Next Generation Science

This is a quote from a New York Times article late last week:

The National Science Foundation and the Microsoft Corporation have agreed to offer American scientific researchers free access to the company’s new cloud computing service. A goal of the three-year project is to give scientists the computing power to cope with exploding amounts of research data. It uses Microsoft’s Windows Azure computing system, which the company recently introduced to compete with cloud computing services from companies like Amazon, Google, I.B.M. and Yahoo. These cloud computing systems allow organizations and individuals to run computing tasks and Internet services remotely in relatively low-cost data centers. The new program was announced on Thursday [2/5/2010] at a news conference in Washington.

via Microsoft to Offer U.S. Scientists Free Cloud Computing – NYTimes.com

Cloud computing is one of the latest IT buzzwords. For those that are unfamiliar with the term, essentially any program or service transmitted via the internet can be considered cloud computing. An outside company runs the servers and software, and is responsible for maintenance, updates and technical issues. Users are charged for access. With cloud computing, software programs you use aren’t run from your personal computer, but are stored and accessed via the Web, typically within a Web browser. If you’ve ever used Google Gmail or Google Docs, you’ve been computing in the cloud.

Microsoft’s announcement comes two years after similar services were offered by Google and I.B.M. to some of the nation’s elite universities, including Carnegie Mellon, Massachusetts Institute of Technology (MIT), Stanford University, the University of California, Berkeley, the University of Maryland and the University of Washington. According to the NYTimes article, Microsoft hopes to differentiate their service by offering scientists a set of custom applications that simplify access to Azure (Microsoft’s cloud services operating system) and the use of older software applications like Microsoft Excel.

This is, however, a step backwards for Open Science. The agreement reached between the National Science Foundation (NSF) and Microsoft only promotes the use of a proprietary data format and application platform — cloud equivalents of Microsoft Office Excel and Microsoft Windows. This does nothing but further entrench Microsoft’s dominance in the scientific computing marktet. Indeed, Microsoft has a track record of using standards that aren’t truly open and leveraging proprietary formats to block commercial rivals and/or free alternatives.

Why is there a time limit on the project? Microsoft could have taken a different path and instead made the service free for academic research without expiration. The company could look to the global business market for a revenue stream. Such an arrangement would have truly been an investment in U.S. science.

With the help of four distinguished life science researchers, The Scientist rounds up the top 10 innovations in the life sciences for 2009.

It’s been a tough year for every industry, and the life sciences are no exception. Yet companies and academic laboratories across the globe have developed innumerable new products designed to take your research to the next level. But with many lab budgets tighter than last year, which technologies are worth the investment?

That’s why, for the second year in a row, we have gathered a panel of expert judges to pick the year’s best innovations to hit the life sciences market in the past year. This year’s winners run the gamut from imaging, genomics, and other tools that stunningly capture both intracellular and extracellular processes. Our judges — Steven Wiley, Jean Wang, Shawn Levy, and David Piston — are all known for pushing the technical boundaries, and have collectively published more than 600 academic papers.

It may have been a tough year for industry in general, but it was a great one for life science innovation.

What’s cool about the article: brief product write-ups, followed by comments from the judges.

Products listed include 3D cell culture, microarray-based sequence capture, an electron multiplication charge coupled device (EM-CCD) camera, cell manipulation with light, and protein-induced pluripotency in mouse embryonic fibroblast cells.

Check it out at The Scientist

More serious competition for Google?

Starting today, Wolfram|Alpha‘s knowledge, computed from expertly curated data, will enrich Bing’s results in select areas across nutrition, health, and advanced mathematics. Wolfram|Alpha provides immediate, unbiased, and individualized information, making it distinctly different from what has traditionally been found through web search. By using Wolfram|Alpha, Bing recognizes the complementary benefits of bringing computational knowledge to the forefront of the search experience.

via: Microsoft’s Bing — Introducing One of Wolfram|Alpha’s First Commercial API Customers

The question is: are the search results truly more relevant?

I’d gladly trade quantity for quality, or simply better navigation options (not just relevance and date). However, it strikes me that the results from one service won’t augment the other: if I use Bing for a computational query, I’m not interested in the search engine results, and if I search for articles on the AKT/PTEN pathway in tumor development, what useful information will Wolfram|Alpha offer?

The Bing-Wolfram|Alpha partnership is interesting but not one that will likely attract more users and increase market share.

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We’ve written previously about DeepDyve, the search engine that searches the deep web, i.e. content that is out of reach of various search engines and other searching algorithms — PDFs, subscription-only archives, databases or other unstructured information located on the “dark web”.

Last week, DeepDyve announced that they are now offering consumers and professionals rental access to more than 30 million articles in their research database. Their new slogan is “Research. Rent. Read.”

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Via BMJ Group blogs:
BMJ » Richard Smith: The beginning of the end for impact factors and journals.

Something has just happened that will almost certainly end the tyranny of impact factors and may well mark another step towards the extinction of most scientific journals. Did you notice it? Probably not, and even if you did you may not have understood what it was or what it may lead to.

It was the appearance of something called rather clunkily “article level metrics.” These are a variety of scores and other bits of information attached to each article in the publications of the Public Library of Science (where I’m on the board). They shift attention from journals to articles, particularly for the academic bean counters anxious to find a convenient and low cost way of ranking academics.

Article-level metrics

Article-level metrics are distinct from the traditional journal-level measures of research quality. The Public Library of Science (PLoS) is the first publisher to implement article level metrics, which currently includes:

• Article usage statistics (pageviews, PDF and XML downloads)
• Citations from the scholarly literature
• Social bookmarks from CiteULike and Connotea
• Reader comments
• Reader notes
• Blog posts aggregated from Postgenomic, Nature Blogs and Bloglines
• Reader ratings

Further measures are being developed. For more information, check out Mark Patterson’s post Article-level metrics at PLoS – addition of usage data.

In the PLoS Conversations video below, Cameron Neylon discusses how article-level metrics can make online research easier and how PLoS is adding support for them directly on their site.

More about PLoS article-level metrics can be found at http://article-level-metrics.plos.org/.

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In December 2001, the private operating and grantmaking foundation The Open Society Institute held a small meeting of 13 leaders in the open access movement with the purpose of accelerating progress in the international effort to make research articles in all academic fields freely available on the internet. The result of this meeting was the Budapest Open Access Initiative, a statement of principle, strategy and commitment:

The literature that should be freely accessible online is that which scholars give to the world without expectation of payment. Primarily, this category encompasses their peer-reviewed journal articles, but it also includes any unreviewed preprints that they might wish to put online for comment or to alert colleagues to important research findings. There are many degrees and kinds of wider and easier access to this literature. By “open access” to this literature, we mean its free availability on the public internet, permitting any users to read, download, copy, distribute, print, search, or link to the full texts of these articles, crawl them for indexing, pass them as data to software, or use them for any other lawful purpose, without financial, legal, or technical barriers other than those inseparable from gaining access to the internet itself. The only constraint on reproduction and distribution, and the only role for copyright in this domain, should be to give authors control over the integrity of their work and the right to be properly acknowledged and cited.

Read the entire document: Budapest Open Access Initiative.

With the principle that all research should be freely accessible online immediately after publication, the Open Access movement experienced rapid growth. As of August 2006, over 360 organizations and 4,000 individuals have signed the initiative. Momentum for Open Access is growing. Recent funder mandates have further strengthened the possibilities for Open Access to all research. Indeed, the National Institutes of Health now has an Public Access Policy that makes it mandatory that all funded research be publicly available no later than 12 months after the official date of publication.

This week, October 19–23, marks the first international Open Access Week. Open Access Week provides an opportunity to broaden awareness and understanding of Open Access to research, including access policies from all types of research funders, within the international higher education community and the general public. For more, see the Open Access Week website.

The Scholarly Publishing and Academic Resources Coalition (SPARC) is a co-organizer of Open Access Week 2009 and offers this welcome to the global celebrations:

For more on Open Access, see Peter Suber’s Open Access Overview.

Also see Bora Zivkovic’s post on Open Access Week, which includes a video by Walter H. Curioso about his views of Open Access and how it can help in developing countries.

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The fourth annual conference on science and the Web is less than four months away. The free three-day event to explore science online will be held in the Research Park Triangle area (North Carolina) on January 15-17th, 2010. Conference sessions will be held in the Sigma Xi building.

The goal of the conference is to bring together scientists, physicians, educators, publishers, journalists, web developers and others to discuss, demonstrate and debate strategies and tools for doing science, publishing science, teaching science and promoting public understanding of science online.
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Monday marked the 40th anniversary of the Apollo 11 moonshot in 1969 by Neil A. Armstrong, Edwin E. “Buzz” Aldrin Jr. and Michael Collins. Ironically, it also marked the 33rd anniversary of the Viking I Mars landing. On Sunday evening, the crew of Apollo 11 spoke together in Washington D.C. at the Smithsonian Institution’s National Air and Space Museum. There, they didn’t recall details from the moon landing, but instead urged mankind to look to Mars.

The UK’s Telegraph has some great footage of the three astronauts speaking at the event. Buzz Aldrin called for a new commitment to travel to Mars, saying [1]:

The best way to honor and remember all those who were part of the Apollo program is to follow in our footsteps. To boldly go again on a great new mission of exploration, we can help make the moon a true stepping stone to more exciting and habitable destinations with the moon acting as a new global commons for all nations. We can venture outward to Mars for America’s future. It may sound like a distant destination beyond our reach but that’s what some called Apollo’s goal to reach the moon. And they were wrong.

Also on Sunday, NASA manager Wayne Hale wrote an interesting entry on his blog called Carrying the Torch. In it he said that the exploration of space reminded him of the Olympic torch relay where “Not everyone who carries the torch is remembered, only a few names are ever announced”. I wonder if he was thinking of the Apollo 11 crew when he wrote that “Not everybody gets to carry the torch up the stadium steps and light the cauldron in the presence of tens of thousands and the virtual presence of tens of millions. Only a very few get to carry the torch in moments of glory.”

And what of the cost to going to Mars? According to Craig Nelson, author of a book on the Apollo program called Rocket Men, the Apollo program was a huge economic stimulus for all of the south. In addition, he cites several economic reasons to go back to the moon [2]:

People think there’s a process of using fusion out of Helium 3, which is a substance that’s very common on the moon and very rare on the earth. And we could have dramatic changes in our energy requirements and needs, if Helium 3 proves to be a useful source of energy. And if it can be successfully mined off the moon and transferred here. There’s also the possibility of using the moon as a giant source of solar energy, since the sun never sets on certain parts of it. So if they can figure out a way to make that practical, and if we have the revolution and booster technology we may have in the next couple of years, both of those things may happen.

The Next Giant Leap

NASA is planning to retire the space shuttle fleet in 2010. The Constellation program is NASA’s new program for human space exploration. The agency’s former administrator, Michael Griffin, called Constellation “Apollo on steroids.” The goal is to return astronauts to the moon by 2020, establish a lunar base, and ultimately travel to Mars.

A board that investigated the space shuttle Columbia disaster in 2003 recommended that the tasks of carrying crew and cargo be divided. To that end, the Constellation program will use two new launch vehicles: Ares I, an in-line, two-stage rocket topped by the Orion crew vehicle and its launch abort system, will carry up to six astronauts while the much more powerful Ares V will carry cargo. However, NASA’s next giant leap has sparked debate because of the estimated $100 billion cost by 2020. An independent panel is reviewing NASA’s plans and is expected to present its results next month [3].

Meanwhile, other nations such as Russia, China and India are increasing their own space programs. Thus, even though the future of U.S. space exploration is under close scrutiny, a new space race may be right around the corner.

What do you think of Buzz Aldrin’s challenge to America? Should the U.S. go back to the moon?

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References

1. Apollo 11 astronauts call for mission to Mars. The Telegraph. 2009 Jul 20.
2. Man’s first moonwalk turns 40. American Public Media Marketplace. 2009 Jul 20.
3. Panel Is Set to Review NASA’s Plan for Human Space Flight. The New York Times. 2009 Jun 2.

The American Recovery and Reinvestment Act of 2009, which President Obama signed today, includes significant investment in scientific research and lays the foundation for long-term economic growth. According to the American Association for the Advancement of Science (AAAS), the economic recovery package contains an estimated $21.5 billion in federal research and development (R&D) funding, $18.0 billion for the conduct of R&D and $3.5 billion for R&D facilities and capital equipment [1].

Major scientific portions of the stimulus include:

• Department of Energy (DOE), Energy Efficiency and Renewable Energy: $16.8 billion, including $5 billion for the Weatherization Assistance Program, $3.1 billion for the State Energy Program, $3.2 billion for Energy Efficiency and Conservation Block Grants, $2.5 billion for applied research, development, demonstration and deployment, $2 billion for Advanced Battery Manufacturing Grants, $400 million for transportation electrification, $300 million for an Energy Efficient Appliance Rebate Program and ENERGY STAR, and $300 million for an Alternative Fueled-Vehicles Pilot Grant Program.
• National Institutes of Health (NIH): $10 billion, which includes $8.2 billion to the Office of the Director ($7.4 billion for distribution to the institutes and centers and $800 million for the Office of the Director for trans-NIH initiatives), $1.3 billion to the National Center for Research Resources (NCRR) ($1 billion for “competitive awards for the construction and renovation of extramural research facilities” and $300 million for shared instrumentation and other capital equipment) and $500 million for improvements to the NIH campus.
• National Science Foundation (NSF): $3 billion for “basic research in fundamental science and engineering”, including $2.5 billion for highly-rated peer reviewed research proposals, $400 million for construction of and equipment in national labs, and $100 million for improving instruction in science, technology, engineering and mathematics (STEM).
• Agency for Healthcare Research and Quality (AHRQ): $1.1 billion for comparative effectiveness research; $400 million will be transferred to the NIH to support comparative effectiveness research. The remaining balance will be used for comparative research of drugs, devices and medical procedures.
• Prevention and Wellness Fund: $1 billion, of which some portion will be allocated to the Centers for Disease Control and Prevention (CDC).
• National Aeronautics and Space Administration (NASA): $1 billion, including $400 million for science missions and climate research, $150 million for aeronautics research, $400 million to maintain access to space as the Space Shuttle is retired, and $50 million for facilities repair and recovery from natural disasters.
• Department of Energy (DOE), Office of Science: $1.6 billion for research funding through the DOE’s Office of Science, including research in areas such as climate science, biofuels, high-energy physics and nuclear physics. Provides $400 million for the Advanced Research Project Agency-Energy (ARPA-E) to support high-risk, high-payoff research into energy sources and energy efficiency in collaboration with private industry and universities.
• National Oceanic and Atmospheric Administration (NOAA): $830 million, including $230 million for NOAA operations, facilities and research, and $600 million for climate modeling, satellite programs and data storage.
• National Institute of Standards and Technology (NIST): $580 million, of which $360 will go to research facility construction.

Andrew at Science Progress has tallied total funding for a number of science-related research and development programs. You can track the progress of the American Recovery and Reinvestment Act at Recovery.gov; the web site features a link to the full text of the Act and a timeline for various milestones.

The Federation of American Societies for Experimental Biology (FASEB) President Richard Marchase, Ph.D. shared his hope for continued support earlier this week [2]:

Ultimately, it is our hope that the economic recovery package is the first step forward towards a long-term, sustainable investment in both biomedical and other scientific research. Stable and predictable budget growth will expedite the research that will improve the health and quality of life of all Americans.

The administration’s commitment to scientific research will become clear later this month when the revised 2009 budget is released. Currently, the NIH is running on extended funding at 2008 levels through March 6th, 2009.

References

1. Final Stimulus Bill Provides $21.5 Billion for Federal R&D. AAAS. Accessed 2009 Feb 17.
2. FASEB Praises Inclusion of NIH, NSF, DOE Science Funding in Stimulus. FASEB press release. 2009 Feb 12.

Additional information was collected from the following sources:

1. Recovery.gov. Accessed 2009 Feb 17.
2. Download the Stimulus Bill. ProPublica. 2009 Feb 13.
3. American Recovery and Reinvestment Act Allots $16.8 Billion for EERE. U.S.Department of Energy, Energy Efficiency and Renewable Energy. 2009 Feb 17.
4. The American Recovery and Reinvestment Act: Investing in Science. Representative Rush Holt, the 12th District of New Jersey. Accessed 2009 Feb 17.

Last summer, Johnson Space Center senior management created seven Employee Engagement teams to focus on recommendations to enhance innovation and open-mindedness at the center [1]. As a member of the Barrier Analysis team, astronaut Andy Thomas wrote and filmed a short, satirical video. The team was asked specifically to look for barriers to innovation and to concentrate on reasons why new ideas get ignored. In an NPR interview, Thomas said [2]:

I wanted to try and capture those in a way that people would understand, in a way that would resonate.

Forget about a PowerPoint presentation. The video is a composite of many people’s experiences at NASA, highlighting many of the obstacles employees face and is generating a lot of discussion within NASA and the space community. To their credit, Johnson Space Center management made sure the video went public so that people could see it.

NASA manager Wayne Hale wrote about the video on his blog just over a week ago, saying that he found it:

… extraordinarily funny and not at all funny. These young people have obviously found themselves in situations RECENTLY in which managers at various levels applied sociological and psychological pressures to keep them from bringing ideas forward.

Looks like we still have a long way to go and the first step is to know that you still have a problem.

What can your organization do to improve collaboration and innovation?

References

1. Video: Barriers to Innovation and Inclusion. Open NASA. 2009 Jan 28.
2. Astronaut’s Video Satirizes NASA Bureaucracy. National Public Radio (NPR). 2009 Feb 9.