moving the lamppost

random musings of a molecular biologist turned code jockey in the era of big data and open science.

Blogging my dissertation

I am not surprised or disappointed that this idea has already been done. In fact, I am quite encouraged that I read that others that have done this so far have had such great experiences with it. I began to think about using my blog to help me get over my reluctance to simply sit down and write for quite a few years. However, I somehow never made the connection that I could also use it to help me actually write the documents themselves. It was only recently, after making a personal promise to engage more frequently and vigorously in the open science endeavor, that I started to research how the idea of blogging a dissertation had worked out for other people.

It’s been normalizing

Gladly, I discover passages about many all-to-familiar feelings I have been having about writing that mystic tome that will represent the sum of my time as a graduate student, yet will most likely be read by maybe ten people... Like many other grad students, I find writing, along with the associated stresses and insecurities, quite intimidating. I fall prey to avoiding such tried and true methods of addressing this as write everyday (even if for just 20 min) because I can’t think of anything to write or because I convince myself that it would be a waste of my time or I feel like if it’s not perfect the first time out of my head then I am a failure or... ad infinitum.

Blogging as document/idea development tool

It’s actually kind of a perfect device for me; I think. Blogs are naturally pretty bite-sized which removes the “Holy FSM! I am NEVER going to be able to finish this!” brake that is a personal favorite nightmare of mine. Because of this, I should be much more likely to write regularly. They are generally aimed at curious non-experts which silences the “What if I show it to my adviser and he/she thinks its so horrible and tells me to start over?!” demon. Blogs have built-in feedback mechanisms in their comments sections which allow input from people you may never have expected. This is great for two reasons:

  1. criticism from people you don’t know can be easier to recover from than from folks you feel like you need to impress

  2. it is exactly these people that a good scientist-communicator should be hearing from, and on a frequent basis

    • shared jargon, background knowledge, etc makes it too easy to write for yourself or other experts in your tiny corner of the community if you truly want to improve your ability to communicate science.
    • it can also be kind of dangerous: group-think is the enemy of innovation and you never know how well you communicated your ideas until you get questions/comments from non-experts.

It’s not bad practice for grant writing either since you need to make sure that everyone on that study section has the best chance possible of understanding the purpose, approach, and awesomeness of your ideas regardless of the referee’s specialty.

The opposite of wasting my time

I have been trying to figure out what to do with the many but short bits of time that I have to myself when I am being a full-time dad two and a half days a week while the little dude is or should be napping. I find that I can not code in that time because I will lose my place and spend half the time reminding myself what I was doing when I left off the last time. This way I am actually making progress towards my major goals and improving an essential skill for any scientist. Granted: I will not be able to simply cut and paste my work from here into submission formats for journals or my committee as a final dissertation. But my thoughts will have been laid out, organized, reworked, and hopefully tested through community involvement in the comments.

What’s it about?

Thanks for asking!

Here is a snippet explaining it:

Comparative transcriptomics of bloodmeal regulated gene expression in mosquito midguts across 150 million years of divergence.

Hematophagy (blood-feeding) is a trait believed to have been present in the common ancestor of modern mosquitoes. The females of many mosquito species must obtain a suitable bloodmeal in order to become competent to mature the first clutch of fertilized eggs, a fact that drives the transmission of many tropical mosquito-borne diseases. 20-hydroxyecdysone (20E) is a well known steroid hormone that is involved in molting and other developmental switches across all of Arthropoda; it is also known to participate in the transcriptional control of bloodmeal regulated genes in mosquitoes.

This work aims to characterize the level of conservation of transcriptional patterns in genes of four mosquito species (Anopheles gambiae, Anopheles stephensi, Aedes aegypti, and Culex quinquefasciatus) as measured using RNA-seq. It specifically aims to focus on genes that may be regulated by the early transcription factors in the 20E transcriptional program. RNA was collected from midguts of mosquitoes 0, 4, 6, 8, and 10 hours post bloodmeal. It represents an effort to combine multiple genome-scale data types including comparative transcriptomics, orthology, evolutionary tree branch lengths (divergence times as old as 150 million years), and putative transcription factor binding sites.

What are your thoughts/experiences with blogs as academic tools?

I would love to hear about your experiences with blogs in academia. Do you have any words of advice or warning? Do you have any favorite academics that you follow? Please comment below and give me your thoughts.

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