Actionbioscience 2

AIBS Submits Testimony to Congress in Support of FY 2013 Funding for USGS, EPA, USFS

2013-03-27T17:51:50Z

The American Institute of Biological Sciences (AIBS) appreciates the opportunity to provide testimony in support of appropriations for the United States Geological Survey (USGS), United States Forest Service (USFS), and Environmental Protection Agency (EPA) for fiscal year (FY) 2013. AIBS encourages Congress to provide the USGS with at least $1.2 billion in FY 2013, with at least $177.9 million for the Ecosystems activity. We further request that Congress provide the USFS Forest and Rangeland Research program with at least $295.3 million, and EPA's Office of Research and Development with at least $600 million.

The AIBS is a nonprofit scientific association dedicated to advancing biological research and education for the welfare of society. AIBS works to ensure that the public, legislators, funders, and the community of biologists have access to and use information that will guide them in making informed decisions about matters that require biological knowledge. Founded in 1947 as a part of the National Academy of Sciences, AIBS became an independent, member-governed organization in the 1950s. Today, AIBS has nearly 160 member organizations and is headquartered in Reston, Virginia, with a Public Policy Office in Washington, DC.

U.S. Geological Survey

The USGS provides unbiased, independent research, data, and assessments that are needed by public and private sector decision-makers. Data generated by the USGS save taxpayers money by reducing economic losses from natural disasters, allowing more effective management of water and natural resources, and providing essential geospatial information that is needed for commercial activity and natural resource management. The data collected by the USGS are not available from other sources and our nation cannot afford to sacrifice this information.

The Ecosystems activity within USGS underpins the agency's other science mission areas by providing information needed for understanding the impacts of water use, energy exploration and production, and natural hazards on natural systems. The USGS conducts research on and monitoring of fish, wildlife, and vegetation - data that informs management decisions by other Interior bureaus regarding protected species and land use. USGS science is also used to control invasive species and wildlife diseases that can cause billions of dollars in economic losses. Collectively, the knowledge generated by these USGS programs is used by federal and state natural resource managers to maintain healthy and diverse ecosystems while balancing the needs of public use.

Other examples of successful USGS Ecosystem initiatives include:

Development of comprehensive geospatial data products that characterize the risk of wildfires on all lands in the United States. These products are used to allocate firefighting resources and to plan fuel reduction projects.
Identification of white-nose syndrome, a fungus that is devastating U.S. bat populations and could jeopardize the multi-billion dollar pest control services provided by bats.
Identification and evaluation of control measures for Asian carp, sea lamprey, Burmese pythons, and other invasive species.
Study of the impacts of solar energy and other next generation energy sources on wildlife and endangered species.

Through the Cooperative Research Units, the USGS and their partners address pressing issues facing natural resource managers at the local, state, and federal levels. Examples of recent research initiatives include studying the effects of the Gulf of Mexico oil spill on wildlife and fisheries, and improving management of elk and waterfowl. In addition to providing research expertise, these partnerships at 40 universities in 38 states serve as important training centers for America's next generation of scientists and resource managers. More than 500 graduate students each year receive training by USGS scientists at Cooperative Research Units. The program is also an efficient use of resources: each federal dollar invested in the program is leveraged more than three-fold.

The National Streamflow Information Program within the Water Resources mission area provides needed information for resource managers and scientists. Its national network of streamgages records changes in streamflow due to alterations in precipitation, land use, and water use. This information is vital to state and local governments, utilities, and resource managers who make decisions about water use.

The requested FY 2013 budget would support several science priorities. The proposed budget would enable the USGS to develop methodologies to better prevent, detect, and control Asian carp and other invasive species. USGS would also be able to provide enhanced surveillance and diagnostic tools, and to develop management tools for white-nose syndrome and other ecologically and economically costly wildlife diseases. Additionally, USGS would be able to study and better inform decisions about new energy sources. Importantly, the proposed budget would increase support for USGS research on high priority conservation and land use issues faced by other Interior bureaus, which lack intramural scientific resources to study these issues.

Although the proposed budget supports many USGS priorities, the requested funding level would result in cuts to other programs that support agency core missions. For instance, USGS would have to diminish efforts to assess the nation's water quality and reduce studies on the impacts of environmental contaminants. Given the agency's critical role in informing the environmental and economic health of the nation, more support is justified. We urge Congress to fully fund the USGS by restoring Administration-proposed reductions to core science programs and operations costs while maintaining the proposed increases for other areas.

In summary, the USGS is uniquely positioned to provide a scientific context for many of the nation's biological and environmental challenges, including water quality and use, energy independence, and conservation of biological diversity. Biological science programs within the USGS gather long-term data not available from other sources. These data have contributed fundamentally to our understanding of the status and dynamics of biological populations and have improved our understanding of how ecosystems function, all of which is necessary for predicting the impacts of land management practices and other human activities on the natural environment. This array of research expertise not only serves the core missions of the Department of the Interior, but also contributes to management decisions made by other agencies and private sector organizations. USGS science is also cost-effective, as the agency's activities help to identify the most effective management actions. In short, increased investments in these important research activities will yield dividends.

U.S. Forest Service

United States Forest Service research provides scientific information and new technologies to support sustainable management of the nation's forests and rangelands. These products and services increase the basic biological and physical knowledge of the composition, structure, and function of forest, rangeland, and aquatic ecosystems.

The FY 2013 budget request would cut funding for the Forest and Rangeland Research by $2.5 million. If enacted, the budget would reduce the Forest Service's capacity to conduct research relevant to wildfires, control of invasive species, and management of wildlife and fish. Given the importance of this scientific work to the management of public and private lands, we urge Congress to fund the program at the FY 2012 enacted level.

Environmental Protection Agency

The Office of Research and Development (ORD) supports valuable extramural and intramural research that is used to identify and mitigate environmental problems facing our nation. ORD research informs decisions made by public health and safety managers, natural resource managers, businesses, and other stakeholders concerned about air and water pollution, human health, and land management and restoration. In short, ORD provides the scientific basis upon which EPA monitoring and enforcement programs are built.

Despite the important role played by ORD, its funding has declined by 11 percent since FY 2004, when it peaked at $646.5 million. At $575.6 million, the budget request for FY 2013 falls far short of addressing past and current shortfalls. We ask that Congress restore funding for ORD to at least the FY 2010 level.

The Ecosystem Services Research program within ORD is responsible for enhancing, protecting, and restoring ecosystem services, such as clean air and water, rich soil for crop production, pollination, and flood control. The program has been chronically underfunded, according to the EPA Science Advisory Board (SAB). Indeed, the current level of funding "provides inadequate funding for research that supports multiple EPA regulatory programs and that the SAB has characterized as transdisciplinary with the 'potential to be transformative for environmental decision making'...," according to an SAB analysis of the FY 2012 budget request. The FY 2013 request fails to correct this problem, instead proposing a reduction of $600,000. Moreover, funding for EPA ecosystem research has been cut nearly in half since 2004. We ask that Congress address the chronic underfunding of the program.

The Science to Achieve Results (STAR) program supports valuable research on human health and the environment through competitively awarded research grants. The program enables EPA to fill information gaps that are not addressed by intramural EPA research programs or by other agencies. A report by the National Academy of Sciences found that the "STAR program is an important part of the overall EPA research program." That same report recommends that funding for the STAR program should be at 15 to 20 percent of the overall ORD budget, "even in budget-constrained times." Despite a proposed increase for the program, the FY 2013 request would fund STAR at less than 15 percent of the overall ORD budget. We urge Congress to fund STAR at the recommended level.

The STAR Graduate Fellowship contributes to the training of the next generation of scientists by supporting graduate students pursuing an advanced degree in environmental science. The National Academy of Sciences called the fellowship "a valuable mechanism for enabling a continuing supply of graduate students in environmental sciences and engineering." Since its inception in 1995, this successful program has supported the education and training of 1,500 fellows who have gone on to pursue careers as scientists and educators. The agency's request would flat fund the program. Given the fellowship's valuable role in preparing environmental scientists and engineers, we ask for the program's funding to be increased accordingly.

ORD's Safe and Sustainable Water Resources program supports research that underpins safe and sustainable water. In addition to helping to ensure safe drinking water for society, the program's research focuses on better understanding resiliency of watersheds to stressors and factors that affect watershed restoration. The budget request would allow the program to pursue research that will inform decisions about water safety and to ensure the sustainability of our coastal watersheds and estuaries.

In conclusion, we urge Congress to restore funding for the ORD to the FY 2010 enacted level. These appropriation levels would allow ORD to address a backlog of research needs.

Thank you for your thoughtful consideration of this request.

AIBS Comments on NPS' Draft Scientific Integrity Policy

2012-04-03T19:39:20Z

Dr. Gary Machlis
Science Advisor to the Director
1849 C Street NW
Washington, DC 20240

Dear Dr. Machlis,

Thank you for the opportunity to comment on the National Park Service's (NPS) draft scientific integrity policy. The policy proposed by NPS upholds the ideals set forth in the directive issued by Secretary Salazar. Although much of the policy is commendable, several areas should be strengthened to ensure the greatest public trust in NPS science.

The American Institute of Biological Sciences (AIBS) is a nonprofit scientific association dedicated to advancing biological research and education for the welfare of society. AIBS works to ensure that the public, legislators, funders, and the community of biologists have access to and use information that will guide them in making informed decisions about matters that require biological knowledge. Founded in 1947 as a part of the National Academy of Sciences, AIBS became an independent, member-governed organization in the 1950s. Today, AIBS has nearly 160 member organizations and is headquartered in Reston, Virginia, with a Public Policy Office in Washington, DC.

Applicability to Employees

We strongly support the agency's decision to apply the policy to all NPS employees and appointees who engage in, supervise, manage, or influence scientific activities; communicate scientific information; or use such information to make decisions. We commend NPS for applying the policy to volunteers, contractors, partners, permittees, and others who develop or apply scientific results.

Universal coverage is essential to guaranteeing that the policy is effective. It is vital that decision makers are subject to the policy, otherwise the potential exists for senior NPS officials to misrepresent, alter, or suppress scientific information. The inclusion of communications staff is key to sustaining public trust in NPS and the information the agency communicates to the public and policymakers.

Foundations of Scientific Integrity

In its December 2010 memorandum on scientific integrity, the Office of Science and Technology Policy (OSTP) outlined several foundational principles that should be included in each agency's respective scientific integrity policy. As currently written, neither the NPS policy nor Interior's Departmental Manual explicitly states the Department's commitment to several of these principles. NPS should rectify this by incorporating the following principles into its final scientific integrity policy.

Require independent peer review of research findings by qualified experts. Peer review is a central tenant of science. NPS should aim for independent review of its research in order to ensure that its work is of the highest quality and to sustain public trust in its scientific work. As currently drafted, the NPS policy requires bureau decision makers to "encourage" staff scientists to seek peer review of their work. This provision should be strengthened by requiring all data and research used to support policy decisions undergo independent peer review by qualified experts.
Establish principles for conveying scientific and technological information to the public, including underlying assumptions, uncertainties, and best-case and worst-case scenarios. Without such information, decision makers and the public are not able to fully comprehend the ramifications of the research nor make appropriate policy and management decisions. The proposed employee code of conduct asks NPS staff to "differentiate among facts, personal opinions, assumptions, hypotheses, and professional judgment" and to report uncertainties. NPS should strengthen this provision by developing and implementing broader principles for communicating scientific and technological information.
Develop a public communications policy that promotes and maximizes openness and transparency. Such a policy should include a provision to allow agency scientists to speak freely to the media and the public about scientific and technological matters based on their official work. Additionally, we encourage NPS to consider following the lead set by the National Oceanic and Atmospheric Administration by allowing its scientists to present viewpoints that extend beyond their scientific findings, for example about policy or management matters, so long as they make clear that they are presenting their individual opinions.

Code of Scientific and Scholarly Conduct

The draft policy outlines a code of ethics for employees, scientists, and importantly those who supervise and manage scientific activities. The proposed code of conduct would benefit from two additions:

The requirement for all employees, appointees, contractors, cooperators, partners, permittees, leasees, grantees, and volunteers to report allegations of scientific misconduct to the appropriate authority.
Include in the code for decision makers that the selection and retention of employees in scientific and scholarly positions is to be based on the candidate's integrity, knowledge, credentials, and experience relevant to the responsibility of the position. Although this principle is currently included in Interior's Departmental Manual, the NPS policy would be strengthened by its addition.

Scientific Societies and Professional Development

We strongly support the policy's encouragement of NPS scientists to serve in the leadership of professional and scientific societies. The participation of government scientists in scientific societies contributes to their professional development and to that of the scientific community.

Additionally, we urge NPS to encourage its employees to publish research findings in peer-reviewed scholarly journals, to present research findings at professional meetings, and to serve as editors of scholarly journals. The December 2010 memorandum on scientific integrity from OSTP explicitly states that agencies should encourage these activities, as well as allow government scientists to receive honors and awards for their research and discoveries. The draft NPS policy does not currently address these matters, nor does Interior's Departmental Manual.

Training on Scientific Integrity

We encourage NPS to include in its final policy a commitment to provide regular integrity and ethics training to its employees, appointees, and contractors. This should include training to new and existing staff. Additionally, NPS should provide information to ensure that employees and contractors are fully aware of their rights regarding dissemination of their research, participation in professional scientific societies, and their responsibility to report waste, fraud, abuse, and scientific misconduct.

Thank you for your thoughtful consideration of these comments. If AIBS may be of further assistance to you on this or any other matter, please contact Dr. Robert Gropp, AIBS Director of Public Policy at 202-628-1500.

Sincerely,

Richard O'Grady, Ph.D.
Executive Director

Fact Sheet on NSF's Investments in Biological Research

2012-03-28T13:18:28Z

Click here to read the PDF.

AIBS Writes to Oklahoma Legislative Leaders in Opposition to Creationist Bill

2012-03-20T19:37:23Z

Senator Brian Bingman
2300 N. Lincoln Blvd., Rm. 422
Oklahoma City, OK 73105

Senator Sean Burrage
2300 N. Lincoln Blvd., Rm. 522
Oklahoma City, OK 73105

Dear Senators Bingman and Burrage:

On behalf of the American Institute of Biological Sciences (AIBS), I write to urge your active opposition to final passage of HB 1551, the “Scientific Education and Academic Freedom Act.” This legislation is bad for science and bad for science education and should not be enacted into law.

Scientists in Oklahoma are deeply concerned about this legislation and the negative message it sends to the rest of the country. The best and brightest scientists, whether working for a university, teaching in a K-12 classroom, or working for a private sector company, want to work in an environment that appreciates the nature of science, not one that periodically redefines science in service to political agendas.

The economy and jobs of the future, whether in manufacturing, research and development, or energy and aerospace, require workers who have an understanding of scientific concepts and are practiced at thinking scientifically. This requires a quality science education, one free of political mandates. If enacted, HB 1551 would merely offer a vehicle for advocates of particular political or religious belief systems to introduce their personal ideologies into the science curriculum.

Advocates for this and similar legislation often assert that evolution and climate change are controversial subjects. Any controversy is purely political. There is no legitimate scientific controversy about evolution or climate change. Scientists have, and continue to, empirically test these concepts and with each test the evidence grows stronger and our understanding more thorough.

This legislation is similar to measures supported by advocates for creationism in other states. We urge you to respect science, science teachers, and religion by opposing passage of HB 1551.

Sincerely,

Richard T. O’Grady, Ph.D.
Executive Director

AIBS Submits Testimony to Congress in Support of the NSF FY 2013 Budget

2012-03-19T18:23:02Z

The American Institute of Biological Sciences (AIBS) appreciates the opportunity to provide testimony in support of fiscal year (FY) 2013 appropriations for the National Science Foundation (NSF). We encourage Congress to provide NSF with at least $7.373 billion in FY 2013.

The NSF is an important engine that helps power our nation's economic growth. Through its competitive, peer-reviewed research grants, NSF is leading the development of new knowledge that will help to solve the most challenging problems facing society, and will lead to new scientific discoveries, patents, and jobs. The agency's education and training programs are helping to ensure that the next generation has the scientific, technical, and mathematical skills employers are seeking. Investments in research equipment and facilities enable the country to continue to innovate and compete globally. These efforts, however, require a sustained and predictable federal investment. Unpredictable swings in federal funding can disrupt research programs, create uncertainty in the research community, and stall the development of the next great idea.

The NSF is the primary federal funding source for fundamental research in the non-medical life sciences at our nation's universities and colleges. The NSF provides approximately 62% of extramural federal support for non-medical, fundamental biological and environmental research at academic institutions.

NSF is a sound investment that pays dividends. The use of peer-review to evaluate and select the best proposals means that NSF is funding the highest quality research. Importantly, the FY 2013 budget request would allow the agency to fund 300 additional research grants, thereby supporting roughly 5,000 additional researchers, teachers, and students.

The research supported by NSF is unique from the science funded by other federal agencies. Unlike most federal agencies, which focus on applied research, NSF supports basic research that advances the frontiers of our knowledge about biodiversity, genetics, physiology, and ecosystems. Recent discoveries that stem from NSF-funded research include:

Creation of designer enzymes that can convert biomass into biofuels faster, more efficiently, and less expensively.
Refined understanding of the mechanism by which the flu virus infects humans. This insight could help to develop more effective treatments for the flu and save lives.
Identification of long-term environmental changes in U.S. ecosystems, such as changes in hydrology and nutrient inputs in lakes in the Midwest.
Knowledge of the physiological effects of human-caused marine stressors, such as pollution and low oxygen, on crustaceans' ability to fend off bacterial infections. This research has ramifications for several economically important fisheries.
Insight into the benefits of anti-microbial plant resins used in beehives on honeybee health. This discovery could have implications for colony collapse disorder, which has devastated bee populations in North America.

Biological Sciences Directorate

The Biological Sciences Directorate (BIO) funds research in the foundational disciplines within biology. These fields of study further our understanding of how organisms and ecosystems function. Additionally, BIO supports innovative interdisciplinary research that improves our understanding of how human social systems influence - or are influenced by - the environment, such as the NSF-wide Science, Engineering, and Education for Sustainability program. In collaboration with NSF's engineering, math, and physical science directorates, BIO is working to develop new, cutting-edge research fields. For example, the BioMaPS program is accelerating understanding of biological systems, and applying that knowledge to new technologies in clean energy.

The FY 2013 budget request for NSF would enable the agency to continue to fund highly competitive grant proposals in BIO's five core programmatic areas: Environmental Biology, Integrative Organismal Systems, Molecular and Cellular Biosciences, Biological Infrastructure, and Emerging Frontiers. Each of BIO's program areas also contribute to the education and training of undergraduate, graduate, and postdoctoral students.

Equally important, BIO provides essential support for our nation's place-based biological research, such as field stations and natural science collections. The Long-Term Ecological Research program supports fundamental ecological research over long time periods and large spatial scales, the results of which provide information necessary for the identification and solution of environmental problems.

The budget request also would sustain an effort to digitize high priority specimens in U.S. scientific collections. This investment will help the scientific community ensure access to and appropriate curation of irreplaceable biological specimens and associated data, and stimulate the development of new computer hardware and software, digitization technologies, and database management tools.

The FY 2013 budget would continue efforts to better understand biodiversity. Funding is included for the Dimensions of Biodiversity program, which supports cross-disciplinary research to describe and understand the scope and role of life on Earth. Despite centuries of discovery, most of our planet's biodiversity remains unknown. This lack of knowledge is particularly troubling given the rapid and permanent loss of global biodiversity. Better understanding of life on Earth will help us to protect valuable ecosystem services and make new bio-based discoveries in the realms of food, fiber, fuel, pharmaceuticals, and bio-inspired innovation.

The budget request includes funding in the Major Research Equipment and Facilities Construction account for the continued construction of the National Ecological Observatory Network (NEON). Once completed, NEON will provide the infrastructure necessary to collect data across the United States on the effects of climate change, land use change, water use, and invasive species on natural resources and biodiversity. This information will be valuable to scientists, resource managers, and government decision makers as they seek to better understand and manage natural systems.

STEM Education

The requested budget would allow NSF to build upon its central role in science, technology, engineering, and mathematics (STEM) education. Support for the scientific training of undergraduate and graduate students is critically important to our research enterprise. Students recruited into science through NSF programs and research experiences are our next generation of innovators and educators. In short, NSF grants are essential to the nation's goal of sustaining our global leadership in science, technology, engineering and mathematics, and reigniting our economic engines.

We encourage the Committee to provide the requested funding for the successful Graduate Research Fellowship program. The budget request would provide funding for 2,000 new fellowships, which are important to our national effort to recruit and retain the best and brightest STEM students. The budget would also provide a needed $2,000 increase to the fellowship's stipend, which has not changed since 2004.

The agency budget request also would provide important research support to early career scientists, helping them to initiate their research programs. The Faculty Early Career Development program (CAREER) supports young faculty who are dedicated to integrating research with teaching and learning. The FY 2013 budget would enable NSF to support approximately 40 more CAREER awards than in FY 2012.

Conclusion

Continued investments in the biological sciences are critical. The budget request for NSF will help spur economic growth and innovation and continue to build scientific capacity at a time when our nation is at risk of being outpaced by our global competitors. Please support an investment of at least $7.373 billion for NSF for FY 2013.

Thank you for your thoughtful consideration of this request and for your prior efforts on behalf of science and the National Science Foundation.

AIBS Writes to Tennessee Governor, Legislative Leaders in Opposition to Creationist Bill

2012-03-16T19:36:00Z

The Honorable Bill Haslam
1st Floor, State Capital
Nashville, TN 37243

The Honorable Ron Ramsey
1 Legislative Plaza
Nashville, TN 37243

The Honorable Beth Harwell
301 6th Avenue North
Suite 19 Legislative Plaza
Nashville, TN 37243

Dear Governor Haslam, Speaker Ramsey, and Speaker Harwell:

On behalf of the American Institute of Biological Sciences (AIBS), I write to respectfully urge your opposition to House Bill 368 and Senate Bill 893. These measures are bad for science, science education, and the future economic health and well being of Tennessee.

The AIBS is a professional society. Our approximately 160 member organizations represent the breadth of the biological sciences and have a combined membership of nearly 250,000 scientists and science educators.

It is important to note that there is no scientific controversy about the legitimacy of evolution or global climate change. These scientific concepts have repeatedly been tested and grown stronger with each evaluation. Any controversy around these concepts is political, not scientific. Indeed, evolution is a core principle that helps to explain biology and informs the development of biology-based products and services, including pharmaceuticals, food, and biotechnology.

As the nation struggles to reignite our economy and prepare our children for the jobs of the 21st century, we should be working to strengthen our science education system - not insert non-scientific concepts into the classroom to placate political special interests.

Please stand-up for Tennessee's students by opposing passage of HB 368 and SB 893.

Sincerely,

Richard T. O'Grady, Ph.D.
Executive Director

cc: Senator Bo Watson
Senator Mark Norris
Senator Jim Kyle
Rep. Judd Matheny
Rep. Gerald McCormick
Rep. Craig Fitzhugh

AIBS Report on the President's FY 2013 Budget

2012-02-20T14:12:57Z

Click here to view the PDF.

AIBS Writes to Indiana Lawmakers in Opposition to Anti-Evolution Bill

2012-02-06T20:27:59Z

Speaker Brian Bosma
Indiana House of Representatives
200 W. Washington St.
Indianapolis, Indiana 46204-2786

Minority Leader B. Patrick Bauer
Democratic Leader
Indiana House of Representatives
200 W. Washington St.
Indianapolis, Indiana 46204-2786

Re: Opposition to SB 89

Dear Speaker Bosma and Minority Leader Bauer:

I write to respectfully urge your opposition to Indiana Senate Bill 89 (SB 89). This legislation, which was approved by the Indiana State Senate on January 31, 2012, would permit the introduction of religious belief systems into your state's science curriculum. If enacted, this legislation would be a disservice to religion, science, and education.

There are many religious traditions that offer explanations for the origin of life. These are, however, not scientific constructs and do not belong in a science classroom.

As I know you are well aware, Indiana has worked hard and successfully to cultivate an educational and business climate that will attract life sciences companies. Indeed, as the Indiana Economic Development Corporation (IEDC) declares on its web site: "Indianapolis was deemed the hottest spot in the country to start a new Life Sciences business by the Wall Street Journal (Aug. 2011)." As the IEDC further highlights, Indiana is increasingly viewed as a global leader in life sciences research and manufacturing in areas such as oncology and biofuels.

Continued growth in these sectors will require an educated and skilled workforce. Thus, it is essential that all students in Indiana receive a quality science education, particularly in the biological sciences. Please support a strong Indiana science curriculum by opposing passage of SB 89 and any similar legislation that would confuse science and religion.

Thank you for your careful consideration of this matter.

Respectfully,

Richard O'Grady, Ph.D.
Executive Director

Cavefish: A Study in Evo-Devo (interview)

2012-01-26T14:53:32Z

Why are cavefish a good example of evo-devo?

The blind Mexican cavefish is one of the few species that has an ancestor on the surface and a descendent in caves.

Jeffery: Scientists study all kinds of organisms in evolutionary developmental biology, but when I started working in the evo-devo field, I decided that in order to understand how development evolved, we would have to look at two closely related species that have diverged recently [developed in separate directions] or to look at the same species in the process of divergence. I looked around for models, and I found several of them. One of them happened to be in caves, and the species is called Astyanax mexicanus, the blind Mexican cavefish. This cave organism is one of the few in which the acknowledged ancestor is still present on the surface, and the descendent organism is still present in the caves. They are the same species but they are in the process of divergence. These species can breed with one another, which allows for the genetic study of interesting traits. This combination of special circumstances fits my criteria for ideal development models. We could determine what the ancestral situation looked like by studying today’s surface fish and examine what the derived species looked like by studying present cavefish.

After the divergence, how do the cavefish differ from their surface counterparts?

Jeffery: Well, actually, we can study this very nicely in caves, particularly in Mexico. Cavefish populations were founded independently of one another and at different times. Which means we have some populations to study that are relatively young, that were founded recently, in addition to some that were founded early on in their evolutionary history. We can look at both the early and the late populations, and we can get an idea of what happened almost immediately when some fish moved from the surface to live in caves.

Interestingly, two things that happened in the changed environment are that the cavefish started to lose its pigmentation [coloring], and it started to lose its eyes (fig. 1). This was not a sudden phenomenon; it took some time, and we know that because the intermediates still have a little bit of pigment, and they have bigger eye remnants than the older forms.

Figure 1. The teleost _Astyanax mexicanus_ has diverged into a surface form (left) and a cave form (right); the cavefish has lost pigmentation and eyes. Research and photos from the laboratory of William Jeffery.

To describe what happened, I would say that first there was a great separation by natural selection as to which organisms could survive and which could not. Second, those that could survive have exacerbated their chances for survival through inbreeding. Then selection acted upon the phenotypes [expressions of genetic traits] that were highly adaptive to their cave environment. This weeding out process is still going on. This is a classic example of survival of the fittest.

An organism’s phenotype refers to how genetic traits are physically expressed in its morphology.

If evolution adapts for survival of the fittest, how is being eyeless a survival mechanism?

Jeffery: Well, eyelessness is not the survival mechanism—I think it is the by-product. When you first look at cave organisms, you are immediately aware of two features: lack of eyes and lack of pigment. But many other things are going on that are not obvious to the naked eye, and if you could look very closely, you would see that there are constructive features that have evolved as well. Some of these features are not found on the body surface—like changes to the brain or sensory organs. In some cases, the fish have a heightened olfactory sensitivity—the organisms can smell better, or they have evolved the ability to detect vibrations.

Cavefish have evolved other adaptations to living in a dark environment, such as the ability to sense pressure changes in the water.

They detect vibrations along their lateral line, a characteristic unique to aquatic vertebrates that sense pressure changes and movement in the water.¹ It is similar to the antennae on insects in its function. These fish have an increased ability to conserve energy and an increased ability to store metabolic products for sparse times. All of these things are beneficial for living in caves.

Now, how is the loss of things like eyes and pigment related to survival? This question has been a big question mark. My personal opinion from doing many experiments is that the lost features are a by-product of those features that are gained. For example, in the case of eyes, eyes are connected in development through a pleiotropic gene [a gene that controls many seemingly unrelated traits²] called Sonic hedgehog [Sonic hedgehog gene (SHh)] with the development of feeding structures, such as the jaws and the taste buds. These traits are enhanced in cavefish; for example, the jaw gets bigger, and perhaps, its function is improved as well. The improvements in this particular case could not have happened without a reduction in the size of the eye because that is just the way pleiotropy works. The evolution of cavefish has happened in a relatively short period during evolutionary time, and because it was so short, it is likely that the easiest changes were made. But there are by-products of those changes, and one of them happens to be the loss of the eyes. Of course, this could only happen in the dark, where eyes are useless anyway.

Pleiotropic genes control multiple, seemingly unrelated, physical traits.

Did the enhanced features come first, and therefore, lead to the degenerating effects, or was it the other way around?

Jeffery: We cannot know for sure but I would say that based upon the theory of pleiotropy, it would be those features that were selected for constructive uses that would adapt a fish or any other animal to the cave. Then, as a by-product, other things were lost, or space was needed to put those other features into action.

When I refer to space, I mean morphological [structural] space. So, for example, to make bigger neuromasts, sensory organs in the skin of the head that are part of the lateral line system and detect water movements, you need more surface space, and with having large eyes there, it does not give you enough surface space. If you are going to have more taste buds, and more sensory structures, a better olfactory system, and a better gustatory system (that is the taste system), you need places in the brain that can integrate the information and convert it into behaviors. Organisms, therefore, need to create space in the brain that controls these places, as well. The space being used for visual input is now defunct, so that space can be taken over; there is only so much space that can fit in a head, and it can be taken over by some sensory functions that are more important now. This is an old idea; in fact, Theodosius Dobzhansky, an evolutionary biologist from the first part of the last century, had this idea but experiments have now been done to support it.

Are the cavefish becoming genetically different from their surface relatives as quickly as the morphological changes are happening?

When scientists breed cavefish and surface fish, they get intermediate forms - these fish have eyes, but the eyes are smaller.

Jeffery: Genetic changes would happen before morphological changes. So yes, they are changing genetically. The gene Sonic hedgehog has not mutated in cavefish—as far as we can tell, the sequences are the same in cavefish and surface fish. Therefore, an upstream gene must control Sonic hedgehog to make it expand its role in cavefish, and therefore, result in more taste buds and bigger jaws. Scientists are searching for these genes but they have not found them yet. When you do genetic crosses with cavefish, you can detect genes and you can study them. When you do crosses with cavefish and surface fish, you get progeny that are intermediate, as far as eyes are concerned—they have eyes, but they are smaller. Then, if you breed the progeny, you get a broad distribution, all the way from animals lacking sight to ones with big eyes. This tells you there are many genes involved in the process and that they segregate independently in that lineage. So, it is a genetic principle that allows you to find this. If there are many genes, there are probably many ways to destroy the eye, and we know a few of them. One example is a pleiotropic interaction with taste buds, but there are probably other examples to illustrate the selection pressure for this phenomenon. A mechanism probably affects eye development; although, in the case of space, we do not know what the exact mechanism is.

Without eyes, how do they sense food, movement, or predators?

Cavefish have developed the ability to detect vibrations in the water, which often indicate the presence of prey.

Jeffery: This is the natural situation in caves. Without eyes, they probably sense food by using novel behaviors; for example, the behavior in which they are attracted to vibrations in the water. Vibrations in the water can result from many things, but often, they indicate food, wiggling crustaceans, which is the case for fish. Additionally, being able to get there quickly, before your competitor does, would be a good thing to do because that food is sparser in the cave than it is on the surface. This evolved behavior is risky for the cavefish because if you are guided to every movement, that is risky—you could be surprised by a moving predator rather than your prey. That would not work on the surface, but it works in the cave because there are very few organisms high in the pyramid of life that could serve as predators. Cavefish do not usually have macroscopic predators in the cave, so they can evolve these risky behaviors. Scientists use this behavior to their advantage. When they go to collect cavefish, they put a net in the water and the vibration alone will attract the fish. That is a risky behavior to have in any other place, and if I were a predator that would be the end of that cavefish.

Is vibration the same as the shadow effect?

Jeffery: No, the shadow effect is something entirely different. The shadow effect is something that is present in surface-dwelling fish [which typically flee from a shadow], as well as cave-dwelling fish. The effect is caused by a temporary shading of light, so it would not happen in a cave. When I talk about that shadow effect, which cavefish have retained, the question is, “Why have they retained it?” Selection is relaxed for anything like that—they have not seen the light for a million years. But those phenotypes are not completely destroyed during life in a cave—even if they are not used, they are kept. As for why they are kept, it may be that these traits are involved in some other phenomenon that we do not know about yet.

Cavefish have retained the shadow effect (the response of fleeing from a shadow) even through they have not been exposed to light for generations.

The shadow response is controlled by the pineal organ [an endocrine gland in the vertebrate brain, also known as “the third eye”³], which in fishes is responsive to light, particularly in photoperiods. The pineal gland produces melatonin, and as a result, organisms undergo circadian rhythms. As far as we know, this does not happen in a cave; although we are not so sure about that because all of the circadian rhythms we know about are dependent upon light. Other types of circadian rhythms that are dependent on things other than light may exist; for example, bats go in and out of caves according to light. When they go back into the cave in the morning, they go back to the roost, and they shake and things fall out, such as ectoparasites [parasites that subsist in or on the skin but not inside the body]. That would be a good time for a cavefish to be swimming right underneath the bat in a pool because of the food provided; so, cavefish can be in tune to things like that. There may be ways other than light in which circadian rhythms are controlled.

Is this loss of pigment a universal feature in cave creatures? And if so, why?

Loss of pigment occurs in organisms that live in caves, deep in the soil, and in parasites that live in the bodies of other animals.

Jeffery: Well, loss of eyes is fairly universal too; but before we go on, I should make the point that some cave dwellers have not lost their eyes. Those animals are just as interesting as the ones that have lost their eyes, and examining them would help explain the loss of the eye too; but they are not studied very often. The situation with pigment is that there is a very broad convergence among different organisms that have lost their pigment in caves. Additionally, this happens not only in caves but also deep in the soil or manmade tunnels, or in parasites existing in the body of other animals. It is very common that pigmentation is lost in all sorts of groups of animals after lack of exposure to light.

Let me digress for a minute—this also happens in humans—there are many different types of albinos [people who lack of pigmentation] in humans. We can study them effectively because there is no natural selection against them, and so there is something that produces albinos frequently in nature, and in environments where it is not adaptive, albino organisms are filtered out. Now, why would they be filtered out? Well, one reason is pigmentation protects organisms from ultraviolet (UV) radiation, so in lighted environments, they could be filtered out because they have less offspring—because they have melanomas, for example. This is probably not so in caves, where UV radiation does not penetrate. So albinism can persist without dire consequences in the dark cave environment, and there may be something good about this trait too. Many bad phenotypes can have good features—sickle cell anemia and so forth. Anyway the question is, “What are these good features?” Well, we will get back to that in a second, but let us just start out with: What is the cause of melanism [dark coloration of skin]? We do not know the cause of albinism in every cave animal, and it is something I am very interested in, and trying to study.

Cavefish have naturally developed albinism using the same genes as humans have.

We know a lot about it in cavefish thanks to the work of Meredith Protas, who was a graduate student in Cliff Tabin’s lab at Harvard University,⁴ several years ago, and she was able, through genetic analysis, to find out what gene was involved in the loss of pigmentation in cavefish. It is actually a longer story than that because perhaps twenty years before, genetic analysis, such as the type that I described to you for loss of eyes, was also done for loss of pigment in cavefish, and actually, a different result was obtained: a single mutated gene was found. To make the story short though, Protas did some crosses of phenotypes like in the earlier experiment. The pathway leading to melanin is very well known throughout the animal kingdom because there are not that many genes involved. It is a very simple, linear path, so Protas worked with just a few candidate genes. She mapped the candidate genes onto the place in the cavefish genome, and she discovered one candidate gene that mapped very closely with the genetic defect. This turned out to be a gene called, Oculocutaneous albinism type 2 (the reason for the long name is that it is an albinism gene that was already known), and it caused a loss of pigmentation in both the eyes and the skin of humans. Cavefish have naturally developed albinism using the same gene as humans have.

In the lighted surface environment, the albinism gene has harmful effects, but it is possible that—in a cave environment—this gene has beneficial properties.

We know this gene is causing albinism in cavefish at least, but we do not know if it is the same gene in other cave animals; I suspect it might be. Maybe this is just a gene that has a high frequency of mutation. So it keeps appearing, keeps appearing, and keeps appearing. On the lighted surface, it is a deleterious feature [having harmful effect(s)] because UV radiation can kill; but in a cave, it is not. It is possible there is something else good about this the mutant form of this gene, but we do not know what it is, although there are a couple of possibilities.

Has any of your research been used to support human medical applications?

Jeffery: Yes, some of it does get used. I have a grant from the National Eye Institute [part of the National Institutes of Health], and they are very interested in the causes of cataracts, for example, and it turns out this happens to be a downregulated gene. Some genes are downregulated in the cavefish lens—one is called alpha-A-crystallin, and that gene is involved in cataract formation in humans.⁵ So studying the deficiency in alpha-A-crystallin could help us understand how cataracts are formed in humans.

Studying a gene in the lenses of cavefish eyes might help scientists understand how cataracts form in humans.

The lens is an often neglected, but it is a very important organizer in the formation of the eye itself. The lens not only controls itself, it also controls other eye tissues around it, so for those tissues to prosper and develop normally, normal lenses are probably required. This has implications for human lens development. We are working on experiments to take a lens out of a surface fish to see what happens, We expect there would be some deficiencies in the retina when the lens is taken out. There may be clues here to understanding more about eye diseases because many eye diseases in humans involve the retina.

Biologists Commend NOAA's New Scientific Integrity Policy

2011-12-13T19:55:45Z

Policy responds to issues raised by AIBS

The National Oceanic and Atmospheric Administration (NOAA) has issued a policy that will promote and protect scientific integrity within the agency. The new policy has been well received by members of the scientific community.

“NOAA’s comprehensive scientific integrity policy should provide a strong foundation for public trust in the agency’s science,” said American Institute of Biological Sciences (AIBS) President Dr. James P. Collins. “Other federal agencies should look to NOAA’s policy as a model.”

The policy outlines goals for facilitating the free flow of scientific information, documenting the scientific knowledge considered in decision making, using information that has been independently peer reviewed, and hiring scientists based on the candidate’s credentials and integrity. Also included in the final policy are codes of conduct for scientists and supervisors.

Notably, the agency’s scientific integrity policy applies to all employees and contractors who directly engage in or supervise research, analyze or communicate scientific findings, or make decisions using science. AIBS previously expressed strong support for application of the policy to all employees, both career and political, involved in NOAA science.

“NOAA should be commended for engaging in such an open process,” Collins said. “Public input and participation helped to improve the draft policy circulated for public comment last summer.”

The final policy includes numerous revisions that respond to public comments. For example, the policy makes clear that all staff scientists may express their personal viewpoints about science and policy matters, holds NOAA grant recipients to the same standards of integrity as federal employees, and provides scientists with the opportunity to review and edit references to their research in official documents.

At the request of AIBS and other organizations, NOAA revised the procedural handbook that will guide investigations of alleged scientific misconduct. AIBS also called on NOAA to make clear that cases involving waste, fraud, and abuse would be referred to the Department of Commerce Inspector General.

“Scientific societies and professional organizations should be pleased with this policy,” stated Collins. Importantly, the policy encourages federal scientists to participate in professional organizations, including as officers and on governing boards, and to serve on scientific advisory bodies. “NOAA now has a clear policy to guide how and when federal scientists may serve their scientific communities. This is good for the agency, for science, and for the public. Federal scientists are often leaders in their fields. Science benefits when they are able to fully participate in their professional communities,” stated Collins.

NOAA developed the scientific integrity policy in response to an Executive Order issued by President Obama in 2009.

AIBS comments on the draft NOAA scientific integrity policy are available online at http://www.aibs.org/position-statements/20110819noaaintegrity.html.

A letter from AIBS to NOAA Administrator Jane Lubchenco regarding the agency’s final scientific integrity policy is available at http://www.aibs.org/position-statements/20111213noaaintegrity.html.

The NOAA scientific integrity policy is available at http://nrc.noaa.gov/scientificintegrity.html.

AIBS Comments on NSF's Draft Scientific Integrity Policy

2011-09-06T16:59:55Z

Dr. Subra Suresh
Director
National Science Foundation
4201 Wilson Boulevard
Arlington, VA 22230

Re: Draft Scientific Integrity Policy

Dear Dr. Suresh,

Thank you for the opportunity to comment on the National Science Foundation's (NSF) draft scientific integrity policy.

The American Institute of Biological Sciences (AIBS) is a nonprofit scientific association dedicated to advancing biological research and education for the welfare of society. Founded in 1947 as a part of the National Academy of Sciences, AIBS became an independent, member-governed organization in the 1950s. AIBS is sustained by a robust membership of individual biologists and nearly 200 professional societies and scientific organizations with a combined individual membership exceeding 250,000.

As is noted in the draft policy, NSF already has in place a number of policies to ensure the integrity of the merit review process and other agency actions. While it is commendable that NSF has been a leader in implementing a conflict of interest policy for investigators, this and other past actions are not sufficient to implement the guidance issued by the Office of Science and Technology Policy. NSF should make several changes to the policy in order to fully ensure the integrity of science.

Applicability to Employees

We strongly encourage NSF to state that the policy applies to all NSF employees, appointees, and contractors who engage in, supervise, or manage scientific activities; analyze or communicate scientific information; or use such information to make decisions. Universal coverage is essential to ensuring that the policy is effective. It is vital that decision-makers are subject to the policy, otherwise the potential exists for decision-makers to misrepresent, alter, or suppress scientific information, as has happened at other science agencies in recent years. The inclusion of communications staff is key to sustaining the public trust in NSF and the information the agency communicates to the public.

Code of Scientific Conduct

Several federal agencies have elected to include in their draft scientific integrity policies a code of conduct to guide the behavior of agency scientists. The National Oceanic and Atmospheric Administration (NOAA) went one step farther and devised a code of ethics for science supervisors and managers.

We recognize that NSF is a very different type of science agency, since it does not employ large numbers of government scientists to conduct intramural research. NSF, however, does employ statisticians, social scientists, and researchers in its National Center for Science and Engineering Statistics (NCSES). According to the NSF website: "As one of 13 federal statistical agencies, NCSES designs, supports, and directs periodic national surveys and performs a variety of other data collections and research." In addition, many staff throughout the agency analyze and communicate scientific results.

It is therefore necessary for NSF to develop a code of scientific conduct to guide employee actions. The codes of conduct included in NOAA's draft scientific integrity policy (sections 6 and 7) could serve as a good model for NSF.

Principles of Scientific Integrity

As currently written, the draft policy highlights many actions that NSF has already completed to address scientific integrity, such as an investigator conflict of interest policy. While these actions are an important part of agency's ability to ensure the integrity of science, they are not comprehensive.

NSF's policy would be much stronger if it included a set of guiding principles on scientific integrity. Other science agencies, such as the Department of the Interior and NOAA included principles of scientific integrity in their draft policies. Examples of principles that are not currently addressed in NSF's policy include:

The selection and retention of employees in scientific positions or in positions that rely on the results of scientific activities shall be based on the candidate's integrity, knowledge, credentials, and experience relevant to the responsibility of the position.
In no circumstance may any agency official ask or direct federal scientists to suppress or alter scientific findings.
The agency will make every effort to establish a culture of transparency, integrity, and ethical behavior among its employees through a combination of policy, opportunities for training, and open communications, both internally and with the public.

We encourage NSF to include these and other principles in their final policy.

Scientific Societies

The draft policy states that NSF staff can "participate in any research or educational institution, scientific society, professional association or editorial board, provided written permission is obtained from the scientist's or engineer's supervisor or ethics counselor." This standard is significantly more restrictive than other science agencies. For instance, NOAA encourages employees to join scientific and professional societies and does not require employees to seek permission beforehand. We strongly encourage NSF to revise their policy to allow employees to freely join scientific and professional societies.

We also urge you to clarify the policy to address the rule recently issued by the Office of Government Ethics that allows federal employees to serve on the board of directors and as officers of non-profit organizations, including scientific societies.

Sincerely,

Richard O'Grady, Ph.D.
Executive Director

AIBS Comments on EPA's Draft Scientific Integrity Policy

2011-09-06T16:57:12Z

Ms. Lisa Jackson
Administrator
Environmental Protection Agency
1200 Pennsylvania Avenue, NW
Washington, DC 20460

Re: Draft Scientific Integrity Policy

Dear Administrator Jackson,

Thank you for the opportunity to comment on the Environmental Protection Agency’s (EPA) draft scientific integrity policy. The policy will help ensure public trust in EPA science. The draft policy, however, could be significantly strengthened with several key additions.

The American Institute of Biological Sciences (AIBS) is a nonprofit scientific association dedicated to advancing biological research and education for the welfare of society. Founded in 1947 as a part of the National Academy of Sciences, AIBS became an independent, member-governed organization in the 1950s. AIBS is sustained by a robust membership of individual biologists and nearly 200 professional societies and scientific organizations with a combined individual membership exceeding 250,000.

Applicability to Employees

The agency’s decision to apply the policy to all EPA employees and appointees who engage in, supervise, or manage scientific activities; analyze or communicate scientific information; or use such information to make decisions is commendable. Universal coverage is essential to ensuring that the policy is effective. It is vital that decision-makers are subject to the policy, otherwise the potential exists for decision-makers to misrepresent, alter, or suppress scientific information. The inclusion of communications staff is key to sustaining the public trust in EPA and the information the agency communicates to the public. For these reasons, we urge you to revise the policy to include all contractors employed by EPA.

Principles of Scientific Integrity

The draft policy outlines a number of important principles that are integral to fostering scientific integrity. The addition of several other principles would significantly strengthen the policy. 1356b2db7529403f2e39751989617dfe

Additionally, the draft policy appears to be inconsistent as to which employees are expected to uphold the principles of scientific integrity. Appendix A states that “EPA employees, whatever their grade, job or duties,” must uphold the principles. Section IV, however, states that “EPA scientists and engineers, regardless of their grade, position, or duties” should abide by the principles of scientific integrity. Section IV of the draft policy should be revised to state that all EPA employees are subject to the principles. Otherwise, it appears only EPA scientists and engineers should “ensure that their work is of the highest integrity, free from political influence.” It should not be the responsibility of scientists alone to ensure the absence of political influence in EPA science. Rather this should be an endeavor that is the responsibility of all EPA employees, appointees, and contractors.

Code of Scientific Conduct

Several federal agencies have included in departmental scientific integrity policies a code of conduct to guide the behavior of agency scientists. The National Oceanic and Atmospheric Administration (NOAA) went one step farther and devised a code of ethics for science supervisors and managers. EPA has already incorporated some, but not all, aspects of such ethical codes into its draft policy. EPA is strongly encouraged to develop codes of scientific conduct to guide the behavior of scientists and managers. The codes of conduct included in NOAA’s draft scientific integrity policy (sections 6 and 7) could serve as a good model for EPA.

Communications with the Media and Public

Although the basic tenants underlying Section IV.B are admirable, the draft policy lacks several specific details that are needed to ensure that the scientific integrity policy is properly implemented.

First, this section of the policy should include managers and supervisors of scientists. The policy should state that managers and supervisors must never suppress, alter, or otherwise impede the timely release of scientific or technological findings or conclusions. Managers and supervisors will not intimidate or coerce employees to alter or censor scientific findings, nor shall they implement institutional barriers to cooperation and the timely communication of scientific findings or technology.

Furthermore, policy officials should be expected to release to the public the scientific or technological findings or conclusions considered or relied on in policy decisions.

In order to fully comply with the Office of Science and Technology Policy memorandum dated December 17, 2010, EPA should “communicate scientific and technological findings by including, when necessary and appropriate, a clear explication of underlying assumptions; accurate contextualization of uncertainties; and a description of the probabilities associated with both optimistic and pessimistic projections, including best-case and worse case scenarios.” Additionally, EPA should publically release “data and models underlying regulatory proposals and policy decisions.”

Lastly, EPA should develop an agency-wide framework for deciding how written and audiovisual materials will be approved for public dissemination. This guidance should include time limits for review and approval, and procedures for redress if time limits are not met.

Scientific Societies and Professional Development

EPA is strongly commended for supporting the participation of agency scientists in the leadership of professional and scientific societies, the publication of results in peer-reviewed journals, the presentation of research at scientific meetings, and active participation in professional societies. As is noted in the draft policy, “scientific leadership is a key component of advancing the mission of EPA.” The engagement of federal scientists in scientific societies is key for the professional development of these researchers and for the advancement of science. To this end, we encourage EPA to state in its final policy that its scientists and engineers are able to accrue the professional benefits of honors and awards for their research and discoveries.

Scientific Integrity Committee

The creation of a committee on scientific integrity and the designation of a Scientific Integrity Official are commendable. The leadership of these individuals should help to ensure that the scientific integrity policy is well implemented across the entire agency. It is particularly valuable that the committee will track and report annually on cases of misconduct. Indeed, this concept was recommended by the Inspector General for the Department of the Interior for the bureaus under its jurisdiction. The development of a training program related to scientific integrity for agency staff is also notable.

Thank you for the opportunity to comment on the draft scientific integrity policy. If AIBS may be of further assistance to you on this or any other matter, please contact Dr. Robert Gropp, AIBS Director of Public Policy at 202-628-1500.

Sincerely,

Richard O’Grady, Ph.D.
Executive Director

Dr. Joseph Travis Honored with E.O. Wilson Naturalist Award

2011-08-31T17:32:31Z

On your receipt of the E.O. Wilson Naturalist Award in June you commented that E.O. Wilson has always encouraged you to stay the course as a real naturalist. What defines a real naturalist in your view?

Real naturalists use their knowledge of nature as a guide to raising and answering questions about what they see.

Travis: In my view a real naturalist is someone who has studied nature, pays close attention to nature in his or her work, and uses that knowledge of nature as a guide to identifying and answering interesting questions. For example, a real naturalist is someone who understands the role of different kinds of soil on plant distribution, and that you can actually see this for yourself by walking around and looking at where certain plants grow. A real naturalist is someone who notices clear patterns in the association of certain insects with certain plants, or that you can learn to identify plants from the structures of their flowers. A real naturalist is someone who feels at home wandering around in the woods, or in the marsh or grasslands just watching—watching birds forage, watching insect flight patterns, watching patterns of phenology in plants over time. A real naturalist is someone who is really engaged with the processes and observations of nature and who notices things and raises questions about what they see.

Source: Florida State University.

You studied biology as an undergraduate at the University of Pennsylvania. What prompted you to choose biology as a major?

Travis: The honest answer is that it seemed like fun! I started college without much inclination as to what I wanted to study. I began my freshman year thinking maybe I’d major in English because I liked reading novels and plays and I liked to write, or maybe I’d major in history because I liked to read about history, or maybe I’d major in something in science because it seemed like a lot of fun. In my very first semester I took a course from Bob Ricklefs called Biology 101: Introduction to Environmental Biology. At that time, the University of Pennsylvania Biology Department had a four-semester introductory sequence in place of the typical Bio I and Bio II two-semester sequence. The first semester was environmental—which meant that it encompassed ecology, evolution and behavior, the second was organismal, the third was molecular and cell, and the fourth was developmental. So I took the course because ecology and evolution seemed like an interesting topic and biology was my favorite science course that I took in high school. By the end of that semester I was all but hooked; it was a great, great course. I just enjoyed every minute of it; I enjoyed the way Bob taught you to think about science and biology, and from that point on I was a biology major.

And then, later, what prompted you to study in Trinidad?

The National Science Foundation, through FIBR, funded the Guppy Project: a five-year project to study the process of adaptive evolution in nature.

Travis: The work I’ve been doing there in the past few years has really been the outcome of my 37-year friendship with David Reznik. David came to the University of Pennsylvania as a first year graduate student to study with Bob Ricklefs in the same year I was a senior undergraduate. We took a course in field ecology together which was a really interesting course taught by three faculty members and in which we were in the field all the time. I’m not sure what we accomplished in terms of projects and academic work, but we sure as heck had a lot of fun and David and I became friends. So when he began his dissertation work in Trinidad I followed his work and we exchanged ideas, corresponded, visited with each other, and even reviewed each other’s papers and grant proposals. We had a close association over a very long time and, when the FIBR (Frontiers in Integrative Biological Research) Program was announced, David approached me and said “I’ve been trying to get you to work with me in Trinidad for years and here’s an opportunity to work on something you’ve thought about for a long time, which is the role of evolutionary and genetic processes on ecological issues. Do you want to finally get involved?” I jumped at the opportunity and that’s how it all got started.

What do you feel are the most important lessons for biologists that have emerged from your studies of guppies and their effects on ecosystems?

Travis: Let me make sure the credit goes to David Reznik for working on the system for 35 years. And John Endler before him and so many others. I’m a late-comer to this system, but a lot of my own work has been in other kinds of systems with similar questions. One of the major lessons from all of this work is that, in many cases, ecological and evolutionary processes unfold on the same timescale. The early ecological geneticists like E.B. Ford, Sir Ronald Fisher, and David Pimentel turned out to be focused on a really important point. Ford argued in Britain in the 1930s that numerical dynamics of populations were intimately entwined with the genetic dynamics on the same timescale. That is to say, as the numbers fluctuated on a scale you could measure, generation to generation, so would allele frequencies, and a process of evolution would unfold in front of you as dynamics unfolded.

One important lesson from the Guppy Project is that ecological processes can be influenced by evolutionary processes on the same timescale.

The real demonstration of this was in Fisher and Ford’s 1947 paper on Panaxia dominula where they actually showed this was true. Now that particular paper had the wrong explanation for what was driving the genetic dynamics, but they showed beyond a shadow of a doubt that genes fluctuate in frequencies and turn over in the same timescale as does the number of individuals. From Ford’s point of view this meant that evolution could be studied experimentally in the here and now. But if you turn it on its head and say that, if evolution can be studied, that also means that ecological processes can be influenced by evolutionary ones on the same timescale, that gives you a different insight into the role of evolution in ecology. If there is one thing I hope I’ve contributed toward advancing the field of natural history over all these years it’s contributing to that particular insight.

What is your assessment of the current state of natural history research, both in the US and around the world—is it healthy?

Travis: It’s very healthy but it’s healthy in a funny kind of way. There’s a lot of great natural history but it doesn’t get the exposure in scientific circles that it perhaps deserves or that it ought to. And I say that because you can certainly see lots of great natural history being done and a lot of people having their research informed by insights from natural history, but most scientific journals are publishing papers that are hypothesis-driven tests of theory or hypothesis-driven planned observations motivated by a concept or idea. They’re not publishing what people consider classic natural history, like descriptions of flowering phenology or narratives of animal behavior. But natural history is alive and well because you can see an appreciation for its motivating the testable hypotheses in the work of many people.

Natural history motivates and informs the work of much of the current research found in scientific journals.

If you look at all of John Avise’s work on phylogeography and genetic population structure, you ought to be astounded by how much he actually discovered, by how many interesting patterns of genes he has documented, and the brilliance of much of what he has articulated as the reasons for those patterns. John is a superb natural historian. I once had a graduate student say something to me along the lines of, “Gosh, how does John Avise do it? How does he come up with these ideas? Everything he touches turns to gold!” I said, “You think this happens by chance? You think he’s guessing? John Avise is a really good naturalist and he draws on that knowledge and intuition for his inspiration.” Beneath the surface of John’s papers you can see really beautiful natural history because you don’t get those ideas and hypotheses without it. So natural history is alive and well in that sense. There are many people who lament the absence of natural history in frontline journals like Evolution and Ecology but I contend it’s actually there motivating a lot of the good work that’s being done; it’s lurking, if you will, just below the surface, because a lot of the people who repeatedly do the best work are really very good naturalists.

Looking to the future, what are the most important questions you’d like to see natural history researchers address over the next twenty years or so?

Travis: I think one of the most important questions that’s both interesting in a scientific sense and important in a practical sense is the spatial scale in which ecosystem processes are connected and the long timescale of influence. For example, if we want to understand the shrimp numbers, scallop numbers, and oyster numbers in the Apalachicola Estuary in north Florida, we have to understand water flow out of the Appalachian Mountains and the water drawn by the city of Atlanta for its citizens to use, because there is a direct and demonstrable statistical connection between water flow in northern Georgia and productivity of the estuary many hundred miles to the south.

In the near future, natural history might investigate how ecosystem processes are connected and over what timescales they operate.

A good natural historian knows that water has to go someplace and that if it starts up in northern Georgia and flows all the way down to the Gulf, then it’s carrying things with it. Ideally, it carries nutrients (which it does in this case) and not pollution. Anyway, those long range connections are very important for us to understand because not only do they connect ecosystems, they connect human actions and decisions in one place with consequences elsewhere. We have water wars in which the states of Florida, Alabama, and Georgia have fought over the water use patterns in the Appalachicola River system. The contention that flow is important for the productivity of the estuary is the sort of thing that, were it not backed up with solid scientific data, would have lawyers arguing it ad nauseum. So I think one of the biggest challenges for natural historians is to expand their scope of thinking from the local woods, the local ponds and lakes, the local rivers, to think broadly on a bigger scale and consider the natural history of extended systems that are connected over long distances, and also how we as a species are going to co-exist with these extensive ecosystems into which we are embedded.

What advice would you give to students who might be interested in pursuing a career in natural history?

Travis: : I think one of challenges is to find clever ways to give students good training in natural history. For twenty years I taught a course in biology of the lower vertebrates - a combination ichthyology and herpetology class—and a lot of our time was spent in the field doing natural history. I told the students that we’d organize our field work around learning which fish occur in which kinds of waters and which herps could be found where. But once you have them outside, you can show them all kinds of stuff. You can say, “Why do you think the water here is so acidic? What do you think about this litter? Why don’t you lick this leaf here and see what it tastes like…it’s bitter isn’t it? Yeah, let’s talk about decomposition of leaves and tannic acid in the water.” You begin to teach students natural history by going out in the field with them and teaching them to observe and ask questions about what they see and perceive. So, one thing we should do as teachers of biology is to find ways to teach students good natural history by taking them out in the field and also by making sure we offer field courses that are not just explorations in quantitative exercises.

Students interested in natural history should take advantage of opportunities to learn and study in the field.

The introduction to tropical ecology course, offered by the Organization for Tropical Studies, that many of us took as graduate students is an excellent model for this. The class would show up at a particular location like the La Selva Rainforest Station and you’d have three days of all-day hikes where the instructor would just teach you the names of things and show you the lay of the land. Then you’d do a couple of projects over the next two or three days, but there was always a significant amount of natural history. We, as instructors, as faculty members in universities and colleges, need to teach natural history more and emphasize it more. At the same time, students should take every opportunity to learn it. When I was a graduate student one of the things I tried to do was to be a field helper for any of my fellow graduate students that would put up with me. I bagged flowers, dug grass tillers, electrofished for catfish, rolled logs for salamanders, trapped mice; I did pretty much everything one of my fellow graduate students was doing just so I could get the exposure and experience and learn from them. And that’s what students need to do. You can learn a lot by just exposing yourself to natural history and, of course, once your curiosity gets whetted by things you observe or see, that motivates you to read a little more, go out a little more, and to keep doing it, and the more you do the better you get at it.

Should students be making a deliberate effort to acquaint themselves with newer biological techniques that we don’t ordinarily think of as being common in the field of natural history?

Natural history forms the foundation for research questions, but students must be familiar with other techniques in order to sufficiently answer those questions.

Travis: They must. Natural history is the underpinning of all of our questions in ecology, evolution and behavior, but it’s not a sufficient route to answer those questions. The first paper I ever published was on downy woodpeckers foraging randomly in summers but very selectively in winters on trees with rough, furrowed bark. And it’s one of those things I just sort of noticed; I liked watching birds and said, “Boy, you know, every time I see them on winter days they’re just on certain types of trees. I wonder if that would actually be true if I were to quantify my observations.” So the question was motivated by the observation. Now in order to get the answer, I actually devised my own rather crude method for measuring how furrowed the bark was so that there would be an objective, repeatable measure of “furrowedness” and not a subjective claim based on what I thought I was seeing. To do this required me to understand what the trees looked like, decipher what “furrowedness” actually implied in terms of a measurement, as well as some basic statistics that would allow me to test the idea objectively. So natural history was the foundation of the question I was interested in, but knowing the natural history wasn’t enough to get the answers in a scientific sense. You have to do experimentation, you have to measure some things objectively that can be very subtle, and you have to be able to keep up with the latest techniques of doing so because those techniques help you answer age-old questions.

Nothing illustrates this better than the development of sequencing technology in genetics and the development of computational power over the last 25 years. We can solve problems we couldn’t solve before, but those have raised questions we didn’t even think to ask before. So, yes, I think students need to familiarize themselves with newer biological techniques in order to obtain answers to questions that emerge from their observations in natural history.

AIBS Comments on NOAA's Draft Scientific Integrity Policy

2011-08-19T16:54:00Z

Dr. Jane Lubchenco
Under Secretary for Oceans and Atmosphere
Administrator, National Oceanic and Atmospheric Administration
1401 Constitution Avenue, NW
Room 5128
Washington, DC 20230

Re: Draft Scientific Integrity Policy

Dear Dr. Lubchenco,

Thank you for the opportunity to comment on the National Oceanic and Atmospheric Administration’s (NOAA) draft scientific integrity policy. The comprehensive policy proposed by NOAA upholds the ideals of scientific integrity. Indeed, NOAA’s draft policy should be used as a model by other federal departments and agencies.

The American Institute of Biological Sciences (AIBS) is a nonprofit scientific association dedicated to advancing biological research and education for the welfare of society. Founded in 1947 as a part of the National Academy of Sciences, AIBS became an independent, member-governed organization in the 1950s. AIBS is sustained by a robust membership of individual biologists and nearly 200 professional societies and scientific organizations with a combined individual membership exceeding 250,000.

Applicability to Employees

We strongly support the agency’s decision to apply the policy to all NOAA employees, appointees, and contractors who engage in, supervise, or manage scientific activities; analyze or communicate scientific information; or use such information to make decisions. Universal coverage is essential to ensuring that the policy is effective. It is vital that decision-makers are subject to the policy, otherwise the potential exists for decision-makers to misrepresent, alter, or suppress scientific information, as has happened at other science agencies in recent years. The inclusion of communications staff is key to sustaining the public trust in NOAA and the information the agency communicates to the public.

Despite the broad coverage established in Section 2.01, the bulk of the draft policy appears to be applicable only to a subset of NOAA employees. Section 5.01 states that “NOAA scientists, science managers, and supervisors shall uphold the fundamental Principles of Scientific Integrity, the Code of Scientific Conduct, and the Code of Ethics for Science Supervision and Management outlined in the following sections of this Order.” Given that these three elements constitute a majority of the substance of the policy, Section 5.01 appears to nullify the coverage established in Section 2.01. The Code of Scientific Conduct (Section 6.01) adds further confusion by stating that it is applicable to the personnel defined in Section 2.01.

In order to clarify the intensions of the policy, NOAA should revise Section 5.01 to state:

“All NOAA employees and contractors identified in Section 2.01 shall uphold the fundamental Principles of Scientific Integrity, the Code of Scientific Conduct, and the Code of Ethics for Science Supervision and Management outlined in the following sections of this Order.”

Scientific Societies and Professional Development

We strongly support the policy’s encouragement of NOAA scientists to serve in the leadership of professional and scientific societies, publish their results in peer-reviewed journals, present their research at scientific meetings, actively participate in professional societies, serve on review panels, and participate in science assessment bodies. As is noted in the draft policy, “scientific leadership is a key component of advancing the mission of government agencies.” The engagement of federal scientists in scientific societies is key for the professional development of these researchers and for the advancement of science.

Communications with the Media and Public

The agency is commended for allowing scientists to speak freely with the media and the public, however, the draft policy’s guidelines for such communications do not provide sufficient detail to inform employees of their rights and limitations under the policy.

The policy states that “NOAA scientists may freely speak to the media and the public about scientific and technical matters based on their official work” (Section 4.03). As currently written, this section does not make clear that NOAA researchers must submit “all written and audiovisual materials that are, or are prepared in connection with, a Fundamental Research Communication” to the head of their operating unit for approval before the information can be publically released (Department of Commerce Administrative Order 219-1 Section 7.01). NOAA should revise Section 4.03 of the policy to make this distinction clear.

NOAA is encouraged to provide information to its employees regarding the use of email to communicate science to the media. Per the June 15, 2011 memorandum from Mr. Cameron F. Kerry, General Counsel for the Department of Commerce: “Electronic communications with the media related to fundamental research that are the equivalent of dialogue are considered to be oral communications; thus, prior approval is not required for a scientist to engage in online discussions or email with the media about fundamental research.”

The agency’s plan for a NOAA-wide framework for review of written and audiovisual science communications, including time limits for review and approval, and procedures for redress if the deadlines are not met, is laudable. Such time frames are important to ensuring that no manager or supervisor can suppress science by refusing to review a document for public release.

Scientific Misconduct

It is commendable that the draft policy offers protection to employees who uncover and report allegations of scientific misconduct, as well as privacy protection to employees accused of misconduct. The agency’s commitment to tracking and annually reporting allegations and findings of scientific misconduct is also admirable. Indeed, this concept was recommended by the Inspector General for the Department of the Interior for the bureaus under its jurisdiction.

NOAA should also be applauded for developing a draft procedural handbook for dealing with allegations of scientific misconduct, and for releasing the handbook with the draft scientific integrity policy. The draft handbook outlines a detailed process for investigating allegations of research misconduct. It is particularly helpful that the process includes the maximum allowable time frame for each step of the process.

Several additional suggestions are offered below that may strengthen the procedures outlined in the draft handbook:

The timeframe for securing evidence, including all original research records and materials relevant to the allegation, should be considerably shorter than is currently proposed. As written, the draft procedures would result in evidence being collected as late as 120 days after the alleged misconduct is discovered. Earlier steps need to be taken to ensure that evidence is collected and secured in order to allow for an accurate and complete investigation.
Allegations of scientific misconduct that involve alleged fraud, waste, abuse, or criminal law violations should be referred to the Department of Commerce Office of Inspector General. The United States Geological Survey (USGS) handles such incidents in this manner.
Guidance, including qualifications and selection criteria, should be added to clarify who can serve as Determining Official when the Deputy Under Secretary for Operations does not fill the role. Given the powerful role this individual could play in the procedures, it is important that an appropriately qualified person is selected.
The Federal Research Misconduct Policy outlines several criteria to guide appropriate administrative actions to respond to research misconduct, including “the degree to which the misconduct was knowing, intentional, or reckless; was an isolated event or part of a pattern; or had significant impact on the research record, research subjects, other researchers, institutions, or the public welfare.” Section 5.04 (a) should be revised to reflect these criteria.
Section 3.02, which outlines how to report allegations of misconduct, should be revised to include a list of the information that is required to be submitted to the Deputy Under Secretary for Operations. The USGS scientific integrity policy could serve as a good model in this regard (see USGS Survey Manual 500.25.8.A.1).
The handbook does not currently address how the review panel will reach a decision. NOAA might consider the model used by the USGS. For the USGS, a Scientific Misconduct Review Panel is directed to “arrive at consensus decision, if possible…. The Panel will take the time necessary to address all of the relevant issues associated with the allegation in order to reach a consensus finding. If, after all efforts are exhausted, the Panel is still unable to reach consensus about whether or not misconduct has occurred, then a majority decision will be made” (USGS Survey Manual 500.25.8.C.4-5). Panel members then write majority and minority reports to record their differences.

Code of Ethics for Science Supervision and Management

The policy outlines a comprehensive code of ethics for those who supervise and manage scientific activities. The inclusion of such a code is an important feature, one that we hope that other federal agencies will include in their respective scientific integrity policies.

Sincerely,

Richard O’Grady, Ph.D.
Executive Director

Multifunctional Magnetic Nanoparticles as Bionanomaterials

2011-07-20T02:59:32Z

Nanobiotechnology focuses on the biological and biochemical applications of nanotechnology.

Multifunctional magnetic nanoparticles¹ are particles about one hundred-thousandth of the diameter of a human hair that combine biologically active molecules with metal particles (occasionally, metal compounds) that respond to a magnetic field. They are considered multifunctional because of the variety of their potential applications, including, in biomedicine, capturing bacteria and purifying proteins. Multifunctional magnetic nanoparticles are recent examples of bionanomaterials. Fabrication and use of such materials is known as nanobiotechnology, and is the branch of nanotechnology that focuses on biological and biochemical applications.² Nanobiotechnology deals with the many molecular processes that occur within living cells on very small (nano-) scales. Improving knowledge of such processes is providing an understanding of many complex cellular functions.

The commonality of “nano” and “bio”

“Nano” and “bio” refer to objects with sizes between 1 and 100 nanometers.

While the objective of nanoscience (nano) is to explore objects and systems that have sizes between 1 and 100 nanometers (nm) in at least in one dimension (Figure 1), biological science (bioscience or bio) primarily focuses on the components and functions of cells. Although the sizes of whole cells range from thousands to tens of thousands of nm, the components of cells usually have sizes below 100 nm in at least one dimension. For example, cell membranes are less than 10 nm thick; the cytoskeletons in mammalian cells are nanofibers of actins and microtubulins tens of nm in diameter; and double-stranded DNA is a nanowire just a few nanometers wide. Therefore, nano and bio share the same range of sizes (1-100 nm), which has allowed scientists to explore the interactions between the two.

Figure 1. Comparison of the sizes of atoms, nanoparticles, and biological entities.

Most importantly, the sizes shared by nano and bio are in a special range. Within this range, new phenomena emerge—that is, the behavior of a group of objects differs drastically from that of each individual object in the group. Figure 2 shows examples of objects and structures in nanoscience or biological science. Figure 2A shows a memory cell from a contemporary computer memory chip; made of a few thousand silicon atoms, it can store bits of information, yet a single atom of silicon (one tenth of a nanometer in diameter) cannot. A phospholipid molecule is useless as an individual molecule; however, when millions of the phospholipids self-assemble in water, they form a membrane 3-9 nm across (Figure 2B) that compartmentalizes a myriad chemical reactions and may have led to the emergence of life. In Figure 2C, although filaments of actin molecules control cell movement, an individual actin molecule has little power to modulate cell behavior. In Figure 2D, although bulk iron-platinum alloy is a “hard” magnetic material (meaning that a large magnetic field is needed to change its magnetization), magnetic nanoparticles of the alloy less than 2 nm in diameter are said to be superparamagnetic—their magnetization is easily influenced by a magnetic field. Clearly, these examples indicate that nanostructures are unique and differ from both the bulk materials and the individual molecules or atoms. Indeed, life itself is fundamentally a collection of processes taking place at the nanoscale within cells.³ It is important, therefore, to understand the interactions between nanomaterials and biological systems and to explore their applications.

Figure 2. Electron-microscope images of some objects in nanoscience or biological systems. (A) A 32 nm node for flash memory⁴ ; (B) the membrane (white arrow) of a bacterium⁵ ; (C) filaments of actin (a cytoskeleton component) ⁶ (©2008, American Chemical Society) ; (D) Iron-platinum magnetic nanoparticles (approximate size 4 nm) (©2003, American Chemical Society).

Molecular interactions as the foundation of nanobiotechnology

Applying nanoparticles requires understanding cellular activities at the molecular level.

Although the functional basic unit of life is the cell, all the processes occurring inside and among cells are sophisticated molecular interactions. Advances in the field of molecular biology continue to reveal details of cellular activities at the molecular level. These have resulted in many extraordinary successes, including:

the discovery of the structures and functions of DNA and RNA;
the elucidations of the structures and functions of numerous enzymes; and
advancements in molecular medicine.

Because molecular interactions dictate biological processes, it would be impossible to explore and apply nanomaterials in biological science without a fundamental understanding of the molecular interactions between nanomaterials and biological entities.

Design and fabrication of multifunctional magnetic nanoparticles

The size and surface chemistry of nanoparticles determines how they interact with biological objects.

Because of the unique response of nanoparticles to a magnetic field, simply attaching them to biofunctional molecules leads to multifunctional nanostructures. Magnetic nanoparticles, therefore, are a favorite choice for the development of multifunctional bionanomaterials. To construct multifunctional nanoparticles, it is necessary to consider both the size and surface chemistry of the nanoparticles in order to control the molecular interactions between nano and bio.

Choice of sizes. Two simple criteria help define the optimal size of magnetic nanoparticles to achieve high affinity, selectivity, and sensitivity in interactions with biological objects:

(1) the nanoparticles should be large enough to allow the presence of multiple ligands (substances, such as neurotransmitters, that form complexes with biomolecules by binding to specific sites). This will allow multiple interactions with a nanoparticle and allow it to bind tightly with biological targets.
(2) the nanoparticles should be small enough to have high surface-to-volume ratios, to be stable when dispersed in a liquid as a colloid, and to move quickly (thus allowing fast reactions). For example, to separate biomacromolecules such as proteins, the size of the nanoparticles should be comparable to the size of the biomacromolecules.

Functionalization Figure 3 shows two ways to anchor molecules on the surface of nanoparticles. In route A, a monolayer⁷ of molecules bearing a reactive group grows on the nanoparticles; specific molecules then react with the monolayer’s reactive groups to yield the functional nanoparticles. In route B, the group that reacts with the surface is joined first to the functional molecule, then the combination reacts with the nanoparticle to yield the desired product. Route A is simple and versatile, but it may leave unreacted sites as defects. Route B produces a well-defined monolayer that has fewer defect sites; however, it can require considerable synthetic effort to engineer the molecules to react with the surface.

Figure 3. Two ways to attach molecules to a nanoparticle (the red fragment represents the surface anchor; the green one, the reactive group to be attached to the nanoparticle).

Applications for multifunctional magnetic nanoparticles

Multifunctional magnetic nanoparticles can be used to detect and capture bacteria.

Capturing bacteria. The ability to detect bacteria at ultralow concentrations without time-consuming procedures is very valuable in clinical diagnosis and environmental monitoring. Doing so using conventional techniques requires an “induction time” of at least 24 hours during the analysis. The use of multifunctional magnetic nanoparticles, as illustrated in Figure 4, can speed this process. After a ligand such as vancomycin [Van] is attached to the surface of the magnetic nanoparticles (e.g., iron-platinum), the magnetic nanoparticles (written as FePt@Van conjugates) become attached to the bacteria, because vancomycin binds to receptors the bacteria carry on their outer membranes—even when the bacteria are present in very low concentrations. A small magnet attracts and enriches the bacteria-nanoparticle composites for analysis. This process takes less than two hours and detects bacteria with very high sensitivity (probably because the FePt@Van nanoparticles are roughly the same size as antibodies, which have evolved to destroy bacteria).

In addition, using functional magnetic nanoparticles to capture bacteria is particularly useful when the polymerase chain reaction⁸ technique is not applicable, which may be the case for biological mixtures. Combining FePt@Van magnetic nanoparticles with fluorescent dyes can achieve quick, sensitive, and low-cost detection of bacteria in a patient’s blood, for example.⁹ Newer strategies based on the same principle detect bacteria by anchoring bacteria-specific antibodies to the magnetic nanoparticles.¹⁰

Figure 4. (A) Interaction between iron-platinum nanoparticles conjugated with vancomycin (FePt@Van) and bacteria (Staphylococcus aureus). The magnet (bottom illustration) attracts the particles and hence the bound bacteria. (B ) There is no interaction with nanoparticles bearing amine groups (NH₂) as the control and so the bacteria are not removed by a magnet. Scanning electron microscope (SEM) images of (C) aggregates of *S. aureus* and FePt@Van nanoparticles, and (D) aggregates of FePt-NH₂ nanoparticles. (E) SEM and (F) transmission electron microscope (TEM) images of a VanA bacteria captured by FePt@Van nanoparticles (inset, high resolution TEM image of FePt@Van nanoparticles). Vancomycin-resistant enterococcus (VRE) is the name given to a group of bacterial species of the genus Enterococcus that is resistant to the antibiotic vancomycin. VanA is one of the six different types of vancomycin resistance shown by enterococcus. VRE(VanA) is resistant to vancomycin and teicoplanin. (Reproduced with the permission from ref. 11. ©2003, American Chemical Society).¹¹

Magnetic nanoparticles can separate different forms of proteins for further study.

Purifying proteins. Studying and developing uses for proteins requires different forms of proteins to be purified and manipulated, which can be challenging because the differences between the forms may be small. Using magnetic nanoparticles to separate the forms can allow exceptionally high selectivity.^12,13 For example, we have used magnetic nanoparticles that are linked to nitrilotriacetic acid, a compound that holds onto certain metal ions, to separate protein variants produced in genetically altered bacteria. The proteins were made bearing special chemical tags that bind strongly to the metal ions.^14,15 Using nanoparticles achieves much higher specificity in separating variant forms of the protein than using microparticles (which are roughly a thousand times bigger). The high surface-to-volume ratios of nanoparticles, together with their ability to disperse easily, also increases their value for separating mixtures and can simplify analytical procedures. In addition, such magnetic nanoparticles are reusable.

Researchers can use magnetic force to control the movement of nanoparticles within cells.

Localizing fluorescent nanomagnets inside a cell. For biological applications, multifunctional nanomaterials have the unique advantage that they can combine superparamagnetism and fluorescence. This means researchers can use magnetic force to control the movement of such particles, which are termed hybrid nanoparticles, within cells, and use microscopes to observe them.¹⁶ Figure 5 shows the movement of such nanoparticles upon applying a magnetic force. Without the magnetic force, the nanoparticles evenly distribute inside the cells due to the lack of specific interactions (Figure 5E). After being attracted by a small magnet, the nanoparticles aggregate on the side of the cell nearest the magnet (Figure 5F). This demonstration of intracellular manipulation of magnetic nanoparticles suggests they could be a useful tool in investigating the different sides of polarized cells. To realize this potential, however, the fluorescent magnetic nanoparticles should have a fast response to the magnetic force, and improvement is still needed.

Figure 5. Intracellular manipulation of iron oxide-cadmium selenide nanopoarticles. (A) Distribution of the nanoparticles in a cell without a magnetic field. (B) Distribution of the nanoparticles with the magnetic field (H represents magnetic field and F represents magnetic force). (C) Aggregation due to strong magnetic dipolar-dipolar interactions (F_D-D). (D) The aggregates of the nanoparticles inside the cells. The confocal images are of HEK293T cells after being incubated with the nanoparticles and a vector (E) without and (F) with a magnetic field (Reproduced with permission from ref. 16. ©2008, American Chemical Society).¹⁶

Summary and challenges

Multifunctional magnetic nanoparticles with high selectivity and high sensitivity not only show promise in the biological applications of bacterial detection and protein purification, they also offer advantages in tumor targeting and multimodal imaging (use of multiple types of imaging simultaneously). Hybrid magnetic nanoparticles open up new avenues for a variety of biomedical applications because of their integrated functions. These two approaches could lead to a wide variety of applications (Figure 6) that are currently under intensive exploration. They include localization of molecules of interest through specific binding to nanoparticles, drug delivery, use with magnetic resonance imaging for research and diagnosis, bacteria detection, protein separation, and use with multimodal imaging. In many of these applications, the ability of nanoparticles to form multiple bonds to a variety of substances of our choosing, and thus to bind tightly where we want them to, is essential to what makes them so uniquely promising.

Figure 6. The scheme illustrates two strategies for fabricating multifunctional magnetic nanoparticles, and their potential applications (QDs represents quantum dots) (Reproduced with permission from the American Chemical Society ©2009).

Despite these exciting potential biomedical applications, challenges and issues remain. For example, heterogeneity of nanomaterials is a major problem and it is still hard to precisely control the number of functional molecules on the surface of nanoparticles. Researchers must develop better strategies for producing nanoparticles that have precise composition, uniform surface modification, and reproducible functionalization. For in vivo biomedical applications, the purity, dispersity, and stability of the multifunctional magnetic nanoparticles in a physiological environment are highly important.¹⁷ It is essential, therefore, to further study and explore the properties of these promising bionanomaterials. We have good reasons to believe that research can create a successful nanobiotechnology that will usher in important biomedical advances.

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