EGN Conference 2013 – Parallel One: Democratising Sequencing: Next generation sequencing and its social, political and ethical frictions

by Simon Read - PhD Student, Cardiff University School of Social Sciences

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The first parallel session of the EGN Conference, chaired by Dr Ruth McNally, concerned itself with debates on open science and its particular resonance in the field of next generation sequencing.

Dr Nick Loman opened proceedings by providing an overview of the crowd-sourcing phenomenon associated with big data. Having started by outlining the volume of sequencers across the world, as well as those involved in the analysis of the results they are offering, Loman then offered a particular case study of an outbreak of E. coli in Germany between May and July 2011. In this example, which resulted in nearly 4000 cases and over 50 deaths, he highlighted the impact of crowd-sourced analysis in offering new interpretations of the ‘sproutbreak’ crisis. The academic community engaged with the available data to present revised analyses from those that initially emerged stating that the strain of E. coli had never been seen before. For instance, academic blogs highlighted similar strains between this particular outbreak and other ten years in the past. The benefits of collaborative and competitive crowd-sourcing were a much more rapid analysis of data which influenced the political response. In addition, the use of blogging, wikis and Twitter enabled, to some degree, subversion of commonly accepted academic publication practice with journal exclusivity being sidestepped in this particular case.

Dr Sabina Leonelli followed this with a summary of her research into open science and ‘data journeys’. The open science movement had invited exploitation of the Internet as a public platform for consultation, exchange and critique. In turn, this facilitated exchange of knowledge claims as well as data, techniques and materials thus driving collaboration and widening participation. However, the novelty of this development was questioned by Leonelli as well as whether free access to all information was practically available given its quantity and consequent immobility. This ‘data journey’ was the core of Leonelli’s research with its various stages being shown to involve huge amounts of labour and to provoke an array of conceptual, material, technical, social, financial and ethical concerns.

Finally, Dr William Spooner closed the session with a presentation that sought to bridge the gap between big data and its practical application. The processing of NGS data typically involves complex routes of independent software components that often provoke variability in response to the same data set. Additionally, ethical concerns around the identification of those individuals submitting their genetic data have been highlighted in recent months. In spite of this, progress is being made in this field. The key issue is how this can be applied effectively within the NHS.

EGN Conference 2013 -- Opening provocation

by Emma Frow - Genomics Forum Associate Director and Lecturer in Science & Technology Studies, University of Edinburgh

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It’s a beautiful spring morning in Westminster, and the cherry blossoms are in full bloom. A fitting occasion to gather and celebrate a decade’s worth of achievements of the ESRC Genomics Network.

The conference opened with a tantalizing film clip (by filmmakers-in-residence Cameron Duguid & Lindsay Goodall) in which several EGN researchers grappled with the question ‘What is genomics?’…more on that later! Genomics Forum Deputy Director CatherineLyall then welcomed everyone to the meeting, and noted that poet-in-residence Samantha Walton will also be capturing this event in verse.

Adrian Alsop (Director of Research at the ESRC) provided some opening reflections regarding a decade of significant change for the ESRC, noting several significant shifts that have taken place in research policy and strategy over the lifetime of the EGN. Notably, ‘impact’ has become an increasingly dominant narrative for UK research, and the ESRC has been influenced by engagement with EGN researchers to define and support a definition of impact that embraces a wide variety of activities. A second big change that the ESRC is working with is the rise of an industrial strategy for science, one that strives to scale up industrial biotechnology with the promise of promoting health, wealth and an increasingly sustainable bioeconomy. Growing investments in ‘big data’ and the increasingly global character of social science research are two further changes influencing the context in which the ESRC operates. How to analyse and engage with these changes is an ongoing challenge and opportunity for social science research.

Adrian noted that EGN research has kept pace with several of these broader changes, and suggested that the interface between the life sciences and social sciences will continue to be a major theme for the first half of the 21^st century. Maintaining quality, impact, and independence in social science research will be critical.

We then moved on to a provocation by Roger Pielke entitled ‘Five Lessons of Science Advice.’ Roger highlighted the ongoing relevance of this topic by flagging up George Monbiot’s column in The Guardian yesterday, which focuses on the role of science advice around the current debates on bee health and pesticide use in Europe. 

Roger drew on over a decade of research, and specifically a series of interviews he has done with 7 US Presidential science advisers, to offer some key lessons about science advice, with some great cartoons to accompany these thoughts: 

Lesson #1: Science advisers are not superheroes. There is still a widespread expectation that ‘science speaks truth to power,’ and scientific evidence should be able to tell us what to do in tricky political situations. The reality is a bit more complicated, and the path between scientific knowledge, advice and decision-making in democracies is messier.

Lesson #2: ‘Science advice’ is a misnomer. Roger argued that we should be thinking instead in terms of ‘political advice.’

Lesson #3: Political advice from a science adviser can take multiple forms. Using a lively example about finding somewhere to eat dinner in London, Roger outlined 4 idealized categories of advice about science, which are expanded on at length in his book The Honest Broker. 

Lesson #4: Institutions matter. Institutional structures can end up having significant effects on decision-making practices, and we need to be sensitive to these broader factors. Roger gave us the example of the US President’s science adviser, who is formally positioned outside the President’s ‘inner circle’ of advisers (in part because science advisers can be called to testify in front of Congress, a level of exposure that precludes participation in highest-level decision-making). 

Lesson #5: “Politics is more difficult than physics” (a well-known quote from Einstein). Political thinking is very different from scientific thinking, and in practice science advisers need considerable experience in politics to do their jobs.

Roger concluded by saying that in the US and Europe, science enjoys enormous respect and authority, and that the ‘mythology of heroic science advice’ lives on – with a growing role for science advice currently being highlighted by institutions including the United Nations and the UK House of Lords.

Imaginative Approaches to Science Writing

by Barbara Melville, Writer in Residence at the MRC Centre for Regenerative Medicine

I was delighted to spend time with the ESRC Genomics Policy and Research Forum, where I prepared and ran a full-day workshop called Nonfiction for Science – Imaginative Approaches to Science Writing. I was fortunate to be co-facilitating with fabulous writer and comedian Siân Bevan, and working with a group of receptive and talented students. Together we explored the theory and practice of creative nonfiction, and its place in communicating science.

Creative nonfiction, like any genre, does a cunning job of resisting definition. Broadly, the aim is to communicate the facts with literary style. These narratives often include personal journeys, like in Primo Levi’s The Periodic Table and Lone Frank’s My Beautiful Genome. But despite the demand for imaginative science writing, there’s a paucity of such works. My guess is people are interested, but don’t feel they have the tools. After all, if you’re used to academic writing, or your background isn’t science, how do you get started? How can you combine fact with subjectivity?

These were among many questions we tackled throughout the day. We worked on drafting personal essays, allowing ourselves to play with ideas before questioning what we’d produced. We studied the underlying principles of narration, including why people tell stories, how to keep writing consistent, and how to combine personal and impersonal information. After lunch, we had a refreshing discussion on accuracy and accessibility in science communication, before spending the final hour reading, rewriting, and brainstorming ideas for essays.

I was thrilled this workshop was so popular, and that I got to run another in partnership with the Beltane Public Engagement Network and the Roslin Institute. I’m now pursuing a website dedicated to this kind of writing, and I hope to run more workshops in the future. I can’t overstate how grateful I am to everyone at the Genomics Forum, our hard-working attendees, my awesome co-facilitators, the Beltane Network and the Roslin Institute for their unending guidance and support in putting these events together. Here’s to many more.

The meme of innate class superiorities

by Leon Feinstein, Genomics Forum Bright Ideas Fellow

I am extremely grateful to the ESRC Genomics Forum in Edinburgh for the opportunity to spend a week there, away from the day job, reflecting on the question of “hereditarianism” and the relationship to it of Socioeconomic Status (SES) and child development, and to discuss this meme with experts. The Forum kindly hosted a workshop on March 6 2013, with a carefully invited group comprising psychologists, geneticists, social scientists, educationalists and representatives from the world of policy. The presentation built on recent helpful discussions at the Institute of Social and Economic Research (ISER) in Essex and at the Centre for the Analysis of Social Exclusion (CASE) at the LSE.

Download - The hereditarian view of social mobility presentation slides >>

I went to the workshop intending to learn how those in biological sciences have been thinking about the challenges of this issue. I motivated the discussion, as they say, with a focus on the technical issue of regression to the mean, which rather dominated proceedings. This has become something of a vexed issue for me, in relation to the graph that some know as “the Feinstein Graph.” I know it as Feinstein, 2003; Fig 2 but I am told I am stuck with the handle.

We didn’t really get into the issue of “hereditarianism” in quite the way I had expected but I arrived with a hope to learn something and was greatly informed by the experience.

I do not attempt a record of the event but I do want to thank participants for attending and their universally helpful contributions.

Please see attached a draft paper in relation to regression to the mean, which I managed to progress due to the discussion at the seminar. I think many participants wanted to have a wider discussion so this may be of minority interest.

As I say in the note, I do not at all accept that I have “misused statistics,” or that the graph "is simply wrong." The first is a glib slur and the second an odd statement because so much of the debate is about what the data mean.

I was further reminded at the Forum that work on this theme must address the changing reliability of the scores as children mature. This is complicated by the fact they are positions in an ordinal distribution of “ranks” in a weighted index of scores, rather than absolute performance on a single, specific test. People tend to forget this. It was helpfully suggested by the inestimable Tim Bates how further research to test the reliabilities of this sort of measure in a new sample might be carried out. I am hoping to discuss further. He said I should read Eysenck and Jensen.

Amongst many insightful points, Wendy Johnson emphasised particularly the importance of recognising that Fig 2, is really just a corollary of Fig 1. I strongly agree with this. I will pick this up in further work.

The fellowship at the Forum was a fantastic opportunity and I am especially grateful to the organisers.

First Fortnight as Forum Poet in Residence

by Samantha Walton - Genomics Forum Poet in Residence

I began my residency at the Genomics Forum staring at a graphic of DNA winding around histones, exposing some genes for activation while spiky epigenetic factors cling to the spools of purple string from worm-like tails. The image claims to describe epigenetic mechanism operating in DNA, and has been one of the many diagrams, images, reconstructions and videos I’ve turned to over the last couple of weeks to try to get a handle on the basics of epigenetics research. This process has also included playing two games – ‘Gene Control’ – in which you can change the shape of your DNA and its levels of methylation by cranking up a volume control, and ‘Lick Your Rats’ where frantic mouse-clicking helps you activate your rat pup’s GR gene. This has, I promise, been a valuable use of my time over the last fortnight as a poet in residence.

Faced with the overwhelming wealth of research being undertaking in the Genomics Network, epigenetics jumped out as a way of honing my focus during my time here. This was in part an acknowledgement of my own ignorance, as by turning focus beyond or ‘above’ the gene, epigenetics upset everything I thought I knew about genomics. I’ll return to the subject of my own ignorance again (and again) later and just admit here that I had never before encountered discussions about the relationship between environment and the genome explored in epigenetics. This is in spite of the field being, according to the programme for the upcoming EGN Conference (April 30^th-1^st May) “one of the most fast-moving and potentially transformative areas of contemporary ‘post-genomic’ science.” The suggestion that environmental influences can cause changes in the structure of the genome, meaning that genes express themselves differently even if the organism is a genetically identical clone, seems of radical importance, not least because ‘environmental influences’ might refer not just to biological factors, but to social, psychological and cultural experiences. The trans-generational considerations of epigenetics make it even more fascinating, and much of the writing on the subject I encountered raised the possibility that changes in gene function might be inherited without the DNA sequence changing, and influenced by factors such as stress, famine, ill-health and parenting.