Category Archives: Water Type Effects on Organism Growth

Repeating Crumley Publication Prep

  1. I need a title for the paper. I’ve always called it Repeating Crumley, and maybe it makes sense to continue that trend, but is there a more fitting/descriptive name? Does it even matter?
  2. I think it makes sense to create .gifs from all the plant germination images for each sample of each experiment.
    1. From RC1-4 I had slideshows, which allowed you to click through each sample at your own pace. Then after I had started making .gifs (especially since that was around the time of memes on the web).
    2. I still think it makes sense to have all the data as pictures as well. If they aren’t already there, I will upload all the images to figshare, and have a separate dataset as gifs.
  3. Should the gifs be stored via my notebook (and thus the Winnower), or figshare?
    1. Both?
    2. Since the Winnower can actively display the .gifs, this has my preference, but I’m not sure. Maybe both… just because.
  4. Making a citation list for every notebook entry may be tiring, but it must be done.
  5. I’ll have to go through my figshare profile to see what data is currently up there.
  6. I worry that I don’t remember some of the data analysis methods. I think the only one I have absolutely no recollection of is the root length vs time graph. I remember it happening but I don’t remember going from Point A to B. I think of this like getting in the car and driving to work. You remember getting in the car, but you have no recollection of the in-between time because you were lost in thought. This is what happens when your brain is in Dissertation/Defense mode.
  7. The primary focus on this paper is going to be about the replication of the Crumley experiment through my methods and the difference in our results. I will include some of the cooler data, but won’t be able to write a follow-up (yet) since there is insufficient data on some of the cooler experiments. But I can show preliminary stuff!

I think that’s all I got now. I’ll keep adding notes like this when I get more ideas, come across roadblocks, or something else.

The Repeating Crumley-ONS Project: Next Steps

Slightly over a month ago, I came across the Winnower and began a project in open notebook science. The concept was to upload notes from my notebook to the Winnower, archive the notes, and get DOI’s for each post. Then I would write 2 papers: one to summarize the experiment and the other to theorize a complete publication system that would incentive open documentation of real-time research (open notebook science). I chose the Repeating Crumley experiment for this experiment in ONS, and you can read about the reasoning here.

Well I’m happy to say that I’ve completed Steps 1, 2, and 3! I’ve posted every notebook entry in the RC series (there’s a physics pun there somewhere) to the Winnower and received DOI’s for almost every post. A few posts didn’t translate, at all, on the platform. They are uploaded, but I didn’t bother with the DOI. Regardless, you can go on any of my Winnower posts and get a DOI (or click through to my notebook),  or look through the RC entries and click the DOI to get to the Winnower archive of that post.

One cool side effect of this project was that a Twitter friend noticed a post that had embedded .gifs and I think I am now credited with being the first to publish a scientific paper with embedded .gif’s.

Now it’s time to write the paper based on all this research. I got the process started a couple years ago with a Google Doc about the project. I think I never followed through, because I didn’t value the traditional publication process. I think open science and peer review publication are on a course to merge and the incentives for ONS will shift, but this is a topic for another time.

Anyway, here is the previous write-up which I’ll work on, merge with some info from my dissertation, and to which add some new thoughts.

This part may take some time…

@BreakingBio Episode 24: #OpenNotebookScience Edition

I totally forgot to post this when it came out about a week after I defended. The folks who run the hilarious video podcast Breaking Bio had me on as their special guest, with Heidi Smith reporting live on location. Check it out:

Arabidopsis Growth Try 4: Week 5

The latest updates are in. Between last week and this week, plants grown in 0% D2O, 30% D2O, 70% D2O, and 80% D2O have died. While this is expected for the larger concentrations, I can’t explain why the 0% D2O sample or 30% D2O sample has died. But I did just think of an interesting effect:

Because the plants are more-or-less sealed from the environment, I have minimized the effects of evaporation and transpiration. I’m not sure if transpired water is harmful to the plants because it basically is their excrement. Regardless, the water in the solid media (the agar) should have a slight rise in D2O concentration due to transpiration processes in the leaves and evaporation of water from the solid media. I’ll have to find the reference for a paper I have that verifies this.

Arabidopsis Growth Try 4: Week 5

Arabidopsis Growth Try 4: Week 3

Growth of Arabidopsis in heavy water

Arabidopsis seeds in DI water (0.0156% D2O).
Arabidopsis seeds in DI water (0.0156% D2O).
Arabidopsis seeds in 33% D2O.
Arabidopsis seeds in 33% D2O.
Arabidopsis seeds in 66% D2O.
Arabidopsis seeds in 66% D2O.
Arabidopsis seeds in 99% D2O.
Arabidopsis seeds in 99% D2O.