We’ve done it! $2000 for open science! http://rkthb.co/7531

I’m truly humbled by the amount of people who have come out to support my project. I am eternally grateful. Honestly, I never imagined that I would hit $2000 but we banded together and got it done.

There is still time though and excess funds would be used to buy even more water (especially since a few new experiment ideas would cost about $400 just for one day!).

If you are in line for a graphic design reward, I’ll get those to you by the end of June. After all, I need to design them!

In the coming days I’ll have posts about my experience with #scifund, making my proposal, and the overall success of scifund along with whatever random thoughts pop into my head.

Thanks everyone for your efforts and showing that the public cares about science and would directly want to support it. I love you all!

Why I became an open scientist…

I was asked a very interesting couple of questions on Twitter last week that got me thinking: Why did I go open? Why do I share my science? To me the answer is very simple: Because science by nature is about knowledge, and in today’s world gaining knowledge cannot be achieved without sharing knowledge. After all, sharing is caring!

Here is the question that sparked a mini-conversation:

@eperlste: @Thescienceofant I noticed your data on Figshare! How many of your peers know about it, express interest when you describe it?

The answer was not many. Honestly, I’m surprised by how many people here at UNM have no idea that open science is a movement and that sharing your data is an option. I get told that last little bit all the time! There are tons of students who get excited when I mention that I share my data and methods and they have no clue that they are allowed to do this too!

Mr. Eperlste (Ethan Perlstein) then asked a follow-up question:

@eperlste: @Thescienceofant so what convinced you to share?

Since it is twitter I had to sacrifice the long and good answer for the stupid answer of “I’ve been a full open notebook scientist for 4 years. I wouldn’t be very good at it if I didn’t share.” But this is my notebook and now I can go into the juicy details…

When I was first introduced to the concept of open science in 2007, I remember thinking “Wait, this isn’t how science is done?” I was new to scientific research and new to graduate school. My PI had just told me some horror stories of his graduate education/career and explained this is why he wants us to be an open lab.

I was so puzzled to learn that there are scientists out there who treated scientific information like it was something to make money off of. The data that we collect isn’t really for the pursuit of knowledge. It’s all about being self centered. Data is for intellectual property. Understanding how the world works seemed to be more about furthering your career than it is improving the place we live.

It didn’t make any sense. And it still doesn’t.

Here I was thinking that science is the most pure field in the world. Everything you do in the name of science is about education, understanding, and building. But the truth was, science wasn’t about any of that.

So at that time, it made sense to share my data. I was just doing what I thought I was supposed to be doing. And back then I thought I would do the world a favor, like Wikipedia. Today, though, I realize that being open is much more than just giving a little help. Being open is bigger than me, bigger than you, and bigger than all the scientific knowledge that exists right now. It’s how science has to be if our culture is going to survive moving forward.

Currently the scientific culture isn’t about education, and it certainly isn’t about sharing. It still is about understanding though. Deep down every scientist is curious, and they all greatly enjoy learning new things. Why else would we be scientists at all? Research certainly isn’t a field that is fun unless you absolutely love science. And after undergrad, you are trained to do something so well that you have trained yourself out of real world job skills, so there isn’t much market for us outside of academia.

Being open allows me to explore the curiosity that I have as a scientist. But it also allows me to be free! I don’t need to rely on people directly teaching me how to perform experiments. I can learn from everyone who shares their experimental technique.

I don’t need to worry that I’m the only scientist doing molecular biology in my building. I can learn from the vast resources made available by people like me. And because they shared with me, I’m sharing back. Because I found their resources useful, I’m sure others will find mine useful (and I’ve heard instances of that being true).

Being open also allows me to educate in a way that has never been seen before. There is a huge disconnect between science and society. Every once in a while, there is a press release about some experiment in Switzerland, or Hawaii, or Japan, or Brazil, etc but those press releases get butchered by the media. By being open, I’m taking matters into my own hands. Who is more capable of properly explaining my research than myself? No one, and that’s why this notebook was created.

Being open allows me to share, and it allows others to build. I’ll only be doing the experiments carried out in this notebook for a short time longer. I don’t want my questions to fade from existence like they did back in the 1950’s. Someone out there is just as interested in these questions as I am. And one day someone will pick up from where I left off.

And they won’t have to start over.

I had to start from scratch. Never again! The next in line, can start from where I ended. And then someone can pick up from where they left off, and so on. And this can happen in every scientific field, for all studies, in all universities/instituions, ALL OVER THE WORLD!

Why wouldn’t anyone want that to happen?

Why don’t we want the public to understand what we do? Why wouldn’t we want them to care about our research like we do? Why wouldn’t I want someone to benefit from both my failures and my successes? Why wouldn’t I want someone to be able to build upon my work without having to waste any time?

And why wouldn’t anyone want to share their discoveries with the entire world, not just the elite few who can access those discoveries through journals?

I want all those things, and that’s why I’m an open scientist.

Yeast and E. coli Growth: What’s next?

There are several things I can do with the yeast experiments:

  • Another but longer time trial experiment (data every hour)
  • Time Trials in larger quantities: maybe 100ml or 50ml – I want to see if the growth in such small volumes affects the measurements any
  • Adapt yeast to D2O and then grow in DDW – I’ll have to do cultures daily in D2O and see if they begin to grow faster in D2O over time. I’m thinking this will let me know they’ve adapted to their environment. I can also try to grow cultures in less D2O (like 10%) and incrementally increase it over time to see if that causes adaptation. Both methods seem viable.

I’m open to suggestions as to what to do next as well.

As for E. coli, those experiments are very inconclusive even in 99% D2O and I wouldn’t have the foggiest as to how to deal with this. Suggestions would be much appreciated here. Ayuda me!

Hourly Yeast Growth Trial 3: Results

Via Figshare:

Hourly Yeast Growth in DDW, DI Water, 30%, 60% and 99% D2O. Anthony Salvagno. Figshare.
Retrieved 21:17, May 30, 2012 (GMT)
hdl.handle.net/10779/03ec08019a22d82c66167d5e7d914de5

This experiment went much better and more predictably. Yeast (unlike E. coli) is more sensitive to deuterium content and grows accordingly. Interestingly (in this experiment) the DDW sample exhibited more growth. I’ll have to experiment on this a bit more.

It should be noted that while it appears that pure D2O grows much slower than the rest (cause it does), I also started with a much lower amount of cells. The cells did not grow well in the starter culture, and they didn’t grow well here either. See the data (or the live results) for starting absorbance readings.

Yeast Time Trial Live Results

Feel free to check in every hour (refresh this page)!

Yeast in DI, DDW, 30%, 60%, and 99% D2O Trial 3: Setup

Yesterday I made starter cultures in D2O, DI water, and DDW. Today I’m doing the time trial experiment and here is the setup:

  1. Setup of five samples:
    1. 9ml of DI YPD + 1ml of DI starter culture
    2. 9ml of DDW YPD + 1ml of DDW starter culture
    3. 6ml of DDW YPD + 3ml of D2O YPD + 1ml of DDW starter culture (30% D2O sample)
    4. 3ml of DDW YPD + 6ml of D2O YPD + 1ml of DDW starter culture (60% D2O sample)
    5. 9ml of D2O YPD + 1ml of D2O starter culture
  2. Measuring:
    1. 400ul of each starter culture in semi-micro cuvettes – to measuring starting absorbance
    2. 400ul of each timed culture (the samples to be measured over time) in semi-micro cuvettes – to measure the time=0 value (should be close to 1/10 of the starting measurements)
    3. repeat B every hour
  3. Blanking:
    1. Before each hourly measurement you need to blank the nanodrop
    2. Blank the DI samples with DI YPD (no yeast added)
    3. Blank the DDW, 30% D2O, and 60% D2O samples with DDW YPD
    4. Blank the D2O samples with D2O YPD

 

Starter Cultures: D2O, DDW, and DI YPD

I just started three new starter cultures for another timed experiment tomorrow. Hopefully this time it goes better than last time.

Setup:

  • 10ml of YPD broth in test tubes
  • The water component of each test tube is different, one is DDW, one is DI water, and the other is 99% D20.
  • The YPD was made last week and stored in the fridge.