Thursday, 7 August 2014

My response to some of the Open Access Myths

This morning there was an #ECRchat on twitter about Open Access publishing.  It's prompted me to write this post because there seem to be some pervasive myths about OA which stick around despite OA advocates best attempts to dispel them .So here's my attempt with 2 of them. It may come across as kinda angry, that would be because it makes me kinda angry.

1. Open Access publishing is less prestigious.

This is the comment I loathe more than anything in debates about Open Access, because although I don't know about other fields, in Genetics it's just not true. I've ranked journals by Impact Factor despite it being a useless metric (debate for another time).

Nature Genetics - 29.6 - 6 month embargo, then Green OA encouraged
Genome Research - 14.4 - 6 month embargo, unless author pays
Molecular Biology and Evolution - 14.3 - Pay for OA
Genome Biology - 10.5 - Open Access
PLOS Genetics - 8.1 - Open Access
Genome Biology and Evolution - 4.5 - Open Access
European Journal of Human Genetics - 4.2 - Pay for OA
Heredity - 3.8 - 6 month embargo, then Green OA encouraged
PLOS ONE - 3.5 - Open Access

So from this list (which I promise I didn't cherry pick to make a point) you can see that other than the Nature journals (Nat. Gen. & Heredity) you either get Open Access as standard, or you can pay to have open access (a whole 'nother can of worms).

I don't think anyone would think that publishing lots in Genome Biology or PLOS Genetics is going to be bad for your career, so at least in genetics, it's just ridiculous to say that OA is less prestigious.

2. Open Access lowers standards

When people talk about this they are conflating a number of different topics: Open Access, Journals which publish without regard to the subject and whether it's 'cool' or not and spam journals.

Lets get spam journals out of the way.

It's not really a problem. Have you seen those emails? Why would you ever publish there? Sure maybe some early Phd students might get duped, but they should have advisors who would protect them from that sort of mistake.  If still in doubt, check to see if the journal is listed here:

So now we'll tackle the difference between OA and journals that publish without regard to fashion, impact, etc.

Most of these journals are open access, e.g. PeerJ and PLOS ONE. But there are plenty of Open Access journals that are really difficult to get into e.g. Genome Research and PLOS Genetics.  Are you really suggesting that the Open Access policy of PLOS Genetics is lowering standards?

Regardless of the journals policy as regards topic, all of these journals have rigorous peer review processes, and it's mostly the same people reviewing for a range of different journals, so there isn't a difference in quality of reviewer.  Some journals (such as PeerJ) are now publishing the review process alongside the article, so you can even check how rigorous it is.

All journals are different and as far as I can see, the only thing that is consistently different across the board between OA journals, and those which aren't, is whether they make your institution's library buy a subscription in order for you to read the articles.  Seriously, that's the whole difference.

Monday, 12 May 2014

Post Phd Story

While perusing twitter the other day I came across a post by Jacquelyn Gill asking about people's post Phd stories.  There are a lot of "why I left academia" stories and you inevitably hear about the superstar stories, but there are a whole lot of us in the middle who never tell their post Phd stories.

So here's mine, take what you will from it.

I did my Phd at the Brighton & Sussex Medical School, and I liked what I was doing there, but I couldn't see myself staying on for a Postdoc (I don't think my supervisors could either...), the topic was fine, but I wasn't really excited by it towards the end of my Phd, and my main supervisor & I used to rub each other up the wrong way.

I had 3 years of funding, so as the three years drew to a close, I started to look for another job.  I was writing up at this point, but I was still quite a way from having the thesis finished.

I applied for a couple of jobs, one at Nottingham University, where I wasn't shortlisted and one at the National Genetics Research Laboratory in Manchester.  It was a 'Clinical Bioinformatician' job (I wasn't really sure what that was, when I got the the interview it turned out it was pretty much a made up job title...) creating tools and teaching bioinformatics for the NHS.

I was offered the job, I took the job, and I moved to Manchester.  For ~ 6 months I was working at NGRL during the day and doing my thesis at night.  Having had no experience with patient centred bioinformatics/genetics, I didn't know how I would take to it.  It turns out, it's not really my thing.  I'm definitely more a blue skies researcher type. However, it was a great job to have while I was writing up my thesis (BTW, it's totally possible, to write up with a new job.  It's not fun, but it's totally possible).

A few months after I'd passed my viva, I decided to start looking around to see if there were any postdoc positions which might be more my style.  I wasn't going to just apply for anything as I was fairly happy in the current job.  Almost immediately, a job came up at Nottingham University (different PI and campus to the last job), I went down for an informal chat before applying and it seemed like a great position.  The PI encouraged me to apply, I did, and I was offered the job.

Three years has gone by since then and I'm now in a second postdoc at Rutgers University in New Jersey.  I'm trying to find either my own money or a lectureship and it's hard.  But I left academia once and came back, so I know that this is the life that makes me happy.  Maybe I'll leave again if things don't work out.  But right now I'm sticking it out.

Thursday, 9 January 2014

The restorative powers of a good conference

It's all been seeming a bit much recently. The year long slog to find a second postdoc, and then finding a really great position that forces me to live halfway across the world from my wife.

The plan for this year (publish enough to seem competitive for fellowships) was starting to seem unrealistic & I could see myself staring down the "what-else-could-I-do" route.

And then I came away to my favourite conference, met up with some old friends, met lots of new interesting people. And they all seem to think I can do this (or if not they're nice enough to do a good job of hiding their doubt!).  I always come away from a conference rejuvenated and with new ideas for what ever project I'm working on, but this conference has reignited my desire for this career. I want to be working with these people, researching the kind of things that make them (and me) excited.

I still know how hard it's going to be, but I've got my drive back, so thanks popgroup47!

Thursday, 12 December 2013

Does playing the publishing game make us hypocrites?

As I'm sure any scientist or academic who spends any time on the internet will know,   Randy Schekman (recent nobel prize winner) wrote an article in the guardian about how we shouldn't be publishing in 'Glamour mags' like Nature, Science and Cell.  Of course his caveat is that we should all publish in his not quite glamour mag (because its open access) e-Life.

Obviously, there's been a lot of talk on twitter about this...

I've seen a lot of "Hurrah!" responses and a lot of re-post with out much comment. But there's also an undercurrent of people who aren't as happy as might be expected.  Mick Watson wrote a really good blog post explaining why some people are annoyed at Schekman and feel he's a hypocryte and that we shouldn't be praising him for something that will ultimately help him out (i.e. get us to publish in his new journal instead).

While I really respect this position, I have to disagree.  While maybe he doesn't deserve praise exactly, we need these people.  He's won a nobel prize, he's published lots in these closed-access journal, his credentials are sorted. So now he has both power and nothing to lose, he can say what he likes.  

I know from trying to persuade my former Boss to go with PeerJ, that people in this position (not that he's won a nobel prize!) aren't always interested in change, they know the system, they've worked out how to do well in the system and while they don't have much to lose, they also don't have much to gain by changing it.  Those of us without much power (Phd student, postdocs, ECRs), we may be idealistic and really want the paradigm to change, but we can't do it on our own, we need the senior people.  I know I have pressure from colleagues and bosses to publish in these journals if I can. Committees for fellowships and future jobs lap these things up, and I'm not in a position to change that.  But Schekman is one of the lucky few who are.

I think on our way up, all of us play the game to some extent.  As long as we know that we're playing the game and doing all we can to change the rules at the same time, I don't think that makes us hypocrites.  We just have to not end up believing in the game if we manage to win it.

Monday, 9 December 2013

Sharing too early or just early enough?

I've been seeing a Guardian article around twitter this week which has kind of hit a nerve.  It was this post about having your blog plagiarised. Not because I've had the same thing happen to me, but because I've been known to be a bit worried about telling people too much, too early about what I'm working on.

This is the second year that I'm going to Popgroup (The UK population genetics/evolution conference) and not talking about the work that I'm hoping to publish in the near future, because we're too worried about plagiarism (Last years work ended up in this paper).  This was due to the fact that both analyses were fairly simple to do, they just hadn't been done that way before, and someone could pretty easily have gone and replicated the study and beaten us to the punch.

But would they?

Although I, along with my colleagues, wanted to protect against competitors, is it actually that likely that anyone would have gone and replicated it?  After all, there would be a room full of people who saw me present the work, it'd be pretty obvious if someone who was there then went and published it a couple of months later.

Science is littered with examples of people 'borrowing' bits of other peoples data (the whole Watson, Crick, Franklin debacle being the main one we think about in genetics).  But, maybe we should give people the benefit of the doubt more.  There are lots of advantages of talking about your science as it progresses, people can pick you up on mistakes and pitfalls and you can get new ideas to improve the work.  So, in the spirit of open science, I think I'm going to try to be a bit more open in the future, I hope it doesn't come back and bite me.

Wednesday, 13 November 2013

Thinking about the next step

So I'm 2 weeks in to this postdoc, which means I pretty much have to start thinking about the next step now.  It seems slightly ridiculous, but I felt I left it too long to start thinking about it during my last postdoc, and its possible that this job may only be 1 or 2 years long anyway.

So what is the next step? I'm on my 2nd postdoc.  Two seems fairly justifiable to me, particularly since I've moved to a really great lab in the US for the second one (where I'm hoping to pump out a lot of papers).  Three would probably be less justifiable...

So this leaves three options a) Lecturship b) Fellowship c) Doing something else.
Lets throw c away now, I'm not ready to contemplate that yet (although one day I might).

When I was looking at postdoc jobs this time around, I did a bit of looking at Lecturing jobs too.  The issue with these seems to be money, in that you need to have had some of your own to be seriously considered, which excluding a small travel grant, I haven't.   Which leads us onto Fellowships.  An enormous unknown for me, its hard to even know where to start really, although I guess by seeing what I'm even eligible for.

A quick look around the internet showed a big lack of information about applying for Fellowships written by people who have do it.  There are quite a lot of pages written by specific universities on their policies, but not much about the experience.  Does anyone know of any links?  I'll continue to document here anyway.

Friday, 8 November 2013

My problems with AcWriMo

AcWriMo stands for Academic Writing Month.  It came about as an off shoot of NANOWRIMO, which stands for National Novel Writing Month and is basically a challenge to try and write a novel in a month.  AcWriMo was started by Charlotte Frost, and if you'd like to learn more, I recommend going to her blog which you can find here -

Both last year and this year I have signed up to AcWriMo full of good intentions to improve my writing habits and to become more productive.

Last year I gave myself a word count for each day, but I think I ended up giving up halfway through as I wasn't really in the right place in my research to do lots of writing, just finished one project, too much actual research to do for the next one.

So this year, I decided that I would just block out an hour a day for writing.  Any writing e.g. this counts as part of today's hour.  But I can already see myself slipping off the wagon.  So I'm going to try and work out the reasons for this and use my realisation of these to re-new my vigour.

1. New Job - The 1st week of November (Academic Writing Month) has coincided with the first week of my new postdoc.  I think because it's a new job and I've had quite a lot of admin things I had to get done etc. I've not found it easy to say "This is my writing hour".  But a lot of those things are over now, so from Monday 9am-10am is going to be my writing hour and we'll see how that goes.

2. I don't have a paper in need of writing up - I think when I envision AcWriMo I think about having a bunch of research that I've done over the Summer that needs writing up into a paper, spending November doing that, and then submitting said paper at the beginning of December.  Of course the big problem with that is that I don't write like that, I do it as I'm going along, so what I actually have is a half written paper that needs more analysis.  However, this year rather than a word count, I've just got an hour I need to write in.  That leaves a lot of other hours to do research in.  Also, since I'm starting some new projects, there's a whole bunch of literature searching to write up.

3. I find writing in chunks kind of boring - I'm going to try and use pomodoros to get over this one.  It makes it into a kind of game - and games I like.  

Does anyone else have a problem like this, i.e. they find the idea of something like AcWriMo really exiting, but the reality seems like hard drudgery?  Anyone got any ideas of how I can buck myself up?