Positive framing of genomics met with scepticism in some communities

Language about genomics used by clinicians and researchers potentially alienates disengaged public audiences. New research suggests that in future, social and historical context should be acknowledged first before discussing scientific detail.

Peer-Reviewed Publication

WELLCOME TRUST SANGER INSTITUTE

 - New research published today in Human Genetics and Genomics Advances reveals the difference between ‘what we say’ and ‘what people hear’ when engaging underrepresented communities around genomics and healthcare.

Genomics datasets, which underpin the ability to interpret all genetic tests, are known to consist of DNA from predominately white, Northern European populations. As genomics becomes an increasingly important part of everyday healthcare*, barriers to diverse participation must be overcome so that everyone can benefit from genomic medicine, not just the privileged few.

The research shows that conversations that lead by positively framing genomics around potential benefits were met with cynicism and scepticism, due to socio-historical inequalities and misinformation that result in widespread mistrust of the healthcare system, private companies, and government.

Researchers from Wellcome Connecting Science, Genomics England, and language strategy firm maslansky + partners leveraged framing theory and behavioural science to develop alternate ways to connect with traditionally disengaged audiences and then conducted focus groups with 100 people from British communities of varying backgrounds.

The groups were mixed in age and genders, and had limited familiarity with genomics. The individuals self-identified as belonging to communities with Black African, Black Caribbean and Pakistani ancestries, as well as people of various ancestral heritage who come from disadvantaged socio-economic backgrounds – all groups identified as missing from genomic datasets.

The groups were presented with short phrases of genomics for non-expert public audiences, framed by what genomics is and what it can offer, such as personal and scientific benefits. The phrases were based on typical text in patient and participant information leaflets used by the NHS and in research studies, and were delivered by an actor – a Black British woman.

In response to the narratives that lead with the positively-framed scientific and health benefits, the participants expressed clear mistrust and cynicism. In explaining their reactions, some participants cited examples of racism in science, including historical injustices, as well as present-day issues and personal experiences, such as a lack of diversity in clinical trials and unequal access to, and quality of health care. Others evoked controversial applications of genomics, such as cloning, gene editing or mentions in dystopian fiction. Some participants expressed suspicion around claims that genomics would benefit everybody, suggesting people like them can be excluded from studies and clinical trials.

Other reasons behind participants’ scepticism around the benefits of genomics included lack of trust in those who should deliver these benefits, including private companies and governments, scientists and the NHS. Others believed these positive phrases were over-promising and perceived as disingenuous, due to the limitations of current genomics knowledge and lengthy clinical trials.

The researchers suggest a more successful approach is to begin conversations by directly and overtly acknowledging and validating their questions and concerns before introducing details about the science. This means recognising and articulating that inequalities exist for people from marginalised communities. As genomics becomes part of everyday healthcare, these realities must be talked about and addressed if diverse public groups are to confidently access genomic medicine equally.

Professor Anna Middleton, Wellcome Connecting Science and Director of the Kavli Centre for Ethics, Science, and the Public, University of Cambridge, said: “Our research has demonstrated that everyday talk about genomics currently, used by researchers and clinicians alike, has the potential to alienate already disengaged public audiences. We interpret our findings, not in terms of illiteracy about genomics, but as illustrative of the very real socio-historical inequities and inequalities that exist for people from marginalised communities. The conversations about genetics that led with the science and its benefits were triggering for participants - this revealed itself as cynicism and mistrust. And thus continuing to frame our science, only through its benefits, however well-meaning, has the risk of doing harm. Moving forward, we will incorporate the results of this research into the tools and training we offer scientists.”

Keith Yazmir, Partner at language strategy firm maslansky + partners, said: “It’s human nature to communicate in ways that you want to be communicated to. But effective communication is based on meeting your audience where they are – not where you are. This is particularly important when connecting on complex topics like genomics and emotional ones like healthcare. Based on our philosophy that it’s not what you say, it’s what they hear, we were honoured to partner with Wellcome Connecting Science and Genomics England on this ground-breaking work.”

Vivienne Parry OBE, Head of Public Engagement at Genomics England, said: “This is a very important piece of research with far reaching implications. We now need to make it widely available and act on its findings. This will help ensure that everyone benefits from genomic medicine, with no-one left behind.”

ENDS

Notes to Editors:

The team had consent from participants to film their focus groups. A summary video of the conversations is available here (credit: Wellcome Collecting Science):

https://www.youtube.com/watch?v=TwvoRss1WGA

The research was designed and delivered by the language strategy company maslansky + partners (www.maslansky.com), which combine linguistics and behavioral science to understand how to optimize message resonance with different audiences.

The team is grateful to all participants who took part in the focus groups for their time and contribution.

* Department of Health and Social Care, Department for Business Energy & Industrial Strategy, Office for Life Sciences, and Lord Bethell of Romford. Genome UK: the future of healthcare. 2020. https://www.gov.uk/government/publications/genome-uk-the-future-of-healthcare

Publication:

A. Middleton, et al. (2023) 'The Legacy of Language: What we say, and what people hear, when we talk about genomics’. Human Genetics and Genomics Advances. DOI: 10.1016/j.xhgg.2023.100231

Funding:

This research was supported by Wellcome Connecting Science, Genomics England and the Kavli Centre for Ethics, Science, and the Public, University of Cambridge. For full funding information, please refer to the publication.

Selected websites:

Genomics England

Genomics England is a global leader in advancing and delivering genomic medicine at scale, for all. Building on our delivery of the 100,000 Genomes Project, we are enabling the world's first national whole genome sequencing service in the NHS Genomic Medicine Service, delivering the most advanced genomic healthcare today. We maximise the patient and participant benefit of this service by using the same trusted and proven infrastructure and expertise, and consent and governance framework, to support the development of the genomic medicine of tomorrow, together with the NHS, industry, and academia. All this focused on delivering our vision of a world in which everyone benefits from genomics.   

https://www.genomicsengland.co.uk [genomicsengland.co.uk]

Kavli Centre for Ethics, Science, and the Public, University of Cambridge

The Kavli Centre is a partner organisation to Wellcome Connecting Science. Based in the Faculty of Education at the University of Cambridge, its mission is: To foster global conversations and build trust by engaging publics and scientists with the ethics of science and its impact on society.

https://www.kcesp.ac.uk/

Wellcome Connecting Science

Wellcome Connecting Science’s mission is to enable everyone to explore genomic science and its impact on research, health and society. Drawing on the ground-breaking research taking place on the Wellcome Genome Campus, Connecting Science inspires new thinking, sparks conversation, supports learning, and understands global attitudes and perspectives. We connect researchers, health professionals and the wider public, creating opportunities and spaces to explore genomic science and its relationship with people, and the world around us.

Wellcome Connecting Science and the Wellcome Sanger Institute are part of the same Wellcome-funded organisation.

https://www.wellcomeconnectingscience.org

About Wellcome
Wellcome supports science to solve the urgent health challenges facing everyone. We support discovery research into life, health and wellbeing, and we’re taking on three worldwide health challenges: mental health, infectious disease and climate and health. https://wellcome.org/

 

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JOURNAL

Human Genetics and Genomics Advances

DOI

10.1016/j.xhgg.2023.100231 

SUBJECT OF RESEARCH

People

ARTICLE TITLE

The Legacy of Language: What we say, and what people hear, when we talk about genomics

 

Study demonstrates adding complex component of milk to infant formula confers long-term cognitive benefits

Peer-Reviewed Publication

UNIVERSITY OF KANSAS

LAWRENCE, KANSAS — Breast milk is widely acknowledged as the most beneficial nutrition for infants, but many families face medical or logistical challenges in breastfeeding. In the U.S., just 45% of infants continue to be exclusively breastfed at 3 months of age, according to the Centers for Disease Control.

For decades, researchers have sought to create a viable complement or alternative to breast milk to give children their best start for healthy development. New research out of the University of Kansas has shown how a complex component of milk that can be added to infant formula has been shown to confer long-term cognitive benefits, including measures of intelligence and executive function in children.

The research by John Colombo, KU Life Span Institute director and investigator, along with colleagues at Mead Johnson Nutrition and in Shanghai, China, adds to the growing scientific support for the importance of ingredients found in milk fat globule membrane (MFGM) in early human development.

The study, which was published in the Journal of Pediatrics, showed that feeding infants formula supplemented with MFGM and lactoferrin for 12 months raised IQ by 5 points at 5 ½ years of age. The effects were most evident in tests of children’s speed of processing information and visual-spatial skills. Significant differences were also seen in children’s performance on tests of executive function, which are complex skills involving rule learning and inhibition.

All forms of mammalian milk contain large fat globules that are surrounded by a membrane composed of a variety of nutrients important to human nutrition and brain development, Colombo said. When milk-based infant formula is manufactured, the membrane has typically been removed during processing.

“No one thought much about this membrane,” Colombo said, “until chemical analyses showed that it's remarkably complex and full of components that potentially contribute to health and brain development."

The 2023 study was a follow-up to one that Colombo also co-wrote with colleagues in Shanghai, China, published in the Journal of Pediatrics in 2019. That study showed that babies who were fed formula with added bovine MFGM and lactoferrin had higher scores on neurodevelopmental tests during the first year and on some aspects of language at 18 months of age.

The global nutrition research community has been looking at MFGM for about a decade, Colombo said. Because the membrane is made up of several different components, it isn’t known whether one of the components is responsible for these benefits, or whether the entire package of nutrients act together to improve brain and behavioral development.

These benefits were seen in children long after the end of formula feeding at 12 months of age.

“This is consistent with the idea that early exposure to these nutritional components contribute to the long-term structure and function of the brain,” said Colombo, who has spent much of his career researching the importance of early experience in shaping later development.

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JOURNAL

The Journal of Pediatrics

DOI

10.1016/j.jpeds.2023.113483 

METHOD OF RESEARCH

Randomized controlled/clinical trial

SUBJECT OF RESEARCH

People

ARTICLE TITLE

Improved Neurodevelopmental Outcomes at 5.5 Years of Age in Children Who Received Bovine Milk Fat Globule Membrane and Lactoferrin in Infant Formula Through 12 Months: A Randomized Controlled Trial

ARTICLE PUBLICATION DATE

1-Oct-2023

COI STATEMENT

J.C. and D.J.S. were provided funding to design the neurodevelopmental testing protocol. B.Y.L. was previously employed by Mead Johnson Nutrition. S.S.W., J.L.W., C.L.H., and W.Z. are employees of ReckittǀMead Johnson Nutrition. All other authors reported no conflicts of interest.

 

Do artificial roosts help bats? Illinois experts say more research needed

Peer-Reviewed Publication

UNIVERSITY OF ILLINOIS COLLEGE OF AGRICULTURAL, CONSUMER AND ENVIRONMENTAL SCIENCES

 

IMAGE: JOY O'KEEFE (LEFT) AND REED CRAWFORD (RIGHT) WITH BAT BOXES INSTALLED FOR A PREVIOUS STUDY. THE RESEARCHERS POINT OUT A NUMBER OF UNKNOWNS RELATED TO ARTIFICIAL ROOSTS AS CONSERVATION TOOLS FOR BATS AND CALL FOR MORE RESEARCH. view more 

CREDIT: LAUREN D. QUINN, UNIVERSITY OF ILLINOIS.

URBANA, Ill. — Artificial roosts for bats come in many forms — bat boxes, condos, bark mimics, clay roosts, and cinder block structures, to name a few — but a new conservation practice and policy article from researchers at the University of Illinois Urbana-Champaign suggests the structures haven’t been studied rigorously enough and may harm bats in some scenarios. The article, published in Conservation Biology, lays out potential dangers and encourages more research on the popular conservation practice.

“The major emphasis among conservation managers using artificial roosts is how to attract bats, typically by modifying design or landscape placement,” said Reed Crawford, doctoral student in the Program in Ecology, Evolution, and Conservation Biology at Illinois and lead author on the article. “Their measure of success is roost occupancy or bat abundance in roosts, but we really have no idea whether artificial roosts positively or negatively affect bats compared with natural roosts. What we do know is there are multiple significant perils associated with these artificial structures that need additional research.”

The dangers associated with artificial roosts mean they could act as ecological traps in some cases, according to Crawford and co-author Joy O’Keefe, assistant professor and wildlife Extension specialist in the Department of Natural Resources and Environmental Sciences and Illinois Extension, both part of the College of Agricultural, Consumer and Environmental Sciences (ACES) at Illinois.

“An ecological trap occurs when animal populations preferentially select sub-optimal habitat when higher-quality alternatives are available,” Crawford explained. “Basically, bats could inadvertently lower their chances of survival and reduce their reproductive success by choosing poorly designed or placed bat boxes.”

The best-documented concern is overheating. People installing artificial roosts often follow scientifically unsubstantiated advice to choose dark-colored structures and place them in sunny locations. The small structures rarely offer any insulation and can quickly reach temperatures beyond what bats can withstand. Unfortunately, there are all too many reports of mass bat deaths, with tiny bodies piled beneath roosts on the hottest days. 

Crawford, O’Keefe, and others have documented thermal gradients inside bat boxes of various shapes, sizes, colors, and materials. Most designs reach dangerous temperatures, at least for short periods. But artificial roosts can also be too cold for healthy pup development. The authors share multiple reports of freezing deaths in bats during cold snaps in Florida and elsewhere. To improve outcomes for bats, the authors suggest assessing the conditions inside new designs before offering them to bats, aiming to strike a balance between reducing overheating risk and offering bats a microclimate suitable for raising their young. 

Another concern is that artificial roosts could provide easier access by predators, such as snakes or raccoons, with little room for bats to retreat or escape. 

When bats roost in trees, they tend to use multiple openings, be higher off the ground, and split up into smaller groups, which might disperse guano and make it harder for predators to see them or to sniff them out. According to O’Keefe, “We need to look at predation rates in natural and artificial roosts and develop effective guards and designs that keep roosting bats safe from predators.”

In their article, the researchers highlight ectoparasite accumulation as another understudied threat associated with artificial roosts.  

“We found more than a thousand bat bugs inside some of the bat boxes we had installed for a previous study. We don't know if that’s normal or if it’s just something that's happening in these artificial roosts,” Crawford said. “It could be a really big deal when you potentially have 10 bat bugs for every one bat. To a bat, those would be like a golfball-sized parasite. They could lose a lot of blood. And we know the bugs preferentially target young bats and pups that can't groom themselves as effectively.”

The researchers note bat boxes may lure bats into low-quality habitat. Urban homeowners or farmers wanting bats for mosquito or crop pest control may inadvertently reduce bats’ diet choices to just a few insect species while likely increasing their exposure to environmental pollutants and novel predators, like prowling cats. Or a well-intended land owner might put up a bat box across a busy road from a forest, increasing the odds of vehicle collisions as bats head for the trees each night.

“There’s a lot more we need to know about bat health in urban and human-altered landscapes to inform decisions about where to place artificial roosts,” Crawford said.

Despite their potential pitfalls, many artificial roosts are “successful” in attracting large colonies of bats, sometimes hundreds of individuals. But Crawford and O’Keefe say those numbers could exacerbate the dangers of artificial roosts. 

“Again, that's deemed a measure of success: if you see 500 bats in one box, that's fantastic. But there's a rare tree that could support that many individuals. In my experience tracking tree-dwelling bats, a colony is often spread across multiple tree roosts in a forest,” O’Keefe said. “And so, in bat boxes, you have this concentration of bats that's potentially more vulnerable — because there's so many of them — to predators, weather extremes, and ectoparasites. Having so many bats together could compound the risks to the population.”

Given that forest habitat is shrinking and bats most definitely need help, what’s a conservation manager or a homeowner to do?

“First, we need much more research on the effects of all of these factors on bats in artificial roosts. But I’d also encourage folks to look more holistically at their landscape and provide additional resources for bats,” Crawford said. “For example, adding clean water sources or maybe putting in pollinator gardens to attract different types of insects for greater dietary diversity. Looking at the artificial roost itself, make sure it’s high enough off the ground and not so small as to heighten exposure to overheating or predators.” 

O’Keefe added, “I encourage people to look beyond their own backyards and think about whether there's a better place to install a roost nearby, like a park, that also offers foraging habitat for bats. Think at the neighborhood or village scale, as bats cover a lot of ground across their roosting and foraging areas. And no one should be putting up artificial roosts and walking away. You should be paying attention to them, keeping an eye on the bats and what's going on in and around the structure, including predators and ectoparasites, to know how bats using that structure might be affected.”

O’Keefe’s laboratory maintains a website with tips for making bat boxes safer for bats.

The article, “Improving the science and practice of using artificial roosts for bats,” is published in Conservation Biology [DOI: 10.1111/cobi.14170].

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JOURNAL

Conservation Biology

DOI

10.1111/cobi.14170 

ARTICLE TITLE

Improving the science and practice of using artificial roosts for bats

SCI-FI-TEK

Department of Energy announces $29 million for research on machine learning, artificial intelligence, and data resources for fusion energy sciences

Nineteen institutions will apply advanced and autonomous algorithms to address high-priority research opportunities in fusion and plasma sciences.

Grant and Award Announcement

DOE/US DEPARTMENT OF ENERGY

WASHINGTON, D.C. - Today, the U.S. Department of Energy (DOE) announced $29 million in funding for seven team awards for research in machine learning, artificial intelligence, and data resources for fusion energy sciences.

Nineteen institutions will apply advanced and autonomous algorithms to address high-priority research opportunities in fusion and plasma sciences. The teams include fusion and plasma researchers working in partnership with data and computational scientists through the establishment of multi-institutional, interdisciplinary collaborations.

“Artificial intelligence and scientific machine learning are transforming the way fusion and plasma research is conducted. These awards will advance a broad set of capabilities across the Fusion Energy Sciences (FES) program, making essential capabilities available for all stakeholders,” said Jean Paul Allain, DOE Associate Director of Science for Fusion Energy Sciences. “The U.S. is leveraging every tool in its pursuit of an aggressive program that will bring fusion energy to the grid on the most rapid timescale.”

The recipients will pursue research in science discovery, diagnostic data analysis, model extraction and reduction, plasma control, analysis of extreme-scale simulation data, and data-enhanced prediction. Multiple awards will focus on establishing new systems for managing, formatting, curating, and accessing experimental and simulation data with research products to be provided in publicly available databases.

The projects were selected by competitive peer review under the DOE Funding Opportunity Announcement for Machine Learning, Artificial Intelligence, and Data Resources for Fusion Energy Sciences.

Total funding is $29 million for projects lasting up to three years in duration, with $11 million in Fiscal Year 2023 dollars and outyear funding contingent on congressional appropriations. The list of projects and more information can be found on the FES program homepage.

Selection for award negotiations is not a commitment by DOE to issue an award or provide funding. Before funding is issued, DOE and the applicants will undergo a negotiation process, and DOE may cancel negotiations and rescind the selection for any reason during that time. 

 

Penn State professor to lead field campaign to study climate in Baltimore area

Kenneth Davis will spearhead the DOE-funded project to investigate influence of surface-atmosphere interactions

Grant and Award Announcement

PENN STATE

UNIVERSITY PARK, Pa. — Kenneth Davis, professor of atmospheric and climate science at Penn State, will lead a team of 23 investigators from 13 research institutions in a new field campaign supported by the U.S. Department of Energy (DOE) to study surface-atmosphere interactions around Baltimore, Maryland, to see how they influence the city’s climate. The new campaign, called the Coast-Urban-Rural Atmospheric Gradient Experiment (CoURAGE), is expected to start in October 2024 and run through September 2025.

CoURAGE will contribute to the Baltimore Social-Environmental Collaborative (BSEC), one of four recently funded DOE Urban Integrated Field Laboratories. BSEC and the three other urban laboratories, located in Arizona, Texas and Illinois, will expand the understanding of climate and weather events and their impact on urban systems.

Davis is the principal investigator for Penn State’s portion of the multi-institutional BSEC laboratory, led by Johns Hopkins University. The CoURAGE science team includes Benjamin Zaitchik, Johns Hopkins professor and BSEC’s principal investigator, along with nine BSEC co-investigators.

With its aging infrastructure, growing susceptibility to heat and flooding, and ongoing issues with air and water pollution, Baltimore is characteristic of many large industrial cities in the Eastern United States. This was a motivating factor in deciding to propose an urban laboratory in Baltimore, Davis said.

“It’s a city that needs to adapt to thrive in a changing climate,” Davis said. “The city also needs sound evidence regarding options for climate change mitigation — options like urban greening. We also need to partner to generate climate science that addresses the priorities of people and neighborhoods in the city that historically have been neglected. Many of our cities face these challenges.”

BSEC will collect long-term data on the urban atmosphere and land-atmosphere interactions. However, it does not have enough resources to observe all the important variables within the city, nor can it cover “the neighbors,” as Davis put it — the atmospheric environments upwind of Baltimore that affect the city’s climate.

DOE’s Atmospheric Radiation Measurement (ARM) user facility will provide instruments and infrastructure for CoURAGE. During CoURAGE, ARM instruments will help provide coverage where BSEC cannot, forming much of what the campaign’s science team calls “a four-node regional atmospheric observatory network.”

CoURAGE is expected to include three ARM nodes. The primary node will be located in Baltimore at Morgan State University’s Clifton Park site, where ARM will operate a portable observatory consisting of instruments, shelters and data and communications systems.

Two nodes will be smaller observational arrays located at key sites outside the city. One will be located in a rural area northwest of Baltimore, on land typical of the plains found between the coast and the foothills of the Appalachian Mountains. Air at this this rural site is often carried into Baltimore by the prevailing winds. The other site will be on an island in the Chesapeake Bay designed to sample atmospheric conditions representative of the bay, the southeastern boundary of the Baltimore metropolitan area.

The fourth node will be an existing long-term observatory operated in Beltsville, Maryland, by Howard University and the Maryland Department of the Environment. Located north of Washington D.C., the observatory will measure the air that is carried into Baltimore when the winds come from the southwest, traveling across the nation’s capital.

With data from multiple sites, CoURAGE will be able to document the degree to which different surface conditions around the region can change Baltimore’s atmospheric environment, according to Davis.

“The CoURAGE campaign will be an important contribution to BER’s urban initiative,” said DOE ARM Program Manager Sally McFarlane. “The ARM observations will help improve understanding of atmospheric processes in urban regions, the surface and environmental conditions that drive them, and how our models of urban systems need to be improved.”

The team will collect what it calls impact and process measurements. Impact measurements are tied to conditions that directly affect residents, such as microclimate, air quality or street flooding in a particular area.

“Those are the properties we want to get right in order to understand the environment people live in,” Davis said. “Most of ARM’s data will be process measurements. These measurements will help scientists determine whether they are getting the right answers in models for the right reasons.”

Davis said his BSEC colleagues have found that wealthier neighborhoods have more existing climate and air quality measurements, so they are focused on putting instruments in lower-income parts of Baltimore. The plan could evolve as the BSEC team hears more from stakeholders in the city.

The project’s community engagement team, led by Tonya Sanders Thach and Samia Kirchner, professors  at Morgan State University; Genee Smith, professor at Johns Hopkins University; and Lisa Iulo, associate professor of architecture at Penn State, has gathered a steering committee that includes a broad array of community members and representatives of city government to guide the scientific effort. The steering committee, in turn, connects BSEC, and now CoURAGE, with a diverse cross-section of Baltimore residents to engage in knowledge co-generation, citizen science activities and educational programs.

Other Penn State faculty who are part of CoURAGE are Kelly Lombardo, Natasha Miles, Ying Pan, John Peters, and Scott Richardson, all faculty in the College of Earth and Mineral Sciences’ Department of Meteorology and Atmospheric Science.

ARM’s last urban campaign, the TRacking Aerosol Convection interactions ExpeRiment (TRACER), took place around Houston, Texas, from October 2021 through September 2022. Led by Penn State alum Michael Jensen, a meteorologist at Brookhaven Lab in New York, TRACER studied the effects of aerosols on storms in the Houston area. Jensen is now a co-investigator for CoURAGE.

The other institutions whose investigators will contribute to CoURAGE include Brookhaven National Laboratory, City College of New York, Columbia University, Howard University, Johns Hopkins University, Morgan State University, NOAA’s Earth System Research Laboratory, Princeton University, University at Albany, University of Maryland, Baltimore County, University of Maryland, College Park and University of Texas at Austin.

 

New odor map helps match perceptions of smells with their chemical structure

Peer-Reviewed Publication

AMERICAN ASSOCIATION FOR THE ADVANCEMENT OF SCIENCE (AAAS)

Brian K. Lee and colleagues have developed a Principal Odor Map (POM) that models the connections between an odorant’s chemical structure with its perceptual property of smell. The map performed as well as some highly trained human “sniffers” in describing odor quality, and could be used for predicting odor intensity and perceptual similarity between odorants. The map moves researchers closer to being able to match molecular properties of odorants to their perceptual properties, a challenge that has proved difficult for olfactory science. (For other senses, neuroscientists have been able to map light wavelengths to color and frequency to pitch, for instance.) Lee et al. used a type of neural network for data processing, called graph neural networks, to develop the POM. One of the things POM could be used for is exploring new odorants; the researchers compiled a list of about 500,000 potential odorants that have never been synthesized, plotting them in the POM to get an idea of how they might smell. Exploring this space would take approximately 70 person-years of continuous smelling time to collect using trained human sniffers. The POM could also aid research on digitizing smells, the authors note.

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JOURNAL

Science

DOI

10.1126/science.ade4401 

ARTICLE TITLE

A principal odor map unifies diverse tasks in olfactory perception

A step closer to digitizing the sense of smell: Monell Center, Osmo model describes odors better than human panelists

Peer-Reviewed Publication

MONELL CHEMICAL SENSES CENTER

 

IMAGE: JOEL MAINLAND, PHD view more 

CREDIT: MONELL CHEMICAL SENSES CENTER

PHILADELPHIA (August 31, 2023) – A main crux of neuroscience is learning how our senses translate light into sight, sound into hearing, food into taste, and texture into touch.  Smell is where these sensory relationships get more complex and perplexing. 

 

To address this question, a research team co-led by the Monell Chemical Senses Center and start-up Osmo, a Cambridge, Mass.-based company spun out of machine learning research done at Google Research, are investigating how airborne chemicals connect to odor perception in the brain. To this end they discovered that a machine-learning model has achieved human-level proficiency at describing, in words, how chemicals might smell. Their research appears in the September 1 issue of Science.

 

“The model addresses age-old gaps in the scientific understanding of the sense of smell,” said senior co-author Joel Mainland, PhD, Monell Center Member. This collaboration moves the world closer to digitizing odors to be recorded and reproduced. It also may identify new odors for the fragrance and flavor industry that could not only decrease dependence on naturally sourced endangered plants, but also identify new functional scents for such uses as mosquito repellent or malodor masking. 

 

“How our brains and noses work together”
Humans have about 400 functional olfactory receptors. These are proteins at the end of olfactory nerves that connect with airborne molecules to transmit an electrical signal to the olfactory bulb. The number of olfactory receptors is much more than we use for color vision - four - or even taste – about 40. 

 

“In olfaction research, however, the question of what physical properties make an airborne molecule smell the way it does to the brain has remained an enigma,” said Mainland. “But if a computer can discern the relationship between how molecules are shaped and how we ultimately perceive their odors, scientists could use that knowledge to advance the understanding of how our brains and noses work together.”

 

To address this, Osmo CEO Alex Wiltschko, PhD and his team created a model that learned how to match the prose descriptions of a molecule's odor with the odor’s molecular structure. The resulting map of these interactions is essentially groupings of similarly smelling odors, like floral sweet and candy sweet. “Computers have been able to digitize vision and hearing, but not smell - our deepest and oldest sense,” said Wiltschko. “This study proposes and validates a novel data-driven map of human olfaction, matching chemical structure to odor perception.”

 

What is the smell of garlic or of ozone? 

The model was trained using an industry dataset that included the molecular structures and odor qualities of 5,000 known odorants. Data input is the shape of a molecule, and the output is a prediction of which odor words best describe its smell. 

 

To ascertain the efficacy of the model, researchers at Monell conducted a blind validation procedure in which a panel of trained research participants described new molecules, and then compared their answers with the model’s description. The 15 panelists were each given 400 odorants as well as trained to use a set of 55 words - from mint to musty - to describe each molecule. 

 

“Our confidence in this model can only be as good as our confidence in the data we used to test it,” said co-first author Emily Mayhew, PhD, who conducted this research while a Monell postdoctoral fellow. She is now an assistant professor at Michigan State University. Brian K. Lee, PhD, Google Research, Brain Team, Cambridge, Mass., is also a co-first author. 

 

The Monell team supplied panelists with lab-designed odor reference kits to teach them how to recognize the smells and select the most appropriate words to describe their perception. To avoid pitfalls from past studies like panelist conflation of “musty,” like a wet basement, and “musky,” like a perfume, training sessions and lab-designed odor reference kits taught each panelist the odor quality associated with each descriptive term.

 

The panelists were asked to select which of the 55 descriptors applied and to rate the extent to which the term best applied to the odor on a 1-to-5 scale for each of the 400 odors. For example, one panelist rated the smell of the previously uncharacterized odorant 2,3-dihydrobenzofuran-5-carboxaldehyde as very powdery (5) and somewhat sweet (3). 

 

Quality control is also important in the final comparison of the human sniffers to the computer model. That’s where co-author Jane Parker, PhD, Professor of Flavour Chemistry, University of Reading, UK comes in. “I’ve worked on smell for many years, relying mainly on my own nose to describe aromas.”Her team verified the purity of samples used to test the model’s prediction. First, gas chromatography enabled them to separate out each compound in a sample, including any impurities. Next, Parker and her team smelled each separated compound to determine whether any impurity is overwhelming the target molecule’s known odor.

 

“We did find a few samples with significant impurities, among the 50 tested,” Parker said. In one case, the impurity was from traces of a reagent used in the synthesis of the target molecule and gave the sample a distinctive buttery smell that overpowered the odorant of interest. “In this case we were able to explain why the panel had described the smell differently to the AI prediction.”

  

CAPTION

Emily Mayhew, PhD

CREDIT

Monell Chemical Senses Center

Better Than a Human?

In comparing the model’s performance to that of individual panelists, the model achieved better predictions of the average of the group’s odor ratings than any single panelist in the study, impurities aside. Specifically, the model performed better than the average panelist for 53% of the molecules tested. 

 

“The most surprising result, however, is that the model succeeded at olfactory tasks it was not trained to do,” said Mainland. “The eye-opener was that we never trained it to learn odor strength, but it could nonetheless make accurate predictions.” 

 

The model was able to identify dozens of pairs of structurally dissimilar molecules that had counter-intuitively similar smells, and characterize a wide variety of odor properties, such as odor strength, for 500,000 potential scent molecules. “We hope this map will be useful to researchers in chemistry, olfactory neuroscience, and psychophysics as a new tool for investigating the nature of olfactory sensation,” said Mainland. 

 

What’s next? The team surmises that the model map may be organized based on metabolism, which would be a fundamental shift in how scientists think about odors. In other words, odors that are close to each other on the map, or perceptually similar, are also more likely to be metabolically related. Sensory scientists currently organize molecules the way a chemist would, for example, asking does it have an ester or an aromatic ring? 

“Our brains don't organize odors in this way,” said Mainland. “Instead, this map suggests that our brains may organize odors according to the nutrients from which they derive.” 

 

Special Notes to Reporters
More information, including a copy of the paper, can be found online in the Science press package at https://www.eurekalert.org/press/scipak/.

This research was funded in part by Google Research and National Institutes of Health grants F32 DC019030 and T32 DC000014. 

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The Monell Chemical Senses Center is an independent nonprofit basic research institute based in Philadelphia, Pennsylvania. Founded in 1968, Monell‘s mission is to improve health and well-being by advancing the scientific understanding of taste, smell, and related senses, where our discoveries lead to improving nutritional health, diagnosing and treating disease, addressing smell and taste loss, and digitizing chemosensory data.

 

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JOURNAL

Science

DOI

10.1126/science.ade4401 

METHOD OF RESEARCH

Computational simulation/modeling

SUBJECT OF RESEARCH

People

ARTICLE TITLE

A principal odor map unifies diverse tasks in olfactory perception