Genes for all
Genes, genomes and genetic technology are playing increasingly important parts in our lives, industries, food and healthcare, and at a point in the not-too-distant future we're probably going to have to grapple with at least some of the contents of our DNA. But is the public really prepared to look inside its genes? Plus, the company aiming to bring molecular biology labs for all, and our gene of the month is crunchy on the outside. This is the Naked Genetics podcast for June 2016 with me, Dr Kat Arney, brought to you in association with The Genetics Society, online at genetics. org. uk.
In this episode
01:16 - Robert Chapman - Public gene knowledge
Robert Chapman - Public gene knowledge
with Robert Chapman, Goldsmiths University of London
Kat - As technology and scientific research gather pace and genomic sequencing procedures become cheaper, having a good understanding of genetics will become more and more important to us all. From getting a genetic test at the GPs surgery to choosing between genetically modified food or its unaltered but selectively bred counterpart or even streaming children in school based on their genetic ability, genes are playing an increasingly prominent role in science and society. But what does the public actually know about our genes and how they work? That's the question that intrigued PhD student Robert Chapman from Goldsmiths, University of London.
Robert - There's been so much development in the area of genetics research and we're not really as a society in a place to debate those developments very effectively. So what I'm trying to workout is why we're not in that place and what we can do to help as a society develop the tools to debate these issues that are going to become more and more important as this research develops.
Kat - I've just written a book that's aimed at the public to help them understand genetics. And I think, "Yeah, yeah! Everyone should just buy my book." But I guess it's not quite as simple as that. How do we find out what people know? I guess that must be the starting point.
Robert - It absolutely is and the first thing we're doing is piloting a research study to look at exactly that question - what people know, what they don't know, and what they think they know. We're hoping to find out also if there's any predictors of areas of knowledge or concern. So for example, to people from certain ethnic groups have different concerns to other groups - are there age differences, are there international differences, is the way that genetics is taught at school a predictor of concerns and things like that. So, we're really trying to do an empirical quantitative study, I believe for the first time, in the broad area of genetics. There has been research in this area, focusing on medical genetics, but not generally the issues that they apply across society so that's the new thing hopefully.
Kat - So everything from pea plants to pandas.
Robert - Exactly, yeah. I couldn't say it better.
Kat - So tell me a bit more about the study. What are you actually doing? What are you asking? Who are you asking?
Robert - So I can't give too much away because we've just piloted it and I'm hoping that some or all of your readers will be interested enough to engage with the study when it is published. But we're looking at what people know about genetics so there are general knowledge questions. We're looking at how they feel about genetics. So do they have concerns for example about genetically modified foods? We're also asking for information about their demographics. So this is very much a first stage. We're hoping to talk to as many people as possible. We're aiming for about 5,000 participants and stratified by profession and country. We're asking people whether they're parents or students so we can really build-up a picture of the demographics of our participants and see if there are any trends that we can spot which might help us target training material information more effectively.
Kat - We've touched on why this is so important but let's dig into that a bit more. Why do the public really need to get to grips with genetics as opposed to any other scientific discipline?
Robert - It's not necessarily as opposed to any other. I think this debate about genetics is at least as important as the debates about climate change. People seem to be very much more informed about those issues for the most part. But what we're learning about genetics, it's providing information that might cause a fundamental shift and how we relate to ourselves and to each other. And so, we are learning what it is to be human and the interactions that make us who we are. If we can then control those interactions or manipulate them - so for example, if we can say this sort of environment is not conducive for this sort of person in the development of reading skills, should we be doing that? So that's why it's important. It fundamentally changes how we relate to ourselves and each other.
Kat - There's been a lot of talk about using genetic tests and things like cancer medicine so you can test someone's tumour and say, "Okay, it's got that gene fault so you need X, Y, Z drug." But you're talking about touching on much more broader social issues - things like, education, lifestyle, upbringing, very much wider issues. These haven't been talked about at all.
Robert - No and that's why it's such a huge project. It's such a huge undertaking and this is just the start of the conversation. It's a huge issue and there are great resources out there from the Sanger Institute, the Wellcome Trust, Nuffield. But most of them focus on biomedical implications or genetic research. What we're hoping to do as part of the Accessible Genetics Consortium which is the consortium I've been part of setting up is look at just improving general genetic literacy so that those issues - but also more general sociological issues can be discussed more usefully.
Kat - This may be an impossible question to answer, but if there was one thing, one concept or one fact that you wanted the public to know about genetics, what would it be?
Robert - It's not a difficult question because I've been thinking about since I was about 15. I think one of the big difficulties is that people consider genetics in quite binary terms. We're taught at school about blue and brown eyes, dominant and recessive alleles, and you will have one or the other. And I clearly remember putting my hand up and asking the teacher, "What about green eyes?" And I was told not to worry as it wouldn't be on the exam.
Kat - I've got green eyes. I always wondered about that.
Robert - So I think if we can work to help people learn a little bit and it's not much more. You don't need to know much more about genetics to understand why that simple Mendelian pattern is only applicable in rare instances. In fact, the principles of Mendelian inheritance work but you've got to remember that this is across multiple genes and those genes have interactions with each other in the environment which is a much bigger issue. But from my mind, one of the fundamental things to address is this idea that there is a gene for A or a gene for B and it's simply not that simple.
Kat - Robert Chapman from Goldsmiths, University of London, and the website for The Accessible Genetic Consortium is http://www.tagc.world/
08:19 - Jon Roberts - From superheroes to genes
Jon Roberts - From superheroes to genes
with Jon Roberts, Wellcome Trust Sanger Institute
Kat - As Robert says, it's vital that we start a public conversation about genes, genomes and genetics. But how? On way, according to a new project launched by the Wellcome Trust Sanger Institute, might be through fictional characters in modern culture, such as the X-Men film franchise. Characters such as Wolverine and Storm have probably done more to increase knowledge of the terms 'mutants' or 'mutation' than any number of biology teachers. Jon Roberts is leading the study.
Jon - So, I was working as a genetic counsellor in Addenbrookes and I was interested in how new genomic technology was sort of going to affect genetic counselling and I wanted to explore how families would communicate not just when they were discussing one gene at a time but how potentially with a whole genome sequence they'll be discussing potentially thousands of genes at a time. So that was the starting point. It was kind of applying idea from genetic counselling. We're looking at how they would impact us in the era of whole genome sequencing.
Kat - Traditionally, people maybe had a family history of a particular disease, they've gone to a genetic counsellor, had a test and said, "Okay, yes. It's this breast cancer gene that you've got" rather than looking at the entire genome and going, "Oh! What's in there?"
Jon - Yes. So, I think that was the point at which I was coming at it is that often, when people have genetic counselling, they're coming with a specific question. Often a lot of times, it can be given to answering that question, kind of going through the ins and outs of a particular gene. Often their family will know about that as well whilst with the genome sequence, there's lots of different questions that could be asked. Often, people might not be familiar with the kind of questions or the answers they might get from a genome sequence. So, it felt as if there was potentially new questions that were going to arise from that, and new ways that families would be sort of interacting with genetic knowledge.
Kat - And are we talking about in-depth genome sequencing, or the kind of after shelf, sort of the 23andMe type kits that people can just buy and do?
Jon - A bit of everything really. I'm kind of interested in both on a kind of a narrow and a broad sense. So, I think I'm interested in what happens when you have a genome sequence or you have a direct to consumer test. And you find out that you've got something very specific. But I'm also kind of interested on the broad sense. What happens if you just go and have a genome test just to find out about your ancestry, kind of how that's going to get talked about in the family, and how that might spark an interest in genetics.
Kat - What are you actually investigating, what are some of the tools that you're using?
Jon - Particularly interested in how we can use people's own interests and their skills and their knowledge to spark interest in genetics. So broadly, it can be thought of as bottom up as opposed to kind of top down. During a particular tour from sociology called funds of knowledge that was developed primarily in the States with disadvantaged families in educational settings that looks to bring children and families' own skills and competencies into the classroom to help with learning experiences.
Kat - As an example, if a family really, really likes football, you could try and steer it around football to help them learn something.
Jon - Exactly. So, it's been showing us quite a good way of helping people engage in topics where they might have been put off before when they sort of think it's not for them. So, there's an issue in science as well with people not thinking science is for them or sort of not thinking they're "sciencey" people. I kind of wanted to make sure that I bypassed and try to engage people who otherwise might be off put by reading something about genetics or genomics. They might see that and think "that's not for me!" whereas I wanted to make sure that I was kind of reaching a wider audience. My starting point is finding out what people are interested in, what they're good at, what they think they're good at, and using that as springboard to engage people with genetics.
Kat - One of the common ways that we hear about genetics is through things like films and popular culture. I'm thinking of the mutants in the X Men or a film like Gattaca or something like that. Is that a really good in road to helping people talk about genes?
Jon - I think it's an excellent way of getting people interested on it. I think it's a huge source of people's language and familiarity with genetics. I think it's something that shouldn't be kind of looked down on but really respected. I think some people worry that the science in films is an accurate or kind of overblown. But I think actually, a lot of new research that looked at how people engage with films recognise the people who know that and they're able to kind of recognise that the science is a bit silly. But it's also they're major in to knowing about science. So an example might be the word 'mutation'. When Stanley created the X Men, he wanted to call it the mutants but it was voted down as a name because nobody understands what a mutation or a mutant is. Yet now, it's a common word used and I think people have a rough idea of what it means. I think that popularisation has come about not necessarily through high end public engagement with science, but through popular culture, films, TVs and comics.
Kat - Sadly, for my friends who've had 23andMe test done, it doesn't tell them that they've got X-ray vision.
Jon - Unfortunately, not. But that would be nice. A friend visited my work at the genome campus in south of Cambridge and a friend visited it rather hoping he's going to get bitten by a spider and become Spiderman, but that wasn't the case. But I think it is often the way people - you talk about films, you talk about books, you talk about comics, and it gets people interested. It gets people talking. It gets their imaginations going and that's what I really want to build on.
Kat - So, tell me a bit more about the specifics of the project. What is this research project actually going to be doing?
Jon - It's going to be split into two parts. The first part is an online survey, sort of a broad survey that looks at people's familiarity with genetics in different contexts. So, how many people have seen it in different films, different books and also, sort of aims to get an idea of kind of broadly speaking, what people's interests are and if there's any overlap with things that would be particularly kind of helpful for thinking about public engagement with genetics. After I've done the survey, I'm going to do some sort of family interviews and some focus groups that are going to look at how people talk about inheritance, how they talk about films, how they talk about what they're interested in, and just sort of try and see that knowledge in context because I'm interested partly in what people know but also, how people use that knowledge in context. The reason for that is knowing about genetics I think is going to be quite important for empowering people and empowering families. And if you're going to empower people, you need to know not just what they know but actually, how confident are they to use that knowledge in different contexts.
Kat - And do you think that one day, we'll see a superhero film that has a genetic counsellor in it.
Jon - I hope so. There's a film called Still Alice that deals with inheritance in quite a sensitive but I would love to see genetic counselling in film and TV and really, kind of get it into the mainstream because I think a lot of the time, people only know about it if they've had genetic counselling. So, I'd love to see, I think a superhero film would be interesting. I think one of the big ways it's going to get into popular culture is through soaps. So there was a big storyline of, I think it was BRCA, that came out in EastEnders. I think that's a really good way of reaching lots of people and getting ideas of genetic counselling, what genetic counselling is into the wider discourse. It's through things like soaps.
Kat - Jon Roberts from the Wellcome Trust Sanger Institute, and you can find out more and even take part in his research project at http://www.characterofdna.com
16:42 - Philipp Boeing - A lab for everyone
Philipp Boeing - A lab for everyone
with Philipp Boeing, Bento Labs
Kat - Imagine all the kit you need to start your very own molecular biology lab, packed down into the size of a laptop bag and perfectly portable. This dream is now becoming a reality thanks to the work of Philipp Boeing and his Kickstarter-funded project, Bento Lab.
Philipp - Bento is this Japanese packed lunch. But yeah, it has that kind of modular look and we like the idea of it connoting portability. It has three or four essential components. The heart is kind of the centrifuge because it's in the middle and it's a pretty powerful small mini centrifuge that you can use to extract DNA from cells for example. And then maybe the most important tool is the PCR machine which is a copy machine for DNA. It's a thermal cycler so it's a block of metal where you can put tubes in and you can programme the temperature very accurately and make cyclic programmes. And then there is a gel electrophoresis chamber with a blue light transilluminator. Now, that's a pretty big word, but basically, it's a little box where you can separate DNA fragments by size or sort them and you can visualise them, so you can make them fluoresce. So you get kind of a bar code image of lines that are actually fragments of DNA of different sizes, and that can tell you a lot of information about the sample.
Kat - Basically, you can purify DNA from a sample tissue, a sample of cells. You can copy it, you can make lots and lots of bits of the bit you're interested in, and then you can see it. I mean, that is pretty much what I spent my PhD doing.
Philipp - Yeah. So now, you can...
Kat - I could've done it all in my bedroom.
Philipp - Yeah, exactly.
Kat - And when it comes to some of the more advanced DNA analysis techniques, here, we talk a lot about gene sequencing or being able to cut up bits of DNA and stick them together. Is it possible to do those kinds of techniques with this setup?
Philipp - We always thought of it as a generic laboratory. Just as you can run many pieces of software on a computer, we wanted you to run many kind of different experiments on this thing. Of course, a lot of the times, it depends on the enzymes that you have and the reagents that you have, these are chemicals that you use to interact with the DNA. There's no reason why you can't for example put two pieces of DNA together and use gel electrophoresis to confirm that for example within Bento lab. So, especially also if you have other tools or you're part of Citizen Science Laboratory, it really slots into other experiments that you can do.
Kat - What about if I wanted to read the DNA sequence of a piece of a DNA?
Philipp - Bento Lab is not a sequencer. That's a much more advance kind of technology but you can work with the tool like the MinION for example which is this USB-sized nanopore sequencer, very kind of advanced, not quite cheap. So I think one experiment costs you like, one of those flow cells costs 1,000 pounds so maybe a little bit out of the reach, but you can also use external sequencing services. In any case, you'll need a tool like Bento Lab to prepare the sample - centrifuge, PCR to prepare a sample and then process it further. So, it's not very expensive to then send a short read out to a sequencing service in a few days get an email it back with the sequence.
Kat - Who do you see using it? who's your target market for this?
Philipp - Well, we have a couple of different ambitions for it. Of course, it's great to have essentially a mini laboratory that's quite affordable and easy to take into the field for example. So a lot of scientists are interested in that. A lot of teachers, they're interested in actually being able to demo or do these experiments with their students in classrooms or in teaching labs in universities. So that's great. We are really driven by movements like the maker movement in electronics and computing, things like Raspberry Pi, things like Arduino. So we do have an ambition that we can have a nice active community of citizens from all walks of life that are doing different projects. There is right now in terms of beta testers a group of pensioners in Wales that are using a Bento Lab setup to analyse different mushroom fungi samples all over Pembrokeshire. There's a seasoned scientist in Switzerland who tests the genetics of yeast found in beer to generate a genetics of taste map. Essentially tests, extracts yeast DNA from beer and looks at the genetics of that yeast and sees how it relates to the taste. So, it's a really great setup for him to drink a lot of beer on his job. But also for me it's kind of a textbook example of, it's a serious scientific project, but it's something that you wouldn't really usually fund or that wouldn't really usually be done if those tools weren't accessible. It's something that's really interesting to so many people. So, that's a project that we really like. So we kind of like all these slightly more - different hobbyists approaches to doing science and we want to have - we want to encourage that kind of community.
Kat - When you say the idea of a lab like this and maybe I've just got a bit of a twisted mind, but I think I could start taking DNA samples from people and testing them. I could work out, is my dad really my dad? Is there a risk that people might start doing that?
Philipp - There's a risk like this already. If you had that kind of ambition which I don't think you have, but if you did have that...
Kat - My dad is definitely my dad.
Philipp - See, there you are. It's always good to trust your parents first of all. But if you really had that ambition, I mean obviously, there's already services that you could use. You have to sign a legal waiver but I guess you already passed that point in this scenario. But even if so, if you really want this equipment, you can get second-hand equipment off eBay. It's going to be more expensive. Not going to mean really it's nice to use but if someone has nefarious ideas of what to do with this equipment, they can do that already. What we want to do therefore is we do want to encourage the science but we also want to raise the kind of maturity of the conversation. So, for most people who are starting for the first time with Bento Lab, they're getting a starter kit with all the reagents and bits and bobs to get started. We really embed that in a context of not just understanding the scientific processes and the kind of craft that goes into it, but also the legal responsibility, the bioethics side of things, understanding how to interpret a result, and how to contextualise it. so not just, "Oh, I found this gene." But actually, what does that mean and what are the consequences?
Kat - What would you hope for if many, many people do get a hands on the Bento Lab and start doing science with it?
Philipp - Well, I think it's really hard to foresee the future and there are many examples of people getting that wrong. I think there are some clear short term examples. So, for one thing, what I would like to see is more people knowing about their genes and genetics as a whole. And also, not just knowing, "Okay, I have genes for this and that like 23andMe" but also, knowing what they can know from that and what they can't know from that. So, it's not just about being able to do more genetics testing but also, being able to understand that result in a context. So we do want to kind of make that a little bit more intellectually serious. We come from the synthetic biology community and those communities. Bento Lab is kind of a start for us, but we do want, just like in software engineering, what's interesting there is that's not just big companies and academics can write software but so many people write software. And so, you can have a very specific app on your iPhone that was made by someone who had exactly the problem that you had. In biology and biotechnology, it's not like that. You really have to have a lot of money and a lot of expertise to be able to do any interesting project. And so, I think what's already happening with the users of Bento Lab is that we're starting to use DNA and genetic technology for much more interesting smaller scale projects like this BeerDeCoded project. So we hope to encourage projects of that kind of scale.
Kat - What are the things could I do if I had one?
Philipp - I mean for sure, Bento Lab right now is mostly about DNA analysis. Unless you have access to other tools and then of course, it just replaces part of your normal lab setup and you can do anything that you can do in a molecular biology lab. I think what would be very interesting is starting to have this community of people who do distributed projects. So, it's not just you doing a project in your garden for example but maybe other people doing a similar project in their gardens in India, in South America, and comparing that. So I think there's a lot of potential for things like ecology and biodiversity studies. I mean also again, I have to come back to this PC analogy but what was interesting there was not like Apple and Microsoft didn't come up with the first examples of what really drive PC adoption. That was for example business people who came up with the idea of Excel. Suddenly, everyone had to have a computer. And so, I think I'm very interested in what happens when people of certain needs maybe in agriculture or healthtech or so on, find out how they can use this because suddenly the technology becomes so available and suddenly every farmer needs one because they found out how to do something with their soil or analyse something with their soil for example that's really relevant.
Kat - I can see a really interesting application in the developing world when you're thinking about tracking outbreaks of diseases like Zika or Ebola to have something that effectively fits in a laptop bag that you can take around and looks very sturdy.
Philipp - There's a lot of interest now also with this new rapid sequencing technology to do these things right in the field. People have always done, taking a sample and get it sequenced but it usually takes 2 or 3 weeks turnaround time because they have to send it to a lab in Europe or the States. By the time it comes back, the information is kind of useless.
Kat - And the person is dead or something.
Philipp - Yeah, but also because they want to do it for epidemiology. That way, they can really trace, "Okay, this new Ebola sequence relates to all these other Ebola cases" and they can really tell how it spreads and when a new strain emerges. So there's an interest for that but it's really difficult and risky, and expensive to bring this lab into those places. So, with Bento Lab, that's definitely much cheaper, much more robust and it's a much smaller footprint. So there's definitely interest in that. We don't market Bento Lab as a medical product, but in this case, it's really a research tool. We have a lot of interest in that area. We're doing some tests and exploring that. It would be really great to see it had such a use.
Kat - Philipp Boeing of Bento Lab. And if you fancy getting your hands dirty with your very own laptop-sized lab, visit their website - https://www.bento.bio/
27:55 - Gene of the Month - Armadillo
Gene of the Month - Armadillo
with Kat Arney
And finally it's time for our gene of the month, and this time it's Armadillo.
First discovered in fruit flies, Drosophila melanogaster, in the 1980s, armadillo was originally thought to be a segment polarity gene in the insects, required to make sure that the different bits of a developing fly know their front end from their back. Fruit fly embryos with a faulty version of armadillo are stubby, hunched little things, with their normally free-moving segments fused together a bit like the plates of an armadillo - the 'crunchy on the outside' creature that gives the gene its name.
So what does it do? Armadillo, or beta-catenin as it's known in other organisms, including mammals like us humans, is a molecular multi-tasker.
It helps to create the junctions in sheet of cells, known as epithelia - such as the skin or lining of the gut. And it also helps to control the activity of genes, responding to signals sent by a molecule made by another important gene, called wingless.
As you might guess, life isn't great for a fly without proper wingless activity, as they don't make wings properly, if at all.
And in humans and other animals, rogue armadillo and wingless activity (or beta-catenin and Wnt, as they're formally known) has been linked to bowel cancer and other types of tumour, making cells grow out of control.