What is eDNA that lingers in water, even your cup of tea and can be pulled from thin air?
New York Times
Researchers are embracing environmental DNA because they only scan for small DNA segments - what they call "bar codes" that identify creatures to species level.
David Duffy is a wildlife geneticist from the University of Florida. He wanted to find a way to better track diseases in sea turtles. He then started finding human
DNA
He looked everywhere.
In the last decade, researchers in wildlife have developed techniques to recover environmental DNA.
eDNA
All living things shed trace amounts of genetic materials. Ecologists can use eDNA as a powerful, inexpensive tool. It is everywhere - in the air or in water, in snow, in honey, and even in your cup of coffee. Researchers have used this method to detect invasive plants before they spread, to track sensitive or secretive wildlife populations, and to even rediscover species that were thought to be extinct. The eDNA is used to monitor Covid, and other viruses in wastewater surveillance systems.
Scientists have been using eDNA to recover human DNA for years. For them, this is pollution, a kind of human genomic bycatch that muddies their data. What if someone deliberately set out to collect eDNA from humans? Erin Murphy, professor of law at New York University School of Law and expert in the application of new technologies to criminal justice, said that the new DNA collection techniques are like catnip for law enforcement officials. The police have been quick in adopting unproven methods, such as using DNA to create probability based sketches of suspects. This could create problems for civil liberties and privacy, as the technology allows more information to come from smaller eDNA sample. Duffy and his co-workers used an affordable and readily available technology to determine how much information could be gleaned from human DNA collected from the environment. This included waterways outside and air in a building. Their research results, published in Nature Ecology & Evolution on Monday, show that scientists can retrieve medical and ancestry data from tiny fragments of DNA lingering around the environment. The findings of the Florida team have prompted forensic ethicists and lawyers to call for a comprehensive regulation on genetic privacy. Researchers say that this also highlights a disparity in US laws regarding such technologies - it's much easier for law enforcement to use a half-baked technology than for scientists to obtain approval for studies that confirm the system works.
Genetic treasure from genetic trash
Since decades, it has been obvious that fragments from our DNA litter the Earth like litter. It didn't matter. Scientists thought that DNA from the environment is too small and degraded to be usefully recovered. It could not even be used to identify a human, unless it was from a distinct sample, such as if someone touched an object or a bloodstain. Researchers are embracing environmental DNA because they only scan for small DNA segments - bar codes if you will - that can identify creatures to species level. After finding "surprisingly high" levels of human environmental DNA while monitoring the disease of Florida sea turtles in their samples, Duffy's team decided to do more to determine the state of human DNA and how much it can reveal about the people living in an area. In one experiment, researchers collected a small sample of water in a St. Augustine creek as a proof-of-concept. The researchers then passed the DNA from the sample into a nanopore sequencing device, which allowed them to read long stretches of the DNA. They used a device that cost around $1,000 and is about the size of an cigarette lighter. It plugs into laptops like a flashdrive. The team was surprised to find that the DNA samples contained much more human DNA than expected. Even limited samples reveal valuable information as our knowledge of human genetics grows. Researchers recovered enough mitochondrial dna - passed from mother to daughter for thousands of years - to create a snapshot of genetic ancestry for the population surrounding the creek. This roughly matches the racial composition reported in the most recent census data for the region (although researchers note that race identity is not a good proxy for genetic origin). One mitochondrial DNA sample was complete enough to satisfy the requirements of the federal missing persons database. The researchers also discovered key mutations that were associated with a greater risk of diabetes and cardiac problems, as well as several eye diseases. According to the data, someone who's genetic material was found in the sample may have a mutation which could lead to a disease causing progressive neurological impairment that is often fatal. It is hereditary, and the illness may not manifest until after a patient reaches their 40s. Duffy couldn't stop wondering: Does this person know? Does that person's family know? Does the person's family?
Surveillance, forensics and other technologies
Anna Lewis, Harvard researcher and expert in bioethics, who studies the ethical implications, legal issues, and social aspects of genetics, stated that environmental DNA had not been discussed widely by experts. After the findings of Duffy and colleagues, environmental DNA will be widely discussed. She said that technology based on eDNA could be used to monitor certain types of people – for example, those with a particular ancestral background, or those with specific medical conditions or disabilities.
Researchers agree that the implications of these uses depend on who and why is using it. While pooled eDNA could help public
Health
Researchers can use the same eDNA samples to identify and target ethnic minorities.
Lewis stated that "this gives authorities a powerful tool." There are many reasons to be worried, I believe, on a global scale. China, for example, already tracks the genetic makeup of minorities such as Tibetans and Uyghurs. She said that tools such as eDNA analyses could make it easier. The ethical minefield that eDNA research presents will also depend on how easy it is to identify a person. In some cases, it is already possible. Robert O'Brien is a forensic scientist at Florida International University, and former crime lab DNA analyst. He said that the genetic data Duffy collected from public places would not work with current methods used by law enforcement in the United States to identify individuals. O'Brien explained that when law enforcement DNA analysts are comparing a crime scene sample with a suspect they look at 20 markers scattered across the human genome, which is tracked by the FBI's Combined DNA Index System (CODIS). These markers can only be useful if it is certain that they all come from the exact same person. Because the eDNA fragments Duffy examined could not capture more than one mark at a given time, a place like the Florida stream would become a nightmare jigsaw. Researchers suggest that eDNA can be used to identify individuals in enclosed areas where fewer people are present. A team from the Oslo University Hospital’s forensic research centre piloted a technique in October to recover human DNA using air samples. They were able to create full CODIS profiles by airborne DNA within an office.
This raises the possibility that police could use eDNA from crime scenes as evidence against people even though the wildlife ecologists behind the technique claim the
science
It's not mature enough to be used for this purpose. Scientists are still trying to understand the basics of eDNA. This includes how it moves through water and air, or degrades with time. Nanopore sequencing, the technology used by Duffy's group to identify longer and more informative fragments of DNA, still has a higher error rate than other technologies. This means that a genetic signature that appears promising could actually be a false lead.
Who has access to DNA when it is available for free?
The rules in the United States vary greatly regarding who can capture and analyze DNA. In an imperfect system, university scientists who want to know more about human eDNA have to justify their research scope and privacy concerns in a process that involves ethics boards from their institutions. These boards can reject or limit the experiments. There are no safeguards in place for law enforcement officials who want to test a new technology. Barbara Prainsack is a professor of medicine and forensics at the University of Vienna. She studies DNA technology regulation. In some countries, such as Germany, there is a green list that includes technologies and evidence forms that can be used by law enforcement. But in the United States, it's the opposite. Murphy said, "It is a Wild West. It's a free for all." "It's understood that police can do anything they want, unless it is explicitly forbidden." Murphy explained that the public, and sometimes other government branches, learn about new techniques used by law enforcement only during a press conference to announce an arrest. She cited the arrest of Joseph James DeAngelo as the Golden State Killer. Police attributed the arrest to genetic genealogy, including entering crime-scene data into family history databases and triangulating an identity based upon distant cousins. She said that in high-profile cases law enforcement relies on "the goodwill they generate when they use the technology to really positive purposes." Some uses may not be revealed. Experts say that the courts are the best place to protect against misuse of a new technology like eDNA. Trial judges should determine if an expert's testimony is "based on a solid foundation" to keep bunk or immature science out of legal discussions. Murphy said that it is unreasonable to expect all trial judges to be up-to-date on the latest scientific advances. She added that the rules of evidence "favor" the admission of proof and rely on the jury to decide what they believe.
Since the 1970s, groups such as The Innocence Project, have been working to eliminate pseudoscience from courts. Microscopical hair analysis, blood-spatter analyses, and bite-marks have all led to the wrong conviction of defendants. Despite the overwhelming evidence that these technologies are not reliable, courts are reluctant to stop using them or to reverse a conviction based on this evidence. This is because they have been used for so long. Aliza Kaplan, a law professor at Lewis & Clark Law School, Portland, explained.
Oregon
The Forensic justice Project is a project of the Forensic Science Institute.
Fourth Amendment prohibitions on "unreasonable searches and seizures" without probable causes are also meant to protect privacy from the powerful new technologies. Since the early 2000s many prosecutors, courts, and police have adopted the view that DNA that is not attached to an individual has been abandoned. This means that the police do not need a search warrant to collect the DNA. It may be impossible to prevent leaving DNA on public property. Duffy and his co-workers found that airborne DNA could be collected from people even when they were wearing surgical masks, gloves or gowns. Vera Eidelman is a staff attorney with the American Civil Liberties Union, who focuses her work on constitutional claims relating to genetic privacy. She was not part of the Florida team's research.
Consent and Genetic Exceptionalism
Comparing human eDNA to other surveillance technologies, like facial recognition cameras, that people don't consent to individually is possible. Experts say that there is a crucial difference. The DNA collection process affects more than just the individual. Sandra Soo Jin Lee, biomedical ethics professor at Columbia University, said that it also affects "family members, and in some cases, communities." Murphy said that DNA can be traced back to ancestors, forward to extended family members, and even to children. Who knows what the DNA of future generations will reveal about us or how we might use it? Genetic information has a broad market - from pharmaceutical companies that develop therapeutics to insurance actuaries to public health researchers. The lack of a legal definition of DNA is preventing the public from being protected. Murphy asks, "Is it property?" What is data? Are medical records always considered data? Once it is collected, who owns it? Duffy's caution, say bioethicists & civil liberties experts, gives decision makers a rare opportunity to discuss ethics and legality before a new genetic technology is widely used. They usually have to play catch-up, but now, thanks to wildlife ecologists they can get a small head start.