What’s in a genome? The quest to decipher human difference

What’s in a genome? The quest to decipher human difference

This article originally appeared inUndark.

Tina Lasisi was 19 when she discovered the scientific question that would take up more than a decade of the rest of her life.

The instructor had made a great discovery in the study of human evolution. People who ancestors lived near to the equator have darker skin than those who lived near the poles.

The detail was a revelation for Lasisi, the biracial child of a Nigerian father and a Bulgarian mom. It wasn’t about race anymore. It was about the amount of UV light her ancestors had seen as they traveled around the globe. Then, almost immediately, another question arose: “What about my hair?”

Lasisi had found a puzzle, a set of puzzles. The color and structure of human scalp hair can vary, unlike hair from wild mammals. It often curls, unlike other hair types. Scientists aren’t sure how this multi-colored hair came about.

Lasisi amassed a collection over the years as she pursued a Ph.D. In biological anthropology. She estimates that she has over 200 samples. Some are kept in small tubes in a refrigerator in her lab, while others are embedded in plastic. She developed rigorous methods to measure the curvature of each hair fiber. Lasisi is now a postdoctoral researcher at University of Southern California. She also studies the genetics of hair. What genes influence the hair type of a person? Why is there so much variation?

Lasisi is also uncomfortable with this work. Scientists have studied variation for centuries in order to group people and establish racist hierarchies. The study of hair has played an important role in this effort. Eugen Fischer, a German anthropologist, was one example.UsedSwatches made of synthetic hair were used to classify mixed-race people living in colonial Africa. (The German regime murdered tens to thousands of people in Namibia, Fischer went on and became a Nazi.

Many anthropologists and geneticists responded to this racist legacy by stating that racial groups are human creations and not natural facts. The now-famous phrase “race” refers to a social construct and not a biological one.

Lasisi and other researchers disagree with this formulation. “There’s this void left by the genuine desire to undo a racist heritage by saying,‘Race isn’t real. Race is not biology. “Race is a social construct.She said. “All of these things have been incorporated into so many syllabuses over the past couple of decades. These things are commonplace among students, and they are not understood by all.

Take hair into consideration. Hair is a complex thing when viewed from one angle. A tightly curled curl can indicate recent ancestry in Africa or Papua New Guinea. A blonde could trace their light hair back to northern Europe or the South Pacific. Hair can also be proof of a relationship.SomethingThe biological aspect of race. An American can tell you about the racial and ethnic identity of a random person, and they will be able to make an educated guess about the color or texture their hair.

There is a void left by the genuine desire to erase a racist legacy. Race is not biology. “Race is a social construct.”

Tina Lasisi

It might be more helpful to say it this way: Race is one crude and complicated way of describing biological variation between humans. Jada Benn Tores, a Vanderbilt University genetic anthropologist, stated that “variation exists.” “It’s the cultural meanings we attach to that variation which will create the different races.” She said that these categories are fluid. A person who identifies himself as White in the United States in 2022 might not have been White in 1922. A person who is called Black in the U.S. may not be considered Black in Brazil. In this sense, race is a social construct.

However, this has not stopped people trying to understand and describe variation. The vast new troves that have been created from genetic data over the past decades have allowed us to study the differences between human beings in great detail and to devise many ways to categorize people. Some of the categories they create are not like U.S. racial classifications. Sometimes, researchers use that data to create clusters that look a lot like race. It is possible to look at differences between existing social racial groups, even if they are not coherent.

Geneticists today are looking into a cloud of trillions upon trillions of datapoints in search of patterns. What they ask — what they are actually looking for — will affect what comes out.

A A person’s DNA can tell many stories at once. Your genome is the result of splicing together the DNA of your biological parents. One half of each parent’s DNA is used, with a few unique mutations added. Zooming back a few generations, you will see that the genome is more like a patchwork made from eight great-grandparents’ DNA. You can go back further and see thousands of ancestors. Most of them have left no legacy to you. It becomes easier to imagine each snippet of your genome as having gone through its own complicated journey, crossing continents and passing through bodies before it landed in your genetic code. At this scale, DNA can provide clues about the origins of a person’s ancestors hundreds of years ago. It also contains faint records about an ancient world, such as the migrations of people around the globe; the mixing and division of communities; and long-ago pandemics or famines.

Human history is a story about churn.Homo sapiensProbably around 300,000 years ago, Africa was where they first appeared. Some groups eventually escaped to that continent. People occupied locations as far-flung and remote as Alaska and Tasmania before long, relatively speaking. They settled on the thin air of Tibet Plateau and pushed into the Americas. More recently, they launched wooden boats into open ocean to populate Polynesian islands. Migrations were a common phenomenon across continents long before the turmoil of the post-1492 colonial era. Recent genetic research suggests that some people whose ancestors left Africa many millennia ago eventually returned to Africa.Migration flowsFrom Eurasia to Africa, and the Indonesian archipelago from theIsland of Madagascar.

These migrations are traced in the human genome, specifically in the millions of spots where the genetic code can differ from one person to the next. One person may have a different entry at a specific spot than another — the nucleic acids cytosine instead of adenine, which is the rough equivalent to swapping one letter out of a word. These small differences often have no apparent effect. Other factors may also contribute to subtle differences, such as why someone has black hair and another person has brown.

This genetic potpourri was subject to changes as human history changed. Some of this was just random. Consider, for instance, a hypothetical population that lives near a mountain range. Half of them carry version A and half have version B of a particular gene. A small group of people, almost all carrying version B, decides to leave their home and cross the mountains. They create a new society and the far side becomes full of people with version A — just by pure luck.

Natural selection drove changes, too. Some people have genetic variants that allow them to thrive in certain circumstances. These genes are passed on to their children. People living high up in the Himalayas, Andes and East African highlands, for example, have developed genetic variants that allow them to thrive with less oxygen. Near the Arctic, people were able to select for paler skin. This is because it is easier to make vitamin D in places with less sunlight.

The genome can also be affected by disasters. A team of researchers recently extracted DNA from the bones of medieval Europeans.FoundAfter the Black Death, certain gene variants that are linked to immune system development became more prevalent in Europe. It seems that people who were carriers of these genes were more likely to survive the pandemic.

These kinds of changes can accumulate over long periods of time and isolated populations of animals, plants, and other organisms can sometimes evolve into distinct groups or even different species. Some scientists believed that this process had also produced racial groups in the 19th and 20th century. They argued that the human species was made up of long-isolated populations with large genetic differences. Experts now believe that this is not true. Joseph Graves, Jr., an evolutionary biologist from North Carolina Agricultural and Technical State University, said that there is very little differentiation among human populations. “And the differentiation that is there, is continuous and not discrete.”

One, humans have only recently emerged in Africa, at least according to the evolutionary clock. It has taken too long for genetic differences to emerge. People didn’t evolve into distinct types by being isolated in small groups. Instead, they moved around and interacted with each other. Agustin Fuentes, a Princeton University biological anthropologist, said that “In most places you have massive movements, intermixing and changing over time.” “There isn’t one thread that ties everything together, like ‘Everyone from Europe has done the same thing.’ThisEvery person from Africa has been doing this for over 10,000 yearsThisFor 10,000 years.

John Novembre, University of Chicago population geneticist, said that the pattern is “diversification followed by contact”. It is a constant dance of new fusions and divisions. According to one estimate, every person alive today has at least one ancestor that lived in the last 3,500 years.

People do not choose their partners by chance. People are more likely to have children with those who live near them or their extended families.

There is therefore a link between geography and genes. To return to the earlier example, people living on the far side are more likely to have version B. People living on the near side have a mix of A andB. If someone randomly picks version B, it’s a good sign.LikelierThey come from the far side. You can repeat this process for several locations on the genome. It becomes possible to guess where someone’s ancestors lived in the past.

Researchers began to develop powerful computational tools to find these patterns in the 2000s.

The most powerful of these tools was, perhaps,All ready to goA trio of young geneticists created the computer program on a single September day 1998 at a workshop near Cambridge, England. The computer program took genetic data.Looked atClusters are groups of people who have genes that are slightly more alike than those belonging to other people. It was known as STRUCTURE.

Humans share more DNA than 99.9% with each other. Researchers have long been fascinated by the many points in the genome that people share.Dovary. Geneticists began to build vast new genetic data libraries, drawing from samples taken from all over the globe, at the time STRUCTURE was created. They hoped that this information would provide clues about human history and small genetic differences that could be useful for medical care. Dorothy Roberts, a sociologist, has a different idea.arguedInnovations in genetic research can sometimes feel like a new expression of the impulse for human beings to be divided into old categories — “a racial science.”

STRUCTURE seemed to be able to feed this impulse, perhaps unintentionally. Researchers used STRUCTURE to draw lines between DNA from two groups: a group made up of white northern Europeans and one made up of black central and southern Africans. This was the first time the tool was published. Soon after, Noah Rosenberg, a geneticist, and his colleagues applied STRUCTURE for genetic data taken from 1,056 individuals from around the globe. Rosenberg and his colleagues instructed the program to create five groups from the people they had collected. These groups were located in Africa, Eurasia East Asia, Oceania and the Americas.

Some observers thought the clusters looked very much like…Race. “The study concluded that people belong to five main groups that correspond to major geographical regions around the world.”SubmittedNicholas Wade, science journalist in The New York Times, said that these regions “generally correspond with popular notions about race.” (Wade elaborated on the idea in a 2014 volume that biologists widely referred to asinaccurate,Intellectually incoherent,racist.)

Many researchers, including Rosenberg at Stanford University, caution against comparing the categories generated by STRUCTURE with racial groups. You can alter the number of clusters that the computer model generates to get different results. You can also adjust the samples that are included in the model. Rosenberg’s team used DNA from far-flung Indigenous groups. Many of these people live in remote areas. The clusters might have looked different if the researchers had chosen 1,056 more subjects, such as people who live in major cities or biracial French citizens or just a random assortment.

Genevieve Wojcik is a geneticist at Johns Hopkins University’s Bloomberg School of Public Health. “There’s no absolute truth when it comes down to groupings,” she said. It’s all about what data you have, who you include, how you use those methods, and what assumptions you make.

She said, “It’s no universal fundamental truth,” and that people “sort of cluster.”

As clustering tools have become more common in the field, the results have varied. Researchers combine scientific judgment with statistical analysis to determine the best number of clusters to examine. A 2009 study on human genetic diversity used a different set to identify 14 clusters. Six of these clusters corresponded with populations that had recently rooted in Africa. Because humans have lived on the continent for so many years, it has more genetic diversity than any other part of the world. Recent research has shown that similar tools were used to analyze more than 30,000 samples taken from New York City residents. The results of this analysis yielded 17 rough-edged clusters with lots of gradation.

Humans share more DNA than 99.9% with each other. Researchers have long been fascinated by the many points in the genome where people differ.

These tools have been criticized by some researchers. Scientists were given a tutorial in 2018 on how to not overinterpret data from STRUCTURE or a related algorithm. Geneticist Eran Elhaik, a professor at Lund University in Sweden, was known for his provocations. He published a paper that described another common tool for visualizing clusters, which he called “the Rorschach” of population genetics.

Experts also believe that the appearance of distinct clusters can exaggerate the differences between groups. There is far more genetic variation within a group of people who can trace their ancestry back to the same region of the world than there is between individuals.AmongGroup members are more likely to be friends than members of other groups.

Rosenberg recently argued that Rosenberg was correct to argue in a paper, quoting an old statement in Nature, that “two random individuals” from one group are almost the same as two individuals from the whole world.

RWojcik describes acial categories as rough maps that are imposed on the mess of human variation — “lines at the beach.” These categories are created and enforced by people. It is now possible to search for genetic differences between socially constructed groups.

It is possible to look for differences in any socially constructed group of people and possibly find something, even if it is only by chance. Deborah Bolnick, an anthropological geneist at the University of Connecticut, created an imaginary group of people, some of whom have purple hair and some who don’t. She said that if we looked hard enough, we might find one point in DNA that everyone with purple hair has and nobody who hasn’t. “So that would indicate a genetic difference between the two groups. Is this meaningful?

Some racial groups may be able to correspond with the geographical distribution of people’s distant ancestors around the world, even if it is only in a limited way. Because genes and geography are linked, racial classifications can capture some of those small genetic differences between people who lived thousands miles apart.

These differences are worth exploring.fraughtBecause the questions are often far from innocent. A small but vocal group has argued for decades that there are significant biological differences between racial populations, particularly in intelligence and aggressive behavior. These conclusions are often based on weak evidence or pseudoscience and tend to reinforce long-standing racist stereotypes.

Some scientists agree that there are good intentions to explore these differences. Akinyemi Oni Orisan, a genetics researcher at UC San Francisco and the lead author of a 2021 paper, stated that there are genetic differences among socially categorized groups.Callingfor the continued use racial categories as part of some medical genetics research. He suggested that acknowledging small genetic differences is not incompatible to a commitment towards racial justice. “I am a geneticist. He said that he knows there are genetic differences among populations based upon ancestry. “I don’t believe I’m a race essentialist.”

These are the places where these differences can be found. One way is to look at those points on your genome, calledlociThese genes appear to have been subjected to recent natural selection. This may vary from one place to the next. Novembre, a Chicago geneticist, said that this signal is visible in predictable places: specifically, “loci which affects things like skin color, immune system biology and pathogen resistance, metabolisms, especially, of new dietary sources.” This means that people adapt to new pathogens and new foods. These adaptations can be seen as minor genetic differences between socially defined groups.

Even if they did exist, it would be difficult to identify differences that relate to intelligence traits. The relationship between genes and the environment — between nurture and nature — can be complex even under the best of circumstances. Even seemingly simple traits like hair color or height can be affected by thousands to hundreds of genes. Intelligence, which is elusive and difficult to define, makes the problem even more complicated.

Although scientists have tried to link intelligence and race for a long time, experts say there is no reason to believe that there are any. Many question the motives of those who are trying to investigate it. Benn Torres (Vanderbilt anthropologist) said, “The more interesting question for me is, why aren’t we asking that question in all of this?” “If intelligence or intelligence is what you are interested in, why aren’t we asking that question?” To what end?

TResearchers are pondering whether big categories are useful. One goal is to find other ways to think about human variation than relying on large categories. Mashaal Sohail is a population geneticist at The Center for Genomic Sciences of the National Autonomous University of Mexico. He said, “Whenever you’re defining population, you’re always forcing discretization.” In other words, categories are always simplified.

Sohail cited an example of a common genetic study. It begins with a subject’s racial identity and then breaks them down into groups based on this — one pool of people of European ancestry and one pool of South Asian ancestry. After the samples have been sorted into groups the geneticists can begin their research. (This sorting can be difficult; some geneticists just throw out samples from biracial people if they are unsure where to place them.

Sohail and other researchers are excited to find ways to do those studies without having to break up the original dataset. Instead, researchers examine how closely everyone is to each other in their sample and how much of their genetic code they share. These large ancestry groups are only rough measures of genetic similarity between people. Sohail stated that relatedness can also be used to measure genetic similarity among people, but without having to artificially group them into groups. Wojcik said that this approach can sometimes enable researchers to use larger datasets, which can help them achieve better results.

These are promising developments, according to Lasisi, the scalp-hair researcher. She said, “We’re now at the point where people pioneer these statistical methods and these data visualization methods. These ways of mathematically understanding relatedness through this way.” It’s like I don’t want to give it a shape. It’s like, I’m not going to try and give it a shape.

UPDATE:An earlier version of this article used a term that some readers might have found inappropriate when describing a hair type that can be indicative of ancestry in more that one geographic region, including Papua New Guinea. These sensibilities have been reflected in the text.

LONG DIVISION Undark Magazine publishes a journalistic project called “The Faulty Legacy of Race Science”. It is an ongoing journalistic endeavor.

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