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Archive for the ‘Deep Thoughts’ Category

Genomics is a Model for a Collaborative Scientific Environment

 :: Posted by American Biotechnologist on 10-22-2014

In an informative study conducted at the University of Michigan, researchers found that 92% of ecologists are reluctant to share their data for fear of being scooped by fellow scientists. Interestingly, the authors suggest that a much more collaborative effort exists among genomic researchers, which they use to explain the tremendous advances in that field (consider the Human Genome Project).

According to study co-author Georgina Montgomery:

Collaboration, rather than competition, is the best way to continue to advance science

Furthermore, Montgomery argues that

increased data sharing will allow more diverse people to actively participate in research, such as early-career scientists and those from underrepresented groups; scientists from smaller or historically less-influential institutions; citizen-scientists; and scientists from the Global South, scientists from Africa, South and Central America, and much of Asia who are often excluded from leading research.

It is quite heartening to hear that Montgomery et al. believe that genomics should be seen as a positive example of open collaboration. Certainly invaluable tools such as ExPASy would not be as successful as it is, (in fact it would not exist), had the world of molecular biology been bogged down by a cutthroat competitive culture. Sharing data is key to our success and I believe that molecular biologists can be proud of the collaborative environment that they have created. Furthermore, recent efforts to encourage scientists to publish their data in open-access journals will surely take the concept of collaboration one step further.

Nonetheless, our world is far from perfect. Regardless of what discipline you are in, the very nature of the grant process and of the tenured university environment, makes the “publish or perish” paradigm very prominent in all of our minds. It is important for us to come up with methods for further increasing shared knowledge which will surely benefit everyone involved.

Click here to read the original story from the University of Michigan.

Saving 600,000 Children’s Lives With a Bar of Soap

 :: Posted by American Biotechnologist on 10-17-2014

The Challenge of Modern Day Science

 :: Posted by American Biotechnologist on 10-14-2014

In recent years, there have been incredible advances in scientific tools available at our disposal. As a result, the rate of scientific discovery and the amount of data produced by molecular biologists and proteomic specialists has been astounding. Projects such as the Cancer Genome Atlas and the ENCODE Project have generated billions of data points and provide opportunities for original researchers and other investigators to use these results in their own work to advance our knowledge of biology and biomedicine. This data explosion has challenged scientists and funding agencies to come up with new models for dealing with this massive amount of data in the most efficient way possible.

In order to tackle this challenge, the National Institute of Health (NIH), has created a Big Data to Knowledge (BD2K) initiative to enable biomedical research as a digital research enterprise, to facilitate discovery and support new knowledge, and to maximize community engagement. So far this year, the NIH has invested $32 Million in BD2K with an additional $624 Million expected to be injected into the project by the year 2020.

According to NIH director Francis S. Collins:

Mammoth data sets are emerging at an accelerated pace in today’s biomedical research and these funds will help us overcome the obstacles to maximizing their utility. The potential of these data, when used effectively, is quite astounding.

Note Dr. Collins’ use of the words “when used effectively.” Effective use and analysis of massive data sets requires open collaboration between scientists across various disciplines and nationalities. Governments play a critical role in facilitating such collaboration and science-friendly collaborative policies are not always forthcoming. Furthermore, lack of data standards for many types of data, and the low adoption of data standards across the research community has also proven to be a significant obstacle to the efficient used of Big Data. In addition, many scientists also do not have the opportunity or facility to use big data and have not been trained in the computational skills to access and analyze large data sets.

Let’s hope that the recent grants awarded by the NIH strengthen the effective use of Big Data so that the time and effort spent in creating this data does not go to waste.

The Cultural Side of Science Communication

 :: Posted by American Biotechnologist on 09-30-2014

Do we think of nature as something that we enjoy when we visit a national park and something we need to “preserve?” Or do we think of ourselves as a part of nature? A bird’s nest is a part of nature, but what about a house?

The answers to these questions reflect different cultural orientations. They are also reflected in our actions, our speech and in cultural artifacts.

A new Northwestern University study, in partnership with the University of Washington, the American Indian Center of Chicago and the Menominee tribe of Wisconsin, focuses on science communication and how that discipline necessarily involves language and other media-related artifacts such as illustrations. The challenge is to identify effective ways of communicating information to culturally diverse groups in a way that avoids cultural polarization, say the authors.

“We suggest that trying to present science in a culturally neutral way is like trying to paint a picture without taking a perspective,” said Douglas Medin, lead author of the study and professor of psychology in the Weinberg College of Arts and Sciences and the School of Education and Social Policy at Northwestern.

This research builds on the broader research on cultural differences in the understanding of and engagement with science.

“We argue that science communication — for example, words, photographs and illustrations — necessarily makes use of artifacts, both physical and conceptual, and these artifacts commonly reflect the cultural orientations and assumptions of their creators,” write the authors.

“These cultural artifacts both reflect and reinforce ways of seeing the world and are correlated with cultural differences in ways of thinking about nature. Therefore, science communication must pay attention to culture and the corresponding different ways of looking at the world.”

Medin said their previous work reveals that Native Americans traditionally see themselves as a part of nature and tend to focus on ecological relationships. In contrast, European-Americans tend to see humans as apart from nature and focus more on taxonomic relationships.

“We show that these cultural differences are also reflected in media, such as children’s picture books,” said Medin, who co-authored the study with Megan Bang of the University of Washington. “Books authored and illustrated by Native Americans are more likely to have illustrations of scenes that are close-up, and the text is more likely to mention the plants, trees and other geographic features and relationships that are present compared with popular children’s books not done by Native Americans.

“The European-American cultural assumption that humans are not part of ecosystems is readily apparent in illustrations,” he said.

The authors went to Google images and entered “ecosystems,” and 98 percent of the images did not have humans present. A fair number of the remaining 2 percent had children outside the ecosystem, observing it through a magnifying glass and saying, “I spy an ecosystem.”

“These results suggest that formal and informal science communications are not culturally neutral but rather embody particular cultural assumptions that exclude people from nature,” Medin said.

Medin and his research team have developed a series of “urban ecology” programs at the American Indian Center of Chicago, and these programs suggest that children can learn about the rest of nature in urban settings and come to see humans as active players in the world ecosystems.

Thanks to Northwestern University for contributing this story.

More Deadly Biohazards Found at the NIH!

 :: Posted by American Biotechnologist on 09-10-2014

So what can you get while working at the NIH? In the past we told you about your risk of exposure to Anthrax, Smallpox, and the Avian Flu Virus. Well, now you can add ricin and Burkholderia pseudomallei, two well-recognized biological weapons, to your shopping list!

The Washington Post is reporting that during a beefed up safety inspection, NIH employees unexpectedly found these and several other deadly biological agents improperly stored among old and long-forgotten stockpiles, some dating back over 60 years.

I must admit that, unfortunately, I have found the news much less shocking this time around than in the past. In fact, I believe that I have now gone through several of the classical stages of grief:

  • Denial (it can’t be that the most respected scientific agency in the United States would irresponsibly allow the dangerous transfer of Anthrax to a low level bio-hazard lab)
  • Anger (what the heck is wrong with the scientist that left Smallpox at the back of the freezer?
  • Depression (we are all going to die from the Avian Flu virus)
  • Acceptance (ricin, staphylococcal enterotoxin, Melioidosis…these are just some of the things you should expect to find at an unsecured government research facility)

There really isn’t much more to say. I applaud the fact that the NIH are trying to introduce measure to more strictly control these substances, but I am not sure that the system will ever be 100% foolproof. There are probably tens, if not hundreds, of dangerous materials floating around labs all over the US, (not to mention the rest of the world). Is this a reason to be scared? I think so. What about you?