How would you describe genomics without using any scientific jargon?

Yesterday was the Annual Student Conference at The Institute of Cancer Research, London. As part of the ICR's Communications team, we helped run a session about the myriad ways that science can (and should) be communicated more effectively.

During this session my colleague Rob Dawson (@BioSciFan on Twitter) introduced a fun tool called the The Up-Goer Five Text Editor. This tool lets you edit text…but only by using the 1,000 most common words in the English language.

It was inspired by an XKCD comic which used the same approach to try to explain how an Apollo moon rocket works. Using this tool really makes you appreciate that just about every scientific word you might use is not on the list. So it is a good way of making you think about how to communicate science to a lay audience, completely free of jargon.

I thought I would have a go at explaining genomics. I couldn't even use the words 'science', 'machine', or 'blueprint' (let alone 'gene', 'DNA', or 'molecule'). Here is my attempt:

In every cell of our bodies, there is a written plan that explains how that cell should make all of the things that it needs to make. A cell that grows hair is very different to a cell that is in your heart or brain. However, all cells still have the same plan but different parts of the plan are turned on in different cells.

We first understood what the full plan looks like for humans in 2003. We can use computers  to make sense of the plan and to learn more about how many parts are needed to make a human (about 20,000). The better we understand the plan, the more we might be able to make human lives better.

You can edit my version online but I encourage people to try explaining your own field of work using this tool.

And the award for the most-retweeted-tweet-of-a-photo-of-a-slide-from-a-presentation-of-mine goes to…

On November 20th, on the last day of my employment at UC Davis, I gave an exit seminar. Jenna Gallegos, a PhD student at UC Davis — who works on the awesome Intron-Mediated Enhancement (IME) project under the supervision of Alan Rose — posted several tweets from my talk including this photo of one of my slides:

This tweet continued to generate interest (retweets, likes, and mentions) for most of the 20th November and for many subsequent days afterwards. The latest retweet of this tweet was today: 16 days after the original tweet! I find this amazing especially as the original slide deals with the topic of genome assembly. At the time of writing the tweet has had 369 retweets and 277 likes

I'm pleased that people have found my jigsaw analogy useful. Some people commented that this isn't the best possible analogy and pointed out various ways that it could be more technically accurate (including suggestions of shredding copies of books and trying to piece together the original).

While I accept that this isn't the most scientific way of depicting the many problems and challenges of genome assembly, it is hopefully an accessible way of illustrating the problem. Nearly everyone has tried putting a jigsaw together, but not everyone has tried reconstituting a shredded book. My exit seminar was aimed at a very broad audience and so I pitched this slide accordingly.

People can follow Jenna on twitter (@FoodBeerScience) and should, at the very least, check out her awesome twitter bio. If you want to know more about her work, here is a recent review of IME that she wrote:

Why I twitter

I cannot sit on the fence. I like twitter and what it offers. I have learned things I never would, built genuine relationships with international people who I would have perhaps have only met over a quick coffee at a conference. And I have changed the way I speak about science.

This post by Mark Brandon sets out nine great reasons as to why he finds Twitter so useful, many of which relate to science communication.

I believe twitter is a strong positive for science, and it is a worthwhile investment of your time.

I completely agree with just about everything he has to say. It's a good list.

ACGT: a new home for my science-related blog posts

Over the last year I've increasingly found myself blogging about science — and about genomics and bioinformatics in particular — on my main website (keithbradnam.com). Increasingly this has led to a very disjointed blog portfolio: posts about my disdain for contrived bioinformatics acronyms would sit aside pictures of my bacon extravaganza.

No longer will this be the case. ACGT will the new home for all of my scientific contemplations. So what is ACGT all about? Maybe you are wondering Are Completed Genomes True? or maybe you are just on the lookout to see someone Assessing Computational Genomics Tools. If so, then ACGT may be a home for such things (as well as Arbitrary, Contrived, Genome Tittle-Tattle perhaps).

I've imported all of the relevant posts from my main blog (I'll leave the originals in place for now), and hopefully all of the links work. Please let me know if this is not the case. Now that I have a new home for my scientific musings —  particularly those relating to bioinformatics — I hope this will encourage me to write more. See you around!

Keith Bradnam

Top twitter talent: UC Davis genome scientists lead the way

The Next Gen Seq website has just published its 2013 list of the Top N Genome Scientists to Follow on Twitter. Over 10% of this International list of scientists are all staff or Faculty here at UC Davis, which says a lot about the quality of genomics talent here on campus:

It is also worth mentioning that there are so many other people at UC Davis who work in genomics and bioinformatics and who use twitter to effectively communicate their research and engage with the community. E.g.

  • @dr_bik - Holly Bik (Postdoc in Jon Eisen's lab)
  • @ryneches - Russel Neches  (Grad student in Jon Eisen's lab)
  • @theladybeck - Kristen Beck (Grad student in Ian Korf's lab)
  • @sudogenes - Gina Turco (Grad student in Siobhan Brady's lab...and winner of best twitter account name)

Great to see UC Davis recognized like this.

 

Update

Updated at 9:09 am to reflect that Next Gen Seq have now added Vince Buffalo to the list (he was apparently meant to be on the list anyway).

How well do UC Davis Graduate Groups communicate their work to the wider world?

PhD students in our lab are mostly split between a couple of UC Davis's many graduate groups. A conversation with some of the students today about 'outreach' and 'social media' led me to wonder how well these graduate groups are communicating their presence to the outside world. The simplest ways of doing this would be:

  • maintain a current website for your graduate group (i.e. with news items)
  • use Facebook (ideally with an open group)
  • establish a blog
  • use twitter

I looked at 11 different graduate groups to see how well they ticked the above boxes. I might be missing some blogs, Facebook groups, and twitter accounts, but if I can't find the relevant details from a Google/Facebook/Twitter search, then I'm assuming that others won't discover them either. This is what I found:

Headline links take you to the home page for the respective graduate group.

Biochemistry, Molecular, Cellular and Developmental Biology (BMCDB)

  • No news page but has an actively maintained blog (easily linked to from above site)
  • Facebook group (open)
  • Active twitter account

Biomedical Engineering (BME)

Biostatistics

  • No news page, though there is a short 'announcements' box on main page
  • No Facebook group
  • No twitter account

Ecology

Epidemiology

  • No news page
  • Facebook group (closed)
  • No twitter account

Integrative Genetics and Genomics (IGG, formerly GGG)

  • Has a news page, but only one item from 2013, remaining items from 2009 and 2008!
  • Facebook group (closed, and have to search for GGG or IGG to find it)
  • No twitter account

Immunology

  • No news page
  • No Facebook group
  • No twitter account

Microbiology

  • No news page
  • Facebook group (closed)
  • No twitter account
  • Has separate website
  • Other: website told me I had to enable Javascript to view their home page even though I have javascript enabled

Nutritional biology

  • No news page
  • No Facebook group
  • No twitter account

Plant Biology

  • No news page
  • No Facebook group
  • No twitter account

Population Biology

  • No news page
  • No Facebook group
  • No twitter account

Please let me know of any updates or additions that I can make to this list

So overall it is pretty poor. BMCDB outshines the others, though BME and Ecology also have a good presence on the web. In many ways, I think it looks worse to do these things badly than to not to them at all. Closed Facebook groups don't send out an inviting message, and having a 'news' page for your graduate group with items from 5 years ago, also sends out the wrong signals.

It takes time and effort to maintain a social media presence, but it doesn't take much effort to at least maintain a news page or simple twitter account (even posting just 1–2 times a week is better than nothing).

Furthermore, the ability to show that you can communicate your work to the wider world is of increasing relevance when applying for grants. It can also raise your profile with your peers and be a useful addition on a resume that helps you stand out from other applicants. Finally, starting a blog or twitter account also helps you hone your writing skills (the latter is great for making you think about how to condense complex thoughts into 'bite size' chunks).

I hope that some of UC Davis's graduate groups make more of an effort in this area (and of course the same can be said for many of UC Davis's departmental and lab websites).

 

Updated 26th September: Added details of some graduate groups that do have blogs and/or websites but which, unhelpfully, are not linked to from their official graduate group webpage.

Slides from a talk on 'the art of good science writing'

I presented in our lab meeting today and used the occasion to talk about writing for science (as well as writing in general). I get to proof-read a lot of texts in the lab (scholarship applications, resumes, grad school applications, manuscript drafts etc.) and I have noticed some common issues that crop up a lot. This talk goes over some of these problem areas and offers some suggestions.

Thanks to the students for letting me share some of their writing.