XSEDE Keynote: Democratizing Scientific Research

By Jan A. Zverina, San Diego Supercomputer Center

August 2, 2013

“As the number of Native American scientists slowly increases to help democratize scientific research for their respective communities, we need to continually train non-scientific researchers on how to work with Native people,” according to LeManuel “Lee” Bitsóí, a member of the Navajo Nation and Harvard University research associate.

“Native people are not anti-science; it’s that we want a pro-indigenous approach to the way science is conducted within our communities,” Dr. Bitsóí told attendees of XSEDE13, the annual conference of the National Science Foundation’s (NSF) Extreme Science and Engineering Discovery Environment (XSEDE) program held July 22-25 in San Diego.

“As Native people, we have always practiced science,” said Bitsóí, who also is the lead Native American scholar for an initiative focusing on young men of color sponsored by the College Board, and secretary for the board of directors for the Society for Advancement of Chicanos/Latinos and Native Americans in Science. “Only we don’t call it science. We just call it a part of life.”

“Like other underrepresented communities, Native people have developed their own diverse scientific knowledge base that includes mathematics, chemistry, and many biosciences typically found in the scientific research community at large,” said Bitsóí, whose focus is on genomics training and epigenetics in particular. But the Natives have passed much of this knowledge on through oral history – which has only recently been recognized as a legitimate source of data by the general scientific community – and this knowledge base also includes areas such as animal husbandry, ethnobotany, and ethnomedicine, as well as “healing” and “arts.”  

“In Custer Died for Your Sins: An Indian Manifesto, Standing Rock Sioux scholar Vine Deloria Jr. argued that non-Native researchers and academics were mainly interested in their own research goals and advancing their careers, and essentially were not concerned about the real challenges that American Indians/Alaska Natives face,” said Bitsóí. “Dr. Frank Dukepoo (Hopi/Laguna) also questioned the bilagáana, or Western, approach to research, especially scientific research in American Indian/Alaska Native communities. Dr. Dukepoo always deferred to his Native culture and upbringing whenever he challenged the status quo.”

Pro-Indigenous Approach

“This type of questioning is what Dr. Kim Tallbear (Sisseton Wahpeton), assistant professor at the University of California, Berkeley, refers to as the first step in democratizing scientific research,” noted Bitsóí. “As Native scientists and researchers, we have made inroads in many disciplines to advance our understanding of how to optimize scientific discoveries for our people.”

The path to a more inclusive science community has not been without challenges, a major one being the lack of effective communication between Natives and non-Natives at the researcher level, as well as society at large. That in turn sometimes discourages Native Americans from pursuing a career in science, instead fostering a widespread reluctance to engage with researchers outside their communities.

During 2007 and 2008 only 522 American Indians and Alaska Natives attained a degree in the biosciences out of a total of almost 78,000 students, said Bitsóí, showing a chart from the U.S. Department of Education. In that same period, 2,203 non-residents attained a degree, according to the same chart.

“What this shows is that higher education in the U.S. is really doing a much better job in educating foreign students than it is in graduating our own people,” said Bitsóí.

Despite science always being a part of Native knowledge bases, there is a real need to train non-Native research scientists on how to work with indigenous communities. That includes learning how to consult with local Native communities and their leaders, better understanding the practices and traditions of those communities, and knowing the complexities of issues such as consent while respecting privacy concerns.

“Implicit is a new definition of rigorous scientific research, one that includes both community development and scientific progress as legitimate objectives of genomic research,” said Bitsóí, who acknowledged his mentors and advisors over the years, including Professors William Gelbart and George Church at Harvard University, and Professors Bette Jacobs and Jeff Collmann at Georgetown University.

Epigenetics and Intergenerational Trauma

Bitsóí, who has devoted his career to enhancing opportunities for underrepresented minority students to become scientists, science educators, and scientifically-informed community members, said his role has been to get those students excited about genomics and connect them with training programs at genome centers around the country.

“The study of genomics is more than discovering similarities between living organisms,” he said, adding that genomic investigations also are responsible for disease prevention and even cures. “Research in this area could lead to the development of new drugs to treat diseases like diabetes, better methods of crop production, better range management of land, and possibly discovering new and innovative ways to sustain the earth.”

In addition to advocacy work, Bitsóí has recently begun to explore intergenerational trauma, or the exposure of an earlier generation to a traumatic event that continues to affect subsequent generations.  As a key area of interest for Bitsóí, he plans to partner with other Native researchers to launch a research project studying the relationships between intergenerational/historical trauma and the relatively new field epigenetics.

“Epigenetics has already demonstrated that certain exposures, especially during periods of developmental vulnerability, can cause long-term harms to exposed individuals and sometimes their progeny,” he said. “Epigenetics invalidates the assumption that nature and nurture operate as independent forces in influencing human development and disease.”

Bitsóí is particularly interested in the numerous legal and ethical issues being raised by epigenetics, notably those regarding individual and societal responsibilities to prevent hazardous exposures, monitor health status, and provide care. 

“Epigenetics…adds a multi-generational dimension to environmentally-caused adverse health effects,” he said. “It also highlights the effects of inequality in living and working conditions, as well as a range of disparities in access to health care and other societal opportunities.

In closing, Bitsóí said that intergenerational or historical trauma has been a controversial topic for non-Native people, since there is an accepted notion that what happened in the past is in the past. However, scientific research in epigenetics has begun to demonstrate that intergenerational trauma is real and has an impact on present-day populations – and what we experience will affect future generations.

Citing the BBC program called The Ghost in Your Genes, he said that epigenetics is based on a simple but contentious idea: that genes have a memory, and that the lives and environments of our grandparents can directly affect us decades later, despite us never experiencing these things ourselves, and the notion that what we do and how we lives could in turn affect our grandchildren.

“Native healers, medicine people, and elders have always known this, and it is common knowledge in Native oral traditions,” said Bitsóí.  To undergird this statement, he cited the work of Bryan Brayboy (Lumbee) in Tribal Critical Race theory: Stories are not separate from theory; they make up theory and are, therefore, real and legitimate sources of data and ways of being.

Subscribe to HPCwire's Weekly Update!

Be the most informed person in the room! Stay ahead of the tech trends with industy updates delivered to you every week!

CMU’s Latest “Card Shark” – Libratus – is Beating the Poker Pros (Again)

January 20, 2017

It’s starting to look like Carnegie Mellon University has a gambling problem – can’t stay away from the poker table. Read more…

By John Russell

IDG to Be Bought by Chinese Investors; IDC to Spin Out HPC Group

January 19, 2017

US-based publishing and investment firm International Data Group, Inc. (IDG) will be acquired by a pair of Chinese investors, China Oceanwide Holdings Group Co., Ltd. Read more…

By Tiffany Trader

Weekly Twitter Roundup (Jan. 19, 2017)

January 19, 2017

Here at HPCwire, we aim to keep the HPC community apprised of the most relevant and interesting news items that get tweeted throughout the week. Read more…

By Thomas Ayres

France’s CEA and Japan’s RIKEN to Partner on ARM and Exascale

January 19, 2017

France’s CEA and Japan’s RIKEN institute announced a multi-faceted five-year collaboration to advance HPC generally and prepare for exascale computing. Among the particulars are efforts to: build out the ARM ecosystem; work on code development and code sharing on the existing and future platforms; share expertise in specific application areas (material and seismic sciences for example); improve techniques for using numerical simulation with big data; and expand HPC workforce training. It seems to be a very full agenda. Read more…

By Nishi Katsuya and John Russell

HPE Extreme Performance Solutions

Remote Visualization: An Integral Technology for Upstream Oil & Gas

As the exploration and production (E&P) of natural resources evolves into an even more complex and vital task, visualization technology has become integral for the upstream oil and gas industry. Read more…

ARM Waving: Attention, Deployments, and Development

January 18, 2017

It’s been a heady two weeks for the ARM HPC advocacy camp. At this week’s Mont-Blanc Project meeting held at the Barcelona Supercomputer Center, Cray announced plans to build an ARM-based supercomputer in the U.K. while Mont-Blanc selected Cavium’s ThunderX2 ARM chip for its third phase of development. Last week, France’s CEA and Japan’s Riken announced a deep collaboration aimed largely at fostering the ARM ecosystem. This activity follows a busy 2016 when SoftBank acquired ARM, OpenHPC announced ARM support, ARM released its SVE spec, Fujistu chose ARM for the post K machine, and ARM acquired HPC tool provider Allinea in December. Read more…

By John Russell

Women Coders from Russia, Italy, and Poland Top Study

January 17, 2017

According to a study posted on HackerRank today the best women coders as judged by performance on HackerRank challenges come from Russia, Italy, and Poland. Read more…

By John Russell

Spurred by Global Ambitions, Inspur in Joint HPC Deal with DDN

January 17, 2017

Inspur, the fast-growth cloud computing and server vendor from China that has several systems on the current Top500 list, and DDN, a leader in high-end storage, have announced a joint sales and marketing agreement to produce solutions based on DDN storage platforms integrated with servers, networking, software and services from Inspur. Read more…

By Doug Black

Weekly Twitter Roundup (Jan. 12, 2017)

January 12, 2017

Here at HPCwire, we aim to keep the HPC community apprised of the most relevant and interesting news items that get tweeted throughout the week. Read more…

By Thomas Ayres

IDG to Be Bought by Chinese Investors; IDC to Spin Out HPC Group

January 19, 2017

US-based publishing and investment firm International Data Group, Inc. (IDG) will be acquired by a pair of Chinese investors, China Oceanwide Holdings Group Co., Ltd. Read more…

By Tiffany Trader

France’s CEA and Japan’s RIKEN to Partner on ARM and Exascale

January 19, 2017

France’s CEA and Japan’s RIKEN institute announced a multi-faceted five-year collaboration to advance HPC generally and prepare for exascale computing. Among the particulars are efforts to: build out the ARM ecosystem; work on code development and code sharing on the existing and future platforms; share expertise in specific application areas (material and seismic sciences for example); improve techniques for using numerical simulation with big data; and expand HPC workforce training. It seems to be a very full agenda. Read more…

By Nishi Katsuya and John Russell

ARM Waving: Attention, Deployments, and Development

January 18, 2017

It’s been a heady two weeks for the ARM HPC advocacy camp. At this week’s Mont-Blanc Project meeting held at the Barcelona Supercomputer Center, Cray announced plans to build an ARM-based supercomputer in the U.K. while Mont-Blanc selected Cavium’s ThunderX2 ARM chip for its third phase of development. Last week, France’s CEA and Japan’s Riken announced a deep collaboration aimed largely at fostering the ARM ecosystem. This activity follows a busy 2016 when SoftBank acquired ARM, OpenHPC announced ARM support, ARM released its SVE spec, Fujistu chose ARM for the post K machine, and ARM acquired HPC tool provider Allinea in December. Read more…

By John Russell

Spurred by Global Ambitions, Inspur in Joint HPC Deal with DDN

January 17, 2017

Inspur, the fast-growth cloud computing and server vendor from China that has several systems on the current Top500 list, and DDN, a leader in high-end storage, have announced a joint sales and marketing agreement to produce solutions based on DDN storage platforms integrated with servers, networking, software and services from Inspur. Read more…

By Doug Black

For IBM/OpenPOWER: Success in 2017 = (Volume) Sales

January 11, 2017

To a large degree IBM and the OpenPOWER Foundation have done what they said they would – assembling a substantial and growing ecosystem and bringing Power-based products to market, all in about three years. Read more…

By John Russell

UberCloud Cites Progress in HPC Cloud Computing

January 10, 2017

200 HPC cloud experiments, 80 case studies, and a ton of hands-on experience gained, that’s the harvest of four years of UberCloud HPC Experiments. Read more…

By Wolfgang Gentzsch and Burak Yenier

A Conversation with Women in HPC Director Toni Collis

January 6, 2017

In this SC16 video interview, HPCwire Managing Editor Tiffany Trader sits down with Toni Collis, the director and founder of the Women in HPC (WHPC) network, to discuss the strides made since the organization’s debut in 2014. Read more…

By Tiffany Trader

BioTeam’s Berman Charts 2017 HPC Trends in Life Sciences

January 4, 2017

Twenty years ago high performance computing was nearly absent from life sciences. Today it’s used throughout life sciences and biomedical research. Genomics and the data deluge from modern lab instruments are the main drivers, but so is the longer-term desire to perform predictive simulation in support of Precision Medicine (PM). There’s even a specialized life sciences supercomputer, ‘Anton’ from D.E. Shaw Research, and the Pittsburgh Supercomputing Center is standing up its second Anton 2 and actively soliciting project proposals. There’s a lot going on. Read more…

By John Russell

AWS Beats Azure to K80 General Availability

September 30, 2016

Amazon Web Services has seeded its cloud with Nvidia Tesla K80 GPUs to meet the growing demand for accelerated computing across an increasingly-diverse range of workloads. The P2 instance family is a welcome addition for compute- and data-focused users who were growing frustrated with the performance limitations of Amazon's G2 instances, which are backed by three-year-old Nvidia GRID K520 graphics cards. Read more…

By Tiffany Trader

US, China Vie for Supercomputing Supremacy

November 14, 2016

The 48th edition of the TOP500 list is fresh off the presses and while there is no new number one system, as previously teased by China, there are a number of notable entrants from the US and around the world and significant trends to report on. Read more…

By Tiffany Trader

For IBM/OpenPOWER: Success in 2017 = (Volume) Sales

January 11, 2017

To a large degree IBM and the OpenPOWER Foundation have done what they said they would – assembling a substantial and growing ecosystem and bringing Power-based products to market, all in about three years. Read more…

By John Russell

Vectors: How the Old Became New Again in Supercomputing

September 26, 2016

Vector instructions, once a powerful performance innovation of supercomputing in the 1970s and 1980s became an obsolete technology in the 1990s. But like the mythical phoenix bird, vector instructions have arisen from the ashes. Here is the history of a technology that went from new to old then back to new. Read more…

By Lynd Stringer

Container App ‘Singularity’ Eases Scientific Computing

October 20, 2016

HPC container platform Singularity is just six months out from its 1.0 release but already is making inroads across the HPC research landscape. It's in use at Lawrence Berkeley National Laboratory (LBNL), where Singularity founder Gregory Kurtzer has worked in the High Performance Computing Services (HPCS) group for 16 years. Read more…

By Tiffany Trader

Dell EMC Engineers Strategy to Democratize HPC

September 29, 2016

The freshly minted Dell EMC division of Dell Technologies is on a mission to take HPC mainstream with a strategy that hinges on engineered solutions, beginning with a focus on three industry verticals: manufacturing, research and life sciences. "Unlike traditional HPC where everybody bought parts, assembled parts and ran the workloads and did iterative engineering, we want folks to focus on time to innovation and let us worry about the infrastructure," said Jim Ganthier, senior vice president, validated solutions organization at Dell EMC Converged Platforms Solution Division. Read more…

By Tiffany Trader

Lighting up Aurora: Behind the Scenes at the Creation of the DOE’s Upcoming 200 Petaflops Supercomputer

December 1, 2016

In April 2015, U.S. Department of Energy Undersecretary Franklin Orr announced that Intel would be the prime contractor for Aurora: Read more…

By Jan Rowell

Enlisting Deep Learning in the War on Cancer

December 7, 2016

Sometime in Q2 2017 the first ‘results’ of the Joint Design of Advanced Computing Solutions for Cancer (JDACS4C) will become publicly available according to Rick Stevens. He leads one of three JDACS4C pilot projects pressing deep learning (DL) into service in the War on Cancer. Read more…

By John Russell

Leading Solution Providers

D-Wave SC16 Update: What’s Bo Ewald Saying These Days

November 18, 2016

Tucked in a back section of the SC16 exhibit hall, quantum computing pioneer D-Wave has been talking up its new 2000-qubit processor announced in September. Forget for a moment the criticism sometimes aimed at D-Wave. This small Canadian company has sold several machines including, for example, ones to Lockheed and NASA, and has worked with Google on mapping machine learning problems to quantum computing. In July Los Alamos National Laboratory took possession of a 1000-quibit D-Wave 2X system that LANL ordered a year ago around the time of SC15. Read more…

By John Russell

CPU Benchmarking: Haswell Versus POWER8

June 2, 2015

With OpenPOWER activity ramping up and IBM’s prominent role in the upcoming DOE machines Summit and Sierra, it’s a good time to look at how the IBM POWER CPU stacks up against the x86 Xeon Haswell CPU from Intel. Read more…

By Tiffany Trader

Nvidia Sees Bright Future for AI Supercomputing

November 23, 2016

Graphics chipmaker Nvidia made a strong showing at SC16 in Salt Lake City last week. Read more…

By Tiffany Trader

Beyond von Neumann, Neuromorphic Computing Steadily Advances

March 21, 2016

Neuromorphic computing – brain inspired computing – has long been a tantalizing goal. The human brain does with around 20 watts what supercomputers do with megawatts. And power consumption isn’t the only difference. Fundamentally, brains ‘think differently’ than the von Neumann architecture-based computers. While neuromorphic computing progress has been intriguing, it has still not proven very practical. Read more…

By John Russell

The Exascale Computing Project Awards $39.8M to 22 Projects

September 7, 2016

The Department of Energy’s Exascale Computing Project (ECP) hit an important milestone today with the announcement of its first round of funding, moving the nation closer to its goal of reaching capable exascale computing by 2023. Read more…

By Tiffany Trader

BioTeam’s Berman Charts 2017 HPC Trends in Life Sciences

January 4, 2017

Twenty years ago high performance computing was nearly absent from life sciences. Today it’s used throughout life sciences and biomedical research. Genomics and the data deluge from modern lab instruments are the main drivers, but so is the longer-term desire to perform predictive simulation in support of Precision Medicine (PM). There’s even a specialized life sciences supercomputer, ‘Anton’ from D.E. Shaw Research, and the Pittsburgh Supercomputing Center is standing up its second Anton 2 and actively soliciting project proposals. There’s a lot going on. Read more…

By John Russell

Dell Knights Landing Machine Sets New STAC Records

November 2, 2016

The Securities Technology Analysis Center, commonly known as STAC, has released a new report characterizing the performance of the Knight Landing-based Dell PowerEdge C6320p server on the STAC-A2 benchmarking suite, widely used by the financial services industry to test and evaluate computing platforms. The Dell machine has set new records for both the baseline Greeks benchmark and the large Greeks benchmark. Read more…

By Tiffany Trader

What Knights Landing Is Not

June 18, 2016

As we get ready to launch the newest member of the Intel Xeon Phi family, code named Knights Landing, it is natural that there be some questions and potentially some confusion. Read more…

By James Reinders, Intel

  • arrow
  • Click Here for More Headlines
  • arrow
Share This