A Blog Around The Clock

Bill Hooker blogs on Open Reading Frame, is a vocal proponent of Open Access publishing, has attended both Science Blogging Conferences to date, and I am happy to call him a friend.

Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Who are you? What is your background? What is your Real Life job?

I’m a molecular biologist.  I did my graduate degree through the University of Queensland, cloning and characterizing proteins from Schistosoma japonicum with potential as vaccine targets.  My first postdoc was with David Harrich, working on the fine detail of HIV-1 replication.  I moved to the US for personal reasons (married a native), and changed fields because most of the HIV work here in Portland, OR is focused on the local primate center, and requires more immunological expertise than I have.  Right now I work with Peter Hurlin, and my focus is on the basic biology of Mnt, a probable tumor suppressor.  I think it’s going to turn out to be quite an important protein in cancer and development, but to date it remains surprisingly under-studied.

But “who am I?” is a much larger question, and by its very nature makes me probably the last person to whom you should look for a direct answer.  I should think anyone who really wanted to know could get as good an answer by reading my blog as by any other method.

What do you want to do/be when you grow up?

i-9222ee4ff4672d14a9ec209f92de652c-an SBC Friday dinner 046.jpgA grownup — that is, a grownup scientist, in the Janet Stemwedel sense.  When Janet talks about “being a grownup in your own profession” she means seeing yourself as a full partner in that profession, with all of the obligations and opportunities that entails.  It’s a subtle transformation that I didn’t have a good name for until Janet’s phrase.  I want to step up, take my own risks and make my own mistakes, and not continue to feel as though I should be checking in with one authority figure or another.

Further, I want to do my research as openly as possible.  Open Source Software is a mainstream concept, and Open Access (publishing) is getting to be one.  What’s not so widely known is the idea of Open Science, which is the application of the same principles — knowledge as a public good, cooperation over competition — to the entire enterprise of research.  The defining edge case for me is Jean-Claude Bradley‘s Open Notebook Science, a wonderful term that is almost self-explanatory.  Jean-Claude is the first to acknowledge that not all research is suitable for an Open Notebook, but I’d like to get as close to that ideal as I can.

Can you tell us more about your scientific research?

As you know perfectly well, I (like any scientist) can talk about that until your eyes glaze over.  But I’ll spare your readers, and try to be brief. 

The small bHLHZIP protein Max is the center of a very important transcriptional control network, the best known player in which is the proto-oncogene MYC.  Depending on how you estimate it, dysregulation of Myc protein is involved in 30-70% of human cancer.  Since mice lacking MYC die very early in gestation, and conditional knockouts of MYC cause a variety of defects, this network is also important in development.  Consistent with that observation, other members of the network play important roles in differentiation.  My main focus is on one such protein, Mnt, which also functions partly as a Myc antagonist.  MNT knockout in cells can rescue the growth arrest caused by MYC deletion, and although MNT knockout mice die late in gestation, conditional MNT knockouts cause tumors similar to those caused by overexpression of MYC.  For such important proteins, we still know surprisingly little about them.  For instance, what I’m doing now is trying to work out the details of post-translational regulation of Mnt (it’s phosphorylated, but where? and by what kinase?) and how that relates to the cell cycle (what does phosphorylation actually do to the molecule’s properties and functions?).  The bigger picture is that Peter, my boss, has some really interesting ideas about connections between mechanisms that underlie both cancer and developmental defects, and so everything the lab does is in a sense digging down towards those mechanisms to see whether Peter is right about the commonalities there.

When and how did you discover science blogs?  What are some of your favourites?  Have you discovered any new cool science blogs while following the Conference?

I think the first science-themed blog I remember reading was Genehack, by computational biologist John Anderson.  (I don’t think the word “blog” had been coined yet, it was just a “website” back then.)  I remember when Nodalpoint started up.  I have also been reading psychiatrist Eliot Gelwan’s Follow Me Here for a long time, but he covers a lot of stuff besides science.  

As to favorites, I simply couldn’t pick.  Even my blogroll doesn’t cover all the science blogs I think are worth reading, because I just can’t keep up.

You are a strong proponent of Open Access publishing.  What was the personal evolution of your views on this topic? Where did it begin?

I was online when things like GenBank and Project Bartleby started up, but I never made the broader connection.  Looking back, the earliest direct influence I can remember was Stefano Ghirlanda’s Free Science Campaign, which started in the late 90′s and has since gone offline.  It is an enduring regret that, although I agreed very strongly with his goals, I didn’t sign his supporters page.  What seems deeply weird to me now is the reason I didn’t do so: I was reluctant to put my name to anything on the internet.  It was a new world to me then, and I wasn’t at home in it.  These days, of course, I am a signatory on every OA petition and declaration that comes my way!

I also remember following Harold Varmus’ doomed E-biomed proposal, which did manage to give us PubMed Central.  All of those ideas sort of fermented away in the back of my mind until I came across BMC, PLoS and Peter Suber’s blog — I honestly can’t say which I found first — and then the light went on and I realized what OA really meant.  I’ve been doing my little bit to help the cause ever since.

How is a scientific paper going to look in 20 years from now?  How is that going to affect the way scientific research (and teaching) is done?

Over the next 20 years, the two most important things that will happen to the scientific paper are: universal adoption of Open Access, and the richly deserved death of the Portable Document Format.

Although it will do a number of wonderful things, Open Access won’t dramatically change the way a paper looks, at least not in the next 20 years.  Both because researchers are a conservative bunch, and because the format has served well for a very long time, I would guess that papers will look something like they do now — Intro/Methods/Results/Discussion — for some decades yet.  The most important things that will change in a 20 year timeframe are the level of detail available with a single click, and the number of entities which can understand the paper. 

Right now, even if you can access a paper what you get is pre-digested in the form of a PDF file — useless for anything except being read by humans (which, of course, is very useful indeed — but nowhere near as useful as a paper could, and should, be).  If there is any supplementary data, which there usually isn’t, it’s another bloody PDF!  In 20 years, something like XML will provide a way to make papers a machine-readable platform for accessing data, not just a pixelated proxy for a hunk of dead tree.  Instead of photocopying that graph three times at 200% so as to be able to draw lines on it and estimate the underlying values, you’ll be able to grab the raw data into your own favorite graphing application, so that you can re-work it and look at it from your own angle.  You’ll be able to zoom in on that spectrum and see the fine details.  You’ll be able to get an unretouched version of that photograph and do the Photoshop work yourself, so as to emphasize whatever you’re interested in.  All of this will be possible, not by writing to the authors and waiting three months for an answer, but with a single click right from the paper itself. 

The other thing that this sort of markup will do is to greatly enhance the number and scope of research tasks that can be automated.  We already rely heavily on search and filtering interfaces (Pubmed, Google, GenBank, and so on) to keep us afloat in a sea of information, and that situation is only going to intensify.  When machines can read papers, they will be able to do something no human can do: read every paper, and find connections among them all.  For a taste of what this might be like, check out iHOP, a text-mining navigation interface to the research literature.  Now imagine what iHOP could do if it could not just read text, but could place that text in context, and then again what it could do if it could access data as well as text.  (Note also that none of this makes sense without OA: good as it is, iHOP is currently crippled because it can only pull sentences from abstracts.  Imagine what it could do with the full text of all those papers!  To fully realize the power of machine readability requires that the entire knowledge base be Open Access.)

What that will mean for research is speed.  You can already see it happening in physics, where OA has been the de facto norm for more than a decade thanks to arXivBrody et al. showed that, in the high-energy physics section, the time between deposit in arXiv and citation in another paper has been dropping steadily since the arrival of arXiv in 1991, and was cut roughly in half between 1999 and 2003.  That’s the research cycle — the uptake of published ideas in further work — accelerating in real time.  Multiply that by the power of text- and data-mining, driven by the combination of OA and machine readability, and you get a tremendous acceleration in the rate of scientific progress. 

I’m not a teacher, so I’m hesitant to make predictions about that field — but what is clear is that teachers and students will have much greater access to detailed information.  On that basis, I guess I’ll venture one (hopeful) prediction: science teaching will focus more on primary sources, on the actual data rather than predigested information in textbooks.  Rather than trying to absorb a body of knowledge being handed down from on high, learning science will become much more like doing science, with students being asked to think, explore and experiment rather than simply memorize.

Is there anything that happened at the Conference – a session, something someone said or did – that will change the way you think about science communication, or something that you will take with you to your job, blog-reading and blog-writing?

Someone — I think it was Moshe Pritsker from JOVE — suggested a possible solution to the scooping problem, which we talked about in one of your posts.  Writing about the conference afterwards, Janet Stemwedel observed that a good conference feels like home, which is exactly how I felt at both SBCs and something I’m going to keep in mind whenever I am involved in organizing any kind of meeting.  The session on open access in developing countries was amazing, and I’ll be thinking about the things I learned there for a long time.  It certainly changed my thinking about science communication, since I tend to focus so much on “first-world” problems in that field — whereas there are all these thousands of scientists for whom detailed definitions of Open Access are all very well but close to meaningless until, say, their dialup connection works more than three days a month.  In conversation over dinner, Aaron Rowe taught me what aptamers are — I’d never heard of them! — and I was just blown away by the potential of these reagents.

In more general terms, I have returned home from each SBC charged up, full of ideas and positive energy, and I definitely take that into my work and my blogging.  My wife says she wishes I could hang out with the people from SBC on a regular basis, as it does me such obvious good.  If I should ever get a foot on the faculty ladder, one of my overarching goals will be to make working in my lab feel like being at SBC every day.

It was so nice to see you again and thank you for the interview.

Likewise, and you’re welcome; and thank you for doing this series of interviews, which I am thoroughly enjoying.


Check out all the interviews in this series.