Category Archives: Uncategorized

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.

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!

Arabidopsis update

This will probably be the last update. I’m going to (1) need to take a break until after I defend, and (2) need to start a new experiment because the plants are running low on media. I did just buy these awesome 1in diameter test tubes which should give the plants all the media and water they could need for a longer period of time. Anyways let’s go to the pictures:

On a lighter note: Gizoogle Biatches!

A friend of mine, sent me to a link for, which customizes a Google Search to make it a bit more hip-hop cultured (my favorite type of culture!). A search for me brings you here. And a click on my notebook reveals this:

Take note of the Water Type Effects on Organism Growth category. Also my favorite quote: “Boy was I stupid. Ya’ll know dat shit, muthafucka!” which actually just reads, “Boy was I stupid.” Ahahahaha. I encourage you to read all my articles Gizoogled! Naaahhhmean?!

And this is just because it’s awesome:

Lab Contamination!!!

This morning while setting up for a time trial experiment, I noticed the 20% yeast sample didn’t smell like yeast anymore. It smelled like a mixture of yeast and something else. So I setup the experiment, took initial measurements, and then analyzed the sample in the microscope. This is what I saw:

Surrounding my slightly modified yeast are these tiny things, that look like super small e. coli so they are probably some bacteria or perhaps they are some kind of spore. Regardless that was not at all in the sample from yesterday (see above), and looks nothing like the e. coli that I temporarily believed was adapted yeast.

So I began a mission to decontaminate the lab. After the cleaning I just did, nothing is alive! Not even myself! In fact I’m not even writing this… (Note to dead future self: Sorry :-\)

Anyways, I began by bleaching the fuck out of everything. The incubator got it the worst as I basically drowned it in bleach. I scrubbed real hard with this super awesome huge bristle brush. I let the bleach sit for about 10 minutes and then wiped it down with clean rags.

Next I used the Activeion Ionator EXP, which was loaned to me by the custodial staff here at CHTM. It’s a spray that ionizes water to clean and disinfect, and supposedly can kill viruses and bacteria. After the bleach treatment on the incubator, I Ionated it and wiped it down and allowed it to air dry.

Then I used the Ionator EXP to clean all the bench tops and all my lab equipment (pipetters, racks, scales, hot plate, etc). I finished by emptying my current supply of YPD and made new stocks for use tomorrow. I feel sad that I had to throw about $80 worth of D2O down the drain, but I gotta be careful in the lab and so it had to go.

Tomorrow I will start the D2O adaptation experiment again (Round 3!) and let’s hope the contamination issues are behind me.


D2O Adaptation Day 54

I’m forgoing future measurements. I have some data to post (in a few minutes) that may reveal potential contamination. And so to verify if the samples are contaminated or if a cool new phenomenon is occurring, I’m growing the D2O adapted yeast in DDW, to see if they revert back. Although, I don’t think that will reveal much either way.

In lieu of the daily measurements I’ll be taking microscope images of the cells as they grow.

Every day I will inoculate a few colonies from the previous generation (similar to what I have been doing, with an inoculating loop) into 10ml of fresh YPD (both D2O and DDW).