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.

Thank you everyone!

Surfing through my site analytics I decided to look at the total number of viewers by their location. Here is what I discovered:



Screen shot 2013-05-05 at 10.13.48 AMIn the 1.5 years that this notebook has been made open, it has spread to almost every country on the planet. I’m not at all surprised that science accessibility could have this kind of influence, but I am in awe that I get to be a part of it.

Hopefully this becomes evidence that open science, science outreach, and science accessibility in general are the keys to the future of the scientific method.

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.

Growth of tobacco seeds in low concentrations of deuterium

Growth of tobacco seeds in DDW.
Growth of tobacco seeds in DDW (0.0001% D2O).
Growth of tobacco seeds in DI water.
Growth of tobacco seeds in DI water (0.0156% D2O).
Growth of tobacco seeds in 1% D2O.
Growth of tobacco seeds in 1% D2O.
tobacco seed root length
Tobacco seed root length growth.

Major Overhaul Coming!

Now that I am done with my Doctoral program, I need to majorly revamp the site:

First, I need to reorganize all of my tags and categories for easier site navigation. I will organize the site by project first:

  • Deuterium Effects
  • Shotgun DNA Mapping
  • Open Notebook
  • Kochlab
  • Art

Next I will organize each project by organism and then experiment. For instance:

  • Deuterium Effects
    • Tobacco Seeds
      • Repeating Crumley
      • Root Hair Analysis
    • Arabidopsis
      • Seed germination
      • Root analysis
      • Plant growth
    • Yeast
      • D2O effects
    • E. coli
      • D2O Adaptation
      • D2O effects
    • Biomolecules
      • Catalase
      • Ovalbumin
      • DNA
    • Water analysis

This will make it much more intuitive to navigate for experiments that are no longer being carried out.

Second, I will also remodel the design of the site so that the design reflects (1) the high quality of science, and (2) reflects the high quality design work that I do. That will just be for fun. With the new redesign, I will also be providing a new weekly column which I’m really excited about. I’m not sure what I’m going to call it yet, but it starts tomorrow and each post will contain real scientific work that reveals exactly how science is aimed to understand the world and better it. Some posts will be very educational, others will be fun and a bit silly but scientific nonetheless, while others will highlight things you didn’t necessarily think about. Regardless, I am quite excited for the series and I hope you are too.

Third, I’ve got a few new projects to unveil. I’m not sure when those will be announced, but two of them I will get to announce this week. I’ll announce the first project tomorrow, and the other project later in the week.

Fourth, my dissertation is 99.9% done and I’m just waiting for my committee to sign the approval cover sheet in order to complete my graduation. Once that is done, I’ll be uploading the document to figshare and will make it available for download. Then after some time, I’ll be uploading a special edition version of my dissertation which will feature some graphic design styling. The special edition is the version that I’ll be getting professionally printed and bound for my advisor, myself, and my parents. I’ll upload that too in case you would rather read the more awesome version.

That is all I have to announce right now. Sorry the site has been kind of dead for the past couple of months. The dissertation work has been beastly, but ONS made it much easier than what I expected the process to be. Now I get to go back to good ole’ fashioned, and fun, science!

Do you?

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