Category Archives: Science

Howard Hughes Medical Institute Takes Big Open Access Step

HHMI Announces New Policy for Publication of Research Articles that will require

its scientists to publish their original research articles in scientific journals that allow the articles and supplementary materials to be made freely accessible in a public repository within six months of publication.

Great news. Some, including me, would prefer a shorter time but this is the limit on the slowest time that will be acceptable not a goal. I don’t know but I wouldn’t be surprised if HHMI is the largest source of research funds outside of the federal government in the USA. This is one more sign the tactics of the old school journals are failing.

HHMI and Public Access Publishing policy

The Howard Hughes Medical Institute has long viewed the sharing of research materials and tools as a fundamental responsibility of scientific authorship. That principle also extends to ensuring that original, peer-reviewed research publications and supplemental materials are freely accessible within six months of publication

Well put; it is amazing how out of touch with the basic concepts of advancing scientific ideas the old style journals are.

Einstein Fellowship for Teachers

Ruth McDonald selected for Einstein Fellowship program:

“As a middle school science teacher, I love science, but I’m no engineering expert,” said McDonald, who has also taught math, social studies, and language arts during her career. “But I can bring in the experts using technology.” Her innovative use of technology – handhelds, laptops, videoconferencing with engineers and scientists – was among the elements leading to her selection.

The fellowship program offers current public or private elementary and secondary mathematics, technology, and science classroom teachers with “demonstrated excellence in teaching” an opportunity to make an impact in the national public policy arena. Fellowships enhance understanding, communication, and cooperation between legislative and executive branches and the science, mathematics, and technology education community.
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McDonald’s 11-month fellowship assignment is with the National Science Foundation. She will receive a stipend for her work from September 2007 through July 2008. “It’s not really a job,” she explained. “It’s a professional growth and development opportunity, with a focus on science, math, and technology. I’m excited about the resources this experience can bring to our district.”

McDonald, who said the district’s willingness to let her take time off to pursue the opportunity “shows how much they value teacher development and achievement,” said she plans to return to LCSD following the fellowship. Until then, she will provide insight into her experience via blogging and videoconferencing, continuing the use of technology that helped land her in Washington D.C. in the first place.

Evo-Devo

Sean B. Carroll discusses the science of evolution and the field of evo-devo in this New York Times Video. Learn more in this extensive article – From a Few Genes, Life’s Myriad Shapes:

evo-devo is the combined study of evolution and development, the process by which a nubbin of a fertilized egg transforms into a full-fledged adult. And what these scientists are finding is that development, a process that has for more than half a century been largely ignored in the study of evolution, appears to have been one of the major forces shaping the history of life on earth.

For starters, evo-devo researchers are finding that the evolution of complex new forms, rather than requiring many new mutations or many new genes as had long been thought, can instead be accomplished by a much simpler process requiring no more than tweaks to already existing genes and developmental plans. Stranger still, researchers are finding that the genes that can be tweaked to create new shapes and body parts are surprisingly few. The same DNA sequences are turning out to be the spark inciting one evolutionary flowering after another. “Do these discoveries blow people’s minds? Yes,” said Dr. Sean B. Carroll, biologist at the Howard Hughes Medical Institute at the University of Wisconsin, Madison.

via: Justin Hunter (Justin and me in Madison) 🙂 Related: Opossum Genome Shows ‘Junk’ DNA is Not Junk – science webcast directory – Learning About the Human Genome – Curious Cat Science and Engineering Search

Tracking the Ecosystem Within Us

Gut Check: Tracking the Ecosystem Within Us

For more than 100 years, scientists have known that humans carry a rich ecosystem within their intestines. An astonishing number and variety of microbes, including as many as 400 species of bacteria, help humans digest food, mitigate disease, regulate fat storage, and even promote the formation of blood vessels. By applying sophisticated genetic analysis to samples of a year’s worth baby poop, Howard Hughes Medical Institute researchers have now developed a detailed picture of how these bacteria come and go in the intestinal tract during a child’s first year of life.
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Before birth, the human intestinal tract is sterile, but babies immediately begin to acquire the microbial denizens of the gut from their environment — the birth canal, mothers’ breast, and even the touch of a sibling or parent. Within days, a thriving microbial community is established and by adulthood, the human body typically has as many as ten times more microbial cells than human cells.
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The results, said Palmer, were striking: the group found that the intestinal microbial communities varied widely from baby to baby – both in terms of which microbes were present and in how that composition changed over time. That finding, she said, is important because it helps broaden the definition of healthy microbial colonization in a baby.

Another intriguing observation, Palmer noted, was a tendency for sudden shifts in the composition of the infants’ intestinal microbial communities over time as different species of bacteria ebbed and flowed.

I find this area and this study fascinating. I’m not exactly sure why this study and the incredibly significant positive bacteria for human life news doesn’t get more notice. Oh well I guess there are not cool pictures of robots or scary stories of potential threats to those reading which makes the news less interesting to some. Still I find this stuff amazing: Energy Efficiency of Digestion – Beneficial Bacteria – Skin Bacteria – Hacking Your Body’s Bacteria for Better Health – Where Bacteria Get Their Genes

Training Grants a Boon to Research and Scientists

Training grants a boon to research, scientists:

According to Petra Schroeder, assistant dean of the Graduate School, there are approximately 30 training grants available at UW–Madison. Most are funded by the National Institutes of Health (NIH), and they direct about $17 million each year toward the training of future researchers.

Each training program has its own specific mission, but most foster interdisciplinary research, providing students with valuable experience in a setting likely to mirror their first job environment. Those involved in the Biotechnology Training Program (BTP) are taught to do research at the juncture of the biological and physical sciences.
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LiGreci is interested in bioremediation, putting microbes to use in cleaning up toxic waste. BTP thrust her into a soil science laboratory on campus. Though LiGreci considers herself primarily a microbiologist, her research lies far outside the comfort zone of most of her peers, involving soil science, chemistry and geology.

According to LiGreci, the exposure she gets to novel lab techniques is eye opening. She learned new modes of culturing bacteria and other lab skills unique to microbiology, expanding her toolkit as a bench scientist. This summer, she will branch out further into the realms of genomics and the intersection between computing and biology when she joins the Joint Genome Institute at Lawrence Livermore National Laboratory as an intern. There, she will work on projects to assemble genomes of soil bacteria.

Mistakes in Experimental Design and Interpretation

Mistakes in Experimental Design and Interpretation:

Humans are very good at detecting patterns, but rather poor at detecting randomness. We expect random incidents of cancer to be spread homogeneously, when in fact true randomness results in random clusters, not homogeneity. It is a mistake for an experiment to consider a pool of 47,000 possibilities, and then only report on the 7 cases that seem interesting.
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A proper experiment states its hypothesis before gathering evidence and then puts the hypothesis to the test. Remember when you did your seventh grade science fair experiment: you made up a hypothesis first (“Hamsters will get fatter from eating Lucky Charms than Wheaties”) and then did the experiment to confirm or refute the hypothesis. You can’t just make up a hypothesis after the fact to fit the data.

This is an excellent article discussing very common errors in how people use data. We have tendencies that lead us to draw faulty conclusions from data. Given that it is important to understand what common mistakes are made to help us counter the natural tendencies.

Scientific Review

This is the way science should always work:

Here’s the short version. Dr. Hall made a mistake in the software he wrote to do something. Another scientist, Dr. Otto, saw the mistake, contacted Dr. Hall and told him about it, and the two of them worked together to confirm that it was in fact a mistake. Recognizing the error, Dr. Hall has now retracted the paper and is working to ensure that people quickly learn that the conclusions are in error. Knowing that will keep others from using Dr. Hall’s original conclusions in their own work, which means that they won’t be starting from a position that’s wrong.

And that, ladies and gents, is exactly how this thing called “science” is supposed to work.

Great post. Interesting comments too. It is not any easier for scientists (than anyone else) to admit mistakes, but scientists view advancing scientific thought as the most important factor. By exposing papers to colleagues the community’s collective effort is brought to bear on finding any weaknesses and to building on the new knowledge to advance scientific understanding further.

Shaw Laureates 2007

Image of the Shaw Prize Medal

The Shaw Prize awards $1 million in each of 3 areas: Astronomy, Life Science and Medicine, and Mathematical Sciences. The award was created in 2004 by Run Run Shaw who was born in China and made his money in the movie industry. According to wikipedia he has “donated billions of dollars to charity, schools and hospitals.” The prize is administered in Hong Kong and awards those “who have achieved significant breakthrough in academic and scientific research or application and whose work has resulted in a positive and profound impact on mankind.”

2007 Laureates:
Astronomy: Professor Peter Goldreich of the School of Natural Sciences at the Institute for Advanced Study, Princeton and the Lee A. DuBridge Professor of Astrophysics and Planetary Physics at the California Institute of Technology, USA, in recognition of his lifetime achievements in theoretical astrophysics and planetary sciences.

Life Science and Medicine: Professor Robert Lefkowitz, an Investigator of the Howard Hughes Medical Institute, the James B. Duke Professor of Medicine and a Professor of Biochemistry at the Duke University Medical Center in Durham, North Carolina, USA, for his relentless elucidation of the major receptor system that mediates the response of cells and organs to drugs and hormones.

Mathematical Sciences: Professor Robert Langlands of the Institute for Advanced Study in Princeton and Professor Richard Taylor, Herchel Smith Professor of Mathematics at Harvard University, USA, for initiating and developing a grand unifying vision of mathematics that connects prime numbers with symmetry.

Goldwater Science Scholarships

I have mentioned previously, I work for ASEE (the curious cat blog is not associated with ASEE). At ASEE, we have started a science and engineering fellowship blog. The latest post covers the Goldwater Science Scholarships – for undergraduate students in science and math. Approximately 300 are awarded each year.

For 2007, 28 mathematics majors, 223 science and related majors, 54 engineering majors, and 12 computer science majors received awards (many of the Scholars have dual majors in a variety of mathematics, science, engineering, and computer disciplines). The one and two year scholarships will cover the cost of tuition, fees, books, and room and board up to a maximum of $7,500 per year.

The Goldwater Foundation is a federally endowed agency established by Public Law 99-661 on November 14, 1986. The Scholarship Program honoring Senator Barry M. Goldwater was designed to foster and encourage outstanding students to pursue careers in the fields of mathematics, the natural sciences, and engineering. Applications will be available starting in September for next year. Schools nominate up to 4 students for the scholarship, see the web site for details on the application process.

Education, Entrepreneurship and Immigration

Education, Entrepreneurship and Immigration: America’s New Immigrant Entrepreneurs is part 2 of a study by Duke’s Pratt School of Engineering and UC Berkeley. Some interesting points from the study:

52 percent of immigrant founders initially came to the United States primarily for higher education, 40 percent entered the country because of a job opportunity, 6 percent came for family reasons, and only 2 percent to start a business.
91 percent of Indian founders, 35 percent of Chinese and 97 percent of Taiwanese founders completed their undergraduate degrees in their home country
Indian and Chinese founders graduated from a diverse set of schools in their native countries, many of which are considered
second- or third-tier universities (only 15 percent of Indian founders were graduates of the IIT).
Immigrant founders of technology and engineering firms have strong backgrounds in science, technology, engineering, and mathematics (STEM) fields. 75 percent had completed their highest degree in a STEM field.
Advanced education in science, technology, engineering, and mathematics is correlated with high rates of entrepreneurship and innovation. The U.S. economy depends upon these high rates of entrepreneurship and innovation to maintain its global edge.