Human genomic bycatch: Our DNA shows up in environmental samples
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If individual's DNA is so ubiquitous, it seems just having it show up in a place wouldn't prove you were there then. I mean you could have come in contact with someone who was there and your DNA was shed as well. Like I would hope it would require more than DNA at this point to get a search warrant, otherwise a search warrant could be issued for pretty much anyone.
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Makes me think of Gattaca, when he's scrubbing his skin to prevent shedding DNA.
Question though, how much DNA are they finding in the air?
Question though, how much DNA are they finding in the air?
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At least zooming in on an image and digitally correcting the quality is still rejected as evidence in court because that's 'image manipulation' and "anything could be added"
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The benefits of DNA bycatch sound interesting, but they may also cross an ethical line. Yes, it might be helpful to find people who have cancer causing mutations, but we can also do that by specifically asking people if they want to be tested for that (and such a method would be more accurate). Using the bycatch method is effectively just an attempt to get around obtaining consent from these individuals, so I don't understand how this is a good thing.
Currently, I imagine the signal will be much to noisy to have a significant impact at an individual level, which is why we need act now to setup strict guidelines to prevent future ethical violations along the lines of GATTACA.
Currently, I imagine the signal will be much to noisy to have a significant impact at an individual level, which is why we need act now to setup strict guidelines to prevent future ethical violations along the lines of GATTACA.
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Came here to say the same basic thing. Even before this, there were problems. Suppose you're a college kid and a search of a victim's dorm room finds some skin flakes that DNA shows are yours. This doesn't even prove you were in the same dorm, let alone the same room. Too many ways for shed particles to hitch a ride from somewhere else.
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While we are at it, it would be good to take a look at all non-human WGS samples so we could recover mostly complete genomes of our all our molecular lab bio technicians. This is actually a problem- particularly for highly amplified dna like ancient material- but there is always a bit of human in every sample. Really this is hard to use any of this material for identification, it’s fragmentary and low coverage at best. And human DNA from shed cells gets totally overwhelmed by environmental DNA pretty much immediately in a soil or water environment. You can still pull it out with PCR if you wanted but the quantities are so low it’s not really going to be effective for much of anything. They collected human microchondiral dna and heavily fragmented material in this study with a sequencer that produces very heavy error ridden sequencing reads.
But for sure you can do this in a hotel room or restaurant and capture more concentrated dna from a single source. Again not particularly practical or high quality - easier to PCR amplify it and send it to a lab than try to piece anything together from nanopore. But this has been doable for many years now say 13 or so, but you don’t see this being used by law enforcement regularly. As it notes in some of the other articles on this story, they still use 20 markers for ID.
But for sure you can do this in a hotel room or restaurant and capture more concentrated dna from a single source. Again not particularly practical or high quality - easier to PCR amplify it and send it to a lab than try to piece anything together from nanopore. But this has been doable for many years now say 13 or so, but you don’t see this being used by law enforcement regularly. As it notes in some of the other articles on this story, they still use 20 markers for ID.
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At grad-school we had a hands-on Mass Spectrometry (MS) , where we took scrupulous care to isolate a protein.
In the result, first peak, keratin.
TLDR; we are still very hairy apes, despite our digital watches...
In the result, first peak, keratin.
TLDR; we are still very hairy apes, despite our digital watches...
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I would imagine one question that's not answered here is how long the DNA is viable for. If I "shed" some DNA that is then carried by you to some other place, how long, realistically, can they collect a sample of my DNA?
Are we talking hours? Days? Years?
It seems like this is a pretty important question to answer before we can really understand the ramifications of any of this.
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Worth looking at figure 2- the environmental samples were very very low, except the samples from sand from bare human footprints.
https://www.nature.com/articles/s41559-023-02056-2.pdf
In the test of enclosed air space 0.5 to 1 percent in supplemental table 3. They did pick the highest with qpcr first out of all samples.
The ST Augustine sampling site is interesting - sampling downstream in water they collected 10 percent. Which seems unlikely. It may be that there was some unintentional or intentional enrichment for longer fragment - aka fresh- DNA. Since nanopore is very sensitive to intact backbone this may have bumped up the recent human. I’m not familiar with the site. Seems like a few too many.
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don't need implanted RFID chips to keep track of imposters with this, as each newborn will get a unique identity signature at conception. we're long past simple fingerprint comparisons, behavior histories and the ugly use of 'blood lines' to ascertain the social standing of populations and the supposed creators of subsequent dynasties.
each individual could be determined acceptable for survival in a society based on less than a few 'desirable' traits that would fall within some 'legally defined' set of parameters. each one becomes a victim by no cause of their own.
culling out the imperfect from the optimal socially useful will be the end use of this 'de-anonymizer' tool. human nature remains as primitive as ever.
each individual could be determined acceptable for survival in a society based on less than a few 'desirable' traits that would fall within some 'legally defined' set of parameters. each one becomes a victim by no cause of their own.
culling out the imperfect from the optimal socially useful will be the end use of this 'de-anonymizer' tool. human nature remains as primitive as ever.
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Depends - it’s all about fragment size- the interesting part of this study is they selected for larger DNA and used nanopore so the reads are somewhat more meaningful to analyze- hence the whole mitochondrial read. But you can detect smaller fragments with more robust sequencing technologies for a long time depending on environmental exposure. But in an environmental sample it would be hard to tell if it wasn’t contaminated from sample collection and handling - the paper does mention that they tried not to contaminate samples - but contaminate here is breathing on the sample collection site or on the filter or on the tube you scraped in the filtered material or numerous places in the extraction or library process.
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I certainly agree it's ethically tricky, but it's probably cheaper to do mass health surveillance screening if you don't have to go round collecting individual samples. Put a litre of grey water from the sewerage plant inlet into the machine, press the button, repeat.
A more voluntary way of sampling could be to have a spittoon at, say, a train station!
They have to clean the tunnels on the London Underground quite often, amazing how much hair gets blown down the tunnels. That's probably biased towards collecting from women; there's a lot more bald men...
These days I'm not sure that ethically sound policy would make enough a difference. There's enough countries out there that'd see an advantage for their repressive regimes that the tech will get developed as a population tracking tool anyway. And once it exists there'll be those in other countries seeking to exploit it commercially, lobbying.
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Could be I guess. But this seems more like a dystopian movie plot where people can’t become pilots because of their bad eyesight- what you telling me you already can’t become a pilot because of your bad eyesight? Damn Air Force- culling out the undesirables- they wouldn’t let me go to Top Gun.
Kidding aside- we can either take advantage of newborn sequencing to mitigate genetic disease and provide informed choice for reproduction options, cure cancers, and provide sustainable energy and food or we could destroy all technology related to genome sequencing to prevent a far future where sometimes you could tell someone had been someplace.
I think the parent was meant to be humorous but not so sure based on previous comments!
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Maybe- but just easier to make everyone carry a cell phone to access basic services and Facebook of course! Or whatever it’s called these days. But you could also do room sampling - be easy to find those Marsley traitors this way.
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CSI caught up to Star Trek: TNG.
I recall an episode in TNG where someone was vaporized and there was a search for their DNA to positively identify them, which (IIRC) was taken from the air and environment since the vaporizing would have degraded DNA.
CSI first aired in 2000, by which time DNA sequencing was already a fairly mature science and it wasn't THAT much of a stretch to imagine a new way to collect DNA. Not so much in the 1980's when TNG was regularly on the air.
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Tech can't beat everything. There no more powerful a surveillance tool than the gossip network in small British villages.
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This technique could find those refusing to carry a mobile, attempting to be off grid. The kind of people a repressive state would like to find most of all...
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Like a team of ex special forces that were inprisoned and forced to escape military prison for a crime they did not commit?
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What are these "ethics" you speak of? Is that a sort of religious culture or something?
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All things in TV and movies that don't actually work or exist IRL, but aren't explicitly impossible due to physics, will (eventually) inspire someone to develop the solution. Whether on purpose or by accident.
This is why we desperately need more positive, utopian fiction, and a lot less police-state, dystopian fiction. Neither will be absolute predictors of future events, but there's nothing in this world that is more powerful than an idea firmly planted in the young minds of a generation.
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"It's been a while since I thought of Gattaca," I thought to myself as I went to comment
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I'll crate dive for classic psych, here: A negative stimulus has, I think it was, 7-8 times the power of a positive one. So, on the one hand, yes, we probably need a lot more positivity. However, you're then up against "Jaded" people who find it "Saccharine"
...and then you need at least a few negative ones to scare them off from the worse stuff. You're talking about overdoing it on negativity and thus fostering it into reality, which is valid. I'd also say you can't completely underdo it and not show Gattaca in biology class as an end of year treat like... well, that's how I saw it
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I would think that you could probably identify how frequently a particular individual's dna shows up in samples, to get an idea whether it was someone shedding dna they incidentally picked up (very low frequency of finding that in samples) vs being nearby themselves (higher frequency of matches).
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If anything, Gattaca was adorably optimistic about the amount of DNA we are shedding and the ease with which it could be collected.
Not to mention DNA databases. You'd never get past their applicant screening. They'll see your borrowed ladder, that you're the one who borrowed it, who you borrowed it from, and the entire family lineage of both sides.
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So there are privacy concerns. About information that our bodies have been spreading hither and yon throughout the environment since long before our ancestors even became human.
We definitely should draw the lines somewhere, but maybe we need to take a deep breath and define what we mean by terms like privacy concerns and rights to privacy.
We need to define what they are, define what is protected by law (and what is merely rude and, possibly, not even that). We also need to specify how law breakers will be detected. This is necessary if they are to be enforced. And we should never have laws that cannot be enforced.
Creating laws which are unenforceable simply weakens respect, observance, and enforcement of all laws. We already have too many laws that the police will not even attempt to enforce, for one reason or another. Legislators need to be incentivized to repeal bad or outdated legislation, as well as pass good and needed legislation, but that's another issue.
On a side note, people forget quickly but, until the Supreme Court ruling in 2013, it was possible for people and businesses to patent your DNA. Your personal DNA. It was a good decision. If anyone should be able to patent your DNA it should be limited to your parents, but even that would be ridiculous. We are not the owners of our DNA, we merely benefit or suffer for being its custodian, but human DNA belongs to all of humanity. This is much the same as saying it simultaneously belongs to no one, and to everyone. In point of fact, with it spread throughout our environment, we are now discovering it simultaneously belongs to nothing and to everything.
We definitely should draw the lines somewhere, but maybe we need to take a deep breath and define what we mean by terms like privacy concerns and rights to privacy.
We need to define what they are, define what is protected by law (and what is merely rude and, possibly, not even that). We also need to specify how law breakers will be detected. This is necessary if they are to be enforced. And we should never have laws that cannot be enforced.
Creating laws which are unenforceable simply weakens respect, observance, and enforcement of all laws. We already have too many laws that the police will not even attempt to enforce, for one reason or another. Legislators need to be incentivized to repeal bad or outdated legislation, as well as pass good and needed legislation, but that's another issue.
On a side note, people forget quickly but, until the Supreme Court ruling in 2013, it was possible for people and businesses to patent your DNA. Your personal DNA. It was a good decision. If anyone should be able to patent your DNA it should be limited to your parents, but even that would be ridiculous. We are not the owners of our DNA, we merely benefit or suffer for being its custodian, but human DNA belongs to all of humanity. This is much the same as saying it simultaneously belongs to no one, and to everyone. In point of fact, with it spread throughout our environment, we are now discovering it simultaneously belongs to nothing and to everything.
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Information that was 100% inaccessible until recent technological advances. You're stating this as if it has been something we've lived with since time immemorial but the problem is the result of brand new technology and therefore is something that hasn't been seen before. Before the advent of this technology our shed DNA was irrelevant because it was literally impossible to use it against someone.
Although the problem does bear similarities to other problems we've been living with for a while (see below). It falls into a category of tracking and discrimination, but via a new industrialized, automatable method.
The right to not be constantly surveilled, profiled, stalked, monetized, and discriminated against by the government, profit motivated corporations, or individuals. The right to not have location, travel, and personal health information compiled into a perpetual database that can be used against you, and the right to redress of grievances when it is.
(Emphasis added.) No we don't. The vast majority of laws are "Don't do X. If we find out you did X you will be in trouble." with no defined mechanism for actively seeking out people doing X. How do we detect that your DNA is being sampled? Innumerable ways. When an inside whistle blower leaks information about an unethical or non-compliant sampling program. When an unexpected DNA sniffing device randomly appears in a public park. When someone observes a suspicious person's pattern of stalker-like behavior and investigates. When an employer accidentally slips up and mentions a genetic condition you have during conversation when they couldn't possibly have known that without sampling or accessing some third party database. When a data breach reveals information that an organization shouldn't have. Et cetera.
That's no different to any other crime. Do we specify how employers discriminating against a protected class like race or sex will be detected? No, we do not. Do we specify how douchebags who upload revenge porn of their ex-partners will be detected? No, we do not. We deal with it when we find out. There is nothing special or magical about DNA sampling that places it outside the normal ways that any other crime is discovered and then prosecuted.
Red herring.
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Arrrgh, you've done it now; I can't get the tune out of my head! Now then, where's my flying tank?
Time for a franchise update? the DNA Team?
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A group of rouge, ragtag scientists (for sure some goofy glasses and the occasional stylish denim lab coat) that go around solving crimes by sucking up e-DNA and running complex but indescribable computational analyses? Sign me up! At least as the consultant of I can visit tropical locations and design new ways to abuse E-DNA studies! You don’t want me acting but I can for sure do an old white guy who says “I love it when the SNPs match!”
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It's already happening for Down syndrome.
https://pubmed.ncbi.nlm.nih.gov/27608174/
What genetic "defect" will be or already is having it?
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