Monday, 5 October 2015

10,000 Up

I've just passed my 10,000th follower on Twitter, and similar to when I went past 5,000 followers this feels like a good point to reflect on this open, 'blog-and-tweet' world evolving around me.

Many of the comments I made two years ago have stood the test of time: Twitter is still fundamentally a conversation, broadcast not just to your lunch queue but worldwide, and blogs remain lightweight, informal platforms for review and commentary. And as with any conversation you have to consider your audience first, and as with all public writing everyone still need and editor [sic].

So, happily, the basic principles hold true. But with this up tick, I want to reflect on whether these media/platforms are actually right for everyone, and the future of open discussion.

You don't have to join Twitter

I get a lot out of Twitter, and part of that includes sharing interesting papers or blog posts I've spotted in my twitter stream or adding new ones to the mix. I find myself asking people if they are on Twitter so I can be sure to reference them when their work comes up. This sometimes elicits a somewhat sheepish response along the lines of, "I don't do Twitter," or "Twitter makes me feel uncomfortable," or, in rare cases, a flash of rage against the world of informal and all-too-short critiques/discussions. 

I try to be positive about my Twitter experience while acknowledging that Twitter is not for everyone, and recognising its pitfalls: it can be distracting, people are often tempted to over-share aspects of their lives, etc. Twitter is certainly not a requirement, and blogs are rather personal. While I am not alone in finding these media useful, I wouldn't say that you are missing out on crucial information if you don't jump in. Mainstream scientific interaction is still via published, peer-reviewed papers and giving talks at conferences and workshops, and that is where the really important stuff is to be found.

You don't have to interact on Twitter

Many people use Twitter as a sort of personalised, text-based radio station: something you can tune into when you want, that gives you a personalised mix of news. I am pretty sure no one else has my mix of interests in worldwide science, UK, European and US politics, cricket and events in the North Tyne valley (in Northumberland). Twitter is useful just in this "consumption" mode.

Twitter is also inherently ephemeral - people shouldn't expect you to be on it all the time (although it seems like some people are!), and no one can expect that a comment (when someone @'s you) will always elicit a response. People have lives, holidays, emergencies and so forth, and all of those things make it perfectly reasonable to ignore this global conversation.

But if you do start a conversation about a topic, I think it is reasonable for others to expect that you will respond and follow through on sensible comments. Some conversations spark a need for deeper discussion (i.e. "we're going to need to meet up face to face for this one..."), and some might dwindle because you have to take your kids to a pirate party, sleep, etc. And that's fine. The instant, global nature of Twitter makes it empowering in some ways, but it also needs to be tamed to fit into your life.

140 characters: plenty of room for misinterpretation

Twitter's limitation of 140 characters can be challenging, and it's surprisingly easy to misinterpret a tweet - in particular when it is intended to be funny, or when it involves a disagreement. Without body language, vocal nuance or the comfort of expository paragraphs, it is extremely easy to blunder on, not realising that the other person has taken offence, become confused or both.

So I stand by my rules of avoiding 'jokes' on Twitter (unless I'm very confident that the people in the conversation will get it), and avoiding disagreements, particularly the complex ones. Science is full of ambiguity and disagreement, which is part of what makes it exciting - but Twitter's natural limitations turn those elements into confusion all to easily. It just is not the right medium for this kind of engagement (more on this below).


Post-publication peer review is cool

The rise of open, “pre-peer review” platforms in molecular biology communication is a big step change. It started with the quantitative biology community putting papers on the Physics Arxiv site, which quickly became the mainstream way to communicate in high energy and theoretical physics. Two platforms have been added to this: Bioarxiv, which has a similar model to Arxiv but with a stronger emphasis on biology papers (e.g., they process Word files). The second is F1000Research which combines submission, peer review and publication production workflows seamlessly as one stream - and insists on open peer review, so the peer-review comments and replies are all published together with the paper – everything in the open.

In this new publishing environment, blogs are starting to feel very … 2000 to me. Why am I am blogging when I could write a pre-publication with a DOI, which can be cited and made a more formal part of the scientific discourse? Blogging is nice, because it is accessible to a broader audience and allows for a more chatty, 'natural language' style – but if the main purpose is to communicate with scientists, pre-publication servers are a better way to go. If the goal is to communicate with a broad set of interested people, an on-line magazine or aggregation site might be better. The independent blog is on borrowed time (which does make me wonder why I’m writing this).

There is a lot of social innovation happening in science, and each one of them takes a bit of adjustment. (For example, keeping track of comments on F1000Research articles can be a bit exhausting.) In general, the move towards a more rapid, open discourse is almost certainly a good thing... Except...

Open, recorded, textual criticism is complex

These new, open communication platforms share three key characteristics: they are text based, they can be close to immediate (like spoken conversation) and, importantly, they are 'on the record', indefinitely.

This is an explosive combination for constructive criticism. The fluid, conversational nature of the media makes it easier to voice criticism, but it demands a certain level of nuanced writing skill to make up for the absence of voice and body language. These platforms make it too easy for people to barrel on with their views, offering no mechanism that advise about, for example, the responding tone of (or meaningful silence from) the other participants. Disagreements can flare up, triggered by trivial things like different use of common definitions, or by deeper problems like a fundamental misunderstanding of the important elements of different positions in a debate. 

The global nature of these communications adds many layers of cultural complexity, as they are (in science) mainly carried out in the English language, which provides endless opportunities for misunderstandings and perceived callousness due to people's different use of English. But it is perhaps the permanent, public, recorded nature of these critical conversations that raises the stakes highest. Onlookers can read motivations in the text that they wouldn’t interpret in the same spoken conversation. One cannot easily forget such a disagreement when it has been so public and lasting, in particular when it becomes personal.

Online constructive criticism in science

I don’t think the social mores are in place for how we handle criticism on these communication media. There are so many cultures and subtleties - there is a reason, after all, why science writing in papers is so dry and literal. In online conversations criticism is often so polite as to be obtuse, or impossible to understand. More upsettingly, criticism can be so vitriolic and personal that it can't be absorbed at all by the person receiving it or the audience observing the dialogue. 

Science is not the only field that has to work out a social contract for on-line communication, and I have a feeling that it’s going to be the generation that grew up with FaceBook, Twitter and SnapChat that's going to work out how best to do this. But I don’t think the current behaviour is right. Constructive criticism – honest but aiming for the best science – is such an important part of our our world that we need to create the right environment for it online. 

Overall, I am still positive about open communication. I find Twitter interesting, informative and fun, and I find blog posts provide an outlet and means of communication that lets me write more broadly and accessibly about science. These media will evolve - just as every other medium has - and be used by more and more scientists. I still enjoy being part of this evolution. 

Wednesday, 16 September 2015

Anatomy of an mainstream science piece

Last week, the Guardian published a Comment by me entitled, ‘Why I'm sceptical about the idea of geneticallyinherited trauma'. In this blog post, I’d like to go through what happened behind the scenes when someone from the mainstream press asked for my views, what my thought process was before I started drafting a response, and why I believe we should all participate more in public discourse on science.

The motivation for the Comment was a short story, published almost a month ago in the Guardian, about a paper that made claims about the transmission of some molecular memory from Holocaust victims to their children via epigenetics. The paper itself was pilloried on Twitter, rightly so in my opinion (one scientist remarked that this is a perfect example of how not to run an epigenetics study). The story was prepared by a reporter covering for Ian Sample (science editor for the Guardian), who was away on holiday; an objective expert opinion was not found for the story, and I think that when Ian returned he felt motivated to redress the balance. Probably because of my active role on Twitter, and with support from other scientists (Matthew Cobb in particular), the door was open for me to pester Ian for a response.

Before you rush to blame the reporter (or journalism, generally) for rushing a story through, it’s important to keep in mind that the media operates under some fairly stringent constraints. First, news must be new, or it isn’t news – so there is always time pressure. In addition, any piece needs to meet two criteria to be broadcast (in print, online, on radio or TV): (1) it must be interesting, and (2) it must be comprehensible to a general audience.


Everyone involved in a large media apparatus (radio, TV, print, etc.), including journalists, editors, subeditors, producers, fact checkers, camera operators and many other professions, aims to maximise interest, accessibility and delivery. For science journalists, “interesting” can mean, broadly, one of three things:

  1. It has, or could have, a direct bearing on the reader/listener/viewer’s life, or in the case of large events, on the lives of a large number of people. Most health pieces and environmental disasters fall into this category.
  2. It is quirky and gives a refreshing perspective on the world, often making use of a cool picture. Big kit falls squarely into this category (robots/satellites sending back the first pictures of a planet / asteroid  / comet automatically max out on this criterion).
  3. It is of global significance and is aligned with burning issues in mainstream politics, for example climate change or epidemics. If this category is mined heavily by many outlets at once (i.e. fuels the bandwagon), then at a certain point everyone has to run some part of the story to avoid alienating their audience.
The best popular science stories weave in elements of at least two categories: e.g. local flooding and epidemics, or a striking image of nature/human anatomy with a healthcare angle. Making a story appealing and digestible is a big part of the science editor’s craft (more on this below), and a priority for the readers/viewers, etc.

Is ‘right’ interesting?

Whether the science is ‘right’ or not doesn't always have a lot to do with whether it is interesting. This aspect of a story is usually the domain of the science journalist and/or editor, whose personal credibility is on the line (and who must avoid landing in legal hot water; though for the purposes of legality, checking the “peer reviewed article” box seems usually to be enough). Science stories can easily be ‘interesting’ but not ‘right’ – and science editors get bombarded with press releases focused far more on the interesting. 

Thankfully, the science editors I know do care a good deal about the correctness of the pieces they put in – but that doesn’t help them find interesting stories that will capture their audience’s attention. And because covering ‘science’ means fielding everything between astrophysics and zoology, it is a lot to expect that everyone involved will have enough of a working knowledge of the science and communities involved to present a balanced view of any subject.

Pitch in.

So, in short, reporting on science is a hard job – though it is also fun to be able to write about science all the time. If you are ever contacted by a science editor to give your opinion, please, please respond! And think carefully about the overall message. If the science is sound, it won’t hurt to allow the ‘interestingness’ to come through. If you do not think the science is sound, say so, outright and clearly (the journalist can canvass others for opinions; be frank, but not harsh).

What’s the angle?

So when I was asked to write the Comment for the Guardian (triggered by that epigenetics piece), here is what went through my head:

  1. I’ll need to explain the hideously complex, overlapping definitions of ‘epigenetics’, and give some insight into the disputes around this. Could easily use as examples the excellent pieces by Mark Patshne, or the (very British) ‘broad church’ compromise definitions by Adrian Bird, and touch on the almost 50 years of debate around this word. Caveat: Good to humanise science, but is this too ‘inside baseball’ (to use an Americanism)? However interesting this is to scientists, it doesn’t score well on any interestingness criteria for the general audience.
  2. I could delight in the sheer inventiveness of biology around epigenetics processes… X chromosome inactivation in females, for example: tortoise-shell (or calico in the US) cats, women with multi-coloured irises. Lots of potential for visuals with those. Or the Calipyge mutation (‘beautiful buttocks’) in sheep: a serious use of differential imprinting, and you get to use the phrase ‘beautiful buttocks’ – a sure win! Plus, pictures of proud farmers looking at their prize lambs... For additional interest, could also write about the long-standing discovery/exploration of epigenetics in flowering time in plants. Absolutely satisfies category 2 criteria: a quirky look at the world, with good visuals.
  3. Is this a good example of the limits of using peer review as the sole measure of quality/correctness? This is a really important issue, but this paper is by no means the first or last case of things going wrong. But, realistically, this is almost certainly uninteresting to most readers. More a matter for scientists to explore amongst themselves in specialised press, or for a science journalism forum.
  4. Use this as an opportunity to explore general misunderstandings of genetics (and, in part, epigenetics)? The theme of genetic determinism is currently too strong in mainstream media, and this needs counter balancing.
Clearly, I went for 4 – but 2 would have been an easy choice (indeed, I think that article should be written sometime!). The other options would never make the cut.

Can I go beyond just explaining this (bad) piece of science?

For a long time I have been watching our culture embrace genetic determinism, more and more. In addition to the commonplace usage of ‘DNA’ as a metaphor for ‘core values’ (see my previous blog post about this, and Private Eye’s satirical weekly column, ‘DNA’), I’ve had conversations with non-scientists about the predictive power of DNA that bring up such concerns as, “I wouldn’t want to know my genome because I don’t want to know the time of my death”. The person I was speaking with in that case was quite convinced that the end point of all these genetic discoveries was a sort of complete roadmap of a ‘healthy’ life, and certainty about which diseases one would get and when. For him, personally, it was simply better ‘not to know’.

In contrast, there is no shortage of opportunities for science journalists to investigate claims made about beauty creams and health schemes ‘tailored’ to a person’s individual genetics. 

The genetics of skin and of exercise response are indeed interesting, but it is hard to establish (to say the least) any clear-cut genotype-specific environment effect. Many of the people marketing these schemes are playing on the ‘DNA is the real you’ meme as if it is a given, rather than checking whether there is any actual scientific basis for that assumption.

The drafting process

As with all my public pieces, the article was a collaboration with both Mary Todd Bergman, who I bounce ideas off and she also edits much of my work (including this blog piece). For the Guardian piece, Ian Sample also went through several iterations with me to improve readability. This process is invaluable – it is so hard as a practicing scientist to read your words back as 'lay person', and to stick with using everyday words rather than using specialised (and thus precise, but inaccessible) terms.

I also had to plot a careful course around the word “epigenetics”. It is a very frustrating topic with at least three 'mainstream' meanings, and numerous attempts to define it. After I had a reasonable draft I sent it around a broader group of people (I will mention many of them below) but in particular to Anne Ferguson-Smith, who I consider one of the best scientists studying epigenetics. She helped change the tone of the piece, in particular stressing the importance and soundness of developmental and environmental changes in the epigenome (contrasting that to trans-generational epigenetics).

Going through multiple drafts greatly improves accessibility (the soul-mate of interestingness) – what you write is not necessarily what people read. Of course, some things are lost in the smoothing process. For example, explaining imprinting didn’t make the cut. Getting across certain ideas was very tricky, for example the fact that in genetics we’re classifying the proportion of variance in some populations, but often deliberately sampling where we fix many other features (I hope the thought experiment of setting the same exam to a mixture of French and English people is a good one).

The broader group?

In science, nobody works alone – just as in writing this piece. But news pieces are written back-to-front, with the conclusion right up top – so things like references, citations and background tend to get squeezed out. (Anyone who writes a lot of science papers will know how weird it can feel not to include a list of references.) It doesn’t feel right to see just my own name at the top of that Guardian piece. Really there are four contributors to this article: myself, Ian, Mary and Anne. Furthermore, the ideas I express here are the result of decades of discussion with people. Science is always a ‘team sport’ and even in a paper you can seldom provide a reference for all the things you’d like to.

I’ve been discussing the ‘over-reach’ of the public’s general grasp of DNA for a while, and as with all really interesting questions my views have been heavily influenced by many of my colleagues. In particular discussions with both George Davey-Smith and John Danesh have really helped me understand the epidemiologist’s view of this. George and John live and breathe human variation every day of the week. Long-standing epigenetics experts like Anne Ferguson-Smith, Stephan Beck, Eileen Furlong and Ian Dunham, and the people I met in ENCODE, including Brad Bernstein, Peggy Farnham and John Stamatopolous, were great teachers in the complex world of histone modifications and (somatic) epigenetic components. Clinician-Scientists such as Nazneen Rahman, Helen Firth and Stuart Cook have opened my eyes to the complexity of ‘well established’ genetic variants, and discussions with people in the broader quantitative genetics community, including Peter Visscher, Trudy Mackay, Jonathan Flint and Chris Haley, and on the Genome Campus Oliver Stegle, Nicole Soranzo, Jeff Barrett, Carl Anderson and Matt Hurles have educated me about the details of these models and the real-life world of complex trait genetics. (I still often only have an intuitive understanding of some of the maths, which gets amazingly tricky – like when you are diagonalising matrices inside equations with Kroneker product schemes, and dealing with non-negative aspects of the matrices, and fixing it all up…).

Discussions with people in all these very different fields have helped shape my position about the way we have communicated with the wider world about genetics and genomics.

DNA is not your destiny, and we need to say it loud

I hope the piece in the Guardian contributes positively to the public discourse around genetics. We are going to be making more and more detailed discoveries about human traits – diseases, yes, but also everyday traits such as human height, normal organ processes, mechanisms that drive behaviours like risk taking, exam achievement, spelling ability, musicality, criminality… Each of these is a totally sensible thing to study. But interpreting the results, both scientifically (read the Methods carefully!) and, more importantly, in a social sense, is going to be difficult and demand a huge time investment.

As practicing scientists, we need to continue laying the groundwork started long ago by many others (see Matt Ridley’s Nature via Nurture, 2003), engaging consistently and non-judgmentally with our communities and policymakers about out work. There is a real task ahead of us in providing an accessible way for people to digest this information. We should take every opportunity to communicate on every level, from the most basic to state of the art. Only then can society really use the hard-earned information gleaned from genetics appropriately, and for the greater good.