The history of a monumental forensic tool and the ethical debate sparked by wrongful convictions based on trace DNA evidence

Tiny Matters

A warning to listeners — this episode contains sensitive material surrounding homicide and assault.

On November 29th, 2012, a group of men broke into the Silicon Valley mansion of 66 year old investor Raveesh Kumra. The men attacked and tied up both Raveesh and his ex-wife who was living there, and then ransacked the home for cash and jewelry. By the time the paramedics arrived, Raveesh — who had also been gagged with tape — had died of suffocation.

A few weeks later, the police arrested 26 year old Lukis Anderson. Anderson, whose DNA had been found on Raveesh's fingernails, was charged with murder. But the night of the homicide, Anderson had actually been at a hospital many miles away, being carefully monitored. So how did his DNA get on Raveesh’s fingernails?

In this episode of Tiny Matters, Sam and Deboki unpack the history and evolution of DNA profiling and how new, more sensitive, technologies can be both incredible tools for picking up trace amounts of DNA to home in on suspects and a huge liability that can lead to wrong convictions.

Transcript of this Episode

Deboki Chakravarti: Hi Tiny Matters listeners, Deboki here. Just a heads up about today’s episode — it tackles some difficult topics related to criminal cases, including assault. That might mean it’s one you or a younger listener would like to skip. We have a pretty hefty back catalog if you’d like to check out another episode instead. OK, on to the show.

Sam Jones: Around midnight on November 29th, 2012, a group of men broke into the Silicon Valley mansion of 66 year old investor Raveesh Kumra. The men attacked and tied up both Raveesh and his ex-wife who was living there, and then ransacked the home for cash and jewelry. By the time the paramedics arrived, Raveesh — who had also been gagged with tape — had died of suffocation.

A few weeks later, the police arrested Lukis Anderson, an unhoused 26 year old man with a list of previous crimes. Anderson’s DNA had been found on Raveesh's fingernails. He was charged with murder which meant that, if found guilty, he could face the death penalty. But the night of the homicide, Anderson had actually been at the hospital being treated for intoxication, carefully monitored all night. So how did his DNA get on Raveesh’s fingernails?

Welcome to Tiny Matters, I’m Sam Jones and I’m joined by my co-host Deboki Chakravarti. 

Deboki: Today’s episode is about forensic DNA evidence — the history of DNA profiling, how it has evolved, and what went wrong in the case of Lukis Anderson. 

Although CSI or Law & Order would like you to think DNA analysis is as easy as pressing a button on a computer and seeing the words “DNA match” pop up on a brightly lit screen, it’s more complicated than that. DNA, or deoxyribonucleic acid, is found in our cells and made up of the nucleotide bases adenine, thymine, cytosine and guanine or A, T, C, and G for short. Sequences of these nucleotides — typically tens of thousands of bases long — code for a huge number of proteins and other molecules found throughout our bodies. 

And my DNA versus Sam’s DNA versus your DNA is all pretty similar. But there are differences, and those differences can be used to tell us apart with remarkable accuracy. This is the basis for forensic DNA profiling. 

Sam: In the United States alone, DNA profiling has led to the exoneration of hundreds of innocent people who were imprisoned. But, in the case of Lukis Anderson, DNA led to a wrongful murder charge. To understand where things went wrong, we need to unpack how DNA profiling works and some of the key criminal cases that pushed it forward. 

For decades, investigators had to rely on forensic evidence like shoe prints, hair, clothing fibers, and fingerprints that a suspect may have left behind at a scene. Sometimes that evidence was helpful...and sometimes it wasn't. But as we learned more about human biology, we also learned more ways to decipher crime scenes. Like in the early 1900s, when we learned that people have different types of blood — A, B, AB, or O.

Deboki: Someone’s blood type is based on the antigens, or proteins, that coat the outside of their red blood cells and the antibodies in their blood plasma — the liquid that our blood cells float in. Knowing a person’s blood type is massively important if they need a blood transfusion. You can’t give type B to a person who has type A blood because it can cause a serious immune reaction that can be fatal. 

So knowing people have different blood types and being able to test for them was an incredible medical advancement. It was also a major win for forensics, because it allowed investigators to home in on, or weed out, suspects. But because there are only four blood types it can really only tell you so much.

Sam: But in the 1960s and 70s, molecular biology took off. Scientists developed different techniques to chop up, separate, and sequence bits of DNA. In the early 1980s, UK scientist Alec Jeffreys and his colleagues invented the first DNA profiling technology — a technique called restriction fragment length polymorphism or RFLP. 

Throughout our DNA, there are specific regions that have nucleotide sequences that repeat, and the number of repeats can vary from one person to the next. That’s what RFLP can detect.

Deboki: Here’s how it generally works: DNA is isolated from a sample of blood, saliva, semen, or other biological material left at a crime scene. Proteins called restriction enzymes are then added to the tube of DNA, and cut up the DNA at specific locations. 

Let’s say the restriction enzymes cut at the end of the sequence ATCG. Maybe the DNA sample left at the crime scene only has that sequence repeating twice — ATCGATCG — but the DNA of a suspect has it repeating 4 times. It’s very clear that the DNA at the crime scene does not match the suspect. 

But let’s say a suspect has it repeating twice — the same as the sample. It doesn’t tell you for certain that the suspect did it, but they can’t be ruled out either. In practice, you need to analyze a bunch of DNA fragments with known repeats to draw a reliable conclusion.

Sam: RFLP DNA profiling was first used in 1986 in the UK. In the United States it was used the following year to convict serial rapist Tommy Lee Andrews in Florida. DNA samples of semen retrieved from the crime scene matched blood drawn from Andrews. But one of the most famous early uses of DNA profiling that helped cement its importance as a forensic tool in this country was the case of Timothy Wilson Spencer, better known as the Southside Strangler. 

Spencer was convicted of raping and strangling four women in Virginia over the course of eleven weeks in 1987. None of the victims survived but DNA in semen from the crime scenes could all be linked to Spencer. On April 28th, 1994, Spencer was put to death in Virginia's electric chair — the first person executed in the United States for a conviction based on DNA evidence.

Deboki: So RFLP analysis was a huge step forward for the field, but it takes a lot of time and requires spit or blood or other biological material the size of a quarter, just so you have enough DNA. 

That all changed with the development of PCR, or polymerase chain reaction. Developed in 1983 by the chemist Kary Mullis, PCR is a technique that makes tons of copies of a specific region of DNA, meaning you can analyze much, much smaller amounts of starting DNA…like invisible to the human eye. Mullis was awarded the Nobel Prize in 1993 for developing PCR, and for good reason. 

It’s an essential technique that I think of as pretty much the foundation of modern molecular biology. Even if you’ve never done a biology experiment, you've probably heard of PCR because it’s used in the more sensitive COVID-19 tests, to detect small amounts of genetic material from the SARS-CoV-2 virus. 

Sam: And in the history of forensic DNA evidence, PCR made it possible to analyze invisible amounts of forensic material. Less than a decade after forensic DNA evidence was first used in the courtroom, PCR allowed for the rise of a new, more sensitive technique called short tandem repeat or STR analysis. 

STR is very similar in concept to RFLP, but it doesn’t require chopping up DNA and it uses PCR, which, remember, means you can start with a teeny amount of DNA as opposed to, say, a drop of blood the size of a quarter. 

Even today, the FBI uses STR as the DNA analysis standard. And I should also just mention that RFLP and STR are not the only forensic DNA techniques out there, but STR is still often the most relevant. 

Cynthia Cale: So when we transitioned to looking at the STRs using the polymerase chain reaction, we didn't realize how sensitive that technology was. So we still kind of focused on those high molecular weight biological materials. So we were still doing blood, semen, saliva and not really doing any kind of the swabbing of a surface of an object at that point. 

Sam: That’s forensic DNA expert Cynthia Cale, who has over 20 years of experience at both public and private forensic laboratories and currently works as a DNA consultant at the company DNA Mavens, which she started with two other forensic scientists.

Cynthia Cale: It wasn't until about maybe the late nineties that literature started coming out saying, hey, I think we could generate DNA profiles from swabbing the surface of an object that somebody may have held and try to determine who that person was. And then after that literature started coming out, we just saw an influx of different items like they were swabbing — door handles, they were swabbing steering wheels, they were swabbing table surfaces. It was just the amount of samples increased exponentially just because we were able to get DNA profiles off of those surfaces.

Sam: Those minuscule amounts of DNA that Cynthia’s talking about are trace DNA, sometimes called touch DNA.

Cynthia Cale: I like to refer to it as trace DNA. I know typically out in the field, a lot of people call it touch or handlers or wearers, but we need to be very careful about the language that we use because we don't want to imply an activity that we don't know actually happened.

Cynthia Cale: If I shake somebody's hand, I could transfer my DNA to their hand and that's a direct transfer event. But then when they go and touch an object and transfer my DNA to that object without me ever touching it, that's an indirect transfer event or secondary transfer.

Meghan Ramsey: You can also imagine situations where through movement DNA can become aerosolized and deposit on surfaces. 

Deboki: That’s Meghan Ramsey, a biologist at MIT Lincoln Laboratory, a federally funded research and development center in Lexington, Massachusetts focused on developing technologies to meet national security needs.

Meghan Ramsey: And so when thinking about sampling these deposits, they're not visible. So you're swabbing or collecting a sample from a doorknob or a keyboard or some surface that's a high touch surface where you think there's a high likelihood that a sample might be present. It's very different than sampling a bloodstain or a blood spatter, which can more clearly be linked to a potential crime that might've occurred. It's much harder to say with confidence how a DNA sample on a surface may have arrived at that point.

Deboki: Every time you touch something, there’s a chance you leave behind DNA, and the amount can vary depending on the material touched and environment, but also the person. Everyone sheds at least some DNA, but people who slough off more DNA are often referred to as “shedders,” leaving it behind on surfaces they’ve touched and spaces they’ve hung out in. There’s also the question of how long that DNA can stick around. 

Natalie Damaso: How long is it going to stay in that environment? And so there's a lot of studies also talking about the differences between the surfaces, the different environments and so on. 

Deboki: That’s Natalie Damaso, who is also a biologist at MIT Lincoln Laboratory and one of Meghan Ramsey’s colleagues. 

Natalie Damaso: And we do have a lot of effective collection methods and extraction methods, but as you go through the DNA analysis process from collection to extraction to analysis, all of those processes lead to some variability as well and interpretation.

Meghan Ramsey: I think when you are going to collect a sample and perhaps it's a crime scene, there's a reason you're there collecting a sample: you want to be able to interpret what that sample means. And so all of those factors that Natalie just brought up really point at the complexity of doing that for trace DNA. So the fact that the amount of DNA that might be left behind is variable based on what that person was doing, is variable person to person, isn't visible. So it's hard to logically draw a conclusion for how it may have gotten there. 

It could also be a mixture, representing a sample from multiple people, which isn’t hard to imagine if it’s some common surface. And then basic questions about how the stability of that DNA changes over time. So how long was it there? How long would you expect to have found it there? So all of those challenges really are central to the question of using trace or touch DNA.

Deboki: Cynthia, like Meghan and Natalie, told us that trace DNA analysis is complex, and so it needs to always, always, always be taken in context.

Cynthia Cale: I’ve always been a proponent for the DNA analysis process. The end result is the end result. It's a great investigative lead, but there are limitations to the testing that we can do. We can tell you possibly who's a contributor to that DNA profile, but how or when that DNA came to be on that object is up to speculation basically. So the sensitivity is great in terms of if you're dealing with a sexual assault and you have minute amounts of male DNA, being able to detect small amounts of that male DNA, that's great. That helps that investigation and you are able to make some kind of investigative lead, but the DNA results shouldn't be taken in isolation. They need to be taken just one piece of the puzzle and everything needs to be looked at as a whole and not just focus on the DNA and say, ‘oh, we have DNA results and we've got to open and shut case.’ Not necessarily.

Sam: So here’s where we get back to Lukis Anderson’s 2012 arrest. Even though his DNA had been found on Raveesh Kumra’s nails, Anderson had been taken to the hospital hours before his murder, after a store owner, seeing Anderson outside and intoxicated, called the paramedics.

As it turned out, the same ambulance and paramedics that brought Anderson to the hospital responded to the homicide a few hours later and treated Kumra with the same equipment, including a pulsometer — a device used to measure a person’s pulse that’s placed on their finger.

Anderson never came in contact with Kumra. And, after months of sitting in prison awaiting a trial, he was cleared of the crime. Three men were later convicted of the murder.

Deboki: And unfortunately Lukis Anderson’s case is not the only one. Another case listeners might remember is that of Amanda Knox, an American exchange student who was wrongfully convicted of murdering fellow exchange student and roommate Meredith Kercher in 2007. Knox spent almost four years in an Italian prison. 

Much of her conviction was based on the trace amounts of both Knox’s and Kercher’s DNA found on a knife recovered from Knox’s boyfriend’s apartment. Trace DNA from Knox’s boyfriend was also found on Kercher’s bra strap. 

After hearing about all of the ways that trace DNA can end up on things, it’s probably very obvious that it could have made its way onto a knife or bra strap without a person placing it there directly. In 2015, the Italian Supreme Court acquitted Knox, partly due to evidence contamination and a misunderstanding of how DNA transfers.

Sam with Cynthia Cale: Just as a bystander, I think DNA evidence for so long has been more or less considered infallible, and I think that depending on the amount of sample that is present at a location, it could be to some degree. If you have a ton of blood from a person and you can identify ‘this is the person,’ it seems pretty cut and dry. But if you're talking about trace DNA it's more complicated than that. 

Cynthia Cale: Right.

Sam with Cynthia Cale: So I’m wondering, where do we go from here? You did talk about how we have to think about trace DNA being part of the picture. It's not this cut and dry thing typically, but are there other things that you want listeners to consider or think about for the future in terms of how things may change?

Cynthia Cale: So there is a push in the field to do what's called an activity level assessment where they're actually taking the DNA profile and trying to decide which activity is more likely than another. That's very difficult to do because, while sometimes the person who maybe handled the object presents as the major contributor to a profile, that's not always the case. So the last person to touch it might not be the major contributor or might not show up at all. You can touch something and not leave your DNA behind. And so if you have other people's DNA on your hands and you're transferring that into the mix, that makes it even more difficult. Really, the only way to do a true activity level assessment is to actually set up the experiments and say, okay, I'm going to have, this is scenario one where this person handles this object and places it here.

And the second scenario is, okay, these two shake hands and the other person puts the object here and then see what kind of DNA profiles you get from those two activities. So that's the push that I'm seeing right now. It kind of bothers me because I know all the factors that influence transfer, and it's very hard to predict how that's going to present itself in a DNA profile. So I worry about how that’s going to be applied or misapplied. 

Sam with Cynthia Cale: Right. So what are some of those variables? Because I do know that some people shed their skin much more than other people, so they're more likely to transfer their DNA…

Cynthia Cale: Yeah, shedder status is one, the type of biological material that's being transferred, obviously based on the literature, body fluids, like your blood semen, saliva are going to transfer farther than skin cells. Wet body fluids you're going to transfer farther than dry body fluids, the type of contact, so if it's just a brief kind of passive contact versus if you're rubbing two objects together, that's going to actually increase the rate of transfer. Environmental factors are going to come into play as well as the type of materials the DNA is deposited on. 

Sometimes I'm watching body cam footage of police officers or searching a vehicle or something like that, and they're moving things around. If you shake out something over a surface, you can dislodge that DNA from that material, and it can be on that surface without either of those two surfaces coming into contact with each other. 

Sam with Cynthia Cale: What would be issue with, like you said, sometimes you'll see on body cam footage, someone shaking out a shirt in a car?

Cynthia Cale: Well, if they happen to find an object of interest, like a firearm, and they had been moving clothing around and shaking it out, there's a potential that DNA from whatever piece of clothing could get dislodged and placed on that surface. And along with, if they're handling it with a pair of gloves and then they go pick up that firearm, they could potentially transfer DNA from that piece of fabric to that firearm inadvertently.

If you happen to be a police officer and you're out there working a scene, change your gloves in between each contact because those gloves can pick up that DNA and transfer DNA from one object to another.

Deboki: In 2018, the Forensic Technology Working Group at the National Institute of Justice called for quote “comprehensive, systematic, well controlled studies that provide foundational knowledge and practical data about ‘touch evidence’ persistence in the real world.”  

Responding to that call, Meghan and Natalie worked on a project looking at the stability of trace DNA in complex real world environments and began quantifying how long touch DNA would persist on certain surfaces under specific conditions. 

Meghan Ramsey: So we generated touch DNA samples, we exposed them to very controlled environmental conditions, and we tried to understand how does the quantity of DNA change, how does the intactness of the DNA change, how does the ability to obtain a DNA profile from those samples change over time? So then we can take those results and help provide recommendations or inform best practices in terms of if you find a sample and you think it's been in a hot, humid environment in the sun for a week, what does that mean for your likelihood of being able to use that sample or gain relevant information out of it? 

Sam: When I started researching this episode, I can truly say I was a little concerned about what I’d learn and if I’d leave feeling disheartened about this incredible technology, but I actually feel a lot better. Is trace DNA legit? Yes. Can it be taken at face value without context and other compelling evidence? No. And it makes me hopeful knowing that this conversation is happening, knowing that we’re putting this episode out into the world for people to hear and better understand that nuance, and knowing that people like Cynthia are working as consultants, so that we can prevent what happened to Lukis Anderson.

Cynthia Cale: I used to love working in the lab, but I find consulting much more rewarding because I can go in and look at the DNA case files and look at body cam footage, look at previous testimonies, and kind of pinpoint where we have weaknesses within our system, and hopefully help promote and get the word out that the indirect transfer of DNA can happen and that we shouldn't disregard it. And that we need to be careful about the language that we use, particularly on the stand, because people's lives are at stake. Not only the victim's lives, but the defendant. And if you mislead the jury into thinking that the only way that a person's DNA can be on an object is through direct transfer or direct contact with that object, you're not giving them the full story and not providing them with the limitations of our testing.

Sam: For my tiny show and tell, I want to talk about something that actually initially inspired this episode but ultimately we didn't cover it all, because the episode ended up going in a totally different direction. In May of this year, a couple studies related to trace DNA came out that really caught my eye. One was about trace DNA in the environment, trace DNA, that's often found in water, soil, air. It's often called environmental DNA or eDNA and it can be really useful for learning about plant and animal health and biodiversity, and even help in identifying potential pathogens in the environment. But it turns out that sometimes there is enough EDNA from humans in an environment that you can actually determine a person's sex and ancestry which, of course, raises some red flags, brings up some ethical questions about if it's okay to be just sequencing strangers' DNA just because they passed by a river or we're in some muddy area or something and we're shedding their DNA.

The other study was about trace DNA being found in microbiome testing, which is fascinating and makes sense, but I hadn't thought about. For decades, researchers have been analyzing DNA in poop, really, let's just say it. They've been analyzing a lot of DNA in poop to determine which microbes and how many of those microbes are present. The general thought was that degraded human DNA that makes it into stool, so essentially the DNA that's not from those microbes, it wouldn't be enough to really tell you much about the person. Well, it turns out that that DNA is not only enough to identify the stool donor's sex and ancestry but also potential disease risks. And, if it's then linked to other databases, it's possible to figure out exactly who the person is.

I'm not bringing this up to freak people out but I think it is really interesting and important that people are identifying these potential ethical issues. Both groups are actually calling for safeguards to really prevent the misuse of this DNA, what you would call human genomic bycatch, which is really the perfect term for it because you're not trying to pick it up, but you are. And then, the question is, is it okay that you are? Is it okay to still analyze it? And so, I think it was really more like a mental exercise to go through after looking at these papers but I thought it was fascinating. It got me on my trace DNA kick. That's why this episode exists. But I was sad that we didn't really cover this because it just felt like it was a little bit too tangential.

But I think it's still really important and important for people to know that this is something that's being considered. Trace DNA is being considered outside of forensics. It's being considered in a lot of different cases, including microbiome stuff and eDNA. 

Deboki: Just the idea that we're just sloughing off DNA like this and that you can really just get this picture of people. But then, yeah, we kind of talk about in the episode, also you can't get the full picture from just the DNA so there's just so many complicated things.

I have so many complicated feelings about stuff like DNA testing, the consumer testing kits, and I still haven't ever done a 23 and me kind of thing partly because I'm so unsure about how I feel about it. I feel like when I hear stuff like this, I'm like, "Yes, I was right," but I still don't really know. Will it ever affect me? I don't know but it's still super ... Just because it doesn't affect me doesn't mean that it's not important to think about because it's going to affect people in general. It's going to affect how we operate. It affects so many different things that happen.

Well, I guess I sort of have ... It's not about trace DNA but it is about studying DNA. There was an article that I picked out for you, Sam. This is from UC Davis. It's actually a description of a research project they did. It is, can golden retrievers live longer? And so, this is about a study on golden retrievers because ... And this is sad but apparently golden retrievers have a 65% chance of dying from cancer, and so researchers wanted to see if they could find just genetically some things. And so, they didn't actually end up looking for genetic factors that would correlate to cancer in the golden retrievers. Instead, what they decided to look at were genetic factors that correlated to a longer life so they studied 300 golden retrievers, which just sounds incredible on its own.

And so, they compared those who were still alive at 14 versus those who had died younger, who had died before they were 12. They compared the genes and the variants in them and they found that those dogs that had a variance of the gene, HER4, which is also known as ERBB4, this is a part of a family of growth factors. The dogs who had this particular variant, they were more likely to have a longer life so they tended to live, on average, 13.5 years versus dogs without the gene tended to live, on average, 11.6 years so that's a long time that you want to spend with your pet. This is just a preliminary thing that the researchers were doing, and so there's more work to be done on what the gene variant is doing. They also noted that dogs get a lot of the same cancers that we do so there's potentially relevance for human cancers as well.

Sam: That's really cool. I also love how they're framing it in a, what is it that these dogs have that allow them to live longer? I mean, I think both are important for people to understand what mutations might put a dog or a person at a greater risk for a certain cancer so they can be on the lookout, so that they can detect it early. I think all of that is so beneficial but sometimes it's really hard to find a mutation or even a group of mutations. And so, looking at what dogs have that are positive versus things that are negative is, I guess, just another way to approach the problem.

Deboki: Yeah, definitely because cancer's so complicated. Like you're saying you can have a complicated set of factors that drive the cancer but could we find something, maybe something a little more straightforward that correlates to survival?

Sam: Yeah. Thanks Deboki, I love that.

Deboki: Thanks for tuning in to this week’s episode of Tiny Matters, a production of the American Chemical Society. This week’s script was written by Sam, who is also our executive producer, and was edited by me and by Michael David. It was fact-checked by Michelle Boucher. The Tiny Matters theme and episode sound design are by Michael Simonelli and the Charts & Leisure team. 

Sam: Thanks so much to Cynthia Cale, Natalie Damaso, and Meghan Ramsey. If you have not rated and reviewed Tiny Matters, please do! We’re trying to grow and that really, really helps us. If you want another way to support the show and look really cool drinking your morning cup of coffee, tea, juice, whatever, we have left a link to our Tiny Matters coffee mug. You can find me on social at samjscience.

Deboki: And you can find me at okidokiboki. See you next time.