Tag Archives: brainstorming

#SciFund Proposal Planning

DDW Project Proposal

Here is the link to my project proposal for the SciFund Challenge. There is nothing there yet, but I’ll fill it up tomorrow and Friday. The video stuff won’t come until next week and images will come after that. Right now I’ll be planning everything out, but first I’m going to do a bit of research. I’m going to read all the SciFund challenges from last year and pick out pieces that seem to really work as compared to how successful they were in their funding goals. I’ll write up a notebook entry on this later tonight.

In the meantime feel free to provide some helpful tips in the comments below.

#SciFund Challenge… I’m in!

I’m super excited because I just received word that I have been accepted to round 2 of the #SciFund challenge. I posted my pre-proposal last week, and from the looks of it I have a lot to do. I received an email that details what needs to be done this week and over the course of the month and some awesome details about the challenge:

  • 140 other researchers got accepted and we’ll all be working together to refine our proposals to make our funding goals. This is going to be a community experience all around: proposal editing will be a collaborative process, and the funding process is crowd based (hence crowdfunding). I’m very much looking forward to this experience.
  • This week my plan is to get familiar with the crowdfunding process and to develop my project proposal. I’ll be developing this in the open as usual so I’ll welcome all your feedback.
  • Next week and the week after, the plan will be to receive feedback for the proposal from others in the competition and hopefully all you who follow my notebook.
  • I’ll also need to develop a promotion strategy. That’s where the world comes in. I’ll obviously be tapping my family’s network, but I’ll also be asking you to tweet, facebook, +1 my efforts to help me reach my goals. I’ll also to to figure out how to get  the university involved and maybe take out an ad in the local newspaper to reach my goal.
  • At some point I’ll need to make a video proposal. So I’ll be needing some feedback on this. While I have video making chops and tools, this project will be the most important thing I do until I graduate so it will have to represent my best work. Anyone interested in helping me story board my proposal should comment below. Again, all that will be open.
  • Finally, I’ll need to come up with a reward program for contributors. This should be fun since I have a multitude of talents that I love to share with all. As an example if anyone contributes $100 I will design business cards for them for free (the printing cost is on the contributor). For a lower level contribution something like for every person who donates $15-25 I will email them a picture of Trex and myself doing experiments in the lab.
  • Finally between this week and next I will need to complete the first draft of my project proposal. According to the welcome email, “This first draft will include the following elements: title, video, rewards, images, and description of your project. Your project description should include the following: a welcome, a call to action, a detailed description of your plans, and a thank you. Please note that the project description should not go on for too long.” I don’t think I’ll be able to have a video done this week, but a story board should not be out of the question. I will look to film it next week.

That’s all for now. Like I said in the coming days, I’ll be setting up a Google Doc to outline and refine my project description, video storyboard, and reward system. Perhaps I’ll mindmap an outline. And remember all of this will be done in the open along with the project as it progresses once the funding is underway and complete! Crowdfunded open science? Yea, that’s awesome!

Project planning notes via Handrite

Here are some notes I took using handrite for android regarding my project plans. I don’t mean to advertise for anything, but I use this app ALL THE TIME and it is super helpful. Typing on my phone is annoying sometimes and Handrite allows me to use my finger to write (albeit sloppily). These notes were taken yesterday while I was meeting with Steve (on my phone) and now I have time to paste them in my notebook. So here is some background on my ramblings:

  • I would like to effectively analyze the amount of hydrogen-deuterium exchange in my samples. This is a phenomenon I’ve talked about a lot, know very little about, and stress a lot over. We tried FT-IR of water samples to see if we can determine differences in the water types. We’ve had mixed results in this regard. It boils down to the fact, that I don’t trust anything. How do I know that deuterium isn’t sneaking into my unopened bottles of DDW, or that hydrogen isn’t getting into my D2O? What about after it’s been opened? What about in my samples? If I’m going to get reliable results with yeast and e. coli I’ll need to know if I can trust commercial products.
  • NMR (nuclear magnetic resonance) seems to be a promising route to try and there may be some equipment either in the Chemistry department or Biomedical Engineering here at UNM that I’ll need to look into.
  • Mass spectrometry may be another avenue to determine precise amounts of deuterium in water.
  • Something not written but that I talked with Steve about yesterday and just remembered is that I need to talk with Sigma to find out how they measure the purity of the DDW and how reliable those measurements are long term. If something sits on a shelf for a year, how do I know it isn’t really just pure natural water?
  • I also have some stuff in my notes about the Repeating Crumley experiment. I just setup a D2O only experiment to show definitively that tobacco seeds do not grow in D2O. Previously I would only track this data for 10-15 days and Crumley went up to a month (if I remember correctly). I’ll write the setup in a minute, but I want to do 30 days so I have some pictures for my open access, self published RC paper (spoiler alert!).
  • Also to show that I’m no slouch, I want to try and repeat Crumley’s original experiment with paper towels to show that the growth of the 100% D2O seeds was due to H-D exchange and other environmental factors and not because they eventually grow in D2O. Yea I’m a badass.
  • The rest of the notes are some ramblings that are not really private but thoughts I would prefer not to elaborate on now.

Tata for now!

#SciFund Challenge Accepted!

If you watch “How I Met Your Mother” you’ll get the title of this post. But if you don’t then I’ll let it be known that I have just completed my submission for the second #SciFund challenge which is hosted by RocketHub.com. Here is my submission:


Effects of DDW on Microorganisms

My #Scifund challenge pre-proposal

I found out about the first round of SciFund too late, but I’ve been on top of it since and I’m going to try crowdfunding for science! Proposals are due by March 29 and must be kept under 150 words. Here is my draft:

Here is the link.

I hope that after initial peer-review, there is an opportunity to explain in more detail the specifics of your project, because 150 words is not nearly enough information to determine if you should contribute any amount of money to a project.

I’m going to request $3000 and during end of this month and into next month I’ll produce an expected budget summary and detailed project outline. All in the open! And if I don’t get into the RocketFund SciFund challenge, I’ll try and crowdfund in other ways or even independently.

Anyways you’re feedback is always welcome!

Spring Break Planning Mindmaps

Spring Break planning map:

Planning for SDM paper mindmap:

Finishing Shotgun DNA Mapping

This isn’t going to make one iota of sense to anyone, so bear with me and I’ll clarify later.

Here are some useful links.

Quick Ideas

I had some thoughts about what I wanted to do next. Now I can’t quite remember what I wanted to jot down (which was the point of this post to begin with) so I’m going to ramble a little until I remember.

The first thing that I wanted to write down was an experiment that Steve and I have talked about a couple of times with regards to the Repeating Crumley Experiments. It seems like the fastest growing plants seem to be right around 1% D2O in DDW (what Molarity would that be? My brain ceases to function right now…). So we want to expand on this a little bit and do small concentrations of D2O in DDW compared to DDW and DI water (with a simulated DI water content sample too) and see if we can find some maximal amount of D2O content for tobacco seed growth.

Since our hypothesis is that life has evolved a use for deuterium (like it has other trace molecules), this should really provide a result and highlight some data that is missing from our current experiments. By this I mean that I have 1ppm deuterium in water (DDW), 156ppm D in water (DI-ish), and whatever ppm 33%, 66%, and 99% are in water (the other D2O) samples. That means there is a major disconnect between the low deuterium content stuff and the high. So this experiment will attempt to fill in the gap. I’ll have to come up with a name for this experiment.

Now that I’ve rambled a bit, I actually remember what the second experiment I wanted to jot down was. Talking with a professor, I explained my results about the root hairs and the seed germination stuff and he found it pretty interesting. Being a physics professor he had no biological intuition about what could be happening, but he did wonder about what could be going on physically. In talking with a fellow grad student I learned about photobleaching experiments that reveal diffusion parameters for a solution. By photobleaching some fluorescent molecules you can watch new fluorescent molecules diffuse into the viewing area, time it, do some simple math, and then get your information.

I’d like to apply this to our water experiments to gain some potential insight about the diffusion of molecules in  D2O, DDW, DI water, and various mixtures of those. I’m guessing it’ll be pretty hard to measure this and so I’m thinking of doing agarose gels to slow down diffusion, or maybe adding some other type of viscous material. In either case, it’s not a fully formed plan, but something to consider in the near term.

Fun conversation between @BoraZ and myself on twitter

I’m trying to figure out how to preserve tweets and in doing so I figured I practice with a conversation I had with @BoraZ (Bora Zivkovic) that started with a joke and evolved into why scientists and students don’t embrace modern methods of collaboration. Here is my attempt to preserve the conversation:

Not pretty, I know. Hopefully this will last longer than 48 hours though because I think this is a valuable conversation to document for future reference.

Preparing for E. coli in DDW, DI, and D2O

Sorry for the lack of notebooking today. I had to send a bunch of emails this morning, catch up on teaching work, and then had to write an informal CV this afternoon. Wanna see it?

Anyways, I’m doing the prep work for the E. coli studies and showing Alex how to use an autoclave. I also am getting into sterile technique and Alex will have something up later about all of this to which I will link.

Tomorrow we are going to mess around (and get triple doubles) in a safe environment and grow some e.coli and see what happens. I also hope to get my hands on some yeast. There are a few barriers before we can get any serious data. First I have to successfully grow microscopic creatures in small containers. I have to get acclimated to using the nanodrop as an OD measuring device. Then I have to do all this with different water types.

Fun times ahead.