265 days to go: What on God's Green Earth Happened to June?

Magnolia in Flower at the Botanics, Edinburgh

How did this happen!? It feels like I only posted the last update a week or two ago, and now more than a month has passed?

*scanning calendar*.

Oh. Right.
Seems like I've since then learned all the ins and outs of the UK renting system (stay tuned for upcoming rant/post on that subject), gotten a pile of moving boxes dumped in my place, found a new apartment, moved house, been a week to sweden and  finally been to St Andrews  for a three day conference ( for which I spend about a week preparing a poster).
Time spent on thesis writing: less than I'd like.

Oh well, at least there's some areas  in which I've been fairly productive since we last spoke:
Me and the supervisors sat down and went through the paper bit by bit. Well, for two hours, at which point we has barely finished the introduction, but still.

The microarray data is still causing loads of head scratching. I managed to isolate one clearcut results, which is great, but that also makes the other indications that the data is composed of pure noise a bit trickier to interpret. It's gonna be interesting to see where this will end up. At least I think I have a clear plan for how to get some methodological research out of it now.

So that's chapter 2 and 3. For the lit review, I've now signed up to an online boot camp to kick start my progress over the next week. Watch this space!

Oh, and I made a poster for the Biometrika Channel networks Conference last week. Got some good chats out of it, a Best Student Poster award, two books and a voucher :-).

One thing I would like to ask you people reading this: When a paper you're writing  has yet another set of revisions with red ink all over the page, a paper that you've been reading over and over and over.  How do you get going and try and make sense of all suggestions, and try and be creative?
I'm really struggling at the moment  - I was hoping to do paper revision on monday, tuesday,wednesday,and thursday this week, but only managed a bit on tuesday, and got stuck really quickly. Fot some rteason, it's almost as if I'm scared of trying to read those comments again, and keep putting it off.

For today, I tried to make a structured todo-list for how to approach the suggestions:

1. Re formulate suggestions as prompts
2. Identify which papers that are  needed for each prompt
3. Freely write from the prompts not needing papers for 10-15 mins each
4. Incorporate free writing as text
5. Read papers needed
6. Reiterate from 3)
7. work on something else when my mind is saturated.

It worked for about an hour and a half, but then life got in the way. And I'm still not sure how to avoid getting stuck. Any tips or sympathy much appreciated!

'til next time,
Gustaf

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Current status of the thesis:
Summary: 774 words, rough sketch.
Introduction: 861 words, rough draft.
Chapter 1: 837 words, rough structure draft.
Chapter 2:5451 words, In yet another revision phase (getting closer though)
Chapter 3:300 words, outline in place,  got some results, goal of what science to get
Chapter 4: 0 words.
Chapter 5: 0 words.
Bibliography:0 words.
Appendix: 0 words.

Total: 8223/50000 words. 0 more since last blog. (gulp!)

Average words per day needed until 01/04/2014: 158. (it keeps rising....)

304 days to go: passed upgrade meeting, cool results, and paper submission in sight. Also work routine.

I’d had a very varying working flow since I last wrote. Some days of working until late late late, some days of literally doing nill, and some days of real “aha!” experience. Overall, I’m pretty happy with what the work that’s been done, but my routine has been in shambles which means that happiness and healthiness has taken a hit.
Ideally, my work routine is something like:

• Get up early-ish, meditate, and eat breakfast (without reading/internetting).
• Have some coffee and spend 10-20 minute freewriting<ref!> On the ipad about work-related thoughts and do a todo list.
• Sit down with the computer, go through my work-related Buddhist contemplations, and start working with a pomodoro timer in 25-50 mins intervals without checking email or using Internet.
• When I’m having lunch, go away from the desk, eat and read something interesting, check email, and take a half-hour walk outside to counter the post-lunch coma.
• Have an evening free of work, and get to bed at a reasonable hour.
  

When I manage to keep on this track, I tend to have a great day, happiness wise and productivity wise. But if I sleep in and start the day faffing about on the net, it’s much more tempting to procrastrinate, compensate by working late, and sleep in the next day. I might get a decent amount done, but the happiness factor is low, and the guilt factor is high. And that’s been the predominately pattern the last few weeks, with some exceptions (like today).

Nevertheless, I have gotten stuff done. I had an upgrade meeting with external examiners two weeks ago, for which I had to write a few pages on my thesis introduction, and make a plan for the rest of my time up ‘til hand-in. (See the fancy GANTT chart above). The meeting went surprisingly well - it’s a rare pleasure to hear other people enthusiastic about your research!

My eternal first paper seems to have an end in sight; I managed to make this interesting simulated example using the uk 2007 Bluetongue outbreak.  What it shows is that if  the outbreak had beens  spreading for two months before being discovered,  then one could have tested a bunch of animals and gotten a pretty good idea of the trend despite not having observed it at the time!
 With this and another example in place, we’ve decided to submit the paper by the end of June to Proceedings of the Royal Society Biology (gulp…). So overall, things are definitely moving forward - there's hope yet.


Current status of the thesis:
Summary: 774 words, rough sketch.
Introduction: 861 words, rough draft.
Chapter 1: 837 words, rough structure draft.
Chapter 2:5451 words, revised yet again since last time.
Chapter 3:300 words, outline in place, research timeline now set up.
Chapter 4: 0 words.
Chapter 5: 0 words.
Bibliography:0 words.
Appendix: 0 words.

Total: 8223/50000 words. 878 more since last blog.

Average words per day needed until 01/04/2014: 137.

338 days to go: current state of the thesis

Since the last time I updated, the first week was quite productive, and the second week terribly unproductive. Three meetings, and some more research work for my second chapter. I haven’t been doing very much writing new stuff; much of it had been incorporating feedback from one of my supervisors about the style of formalization the paper I’m writing should have, and discussing with my other supervisor about the structure of my introduction. Little done in terms of number of words, but hopefully a fair lift in the article quality.
The difficult thing about editing stuff is that (at least for me) it is easy to feel like I’m just stuck in one place forever and ever - getting an objective measure of how much progress I’ve actually made that can convince my self doubting mind seems nigh impossible.
For the coming weeks, I have an upgrade meeting coming up in a few weeks time that is intended to check that I’m on track for finishing my phd. For this I need one to two draft chapters written, a cover letter introducing my research, a list of “training"a planned structure of the thesis, and a concrete time plan for the coming year. I also got a poster accepted to a conference in July, so that needs to be written as well. I do tend to be able to work towards deadlines quite well, so that should move the word count upwards somewhat.
Current status:
Summary: 774 words, rough sketch.
Introduction: 800 words, rough draft.
Chapter 1: 837 words, rough structure draft.
Chapter 2:5206 words,revised 1 time since last time.
Chapter 3:300 words, outline in place, research to do.
Chapter 4: 0 words.
Chapter 5: 0 words.
Bibliography:0 words.
Appendix: 0 words.
Total: 7345/50000 words. 472 more since last blog.
Average words per day needed until 01/04/2014: 126.

356 days to go: countdown to thesis submission

I am currently registered as a PhD student, funded by a EU project to research novel statistical methods for analysing test results on the presence of pathogens in wildlife. I have been trying to do this for the last two years, and in a little less than one year  my funding runs out (my last quarterly payment is on 31st of December 2013, and 1st of April 2014 marks the end of my third year).

 Hm... That sounds scary.

In order to help produce a neat, 50k word package of novel research by that date, I have decided to start documenting my progress on a weekly basis.  This is both so that I can get a nice carrot of "wohoo! look how much I've got done in the last week", and a stick of risking publically admitting any woefully meager posts the times I fall prey to my all-too-common tendencies of plenty of procrastination. 

So! Here goes. A rule of thumb for a UK thesis seems to be 50 000 words, and somewhere between 60 and 300 pages.  This is a sketch of my thesis structure together with how much, or little, I have completed on each chapter and section thus far:

-----------------

How to count bugs in wild animals:

Some statistical methods for wildlife disease surveillance

[Note: This is a non-approved, silly title that most likely is very far from the final one]

Contents

Foreword

Current word count: 91

Current status: Dreamy visualisation of when I can afford to thank everyone for my finished, wonderful thesis.

Summary

Current word count: 200 

Current status: random scribbles

Introduction 

Current word count: 482

Current status: start of a rough structure

Chapter 1: 

A review of statistical methods used  in wildlife disease surveillance

Current word count: 800

Current status: Rough structure draft, and some structured reading done

Chapter 2:

Recovering dynamic trends from multiple test data

Current word count: 5000 words

Current status: Journal article in the final rounds (i.e. five more or so) of review before submission.

Deadline: Submission before summer, i.e before end of May.

Chapter 3. 

Correlation and causation in multi-pathogen arrays

Current word count: 300

Current status: First research phase

Deadlines: Preliminary first report due in two weeks,  Chapter draft by September 1st.

Chapter 4: ?

[Another method chapter, the content of which depending on data and what seems like a logical expansion]. 

Current word count: 0

Current status: Not started

Deadlines: Chapter Draft finished by Dec 1st.

Chapter 5:

Statistical results from the WildTech project

Current word count: 0

Current status: Not started

Deadlines: Chapter draft finished by Jan 1st.

Bibliography

Appendix

Total: 6873/50000 words.

Average words per day needed until 01/04/2014: 118

Pappor är farliga? Inte enligt avhandlingen...

Enligt Eva Sternberg skulle hemmapappor vara "livsfarliga för barnen". Vad hon grundar det påståendet på är oklart, mer än hennes egen (skeva?) bild av verkligheten. Eva ger nämligen ingen källhänvisning mer än att säga att en avhandling av Anna Carlsson "bevisar" en 30%-ig ökning av skador de senaste tre åren. Detta länkar Eva samman med en ökning av antalet föräldralediga pappor. Såvitt jag kan förstå gör hon den kopplingen alldeles själv. Avhandlingen i fråga heter "Child Injuries at Home - Prevention, Precautions and Intervention with focus on scalds" (den borde dyka upp på Malmö Högskolas databas inom några dagar). Tyvärr går den ännu ej att läsa, och söker man efter Anna Carlsson på PubMed dyker bara två artiklar upp: Compliance with child accident precautions by child health nurses

och

Burn injuries in small children, a population-based study in Sweden.

Gissningsvis är det ytterligare artiklar på ingående (en avhandling brukar innehålla fyra artiklar, men ett antal av dom kan fortfarande vara på väg genom peer-review-maskineriet när man disputerar). Dock, ingen av de publicerade artiklarna nämner någonting om vare sig en ökande trend eller om vaktande förälderns kön. Ännu så länge verkar alltså Evas påstående vara helt grundlöst. /G

Om att slopa karenstiden för män som har sex med män.

På Isobels Verkstad har Isobel tagit upp den länge debatterade frågan om män som någon gång haft sex med män ska få ge blod. Diskussionen ramlar direkt ned i ett jämförande av olika grupper med varandra: Thailand-torskar (får inte ge blod), invandrare (personer uppväxta i syd- och mellanamerika får aldrig ge blod), och MSM ( män som har sex med män) , som får ge blod ett år efter det senaste samlaget. Anlägger man ett rättviseperspektiv på frågan kan det naturligtvis verka orättvist att de flesta bögar inte får ge blod. Men betänk följande:

• Det finns alltid en viss risk att man missar HIV-virus vid testning av givet blod.
• Risk för att vara HIV-smittad finns i alla grupper, och det mest rättvisa sättet att uppskatta hur stor denna risk är är att se på HIV-incidensen i respektive grupper.
• 56% av alla rapporterade HIV-fall 2008 i Sverige inträffade bland nyligen invandrade som blivit smittade i sitt hemland. Dessa skulle aldrig vara aktuella för blodgivning innan HIV redan hade upptäckts. Av övriga fall inträffade 39% bland MSM.
• Att låta MSM ge blod utan karenstid skulle därmed öka den befintliga risken för att någon blir HIV-smittad av en transfusion med 40%.

Om man ska argumentera för att låta MSM ge blod ska man åtminstone vara hederlig nog att erkänna att man tycker att rättviseargument och 5% mer blod (grov gissning på andel MSM i befolkningen) är viktigare än den där 40%-iga ökningen av risken för HIV via transfusion. /G.