Home // Speaker Feature // Writing the Books on Forensic DNA: Dr. John Butler
Apr 29 2020
Writing the Books on Forensic DNA: Dr. John Butler
Dr. John Butler has both taught and inspired many in the field of forensic DNA. In this interview, Mirna Ghemrawi, PhD student at Florida International University and former ISHI student ambassador, helps us to get to know John a little better.
She asks him about what led him to become an author, what advice he has for students deciding on a college program, how he envisions emerging technologies will complement DNA sequencing, and much more.
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Mirna: Hi, my name is Mirna, and I am a PhD student at Florida International University. Today, it’s my first time being an interviewer, and I’m so excited, because I’m with Dr. John Butler. The first time, the ISHI crew asked me if I was interested in interviewing anybody, the first thing that came to my mind was Dr. Butler.
The first time that I had an encounter with him was back in 2016, and it was when I first got introduced to forensic DNA typing. I had a question about one of the pages of his book. By the way, his books are awesome, and we’re going to talk about it in a minute. Then I emailed him, but I thought, “Who am I for him to respond to my email asking for clarification?” So, I forgot about it, and just two weeks after that, I got an email back saying, “Hey, sorry, I was at a conference, but this is my explanation.” I was so happy, and was like, “Oh my gosh, he responded, and it was just… For me, it was actually my first time sending an email for an author and getting a reply, so I was like, “Ok, that’s awesome.”
So, with no further ado, I’m so glad that you accepted my invitation for an interview with you.
Mirna: I think in the forensic field, you are a leader in forensic DNA typing, and I am one of the big fans of your books and your knowledge. I’ve learned a lot. I’m just curious to know what was your trigger to actually write those books that a lot of students and practitioners are actually using?
John: So I grew up in a home with books. My father and my mother were both teachers. My dad was a college professor, and he’s written about 12 books on farrier science. On how to make horse shoes and put them on horse feet. And so, since I was a kid, my dad wrote books, and I was supposed to write books eventually. I didn’t know what the book was going to be on. I like history quite a bit, but I’ve always loved science. So, I had four years of biology in high school, so I got interested in forensic science, and I learned about that as a profession. This was before CSI became popular, I think. And then, just started learning about DNA and started working in it, and started realizing that there’s lots of information that I’ve gathered as part of my PhD dissertation. So I built a website. That was the STRbase website. And then I wanted to write those things down and make them available and kind of teach people step by step how to do the process. So those were the first books. It’s been 20 years since those books first started, and I’ve done 5 so far.
Mirna: That’s awesome. I can say when I read through them, the word flow or the way you wrote them is so easy to grasp and so easy to understand. You go to the table of contents, and you need specific information, you just find it like that. I just find everything I need in those books.
John: There’s a reason for that. It’s call pedagogy – the process of thinking about how to teach something, and the process of helping people learn. And so, I spent a lot of time with a white board thinking about each step of the process and how to design the teaching for that. So, each chapter has been thought through many, many times, and re-adjusting things to the right order. Then, my wife, who’s not a scientist reads what I write, and if she can’t understand it, then I have to re-write it. She helps make it understandable, so you can thank her for.
Mirna: Oh definitely a big thanks to her as well. That’s really so inspiring, and I’m sure that’s not only opinion, but also a lot of other people who are using your books have that exact same, if not more feeling about your books.
So, as a student, my interview might focus a little bit about some advice for some new people in the field. New scientists are really interested in forensics. Based on your experience, if we give an example about the United States or other countries there are programs (specifically we are talking about graduate level) that offer either degrees just as forensic science or others that are STEM, like biology or chemistry or biochemistry, but then have forensics as a track. Do you see any difference between the two, or one that is better than the other?
John: It depends on two things. One is the professor and the next is the curriculum. So, who’s teaching it, and what’s being taught. So, there is three PhD programs right now at FIU, one at Sam Houston State, and one at West Virginia University in forensic science, and you can get biology tracks or toxicology tracks and stuff. But, I think in general, it’s typically if you get a degree in analytical chemistry or molecular biology, you’re probably better off right now until those programs are developed further. It depends again on the professor. So, if you have a good professor to work with, and I know you do, because he helped teach me many years ago, that helps, and I think you can be a very effective program in any school.
Mirna: That’s interesting. So, to be on the same flow here, we’re talking about PhD programs, but there are also countries that are not as developed as the United States, and a lot of them are now entering the DNA field. If we compare what we are doing here of Rapid DNA, genealogy, it’s way… Microbiome, we’ll talk about that in a little bit. But, what advice can you give them to accelerate, maybe, and to be on the same level as other labs?
John: I think part of it is what question you’re trying to answer. So, to address sexual assault cases or homicides, to focus on the simple things to begin with, and not try to think that I need to have all the tools in place like what happens in the United States or the UK or somewhere else, and just realize that it takes a lot of work to get there. So, it’s the small and simple things that will get you to the big things eventually, but I would say focus on getting started and just the process of handling samples, for example, and to be able to extract DNA effectively, and not have to worry about the fanciest equipment to begin with at first, until you can build up the expertise there.
I’ve had the chance to visit almost 30 countries and see labs in many of these countries and see some that are very well funded, and some are not. It’s very dependent on the country and the individual laboratories.
Mirna: That’s interesting. Have you visited Lebanon, or…
John: Not yet.
Mirna: Maybe we’ll invite you when I work there.
John: I’ve corresponded with a number of people from Lebanon, just answering email questions and stuff.
Mirna: As usual, your humbleness and your help for everyone is just…
John: I enjoy helping other people. I try to live up to my name. You know, I’m a Butler, so I have to serve other people.
Mirna: That’s a good one! So, now a little bit into some technical science questions. Can you envision a system like the beads cleanup or the magnetic beads that can substitute or delete the need of quantifying DNA for DNA typing?
John: It depends on the type of sample, because if you have something where you’d expect to have lots of bacterial DNA, and if the beads could tell the difference between human DNA and bacterial DNA, that would be fine, just hybridonize to the human DNA, but usually it’s capturing DNA in general, so you’re going to have a hard time separating whether it’s plant DNA or microbial DNA away from the human DNA. For some samples, I think it could be quite effective, just doing a bead-based quantitation.
Mirna: When you’re not expecting bacteria and a specific type of sample.
John: Yep, it would depend a lot on the sample type.
Mirna: Gotcha. That’s interesting. So, we’ve seen in the last two days, at the ISHI conference, that a lot of focus nowadays in forensic DNA is going towards other subdivisions than DNA typing, such as DNA phenotyping, microbiome, proteomics. I would like to know your opinion about each of those three, mainly, and how far they are from being admissible or used in actual casework?
John: Again, it depends on the questions being asked and the types of samples being processed. There may be some situations where the microbiome can be very useful and I think it’ll serve more as a supplemental to the core work that’s being done with the STR typing and so on, because of the databases. Everything comes back to how do you match data to somebody else or connect to other potential people, and that’s where databases come in. So, if you don’t already have something in the database, it can provide an investigative lead and assist in some things, but probably not going to provide the full solution. Nothing’s going to provide a full solution. So, whether it’s the proteomics or the phenomics, where you look at the phenotype of something, or the microbiomics as you’re always going to have some… It’ll help in some aspects, but it’s not going to provide the complete solution to anything.
Mirna: Because, again, it’s not confirmatory as the STRs for example, to compare and use some statistics, but there might be, as you say, some investigative leads.
John: Correct. And that’s what the genealogy is doing. It’s providing a new avenue to access samples that you couldn’t or people that you could access previously. So that’s where the microbiome can do the same kind of thing. You can answer a question from a different angle, and that can be very useful.
Mirna: Yeah, that’s very interesting. That’s a question that probably backs up what you were saying. Do you think that proteomics or any other discipline might just replace DNA typing at some point in the future?
John: Again, you have to have something to compare it to. Because in forensics, there’s always a Q versus a K. A question and a known. And if you don’t have knowns to compare to… So, it takes time to build that database of knowns, if you will to be able to make a comparison. So, as proteomics becomes more prevalent, and that could certainly happen as more research occurs there and gets implemented, you still have the challenge of what are you going to compare it to, and that will take time to build it up. So, I think time will tell.
Mirna: Yeah, probably also financially. Whether they can build this big database like a CODIS.
John: Right. So, you have the expense of the instrument and research often you don’t think about the practicality. It’s just can we do this? So, academic research has a different purpose, which is can we publish a paper? Can we learn something new from this? Can we extend the field? But, at the end of the day, in the forensic lab, we have to make it a practical solution. What can we do to actually help solve this case?
Mirna: That’s very critical, yes, thinking business wise or how you can implement it. Is it practical to implement it? That’s true. In the past 10-20 years, what have you seen that has been the biggest breakthrough. After PCR and that breakthrough, but in the field of forensic DNA typing.
John: I’d say the biggest breakthrough has been standardization. The fact that you have core loci and that’s what enables then the database to be built and everything else to come around after that. So, it’s not really innovation in that way, but it enables everything else. There’s always cool new things, like new software or new tools or new ways to sequence the DNA. Those are wonderful and they extend the capability, but at the end of the day, you can help solve more crimes. You can connect more things, and I think that’s going to lead to having lots of knowns to compare to is what that enables to happen.
Mirna: And I can say that the work that’s been done for creating and maintaining those standards through NIST and other organizations is just very important. Providing labs who are trying to do validation and some controls and some known samples so you can verify and do accreditation for those labs, as you mentioned, is very critical point. Because, you cannot trust any results if you’re not sure that they’re doing the right…
John: Yep, you need data that supports the conclusions. That’s the bottom line.
Mirna: Exactly, exactly. And, what is the strangest profile that you’ve ever seen, because I’m pretty sure that you’ve seen so many DNA profiles.
John: Well, working with the STRbase website, we take in duplicate alleles, tri-allelic patterns and so on. Those are fascinating to see, and those are chimeric sometimes. Seeing chimeric profiles where you’ll see mixtures from two different individuals where they’re part of one individual. That’s fairly rare, but those do occur. Probably the most interesting one was we saw a very large… It was a 29 allele at the D5S818 locus and it was an insertion. After the sequence, there was a big insertion that occurred, so it was just a very unusual insertion that occurred right next to the repeat, so the primers made it very large. So, just 29 alleles way outside the range you would expect for that locus. So, that would be one of the more unusual ones I would say.
Mirna: That’s interesting. You sequenced the sample to be able to know if there was this…
John: Yeah, it was a 48 base pair insertion that occurred. So, Margaret Kline at NIST sequenced the sample and found it. So, it was very interesting to see. So, people for a while would send us samples to sequence, and you’d kind of see these odd ball situations. What’s going on. Sometimes you see a primer binding site mutation. Those are fascinating to see. Why doesn’t the primer bind properly, because the sequence has changed compared to the normal templates.
Mirna: That’s interesting. Yeah, I can say, actually, during my Masters, I did collect some Lebonese samples, and we did to the conventional STR on them with NIST with Dr. Pete and Dr. Sara, and we did see tri-alleles in autosomal STRs and bi-alleles in one YSTRs as well. And not conventional like in the database. They were not found yet or no one has observed. So yeah, those are unique and interest to sequence, I think.
John: And it’s fun to be able to share those with others. So when people would submit them to STRbase and we’d put them up there, there’s hundreds of those available now, so having a catalogue of that so anybody could go look and say, “Oh, someone else has seen that same duplication, or that tri-allelelic pattern, or whatever.”
Mirna: I think, is it true that nowadays if they want to do compute the forensic parameters they remove that from the…
John: Typically that’s done, because it’s not… We don’t understand the mechanisms that by which they’re really copy number variants, so an extra number of the section of the DNA gets inserted in there, but how often does that happen and how do you compute that from a statistical standpoint? Usually it’s just left out of the calculations.
Mirna: But that gives more uniqueness for the profile. So as a forensic application I think it’s more unique. We can catch more criminals that way.
John: Well they don’t occur all the time.
Mirna: Of course, that’s true. So, now a fun question. Can you juggle and do rope tricks at the same time?
John: So, I learned how to spin ropes and stuff. I’ve shown that at meetings in the past, and I also learned how to juggle when I was in college and stuff, but I don’t normally do those at the same time, so I’m not going to try to demonstrate that here today.
Mirna: Maybe some practice and then…
John: Yeah, maybe. Maybe it’s something I’ll try someday.
Mirna: At another ISHI conference maybe.
John: There ya go. It’s fun just to attempt those things sometimes. People don’t expect that from me, I think. So, to spin a rope or to juggle.
Mirna: Wow, I mean that’s not easy.
John: It just takes some practice, that’s all.
Mirna: I barely know how to play ping pong, but other than that, I don’t know. Awesome! So, we know that you are going to be the president for ISFG and it’s going to be held in Washington D.C.
John: Yes, in two years.
Mirna: That’s exciting and I’m looking forward for that one. Are you planning as president and in D.C. to go to the White House?
John: I don’t know if that’ll happen. In terms of for me personally, I’ve been to the White House before, but not in this capacity, I probably wouldn’t. But, the president of ISFG will have a chance to welcome people to come to the United States, which will be exciting. There’s 84 countries that are a part of ISFG right now, so that’s exciting. My goal is to learn how to say thank you in many of their languages. I think that’ll be kind of fun to greet people and to make those connections. But to me, I think the neatest thing is ISFG is a chance for the scientific community to come together, and I’m excited to see people come to the United States, and also for the United States scientists who don’t normally get to go overseas to be able to see some great science, so I think it’ll be fun to see that.
Mirna: That’s going to be really interesting. I can teach you the Lebanese way of saying that. I say Lebanese and not Arabic, because each of the dialects are different. I will be definitely looking forward to this meeting as well and I’m pretty sure it’s going to be just perfect.
I think I would sit here for hours just speaking with you, because every time I talk to you I learn a lot, but I think I would like to make it a little bit shorter this time. Last funny question, I think. If aliens exist, and they come here, do you think they would have the same DNA that we do, and if not, what kind of DNA typing would or what kind of method would we need to identify them?
John: Well first, you’d have to swab them and get a DNA profile from them. But, my philosophy is if the primer doesn’t bind, a DNA profile you will not find. So, there you go. It’ll depend on whether or not the primers will bind to the sequence and so, we wouldn’t know until we were able to sequence them or at least attempt it. As with anything in science, give it a try and see what happens.
Mirna: Exactly, just do an experiment and see.
John: And if it fails, then you have a species not specific to them, so then you know you have a null allele, because the primer’s not going to bind properly.
Mirna: Yeah, we won’t speak sciency. I really appreciate it. I cannot find the words to say thank you, I think. I would say thank you in Arabic, and I look forward to meeting you again and learning things, and keep this connection. I really appreciate everything, and I don’t know if you want to say anything?
John: I think one of the things you learn is asking a question is critical to learning, so I would say just like you did when you first contacted me and asked about the different types of errors that were being reported in the appendix in that book, and did I classify them correctly, and questioning that is a wonderful thing. So, that’s what a scientist does is ask questions, so if you’re afraid to ask questions, then you’re not able to learn further, so keep asking questions, and don’t feel afraid to ever ask me a question. I’m happy to try and help.
Mirna: Thank you, I really appreciate it. That’s for sure very important advice for new researchers and new scientists in this field and other fields as well. As you said, in the beginning, I will tell you that I was very afraid to ask.
John: Sure, people get intimidated, but I’m just a regular person, so ask a question.
Mirna: Yeah, like you said no question is dumb. You need to learn and understand. Thank you so much for your time and thank you for watching.
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