Fairy Circles have been found in Australia! #cool #weirdscience

This is just cool! Smithsonian Mag does a good job summarizing:

brad_howe_heliwest_group_aerial_1.jpg__800x600_q85_crop.jpg

The highly regular spacing of fairy circles in Australia becomes visible in dense vegetation. The grasses in the foreground of the image are patchy as they are rebounding from fire. (Brad Howe, Heliwest Group)

Mysterious Fairy Circles Have Been Found in Western Australia
Once thought to exist only in Namibia, circles spotted 6,200 miles away are helping sort out how these odd features form

smithsonian.com
March 14, 2016
In certain spots, the Namibian plain looks like a scene from a Dr. Seuss book—large, regularly spaced circles dot an otherwise grassy landscape, the red dirt glaring like a beacon against the pale tufts of grass. Guesses about how these bizarre formations came to be range from the practical to the fanciful: underground gas, termites, radiation, dragons and giants.

Whimsically dubbed fairy circles, the strange shapes had only been spotted in Namibia—until now. This week scientists report their appearance roughly 6,200 miles away in the desolate outback of Western Australia. The discovery is already helping scientists tease through the mystery behind these natural patterns.

Scientists from many fields have previously tackled the perplexing question using mathematics, biology, ecology and entomology. Recently the debate has homed in on two theories: Either termites killed rings of plants by munching on their roots, or the grass self-organized to best take advantage of resources in the harsh desert landscape.

The discovery of fairy circles in Australia, described this week in the Proceedings of the National Academy of Sciences, now has the team leaning strongly towards the answer of self-organization.

“Water is limited, and because water is limited it cannot sustain a continuous vegetation coverage,” explains lead author Stephan Getzin at the Helmholtz Centre for Environmental Research – UFZ in Germany. So “we have gaps and other patterns like labyrinths and stripes or even spots.”

Continue reading

Women view professional advancement as equally attainable, but less desirable #GirlPower

For all who have access to PNAS, this is a fascinating study on why women are not found in higher-level positions in the workplace.  This “leaky pipeline” phenomenon has been investigated for years. Women now represent a majority in college and graduate schools, however, moving up the career ladder, they are less and less represented.  While in the past, a lot of this has been attributed to gender inequality, this study shows that while women believe higher-level positions are obtainable, they find them less desirable and opt away from taking them. A summary of this research can be found in the abstract:

Women are underrepresented in most high-level positions in organizations. Though a great deal of research has provided evidence that bias and discrimination give rise to and perpetuate this gender disparity, in the current research we explore another explanation: men and women view professional advancement differently, and their views affect their decisions to climb the corporate ladder (or not). In studies 1 and 2, when asked to list their core goals in life, women listed more life goals overall than men, and a smaller proportion of their goals related to achieving power at work. In studies 3 and 4, compared to men, women viewed high-level positions as less desirable yet equally attainable. In studies 5-7, when faced with the possibility of receiving a promotion at their current place of employment or obtaining a high-power position after graduating from college, women and men anticipated similar levels of positive outcomes (e.g., prestige and money), but women anticipated more negative outcomes (e.g., conflict and tradeoffs). In these studies, women associated high-level positions with conflict, which explained the relationship between gender and the desirability of professional advancement. Finally, in studies 8 and 9, men and women alike rated power as one of the main consequences of professional advancement. Our findings reveal that men and women have different perceptions of what the experience of holding a high-level position will be like, with meaningful implications for the perpetuation of the gender disparity that exists at the top of organizational hierarchies.

As a woman in science, I am thrilled to see this study as it completely echos my own personal sentiments.  I am fortunate enough to say I have not personally experienced any discrimination based on gender thus-far in my career (that I know of), yet, attaining a high-power career position still doesn’t seem all that desirable. Not because I don’t think it’s possible, but mainly because I just can’t decide if it’s worth it. In science, for example, becoming a principal investigator at a research institution requires an incredibly demanding workload: long hours in the lab, working on weekends, etc. There are some flexibilities in your schedule, but from my observations, most mothers are back in the lab (or at least very present through email) as little as one week after delivering their child. For many, the job description is just not desirable enough.

While this study certainly shows a realistic reason why women are not in these high-level positions, I think it raises another issue: WHY are women (and even some men) finding high-power positions less-desirable?  I think to really close the gender gap in high-power positions, all places of work must make these positions more desirable: provide adequate maternity (and paternity) leave/care, allow for flexible work hours, create opportunities to telework, etc. Maybe then we can finally mend the “leaky pipeline.”

Scientists “delete” HIV virus from human DNA!

A lot of progress has been made in the past 30 years in understanding, preventing, and treating HIV (previous post), and now scientists have figured out a way to essentially delete the HIV virus from human DNA.  To date, no cure exists for HIV/AIDS, but new developments from a group out of Temple University, published in PNAS, shows promise for suppressing viral gene expression and replication, and immunizing uninfected cells against HIV infection.

This finding is nicely summarized by the Daily Mail.  The scientists have developed molecular tools to cut out the HIV gene from our genome.  Here’s how it works:

  • Researchers based the two-part HIV-1 editor on a system that evolved as a bacterial defence mechanism to protect against infection. 
  • When deployed, a combination of a DNA-snipping enzyme called a nuclease and a targeting strand of RNA called a guide RNA (gRNA) hunt down the viral genome and remove the HIV-1 DNA. 
  • Dr Khalili’s lab engineered a 20-nucleotide strand of gRNA to target the HIV-1 DNA and paired it with a DNA-sniping enzyme called Cas9 and used to edit the human genome.
  • From there, the cell’s gene repair machinery takes over, soldering the loose ends of the genome back together – resulting in virus-free cells. 

This next step is to develop the construct in order to conduct preclinical studies.  There is still work to be done in fighting this disease, however, this new cas9 system for editing out HIV from the human genome is a step in the path towards finding a cure.

Scientists discuss the Future of Research at #ASCB2014 #FORsymp

Superstar Scientists Share visions for the Future of Research at ASCB/IFCB Meeting

by Christina Szalinski

A panel of bioscience superstars tried to throw some light on the gloomy outlook for cell research Saturday at the ASCB/IFCB 2014 meeting in Philadelphia. As NIH funding shrinks, graduate programs grow, and fewer than 10% of PhDs go on to tenure-track position, Bruce Alberts, professor at University of California, San Francisco, best-selling textbook author, and newly minted National Medal of Science winner, wondered aloud, “What brilliant young person wants to become a scientist… if they have to wait until they’re 42 to get their first independent grant?” Alberts continued, “You’re supposed to be famous to get a job as an independent investigator. You would have laughed at my CV when I got hired.” Alberts was joined on the panel by Shirley Tilghman, ASCB president elect and president emerita at Princeton University; Jon Lorsch, Director of the NIH National Institute for General Medical Sciences; and Marc Kirschner, past president of ASCB and chair of the Department of Systems Biology at Harvard Medical School (HMS); and more.

 

HMS postdocs Jessica Polka and Kristen Krukenberg believe that it’s time for researchers to face the new realities. To that end, they initiated this panel in Philadelphia on the “Future of Research,” pulling in leaders from across the biomedical research enterprise to a special interest subgroup session at the ASCB/IFCB meeting. Krukenberg opened the session by summarizing an earlier Future of Research symposium they organized for postdocs in Boston in October. Krukenberg reported that working groups at the Boston symposium recommended a broadening of training, changes in lab structure, diversification of funding mechanisms, and rewards for scientists who interact with the public.

 

In Philadelphia, Alberts had his own recommendations—techniques and equipment should be freely shared to minimize waste, scientific risk-taking should be encouraged, and labs should be a more moderate size, with 9 to 12 as the maximum. “Howard Hughes (Medical Institute) chose individual scientists to double the size of their labs, thinking they’d do twice as much work, but they started doing less interesting things because they had to manage an enterprise,” Alberts explained.

 

Connie Lee, Assistant Dean for Basic Research at the University of Chicago and chair of ASCB’s Public Policy Committee, said while the research situation at her university wasn’t dire yet, bridge funding for PIs caught between R01s had been increased four-fold in recent years. Lee urged institutions and researchers themselves to find other sources of funding.  “Think outside the NIH box,” Lee said. Chicago now has grant writing-workshops to give critical feedback on first drafts of grants, and someone in Washington, DC, to help them identify new sources of funding. Lee said that institutions have to help create new avenues for scientists to innovate.

 

Kirschner said that science best proceeds in an environment of free inquiry. He cited the example of the Hamilton Smith, who was working in the obscure field of bacterial immunity and discovered restriction endonucleases, which revolutionized DNA modification and earned a Nobel Prize. “These are the kinds of things we should promote that the system is working against,” Kirschner said. “Science progresses most rapidly when scientists can focus on science. Writing grants can stimulate creativity, but rewriting them does not.”

 

Referring to her time as Princeton president, Tilghman joked, “I had a 12 year sabbatical thinking about binge drinking, and college football, and financial aid… In the years that I had been away [from science] the sense of optimism had been eroded… The ground conditions we’re laying out for the next generation… are not the conditions that create the very best science.” The problem, said Tilghman, is too many people chasing too little money. An easy first step, she believes, would be to require every graduate training program that gets NIH funding to post the career outcomes of their students. “I’m begging the NIH, on my hands and knees if I have to, to do this at minimum so students can make informed decisions,” Tilghman declared. She said it’s hard to say where the workforce pipeline could or should be narrowed just as it’s hard to predict who will do well in grad school. But Tilghman said one thing is clear: “We can’t afford to send 75% of students onto postdocs.”

 

Kenneth Gibbs, a Cancer Prevention Fellow at the National Cancer Institute, expressed concern about the “shearing forces inside the biomedical research pipeline.” At NCI, Gibbs investigates biomedical graduate student and postdoctoral training. He said that his data indicate that many PhDs entered graduate training with poor knowledge of career options and that over time in graduate programs, students move away from the goal of reaching a faculty position.

 

Lorsch, whose NIH institute is the primary source of federal funding for basic cell science research, wants to change the way grants are awarded. “RNAi wouldn’t have been discovered if the PI had said, ‘That’s not one of the specific aims, so you’d better get back to working on those so we can get the grant renewed,’” Lorsch said. Soon NIGMS will be piloting a program called Maximizing Investigators’ Research Award (MIRA), which aims to provide one grant per PI that’s bigger and longer than R01 averages and not tied to specific aims, according to Lorsch. The review will be based on track record and overall research ideas and there will be modified review considerations for early-stage investigators. “NIH is taking seriously all these problems, but without reciprocal changes at institutions it won’t work. Everyone is going to have to change what they do in order to right the sinking ship,” Lorsch said.

*This article is from the ASCB Post

Problems in Science Part 1: the broken economics of academic publishing

For the introduction and background on this series of posts, see this post.

bundles

A great article by Bob Yirka on Phys.org summarizes a recent PNAS paper describing how universities and academic institutions are being scammed (more or less) by publishers when purchasing bundled subscriptions to academic journals (during the writing of this post, Science published a similar review article by John Bohannon).

In looking at the contracts, the researchers found widely different charges to universities for the same bundles. They found for example, that the University of Michigan paid $2.16 million in 2009 for a bundle from Elsevier, while the University of Wisconsin, paid just $1.22 million the same year for the same bundle from the same company. They note that the two universities are similar in the size of their staffs and the number of PhD students, yet one school paid considerably more than the other.

That is crazy right? The publishing companies make the universities sign confidentiality agreements, so they can’t discuss how much they pay with other universities, hence the huge discrepencies. But that only scratches the surface of craziness in academic publishing. As a taxpayer, you fund much of the research that is published in academic journals. Scientists, whose salaries and research likely include funding from tax dollars, usually have to pay academic journals to publish papers (using taxpayer money again). In the editing process, journals utilize a peer-review system. In almost all cases, scientists, most of who are again at least partly funded with tax dollars, do this peer-review FOR FREE. The academic journals then publish the accepted articles that were paid for by taxpayers all along the way. However, many (most?) academic journals require subscriptions to view the published articles. Meaning that scientists and the public have to pay, or be part of an institution that pays, in order to see science that they essentially funded each step of the way. This process, with profit numbers, was described in the Economist:

In 2011 Elsevier, the biggest academic-journal publisher, made a profit of £768m ($1.2 billion) on revenues of £2.1 billion. Such margins (37%, up from 36% in 2010) are possible because the journals’ content is largely provided free by researchers, and the academics who peer-review their papers are usually unpaid volunteers. The journals are then sold to the very universities that provide the free content and labour. For publicly funded research, the result is that the academics and taxpayers who were responsible for its creation have to pay to read it. This is not merely absurd and unjust; it also hampers education and research.

And even though it IS absurd and unjust, there is some noise from the opposing side!! Publishing companies and academic journals disagree that the system is as bad as I have described, and granted, I may have described a worst case scenario (but not uncommon). But, then again, who wouldn’t disagree when you’re company is making those kinds of profits (see above: $1.2 billion!). A recent Nature article does include some arguments in support of publishers and journals. For example, prestigous journals have a higher workload due to higher rates of submission, and that requires more time and workers. Not too mention the claim that these journals have a ‘higher’ caliber of science (a topic of a later post in this series).

However, there is some hope on the horizon of fixing this broken system. In the US, the White House has mandated that taxpayer funded research must be open access… after one year. This means that taxpayer funded research that is published in any journal must be freely available after one year, which is a good start, but a lot of science happens in a year. There is also the problem of whether journals are actually following these rules and making these articles available. Furthermore, this is in the US. Turns out that other countries also do science, and many American scientists want to collaborate with international scientists. Access to scientific articles in other countries can be much more difficult and expensive, which definitely holds back science in these countries and hampers international collaboration.

There is also a trend of increasing numbers of publications in open access journals (journals like PLOS, public library of science, and eLife). These types of journals are becoming more and more popular, and new ones are sprouting up everyday (Society for Neuroscience announced its new open access journal this week, eNeuro). They are freely available to the public, and the costs of publishing in these journals is considerably cheaper.

More work needs to be done to address the crazy economics of academic publishing. Right now it seems like taxpayers are on the losing side for supporting science, with a lot of money going toward publication and not actual science. Not to mention that the public has limited access to this science (See one of the many posts where I can’t link to the full article, only the abstract. Or have to apologize that not everyone will have access to the article). Lastly, it is mind-boggling that universities and research institutions are allowing themselves to be taken for a ride. To me it seems that research centers are the majority of both the supply and demand for academic journals (supporting the scientists, science, publication, peer-reviewers, and also use these publications as a metric for scientific success). Doesn’t that mean they have a lot of negotiating power. Hopefully with the report in PNAS, universities will take a closer look at how they deal with academic publishing, which in turn will hopefully benefit the economics of publicly funded science and in turn the science itself.

 

Can we make scientific research sustainable?

Kirshner

With the current popularity of sustainable goods, including food, fuel, energy etc, it seems like a great time to discuss the UN-sustainability of the current system for scientific enterprise.

This is a great interview with Marc Kirshner about a recent article he recently published in PNAS along with a powerhouse list of authors (nobel laureate included) about the systemic flaws in scientific research, including why it is not sustainable. Interview here. Original PNAS Article here.

The take away point is that the system is broken and is completely unsustainable. The interview and article also include some ideas for how the system can be changed for the better. The interview is amazing quote after amazing quote about the problems with the research system, but also includes amazing quotes about how we can fix it. A few examples:

“And science is more expensive. Science is going very, very well in many ways. But that has created a situation where there’s a tremendous amount of stress in the system. And the stress itself is operating not to support the best science, but actually to discourage some of the best science.”

“Competition itself at some level is a good thing. But when people’s livelihood depends on getting the grant, it undermines a lot of the cooperative nature of science, the open and sharing nature of science.”

“By hampering basic science you inhibit translational science. I am just not convinced that the barrier to new developments in science is at the translational level; it’s really at the more fundamental level.”