How scientists are subtracting race from medical risk calculators

Posted in Articles, Health/Medicine/Genetics, Media Archive, United States on 2021-08-12 22:15Z by Steven

How scientists are subtracting race from medical risk calculators

Science Magazine
2021-07-22

Jyoti Madhusoodanan
Portland, Oregon


Anuj Shrestha

To pediatrician Nader Shaikh, the rhythm of treating babies running high fevers is familiar. After ruling out the obvious colds and other common viruses, he must often thread a catheter into a months-old baby to draw a urine sample and check for a urinary tract infection (UTI). “You have to hold the baby down, the baby’s crying, the mother is usually crying too,” says Shaikh, who works at the University of Pittsburgh. “It’s traumatic.”

UTIs, although relatively rare in children under age 2, carry a high risk of kidney damage in this group if left untreated. Often, the only symptom is a high fever. But high fevers can also signal a brain or blood infection, or a dozen other illnesses that can be diagnosed without a urine sample. To help clinicians avoid the unnecessary pain and expense of catheterizing a shrieking infant, Shaikh and his colleagues developed an equation that gauges a child’s risk of a UTI based on age, fever, circumcision status, gender, and other factors—including whether the child is Black or white. Race is part of the equation because previous studies found that—for reasons that aren’t clear—UTIs are far less common in Black children than in white ones.

The UTI algorithm is only one of several risk calculators that factor in race, which doctors routinely use to make decisions about patients’ care. Some help them decide what tests to perform next or which patients to refer to a specialist. Others help gauge a patient’s lung health, their ability to donate a liver or kidney, or which diabetes medicines they need.

In the past few years, however, U.S. doctors and students reckoning with racism in medicine have questioned the use of algorithms that include race as a variable. Their efforts gained momentum thanks to the Black Lives Matter movement. In August 2020, a commentary published in The New England Journal of Medicine (NEJM) highlighted the use of race in calculators as a problem “hidden in plain sight.” It’s widely agreed that race is a classification system designed by humans that lacks a genetic basis, says Darshali Vyas, a medical resident at Massachusetts General Hospital and co-author on the paper. “There’s a tension between that [understanding] and how we see race being used … as an input variable in these equations,” Vyas says. “Many times, there’s an assumption that race is relevant in a biological sense.”…

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The Disordered Cosmos: A Journey into Dark Matter, Spacetime, and Dreams Deferred

Posted in Books, History, Media Archive, Monographs, Philosophy, Politics/Public Policy, Social Justice on 2021-03-11 00:15Z by Steven

The Disordered Cosmos: A Journey into Dark Matter, Spacetime, and Dreams Deferred

Bold Type Books (an imprint of the Hachette Book Group)
2021-03-09
336 pages
Hardcover ISBN-13: 9781541724709
eBook ISBN-13: 9781541724693
Audiobook ISBN-13: 9781549133961

Chanda Prescod-Weinstein, Assistant Professor of Physics and Astronomy; Core faculty in Women’s and Gender Studies
University of New Hampshire

From a star theoretical physicist, a journey into the world of particle physics and the cosmos — and a call for a more just practice of science.

In The Disordered Cosmos, Dr. Chanda Prescod-Weinstein shares her love for physics, from the Standard Model of Particle Physics and what lies beyond it, to the physics of melanin in skin, to the latest theories of dark matter — all with a new spin informed by history, politics, and the wisdom of Star Trek.

One of the leading physicists of her generation, Dr. Chanda Prescod-Weinstein is also one of fewer than one hundred Black American women to earn a PhD from a department of physics. Her vision of the cosmos is vibrant, buoyantly non-traditional, and grounded in Black feminist traditions.

Prescod-Weinstein urges us to recognize how science, like most fields, is rife with racism, sexism, and other dehumanizing systems. She lays out a bold new approach to science and society that begins with the belief that we all have a fundamental right to know and love the night sky. The Disordered Cosmos dreams into existence a world that allows everyone to experience and understand the wonders of the universe.

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Public Thinker: Chanda Prescod-Weinstein on Dark Matter and White Empiricism

Posted in Articles, Interviews, Media Archive, United States, Women on 2019-09-18 18:59Z by Steven

Public Thinker: Chanda Prescod-Weinstein on Dark Matter and White Empiricism

Public Books
2019-09-17

Lawrence Ware, Co-director of the Africana Studies Program; Teaching Assistant Professor and Diversity Coordinator in the Department of Philosophy
Oklahoma State University


Chanda Prescod-Weinstein. Photograph by Lisa Longstaff

Dr. Chanda Prescod-Weinstein is one of fewer than a hundred Black American women to earn a PhD from a department of physics. Being part of an all too rare group has given her a glimpse into the way the world of physics works—through not just equations and experiments but also human social interactions. The child of grassroots political organizers, Prescod-Weinstein is a theoretical physicist and a self-taught Black feminist philosopher and scholar of science, technology, and society studies. She is also vocal about social problems within science and the way science contributes to problems in the larger world. I caught up with Dr. Chanda, as she is known to many on Twitter (@IBJIYONGI), via Skype, and what follows is a discussion that goes from dark matter to how whiteness operates in physics.

Lawrence Ware (LW): Can I ask you to explain to me, almost like I’m an eight-year-old, what you do?

Chanda Prescod-Weinstein (CP): I think about the origin of spacetime and the origin of everything inside of spacetime. It’s the question of how we get from the beginning of the universe to us sitting in the rooms that we are sitting in now. How do we get from point A to point B? And does the universe even have a beginning? What happened at the very beginning?

LW: But I am still very confused about what you do. Help me understand.

CP: I just do math all day.

LW: How do you bring your interest in race and gender into conversation with what you do with physics, then?

CP: When I was 10 years old, I began getting really excited about theoretical physics. And I was really excited about doing theoretical physics specifically because I thought it would get me away from human problems. My parents were both activists; I spent my entire childhood hearing about the ways the world is messed up. I think I saw theoretical physics as an exit from having to worry about the human condition.

Then, when I was in high school, I became aware that I might stand out in my classes, because my background was a little bit different from that of the typical physicist. I was aware that there weren’t a lot of Black women in physics. I had never heard of one. This generation might have a very different experience now, because of Hidden Figures, but there was nothing like that when I was in high school.

So I thought I would just stand out, but I didn’t really think much of it. I had no intention to go into college thinking about race or gender or anything like that. And then I started experiencing racism and sexism in physics environments and started trying to make sense of it. That was how it started to come together…

Read the entire interview here.

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“There is so much diversity in Africans that there is no such thing as an African race.”

Posted in Excerpts/Quotes on 2018-02-20 00:57Z by Steven

The study adds to established research undercutting old notions of race. You can’t use skin color to classify humans, any more than you can use other complex traits like height, [Sarah] Tishkoff says. “There is so much diversity in Africans that there is no such thing as an African race.”

Ann Gibbons, “New gene variants reveal the evolution of human skin color,” Science, October 12, 2017. http://www.sciencemag.org/news/2017/10/new-gene-variants-reveal-evolution-human-skin-color.

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New gene variants reveal the evolution of human skin color

Posted in Africa, Articles, Health/Medicine/Genetics, Media Archive on 2018-02-20 00:53Z by Steven

New gene variants reveal the evolution of human skin color

Science
2017-11-12

Ann Gibbons, Contributing Correspondent


Researchers have identified genes that help create diverse skin tones, such as those seen in the Agaw (left) and Surma (right) peoples of Africa.
ALESSIA RANCIARO & DR. SIMON R. THOMPSON

Most people associate Africans with dark skin. But different groups of people in Africa have almost every skin color on the planet, from deepest black in the Dinka of South Sudan to beige in the San of South Africa. Now, researchers have discovered a handful of new gene variants responsible for this palette of tones.

The study, published online this week in Science, traces the evolution of these genes and how they traveled around the world. While the dark skin of some Pacific Islanders can be traced to Africa, gene variants from Eurasia also seem to have made their way back to Africa. And surprisingly, some of the mutations responsible for lighter skin in Europeans turn out to have an ancient African origin.

“This is really a landmark study of skin color diversity,” says geneticist Greg Barsh of the HudsonAlpha Institute for Biotechnology in Huntsville, Alabama.

Researchers agree that our early australopithecine ancestors in Africa probably had light skin beneath hairy pelts. “If you shave a chimpanzee, its skin is light,” says evolutionary geneticist Sarah Tishkoff of the University of Pennsylvania, the lead author of the new study. “If you have body hair, you don’t need dark skin to protect you from ultraviolet [UV] radiation.”

Until recently, researchers assumed that after human ancestors shed most body hair, sometime before 2 million years ago, they quickly evolved dark skin for protection from skin cancer and other harmful effects of UV radiation. Then, when humans migrated out of Africa and headed to the far north, they evolved lighter skin as an adaptation to limited sunlight. (Pale skin synthesizes more vitamin D when light is scarce.)…

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Loci associated with skin pigmentation identified in African populations

Posted in Africa, Articles, Health/Medicine/Genetics, Media Archive on 2017-12-04 01:50Z by Steven

Loci associated with skin pigmentation identified in African populations

Science
2017-10-12
eaan8433
DOI: 10.1126/science.aan8433

Nicholas G. Crawford, Derek E. Kelly, Matthew E. B. Hansen, Marcia H. Beltrame, Shaohua Fan, Shanna L. Bowman, Ethan Jewett, Alessia Ranciaro, Simon Thompson, Yancy Lo, Susanne P. Pfeifer, Jeffrey D. Jensen, Michael C. Campbell, William Beggs, Farhad Hormozdiari, Sununguko Wata Mpoloka, Gaonyadiwe George Mokone, Thomas Nyambo, Dawit Wolde Meskel, Gurja Belay, Jake Haut, NISC Comparative Sequencing Program, Harriet Rothschild, Leonard Zon, Yi Zhou, Michael A. Kovacs, Mai Xu, Tongwu Zhang, Kevin Bishop, Jason Sinclair, Cecilia Rivas, Eugene Elliot, Jiyeon Choi, Shengchao A. Li, Belynda Hicks, Shawn Burgess, Christian Abnet, Dawn E. Watkins-Chow, Elena Oceana, Yun S. Song, Eleazar Eskin, Kevin M. Brown, Michael S. Marks, Stacie K. Loftus, William J. Pavan, Meredith Yeager, Stephen Chanock, Sarah Tishkoff

Despite the wide range of skin pigmentation in humans, little is known about its genetic basis in global populations. Examining ethnically diverse African genomes, we identify variants in or near SLC24A5, MFSD12, DDB1, TMEM138, OCA2 and HERC2 that are significantly associated with skin pigmentation. Genetic evidence indicates that the light pigmentation variant at SLC24A5 was introduced into East Africa by gene flow from non-Africans. At all other loci, variants associated with dark pigmentation in Africans are identical by descent in southern Asian and Australo-Melanesian populations. Functional analyses indicate that MFSD12 encodes a lysosomal protein that affects melanogenesis in zebrafish and mice, and that mutations in melanocyte-specific regulatory regions near DDB1/TMEM138 correlate with expression of UV response genes under selection in Eurasians.

Variation in epidermal pigmentation is a striking feature of modern humans. Human pigmentation is correlated with geographic and environmental variation (Fig. 1). Populations at lower latitudes have darker pigmentation than populations at higher latitudes, suggesting that skin pigmentation is an adaptation to differing levels of ultraviolet radiation (UVR) (1). Because equatorial regions receive more UVR than temperate regions, populations from these regions (including sub-Saharan Africans, South Asians, and Australo-Melanesians) have darker pigmentation (Fig. 1), which likely mitigates the negative impact of high UVR exposure such as skin cancer and folate degradation (1). In contrast, the synthesis of vitamin D3 in response to UVR, needed to prevent rickets, may drive selection for light pigmentation at high latitudes (1).

The basal layer of human skin contains melanocytes, specialized pigment cells that harbor subcellular organelles called melanosomes in which melanin pigments are synthesized and stored and then transferred to keratinocytes (2). Melanosome morphology and content differs between melanocytes that synthesize mainly eumelanins (black-brown pigments) or pheomelanins (pigments which range from yellow to reddish-brown) (3). Variation in skin pigmentation is due to the type and quantity of melanins generated, melanosome size, and the manner in which keratinocytes sequester and degrade melanins (4).

While over 350 pigmentation genes have been identified in animal models, only a subset of these genes have been linked to normal variation in humans (5). Of these, there is limited knowledge about loci that affect pigmentation in populations with African ancestry (6, 7).

Skin pigmentation is highly variable within Africa

To identify genes affecting skin pigmentation in Africa, we used a DSM II ColorMeter to quantify light reflectance from the inner arm as a proxy for melanin levels in 2,092 ethnically and genetically diverse Africans living in Ethiopia, Tanzania, and Botswana (table S1 and figs. S1 and S2) (8). Skin pigmentation levels vary extensively among Africans, with darkest pigmentation observed in Nilo-Saharan speaking pastoralist populations in Eastern Africa and lightest pigmentation observed in San hunter-gatherer populations from southern Africa (Fig. 2 and table S1)…

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Departure of U.S. Census director threatens 2020 count

Posted in Articles, Census/Demographics, Media Archive, Politics/Public Policy, United States on 2017-05-11 02:01Z by Steven

Departure of U.S. Census director threatens 2020 count

Science
2017-05-09

Jeffrey Mervis


John Thompson will leave the Census Bureau on 30 June. U.S. Census Bureau

John Thompson is stepping down next month as director of the U.S. Census Bureau. His announcement today comes less than 1 week after a congressional spending panel grilled him about mounting problems facing the agency in preparing for the 2020 decennial census. And Thompson’s pending retirement is weighing heavily on the U.S. statistical community.

Thompson is leaving halfway through a 1-year extension of a term that expired last December. His departure will create what a 2011 law was expressly designed to avoid—a leadership vacuum during a crucial time in the 10-year life cycle of the census, the nation’s largest civilian undertaking. The immediate concern is who the Trump administration will appoint, and how soon it will act…

Ken Prewitt, who led the agency from 1998 to 2001, worries that a long delay in naming a well-qualified replacement for Thompson could be the first step of a long, steep decline in the quality of the federal statistic system, which spans 13 agencies. “That system is fragile, and it wouldn’t take much to damage it severely,” says Prewitt, a professor of social affairs at Columbia University. “My real fear is that they don’t care enough to do a good job with the 2020 census. And then after doing a bad job, they decide to let the private sector take over.”…

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Taking race out of human genetics

Posted in Articles, Health/Medicine/Genetics, Media Archive, Politics/Public Policy, Social Science on 2016-02-06 17:35Z by Steven

Taking race out of human genetics

Science
Volume 351, Issue 6273 (2016-02-05)
pages 564-565
DOI: 10.1126/science.aac4951

Michael Yudell, Associate Professor
Dornsife School of Public Health Department of Community Health and Prevention
Drexel University, Philadelphia, Pennsylvania

Dorothy Roberts, George A. Weiss University Professor of Law and Sociology and the Raymond Pace and Sadie Tanner Mossell Alexander Professor of Civil Rights
University of Pennsylvania

Rob DeSalle, Curator, Molecular Systematics; Principal Investigator, SICG Genomics Lab; Professor, Richard Gilder Graduate School
American Museum of Natural History, New York, New York

Sarah Tishkoff, David and Lyn Silfen University Professor in Genetics and Biology
University of Pennsylvania

In the wake of the sequencing of the human genome in the early 2000s, genome pioneers and social scientists alike called for an end to the use of race as a variable in genetic research (1, 2). Unfortunately, by some measures, the use of race as a biological category has increased in the postgenomic age (3). Although inconsistent definition and use has been a chief problem with the race concept, it has historically been used as a taxonomic categorization based on common hereditary traits (such as skin color) to elucidate the relationship between our ancestry and our genes. We believe the use of biological concepts of race in human genetic research—so disputed and so mired in confusion—is problematic at best and harmful at worst. It is time for biologists to find a better way.

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How Europeans evolved white skin

Posted in Articles, Europe, Health/Medicine/Genetics, Media Archive on 2015-04-06 01:26Z by Steven

How Europeans evolved white skin

Science
2015-04-02
DOI: 10.1126/science.aab2435

Ann Gibbons, Contributing Correspondent

ST. LOUIS, MISSOURI—Most of us think of Europe as the ancestral home of white people. But a new study shows that pale skin, as well as other traits such as tallness and the ability to digest milk as adults, arrived in most of the continent relatively recently. The work, presented here last week at the 84th annual meeting of the American Association of Physical Anthropologists, offers dramatic evidence of recent evolution in Europe and shows that most modern Europeans don’t look much like those of 8000 years ago.

The origins of Europeans have come into sharp focus in the past year as researchers have sequenced the genomes of ancient populations, rather than only a few individuals. By comparing key parts of the DNA across the genomes of 83 ancient individuals from archaeological sites throughout Europe, the international team of researchers reported earlier this year that Europeans today are a mix of the blending of at least three ancient populations of hunter-gatherers and farmers who moved into Europe in separate migrations over the past 8000 years. The study revealed that a massive migration of Yamnaya herders from the steppes north of the Black Sea may have brought Indo-European languages to Europe about 4500 years ago.

Now, a new study from the same team drills down further into that remarkable data to search for genes that were under strong natural selection—including traits so favorable that they spread rapidly throughout Europe in the past 8000 years. By comparing the ancient European genomes with those of recent ones from the 1000 Genomes Project, population geneticist Iain Mathieson, a postdoc in the Harvard University lab of population geneticist David Reich, found five genes associated with changes in diet and skin pigmentation that underwent strong natural selection…

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Mexico boasts a staggering genetic diversity, study shows

Posted in Caribbean/Latin America, Health/Medicine/Genetics, Media Archive, Mexico on 2014-07-02 01:45Z by Steven

Mexico boasts a staggering genetic diversity, study shows

Los Angeles Times
2014-06-12

Geoffrey Mohan

SHARELINES

▼ DNA offers a nuanced answer to what it means to be Mexican
▼ Ancient genetic signal survived conquest in Mexico
▼ Latino and Hispanic labels don’t do justice to Mexico’s genome

Writers, artists and historians have long pondered what it means to be Mexican. Now science has offered its answer, and it could change how medicine uses racial and ethnic categories to assess disease risk, testing and treatment..

The broadest analysis of the Mexican genome ever undertaken reveals a nation of staggering genetic diversity, where European conquest only thinly masks the ancestral DNA of Native Americans, and where some populations remain as distinct from one another as Europeans are from Chinese, according to findings published Thursday in the journal Science.

Forty researchers, who share Latino heritage as well as professional qualms over the significance of ethnic and racial categories, teamed up across borders to analyze more than 1 million variations in the building blocks of DNA. They examined more than 500 samples collected in Mexico’s remote Indian villages and polyglot cities, and from Mexican Americans in California.

“Because these populations are so rich, so genetically differentiated, you can’t just lump them all in,” said lead investigator Carlos Bustamante, a population geneticist and co-director of Stanford University’s Center for Computational, Evolutionary and Human Genomics. “You really have to embrace that diversity and think about doing medical genetic studies on a very large scale.”

To illustrate their point, the researchers compared their new genetic data with the results of lung function tests for children in Mexico City and Latinos in the San Francisco Bay Area. They discovered that pulmonary function varied in ways that were mirrored in DNA. It was as if someone with a fraction of Maya ancestry had lungs that were 10 years older than someone with a bit of northern indigenous heritage…

…Researchers not involved in the study, however, caution that correlations between disease risk and ancestry may not have much of a genetic basis at all. In many cases, they might mask socioeconomic or environmental factors — where and how you live.

The suggestion that differences in DNA are responsible for observed differences in lung capacity “is an enormous leap,” said UC Berkeley sociologist Troy Duster, who has written extensively on the intersection of race, biology and public policy.

Lundy Braun, an Africana studies professor at Brown University who studies the intersection of race and medicine, said medicine’s focus on genetics may be overshadowing other avenues of research.

“The effects of social class on lung function have been largely ignored in favor of the focus on race and ethnic difference,” she said.

Braun and Duster worry that such genomic studies may unwittingly lend legitimacy to widely discredited ideas about racial disparities.

“There is always lurking danger that this kind of research, which emphasizes the genetic structure of ethnic and racial groups, fuels the notion that the biology or genetics of those groups explains their condition,” Duster said…

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