Monday, August 12, 2013

Paper one - a PhD's journey


Each journey to the publication of your first peer-reviewed paper for a PhD student can be wildly different.

So in an act of relief or perhaps frustration I thought I would share with you the journey mine took.
I think it would be fair to say that the language I use is a reflection on the emotions I went through at the time but as we all know hindsight is a wonderful thing, so hopefully I manage to round it off with a more level view of the ordeal. See there I go already.

Over a year ago on July 9th I received my first set of data from the large Hubble Space Telescope program headed by P.I David Sing, my supervisor. The data is near-infrared low-resolution grism spectra of the hot Jupiter host star HAT-P-1 from Hubble’s Wide Field Camera 3.
My job is to see if we could identify any chemical signatures in the atmosphere by producing a transmission spectrum, a measurement of the planets radius at a number of different wavelengths.

After reading a lot of papers in great detail and dissecting a few codes so I could write my own, I had my preliminary results in place. Just in time for my 2nd year assessment presentation at the beginning of October to the whole college of Physics. As I am still here I am going to assume it went well.

Next is when the delusions start. I remember thinking great I have results. I had the models from the theory fairies and it all looked great. We had water!

The hard part was over; I could now go on my holiday leaving my first draft with my supervisor to look over.
I know what you are thinking, poor sad naive/delusional student, don’t worry so am I now.
I remember arrogantly wondering how other people had such trouble and that it all was very easy - I had my transmission spectrum, I had a pipeline to reduces the data quickly, and the paper is written – it will be out in no time.
You will be glad to know my internal monologue and ego have been taken down a few pegs since then.

Over the Christmas break I received similar results from a few of our collaborators, which nicely backed up my own. So 6 months after the data was received I sent off the paper to the CO-I’s, people whose names would appear on the paper who either directly contributed to the content of the work or were part of the group who acquired the data used.
Now as a lowly PhD student you are on the lowest of the unevenly distributed rungs of the academic ladder and with an increasing number of CO-I’s the percentage of responses you will receive reduces considerably. So deploy your patience and give it some time it will more than likely be worth it. By the middle of February I had naively named my LaTeX document ‘final draft’ and vowed to never have to run my seizure inducing code again - in hindsight perhaps removing all of the plotting commands would have been the best idea but seeing exactly what is going on in your code is very useful.
Of course this bout of confidence would not last long and just 3 weeks later I was on ‘final draft 7’. Which turned out to be the lucky one that once again got sent around to the CO-I’s; this time with a two-week deadline, which of course they frustratingly defied.

I think it is safe to assume that this was when my housemate learnt to not respond to my external monologue as I paced around the apartment with pen and paper in hand endlessly checking for mistakes or searching for clarity. Only one problem, now I can never get him to respond as he assumes everything I say is my brain externally questioning itself and the world around it – to be honest it is scarily a more accurate assumption than it once would have been.

The Trumps card for our observations
Finally on April 4th I uploaded the manuscript to MNRAS and satisfyingly clicked submit.

I wish I could tell you that were the end, I truly do, but peer review rightly requires a peer response. Now when I say peer I mean someone else on the academic ladder, and as I am a PhD student and this is my first paper, that peer will be several seemingly unattainable rungs above me on that ladder.

Once you have submitted your paper and a reviewer has been selected you just have to sit and wait. We were lucky to get a response within a month and quickly got back to work. The reviewer recommended moderate revisions before it could be reconsidered for publication, which is the middle ground between major and minor revisions. I was really happy with some of the comments, I remember printing them out and highlighting them according to how much work needed to be done. There were a few that would require a lot of work and it took over a month with over 100 program re-runs before the responses were diplomatic and constructive enough to send back with the revised version of the manuscript.

The comments and the revised manuscript then are sent back to the reviewer for them to look over your changes and are given an additional 3 weeks to respond. They can then either then recommend more revisions or suggest to the editor that the manuscript is ready for publication. Just before the 3-week deadline we received a second report again with moderate revisions, something I would have been again happy with if only the response was logical and correct which, as I am sure you can guess by the tone it was not. I was having my first lesson in scientific politics.

After taking the evening to calm down in the pub with a glass of wine and some friends I sat down to write the response. Luckily my friend was on hand to moderate my responses before I could even show them to my supervisor. Let’s just say that the phrase ‘it appears the reviewer has misunderstood …’ was used in the response more than once. Which is a far more diplomatic statement than I could conceivably come up with myself. But the changes were quick and trivial so to appease the reviewer we made them and re-re-submitted it the next afternoon.


Four days later we got on a plane headed for St Andrew’s and this years RAS National Astronomy Meeting where my work would be presented as a poster and through a press release along with a colleagues work.
Three weeks later at the end of the reviewer’s deadline we received another set of comments and a re-re-re-revision was made. This time with some more trivial corrections, adding plots, tables, and references, I waved it goodbye and revision III was submitted.

But we have still not quite reached the end; I did warn you it was an ordeal.

Another three weeks passed and we received our 4th set of comments from the reviewer, thankfully this time with only ‘minor’ revisions suggested before consideration for publication was suggested. Those minor suggestions, ‘Please add in reference XX and reference YY to the manuscript’ and guess what, those papers had an author in common with all previous papers suggested by the reviewer in previous comments – it is safe then to assume whom it is at that point.
Water, water, everywhere - well at least in HAT-P-1b's atmosphere

And it is here that you find me over a year since I first received the data to the day that it is up on Astro-ph/ArXiv. Although it has been an incredibly frustrating journey, for which I am forever marked with my first grey hairs, I am truly grateful because although patience is most certainly still not in my nature some aspects of caution have been added, and the paper is now far better than it was before.

See I told you I could end on a happier more leveled view of it all.

Thank you for joining me on the journey let’s hope the next one is not so stressful as I would very much like to keep my brown hair just a little longer.