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.
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 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.
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
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.
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.
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!
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