonomy and other reference managers, possibly in conjunction with Open Library, scholarly search engines and tools like Scribd, Mendeley or Papers. One problem wikis cannot solve is that of access to paper-based research publications, but due to the current spread of Green and Gold Open Access initiatives, this is likely to change in the next few years anyway if authors decide to follow suit in a consistent manner and act accordingly for their own contributions.
- The External Links subpage is a context-based alternative to conventional social bookmarking as known from delicious and simpy
- Additional subpages could be tailored to meet the needs of individual categories of articles (e.g., properties of chemical elements, genes, stellar constellations etc.) or more general scholarly needs (e.g., peer review, slides, code, protocols, or bot-generated transcripts from video lectures)
Besides, User pages may provide context-based alternatives to individual pages at different networking sites, and possibly even to blogs like this one, while the Recent changes page could turn into an alternative for friendfeed, with items on your Watchlist (if you are logged in) equivalent to friendfeed rooms or personal feeds you are subscribed to.
For the record, this social networking component of Citizendium has already been discussed three years ago, prior to its official launch and thus at a time when many of its current structures and their implications were not known yet.
Finally, and importantly, the easy availability of context (once the system is reasonably well adopted by scholarly communities, and the encyclopedic corpus thus reasonably complete) would make it more easy to guide expert attention and thus to identify obvious gaps in current knowledge (e.g., by means of an expert evaluation of items listed on the Most Wanted page). Science funders (or indeed anyone) could then put forward research proposals on such topics (e.g., via a Calls subpage, FundScience, InnoCentive, Mechanical Turk or by more traditional means). And while we are at it, we think science funders, job committees and review panels would profit from familiarizing themselves with the workings of collaborative platforms like wikis, particularly the aspects relevant to reliability, attribution, and outreach. Your organization, company, university, research subject or methodology probably has a page on some of the wikis described here — take a look at it, along with its history and talk pages, and you will almost certainly find something that needs improvement.
To sum up, the still fledgling Citizendium currently seems to be the closest match for a cross-disciplinary scholarly wiki anchored in the real world, and independent of whether it will allow original research to be posted in the future or not, this essential function in scholarly communication can be fulfilled by OpenWetWare (indeed, a similar separation of powers is one of the most healthy elements of most democracies). If widely adopted, this would entail a major shift in the way research is being done and communicated, towards what has come to be known as open science. As a side effect, commercial publishers would have to look for new things to publish, other than original research (non-commercial publishers like scholarly societies may, after the usual period of resistance, see more advantages than disadvantages in the groupware model). Reviews at different levels of expertise may be one option, also tutorials or other learning tools. All of this could be undertaken via some intelligently structured sets of groupware, too, depending on the incentives involved (in fact, such reviews are the scope of Scholarpedia). A side effect for researchers would be that they could use the author fees, page and figure charges and all other sums currently spent for publishing a paper for other purposes, including the maintenance of the shared public knowledge environments of the kind described here.
Of course, there are potential problems with such an enormous concentration of knowledge (e.g. for attacks and misuse, especially in relation to an international author identification that is currently being discussed). The obvious solutions are appropriate mirroring and otherwise transparency. Similar concerns would apply to a journal like PLoS ONE that does not have a scope in the traditional paper-limited sense mentioned above, yet one year after launch, it is doing pretty well. If it were to adopt a symbiosis with a suitable wiki in a way similar to the RNA Biology initiative — which requires authors to submit “a short manuscript, a high quality Stockholm alignment and at least one Wikipedia article” (emphasis added) — it might do even better. The first steps in this direction have already been taken.
This blog post was written and structured collaboratively by Daniel Mietchen, Claudia Koltzenburg and François Dongier, with further input received via the FriendFeed thread embedded below. As you can infer from the mindmap, the originally two-part series is now going to be continued, and as always, you are warmly invited to join the drafting of the next part, which will deal with the implications of the paper-to-digital transition for research funding.
This text and the associated mindmap are available under a CC-BY license.
Challenge Grant Applications and General Government News
05.21.09 by Daniel Gaddy
Predictably, the National Institutes of Health is reportedly overwhelmed by the submission of approximately 20,000 Challenge Grant applications, which is more than double the amount typically received in a normal review period. NIH is supposed to award the grants by the end of September. In order to review this number of grants in such a short time period, it has recruited more than 15,000 extra reviewers and will take an editorial board-style approach. One obvious issue with so many applications and reviewers is that the pool of reviewers comes from the same pool of applicants. This creates potentially serious conflicts of interest, and unprecedented headaches for the NIH staff to find reviewers with expertise in a particular field, but who did not submit grant applications to the NIH branch that represents their field of interest!
Furthermore, grants are primarily submitted through the website Grants.gov, which accepts grant applications from 26 federal agencies including the Department of Health and Human Services, Department of Energy, and National Science Foundation. The system is already inundated with around 20,000 submissions, causing countless submission problems ranging from generally sluggish performance to system crashes. With the application deadline of May 29th looming, many more applications are expected, along with additional problems. As alternatives to Grants.gov, DoE is accepting applications through their e-Center portal, NSF is accepting applications through Fastlane, and other agencies have established alternative mechanisms of grant submission. However, it would not be terribly surprising if the grant awards were delayed due to the unprecedented number of submissions.
In related news, NIH is examining its financial conflict of interest policies following a number of high-profile incidents involving extramural researchers. Comments are due by July 7.
Finally, in accordance with President Obama’s Open Government Initiative, the federal website Data.gov has been created. The website has the following to say:
The purpose of Data.gov is to increase public access to high value, machine readable datasets generated by the Executive Branch of the Federal Government.
As a priority Open Government Initiative for President Obama’s administration, Data.gov increases the ability of the public to easily find, download, and use datasets that are generated and held by the Federal Government. Data.gov provides descriptions of the Federal datasets (metadata), information about how to access the datasets, and tools that leverage government datasets. The data catalogs will continue to grow as datasets are added. Federal, Executive Branch data are included in the first version of Data.gov.
Participatory Democracy
Public participation and collaboration will be one of the keys to the success of Data.gov. Data.gov enables the public to participate in government by providing downloadable Federal datasets to build applications, conduct analyses, and perform research. Data.gov will continue to improve based on feedback, comments, and recommendations from the public and therefore we encourage individuals to suggest datasets they’d like to see, rate and comment on current datasets, and suggest ways to improve the site.
Goal
A primary goal of Data.gov is to improve access to Federal data and expand creative use of those data beyond the walls of government by encouraging innovative ideas (e.g., web applications). Data.gov strives to make government more transparent and is committed to creating an unprecedented level of openness in Government. The openness derived from Data.gov will strengthen our Nation’s democracy and promote efficiency and effectiveness in Government.
Some existing datasets relate to Health/Nutrition and Science/Technology. It will be interesting to see what types of datasets appear on this site in the future.
The White House Office of Science and Technology Policy Needs our Help!
05.7.09 by Daniel Gaddy
I received the following information from Sciencedebate.org. Over the past several months, and again last week at his address to the National Academies of Science, President Obama pledged to restore scientific integrity to government. Of course, that is easier said than done. Apparently Obama recognizes this, and has asked for input from us, the concerned public.
On March 9, the president formally asked the White House Office of Science and Technology Policy (OSTP) to make recommendations on how the executive branch can meet this pledge.
The OSTP has opened a public comment period regarding this directive, giving you the opportunity to share your thoughts on what the next steps should be. Comments are due by Wednesday, May 13.
The OSTP is looking for recommendations on the six issues President Obama identified in his memo:
- hiring and keeping qualified scientists
- defining new policies to ensure integrity
- using “well-established scientific processes” like peer review
- disclosing scientific findings
- ensuring that principles of scientific integrity are being adhered to
- adopting additional policies like whistleblower protections
The OSTP is accepting comments via email and through their blog, here.
Their original request for input can be found here (pdf).
Many organizations in Washington will be giving their opinions of what the OSTP plan should entail. We believe it is important for scientists and other science supporters to be included in that process, and for you to indicate to the White House how science and scientific integrity affect your work, your families, and your communities.
If you’re interested in more background information, visit the scientific integrity site of our friends at the Union of Concerned Scientists here.
Bail Out the Education System!
04.3.09 by Daniel Gaddy
Recently, a lot of discussion has taken place about Wall Street and automotive company bailouts. Another bailout, a worthy one, is beginning to finally get some press. It is not breaking news that the education system in the United States has struggled for some time now, particularly when compared to the education systems of other nations around the world. According to a Washington Post article published late last year, as the cost of college soars, the United States is lagging behind much of the world in terms of providing access to higher education.
During the past two decades, some other nations have made the kind of effort to improve access to higher education that the United States undertook in the 1950s, ’60s and ’70s, said Patrick Callan, president of the research group.
In the United States, by contrast, college costs keep rising; more students are dropping out of high school; and large gaps remain in the success rates of students of different races, incomes and states. “We’re one of the few countries where our older population is better educated than the younger population,” Callan said.
The study gives a failing grade for college affordability to every state but California, which received a C because of the relatively low cost of its community colleges. Researchers said the percentage of an average family’s income needed to pay for a public four-year college has risen from 20 to 28 percent, after financial aid. For community colleges, the burden has risen from nearly 20 percent to nearly 25 percent.
…In the past decade, student borrowing has more than doubled, and as the economy worsens, the researchers warned, many states have predicted cuts in higher education funding.
Since the early 1980s, college tuition and fees have jumped nearly 440 percent, far more than health-care, food, housing and transportation costs. The median family income rose less than 150 percent.
So, while we can pour as much money as we want into the current economic crises, the failure to fund and improve our education systems means one thing: our future generations will be grossly unprepared to compete with their better-educated, better-trained, and overall superior peers from around the world. What does that mean? The financial “crisis” we are experiencing today may be nothing compared to the crises we may face a generation or two down the road. Imagine unemployment soaring as Americans can’t get jobs because they can’t compete with superior foreign applicants. Imagine our economy crumbling as companies leave our shores for better opportunities in Europe or Asia.
To some degree, this is already happening, particularly in the sciences. A recent UK study revealed that only 28% of British 16-18-year-olds believe that science is a relevant career choice, and no survey is needed to see that similar attitudes prevail in the United States. The majority of Postdocs and Graduate Students I work with on a daily basis and interact with at meetings are Asian, mostly from India, China and Korea. The reason is simple: science is still perceived as a meaningful, dignified, and, perhaps most importantly, well-paid career choice in these countries, while the negative stigmas that are associated with science in much of the western world are nowhere to be found. A lot could be said about the lack of funding for science in the US and the poor salaries scientists endure compared to the enormous time we put into our education and careers. What I want to talk about here is the education process. The negative stigmas associated with science are ingrained in our youth early: science is too hard, not interesting, not fun…. It is true that science is hard, but it most certainly is interesting and fun! We can change these perceptions with early education. Science is all too often presented as boring and stuffy, and the image of a scientist is the disheveled, lab coat-wearing Einstein look-alike. Who can blame kids for immediately coming to negative conclusions. When taught properly, science can be seen as an interesting series of puzzles, in many ways like a game, but potentially a game of life and death. Depending on the field of science, of course, there may be good guys and bad guys (the good guys being the scientists and the bad guys being, for example, deadly diseases the scientists are trying to cure). There is a great deal of strategy involved in defeating the villains, as there is in the most popular video games of today, which kids (and many scientists I know) devote almost all of their free time to playing. In the end, if presented properly, the difficulty involved in science can actually be a good thing because it provides a challenge, and we all know that kids are quickly bored by easy games. This analogy may be tedious, but it makes sense to me.
But all of this is for nothing if our education system continues to fail our youth. Therefore, the bailout of the education system is a bailout I can firmly stand behind. Of course, simply throwing money at a problem never actually solves the problem. Our education system needs an overhaul on a variety of fronts, but an affordable education must be a top priority.
Robert Reich provides more justification for bailing out the education system:
It’s absurd. We’re bailing out every major bank to get financial capital flowing again. But we’re squeezing the main sources of our nation’s human capital. Yet America’s future competitiveness and the standard of living of our people depend largely our peoples’ skills, and our capacities to communicate and solve problems and innovate – not on our ability to borrow money.
What’s more, our human capital is rooted here, while financial capital moves around the globe at the speed of an electronic blip. Right now global capital markets are frozen, but the big money — mostly in Asia and the Middle East — and will come here, bailout or no bailout. At this point it’s coming back as purchases of dollars or in the form of T-bills that are financing the Wall Street bailout. Eventually American assets will become so cheap that the money will come rushing here to buy up the bargains.
It’s our human capital that’s in short supply. And without adequate public funding, the supply will shrink further. Don’t get me wrong: I’m not saying funding is everything when it comes to education. Obviously, accountability is important. But without adequate funding we can’t attract talented people into teaching, or keep class sizes small enough to give kids a real chance to learn, or provide them with a well-rounded curriculum, and ensure that every qualified young person can go to college.
So why are we bailing out Wall Street and not our nation’s public schools and colleges? Partly because the crisis in financial capital is immediate while our human capital crisis is unfolding gradually. But maybe it’s also because we don’t have a central banker for America’s human capital – someone who warns us as loudly as Ben Bernanke did a few months ago when he was talking about Wall Street’s meltdown, of the dire consequences that will follow if we don’t come up with the dough.
Dire consequences, indeed.
Science Stimulus
03.10.09 by Daniel Gaddy
On February 13th, the United States Congress passed an economic stimulus bill that provides significant improvement to federal science funding, and President Obama signed the bill into law on February 17th. Below are two newsletters that have been forwarded to many of us in the science community. These reports provide details about the package and its impact on science funding. The first report is from the US Congress, outlining where the $787 billion will be spent. The second report is from Howard Garrison, the Director of Public Affairs at the Federation of American Societies for Experimental Biology, and specifically deals with the funds allocated to the NIH.
United States Congress
The American Recovery and Reinvestment Act of 2009
Creating Jobs, Supporting the States and Investing in Our Country’s FutureThe United States is facing its deepest economic crisis since the Great Depression, one that calls for swift, bold action. The goals of this legislation are the same as they have been from day one: to strengthen the economy now and invest in our country’s future.
This legislation will create and save jobs; help state and local governments with their budget shortfalls to prevent deep cuts in basic services such as health, education, and law enforcement; cut taxes for working families and invest in the long-term health of our economy. We do all of this with unprecedented accountability, oversight and transparency so the American people know their money is being invested responsibly.
To accomplish these goals, The American Recovery and Reinvestment Act provides $311 billion in appropriations, including the following critical investments:
- Investments in Infrastructure and Science – $120 billion
- Investments in Health – $14.2 billion
- Investments in Education and Training – $105.9 billion
- Investments in Energy, including over $30 billion in infrastructure – $37.5 billion
- Helping Americans Hit Hardest by the Economic Crisis – $24.3 billion
- Law Enforcement, Oversight, Other Programs – $7.8 billion
Investments in Infrastructure and Science include:Infrastructure Improvements
- $7.2 billion for Broadband to increase broadband access and usage in unserved and underserved areas of the Nation, which will better position the U.S. for economic growth, innovation, and job creation.
- $2.75 billion for the Department of Homeland Security to secure the homeland and promote economic activity, including $1 billion for airport baggage and checkpoint security, $430 million for construction of border points of entry, $210 million for construction of fire stations, $300 million for port, transit, and rail security, $280 million for border security technology and communication, and $240 million for the Coast Guard.
- $4.6 billion in funding for the Corps of Engineers.
- $1.2 billion for VA hospital and medical facility construction and improvements, long-term care facilities for veterans, and improvements at VA national cemeteries.
- $3.1 billion for repair, restoration and improvement of public facilities at on public and tribal
lands.
- $4.2 billion for Facilities Sustainment, Restoration and Modernization to be used to invest in
energy efficiency projects and to improve the repair and modernization of Department of Defense facilities to include Defense Health facilities.
- $2.33 billion for Department of Defense Facilities including quality of life and family-friendly
military improvement projects such as family housing, hospitals, and child care centers.
- $2.25 billion through HOME and the Low Income Housing Tax Credit program to fill
financing gaps caused by the credit freeze and get stalled housing development projects
moving.
- $1 billion for the Community Development Block Grant program for community and economic
development projects including housing and services for those hit hard by tough economic times.
- $1 billion for the Bureau of Reclamation to provide clean, reliable drinking water to rural areas
and to ensure adequate water supply to western localities impacted by drought.Transportation
- $27.5 billion is included for highway investments
- $8.4 billion for investments in public transportation.
- $1.5 billion for competitive grants to state and local governments for transportation
investments.
- $1.3 billion for investments in our air transportation system.
- $9.3 billion for investments in rail transportation, including Amtrak, High Speed and Intercity
Rail.Public Housing
- $4 billion to the public housing capital fund to enable local public housing agencies to address a $32 billion backlog in capital needs — especially those improving energy efficiency in aging buildings.
- $2 billion for full-year payments to owners receiving Section 8 project-based rental assistance.
- $2 billion for the redevelopment of abandoned and foreclosed homes.
- $1.5 billion for homeless prevention activities, which will be sent out to states, cities and local
governments through the emergency shelter grant formula.
- $250 million is included for energy retrofitting and green investments in HUD-assisted housing projects.Environmental Clean-Up/Clean Water
- $6 billion is directed towards environmental cleanup of former weapon production and energy
research sites.
- $6 billion for local clean and drinking water infrastructure improvements.
- $1.2 billion for EPA’s nationwide environmental cleanup programs, including Superfund.
- $1.38 billion to support $3.8 billion in loans and grants for needed water and waste disposal
facilities in rural areas.Science
- $1 billion total for NASA.
- $3 billion total for National Science Foundation (NSF).
- $2 billion total for Science at the Department of Energy including $400 million for the
Advanced Research Projects Agency—Energy (ARPA-E).
- $830 million total for the National Oceanic and Atmospheric Association (NOAA).Investments in Health include:
- $19 billion, including $2 billion in discretionary funds and $17 billion for investments and
incentives through Medicare and Medicaid to ensure widespread adoption and use of
interoperable health information technology (IT). This provision will grow jobs in the
information technology sector, and will jumpstart efforts to increase the use of health IT in doctors’ offices, hospitals and other medical facilities. This will reduce health care costs and improve the quality of health care for all Americans.
- $1 billion for prevention and wellness programs to fight preventable diseases and conditions with evidence-based strategies.
- $10 billion to conduct biomedical research in areas such as cancer, Alzheimer’s, heart disease and stem cells, and to improve NIH facilities.
- $1.1 billion to the Agency for Healthcare Research and Quality, NIH and the HHS Office of
the Secretary to evaluate the relative effectiveness of different health care services and treatment options.Investments in Education and Training include:
- $53.6 billion for the State Fiscal Stabilization Fund, including $39.5 billion to local school
districts using existing funding formulas, which can be used for preventing cutbacks, preventing layoffs, school modernization, or other purposes; $5 billion to states as bonus grants for meeting key performance measures in education; and $8.8 billion to states for high priority needs such as public safety and other critical services, which may include education and for modernization, renovation and repairs of public school facilities and institutions of higher education facilities.
- $13 billion for Title 1 to help close the achievement gap and enable disadvantaged students to reach their potential.
- $12.2 billion for Special Education/IDEA to improve educational outcomes for disabled children. This level of funding will increase the Federal share of special education services to its highest level ever.
- $15.6 billion to increase the maximum Pell Grant by $500. This aid will help 7 million students pursue postsecondary education.
- $3.95 billion for job training including State formula grants for adult, dislocated worker, and youth programs (including $1.2 billion to create up to one million summer jobs for youth).Investments in Energy include:
- $4.5 billion for repair of federal buildings to increase energy efficiency using green technology.
- $3.4 billion for Fossil Energy research and development.
- $11 billion for smart-grid related activities, including work to modernize the electric grid.
- $6.3 billion for Energy Efficiency and Conservation Grants.
- $5 billion for the Weatherization Assistance Program.
- $2.5 billion for energy efficiency and renewable energy research.
- $2 billion in grant funding for the manufacturing of advanced batteries systems and
components and vehicle batteries that are produced in the United States.
- $6 billion for new loan guarantees aimed at standard renewable projects such as wind or solar
projects and for electricity transmission projects.
- $1 billion for other energy efficiency programs including alternative fuel trucks and buses,
transportation charging infrastructure, and smart and energy efficient appliances.Help for Workers and Families Hardest Hit by the Economic Crisis includes:
- $19.9 billion for additional Supplemental Nutrition Assistance Program (SNAP), formerly Food
Stamps, to increase the benefit by 13.6 percent.
- Child Care Development Block Grant: $2 billion to provide quality child care services for an
additional 300,000 children in low-income families who increasingly are unable to afford the high cost of day care.
- Head Start & Early Head Start: $2.1 billion to allow an additional 124,000 children to participate in this program, which provides development, educational, health, nutritional, social and other activities that prepare children to succeed in school.
- State and Local Law Enforcement: $4 billion total to support law enforcement efforts.
- $555 million to expand the Department of Defense Homeowners Assistance Program (HAP)
during the national mortgage crisis.
Unprecedented Oversight, Accountability and TransparencyThe American Recovery and Reinvestment Plan provides unprecedented oversight, accountability, and transparency to ensure that taxpayer dollars are invested effectively, efficiently, and as quickly as possible.
- Funds are distributed whenever possible through existing formulas and programs that have proven track records and accountability measures already in place.
- Numerous provisions in the bill provide for expedited but effective obligation of funds so that
dollars are invested in the economy as quickly as possible.
- The Government Accountability Office and the Inspectors General are provided additional funding for auditing and investigating recovery spending.
- A new Recovery Act Accountability and Transparency Board will coordinate and conduct oversight of recovery spending and provide early warning of problems.
- A special website will provide transparency by posting information about recovery spending,
including grants, contracts, and all oversight activities.
- State and local whistleblowers who report fraud and abuse are protected.
- There are no earmarks in this bill.
The full text of the bill can be found here.
From FASEB:
” I have just finished speaking with Raynard Kington, Acting Director of the NIH, and he has given me the basic outline of how NIH will allocate the new funding from the stimulus bill:
As we know, the legislation provided a total of $10.4 billion. Of this sum, 1.3 billion will go to NCRR [National Center for Research Resources] ($1 billion for competitive extramural facilities; $300 million for shared instrumentation). Another $500 million goes to intramural facilities and $400 million gets transferred to the Agency for Healthcare Research and Quality.
A total of $8.2 billion goes to the NIH Office of the Director [OD], of which $7.4 billion is transferred to the I/Cs [Institutes/Centers] with $800 million remaining in OD for trans-NIH initiatives.
Here is the basic outline of how the $8.2 billion will be spent. There will be three major mechanisms with the bulk of the funding going to mechanisms 1 and 2:
1. R01 applications already in the funding queue Two years of funding will be provided for those applications that can benefit from two years of funding and align with I/C priorities. A few applications may get four years of funding
2. Administrative Supplements to existing grants Existing grants with at least one year to run may be given the opportunity or asked to submit supplements that further the goals of the I/Cs. These will be handled at least in part by requests from the I/Cs and likely with some calls for proposals and could involve equipment, extended funds for postdocs who were not able to move to their own position, summer students, related projects, etc. There may be other priority issues that the I/C staff want to see funded.
3. Challenge Grants
A new RFA [Request For Applications] will be released within a week or two for a new, two-year program of cross-cutting, highly innovative projects, $1 M total per project.Mechanisms for the $400 M for AHRQ [Agency for Healthcare Research Quality] are not yet finalized.
>From what I have learned, this is excellent news. More information will be available shortly.”
Sincerely,
Dick
~~~
Howard H. Garrison, Ph.D.
Deputy Executive Director for Policy and Director, Office of Public Affairs Federation of American Societies for Experimental Biology 9650 Rockville Pike Bethesda, MD 20814
A lot of this may be incomprehensible to the layperson, but what it basically means is a lot more money has been made available for science funding via the NIH, as well as other agencies. The basic mechanisms of the NIH funding are to provide additional money to existing, qualified grants, and to begin funding many new, short-term grants (RFAs). This could go a long way toward stimulating the sciences, as well as the economy as a whole. Much of this money will go toward infrastructure, meaning the construction of new research buildings and laboratories, which provides jobs to the construction industry. When the new labs are constructed, institutions will need to hire new faculty, new Postdocs, new students, and new technicians. This is very good news for those of us in the science community, who have felt a significant crunch over the past several years. Nonetheless, it cannot be overstated that this is a short-term fix – a bandage to stop the bleeding, so to speak. Long-term solutions to science funding will depend upon multiple avenues of support, not solely federal funding. This will also require a fundamental change in our values – as a nation, it is time that we, once again, begin understanding and advocating the importance of science and science education.
The complete list of NIH challenge grants resulting from the American Recovery and Reinvestment Act of 2009 can be found here.
Economy and Madoff Scheme Affect Science Funding
01.23.09 by Daniel Gaddy
By now, everyone should be aware of the Bernard Madoff ponzi scheme, which swindled $50 billion from investors. What you may not be aware of is the impact of this scandal on science. Multiple private foundations that fund research have announced that they were victims of Madoff’s scheme. These organization include the Carl and Ruth Shapiro Family Foundation, the Picower Foundation, and the Wunderkind Foundation, and potentially others that have not publicly announced they are victims. When we combine the funds lost as a result of the Madoff scheme with the effects of the current economic downturn, which has cost some private foundations up to 30-40% of their assets, we begin to paint a frightening picture of private research funding. Many of these organizations have announced that they will not be able to fund new research projects in the coming fiscal year, while others have ceased all grant-making, including the payment of grants that have already been awarded, for at least the coming fiscal year.
The effects of this are already being felt at research institutions around the country, including right here in Pittsburgh. Timothy Greenamyre, a Parkinson’s Disease researcher at the University of Pittsburgh, has announced that he lost a $750,000/year grant from the Picower Foundation, which will be closing its doors altogether in the next few months. Furthermore, my own boss has announced that he will not receive renewals of previously-awarded grants from both the Juvenile Diabetes Research Foundation and the Cystic Fibrosis Foundation, two organizations that have suffered losses due to the poor economy.
If you have read this blog before, you know that most funding for biomedical research is awarded through the National Institutes of Health (NIH). You should also be aware that the funding levels of the NIH are among all-time lows as the budget of the NIH has effectively been dropping for the past 8 years. Unfortunately, with the inability of private foundations to fund new awards, and in some cases not even being able to honor their previous obligations, more and more researchers are going to turn to the NIH, and the percentage of funded grants will undoubtedly drop even further over the next year. As a result, many outstanding research projects will not be funded, and many academic scientists may even lose their labs if they are not able to replace lost funding.
We all suffer from this. Scientific advancement requires money, and lots of it. Without science funding, diseases remain uncured and unchecked, healthcare practices and techniques are unimproved, and our overall technological advancement is inhibited. While no one can accurately predict what the coming year holds, we can say that, right now, the foreseeable future of science funding looks grim.
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Cut your energy consumption to save your environment, and your money
01.14.09 by Daniel Gaddy
I was recently made aware of a free online service called WattzOn. WattzOn allows users to measure personal energy consumption, compare consumption over time and with other users, and analyze data that may allow users to cut back on energy consumption, thereby saving money, and potentially the environment.
The United States is the world’s largest energy consumer in terms of total usage, and is seventh in the world in per-capita consumption. Moreover, our energy usage is dramatically outpacing our population growth, suggesting that each one of us is using far more energy than we should be. Furthermore, our energy consumption is only expected to increase over the coming years. With this in mind, those of us who are environmentally-conscious should do everything in our power to cut back on our consumption.
WattzOn is an example of a free service that may allow us to begin doing this. If enough of us make small changes to our lifestyles, large results can be obtained. If doing a small part to save the environment is not enough to motivate you to monitor and alter your energy consumption, perhaps the current economic downturn will provide some additional motivation to cut back on usage and save some money each month.
The reason for FundScience
12.21.08 by Sharmila Pejawar-Gaddy
As a member of The American Association of Immunologists (AAI), I receive the monthly AAI newsletter that keeps me up-to-date on current happenings in the world of Immunology (and sometimes science in general). This month’s newsletter also included a letter to members from the Executive Director of AAI, where she was asking members to “continue their support to AAI by renewing their membership, which is so important specifically in this current economic climate, where a strong AAI voice in Washington is essential to Immunologists”. The letter continued to tell us, in actual numbers, what a hard hit science has taken in these last 8 years. According to this newsletter, the NIH has had a 14% loss in purchasing power since 2003. 14% in 5 years, think about it! Stepping out of my scientist-skin, I ask a serious, unbiased question: what type of a society takes money away from medical advancement? As a person who is witnessing this first-hand, I cannot tell you how many cases I have heard off in which brilliant scientists have lost their funding and have either had to leave research all together or move to another country like Singapore, which has realized that advancement in science and healthcare is the touchstone of any successful civilization. If history has taught us a few things it is that many ancient civilizations were wiped off the face of the earth due to their inability to deal with disease, famine and draught, all which can have solutions in science.
This is where non-profit organizations like FundScience come into play. The unique thing about FundScience is that the general public is put in direct access with the scientific method. This begins to disslove the misunderstandings about science, scientific techniques and the timeline from the advent of a thought/idea to the fruition of that idea.
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How some research is never published.
10.31.08 by David Vitrant
One issue that you will hear us gripe about here (and try to find a solution for) is the lack of mediums to discuss or publish “non-data”. What i mean by non-data is anything that can’t be published but might be useful. In that list I include hypotheses that were not correct, or data that is unpublishable or unreproducible.
You ask why non-data would ever be published eh ? Well while positive results are great and lead to new avenues, all the negative results help others not waste time doing useless time consuming experiments. Another reason why non-data is important is that your non-data may actually support somebody else’s research (some examples I will get to in another post). The problem is how to organize it, and how to constitute exactly what a piece of non-data entails.
Anyway. on to the meat of this “depressing” story. Let’s talk about Antidepressants 
This NYT article describes how some makers of antidepressants didn’t disclose about 1/3 of their drug related studies. This is nothing new for most of us in the scientific field. Many times when we receive funds from biotech firms or pharmaceutical firms to do research there are strings attached. That’s not to say the strings are all bad. The funding is necessary to bring some research into industry but one of the most prevalent string is that the corporation funding a research project usually has the final say on what data can be published, and when. They pay the research, they own the rights, and are accountable to shareholders.
Most of the time that is alright, but for drug trials that is another story. When patients are involved it is important to weigh the good aspects of a drug to the bad aspects. Well what if the FDA never sees the really bad data? Can they still make an informed decision on the safety of a drug? I’ll let the public think about that one. To be fair it’s not the FDA’s problem if information doesn’t come their way. There needs to be less ambiguous congressional guidelines set to monitor drug studies either earlier on in the process, or to require full disclosure.
David Vitrant
Does Open Source Apply to Science?
10.24.08 by Syam Anand
Release early, release often- the mantra of open source softwares- can it be applied to Fundscience?
By Syam Anand
I want to first introduce the mantra of open source softwares to the small minority of those who may not be aware of it. “Release early and release often” summarizes the philosophy of people who work and support open source softwares. Open source softwares thrive on the committed efforts of groups of people who work from different parts of the world. They put their brains together for a common goal- constant improvement based on feedback. They are not part of any real organization. But they always evolve into an organization of sorts that is governed by operating principles that co-evolve with them keeping in tune with changing priorities. The good thing about evolution is, it tests and selects the fittest. Being more flexible thus makes them more adaptable as an organization.
From a strategic perspective open source softwares thrive on “real” feedback and “real” solutions. People who actually uses these softwares work on it and to improve it and keeps on improving it. First, they don’t wait to come up with packages such as version x or version y and then try to sell it in a form that cannot be tinkered with (similar to a biology kit whose information in “proprietary” and you don’t have access to it, even if you own the kit!). Second, they don’t set the intervals with which they come up with updates, beforehand. They do it on a regular basis. If a software has a bug, it is explained in the open for possible solutions. When a solution is found, it is notified to everyone. As a practicing scientist, it seems very similar to what we do everyday for every aspect of laboratory life, except for funding. We regularly do experiments, we regularly improvise and find better ways to ask questions and get answers. But when it comes to funding, we can do it three times a year for NIH and once a year for the foundations. Of course, we regularly work towards getting funded!
When you talk to any scientist (established or beginner) about funding avenues that are currently available, one constant complain you hear is that it takes a huge amount of time to get a proposal reviewed and funded. This is true for NIH (since I am a biologist, I would restrict myself to NIH) and foundations that fund research. By huge I mean, upto ONE WHOLE YEAR! Herculean efforts, planning and lots of luck seem to be a requirement to survive the transition periods. Consider the rate at which funding is granted nowadays- 10% of grants that require substantial amounts of preliminary evidence (which in turn takes money, time and manpower to generate!). This means if one has to rewrite and resubmit, which takes another year, a few lives and careers will be on the line and soon off the line. And it actually happens in real life. A glaring example is that of Dr. Prasher who did not win the nobel for GFP because he ran out of funds and had to give his GFP clone to two other scientists who went on to win this year’s nobel in chemistry. It seems he is driving a courtesy shuttle now! (read the blog by dgaddy in fundscience.org on GFP). This brings me to the point I wish to make- fund early and fund often is the way to go, if anyone wants to be different and make a difference in the way research is funded.
Fund early and fund often is easier said than done, as one has to consider the availability of funds, availability of reviewers and the time constraints this would place on the reviewers. Since the success of open source strategies depends on cooperation between individuals who are knowledgeable, building an interactive community and providing a forum for concurrent evaluation of proposals are the starting steps. The next step would be to remain flexible. Too many rigid rules for submission, evaluation and granting funds would make it look the same. Make it simple and flexible and let it evolve.
If there is a possibility of funding one project every month, I would rate that as more rewarding for supporting science ON TIME, rather than 12 grants at the end/beginning of every year. Fund early and fund often. If fundscience can adapt this mantra, it will address one low point of every funding agency that I know- TURNAROUND TIME. This is a niche that fundscience can evolve into and make its own habitat. How to achieve this objective is a matter of discussion, debate and planning. But this is one requirement that is yet to be a major focus for a scientific funding agency. One argument against this would be that competition is not going to be uniform in every month. My answer to that is that competition wont be uniform no matter how it is done, as scientists come up with fresh ideas regularly and there is no clear way to mark a genius from a dumbo other than wait and see how and what he/she does in a relatively long period of time. There is no point in holding a science Olympics to see who wins!
As a closing argument, I feel that if a scientific paper can be reviewed in two weeks time (accelerated papers take this long) and a suitability report for a journal (such as science/ nature) can be obtained overnight from their editorial boards, a short write-up (one-three pages) can be read and reviewed and put to vote within a month. Another fresh beginning would be to put the submitted proposals for a vote not just by the “experts” (for which there are other forums such as NIH and the innumerable foundations) but by everyone including Ph.D students, post-doctoral fellows, doctors, engineers and people who are curious and interested to participate. If you can vote for electing your president, you could vote on the science that you wish you fund directly too! The role of experts will be to moderate the discussion and voting in a fruitful and non-partisan manner.
As for which projects can be funded (since the public is directly involved, this is a concern for a lot of people), the institutional review board and research administration to which the scientist making the proposal is answerable will ensure that all rules and regulations are met with and research is conducted ethically and responsibly.
Syam Anand
Pittsburgh, USA.
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