Tag Archives: ideas

Deuterium exchange analysis experimental planning

The future direction of the experiment using the ring down cavity spectroscopy device will be planned here. This should be a fun collaboration between Scott Jasechko (Earth and Planetary Sciences) and myself (Physics). Join the conversation!


An alternative analysis to FT-IR to study deuterium exchange

Via figshare:

Deuterium Content of Deuterium Depleted Water: 1st Trial. Anthony Salvagno, Scott Jasechko. figshare.
Retrieved 21:24, Jul 20, 2012 (GMT)

A few days ago I made a new friend named Scott Jasechko. We met to discuss the possibility of creating a TED branded forum to UNM. We got to talking about our research and it turned out that our research interests are very much aligned and he studies water isotope amounts with relation to natural water around the planet. He’s about to publish his findings and once that goes through I’ll link to that.

It turned out that his lab has a device that can very accurately measure small concentrations of deuterium and oxygen-18 in water samples. I told him about my DDW experiments and how deuterium exchange may affect my experiments, but that I can’t quantitatively measure it’s affect or the process in general. So we got to talking and he wanted to help me out.

The data linked above is the results of the mini-collaboration that I predict will turn into more. Scott used his Picarro cavity ring down spectroscope, which means very little to me right now, to analyze the water samples I gave him. The water was used in these two experiments (each word is a separate link). And was then stored in our desiccator (with drierite to reduce moisture exchange) until yesterday (July 19, 2012).

Surprisingly, the data shows very little change from what Sigma claims (less than 1 part per million D to H) to yesterday, showing very little exchange. There are two things to consider here: (1) the machine wasn’t calibrated for such low levels of D, which skew the readings (since they actually give us negative ratios), and (2) volume may play a part in exchange.

I don’t understand the mechanism very well but I suspect that surface interactions play the largest role in deuterium exchange. Once deuterium is introduced into the sample, then I would guess diffusion takes over, but this is probably slower in nature than evaporation/other mechanisms that are involved on the surface. Basically this is a thermodynamics problem that I would need to spend 3 months thinking about to compare with experimental analysis (since that is how long the Thermo class is, 1 semester).

The follow up to this experiment should be better organized. Obviously we’ll need to redo this experiment. Scott and I are also performing another experiment where Scott has left the lid off the samples I gave him so he can see if there is a new value the spectroscope provides. From here we may want to do some longer time analysis and some other studies that we’ll have to plan. I’ll start a new thread for that, in the mean-time I hope he’ll introduce himself in the comments of this post.

Some other notes:

  • I geeked out when I realized the power of this sort of collaboration. If I hadn’t been affiliated with TEDxABQ and thus this new idea of TEDxUNM (not officially licensed), I would have never met Scott. These are the sorts of collaborations that I hope can be introduced because of the Open Research IGERT proposal.
  • I mega-geeked out when I realized I can do a project planning thread with someone here at the university in another lab that can also participate in the project! Open science at the core all the way.
  • I super-mega-geeked out when I realized that I implemented a crucial aspect of ONS. As I wrote this post I wondered what experiments I had used the water for. Then I realized that it’s all documented and that I can show everyone what those experiments are. It’s not enough that I have it recorded by date, but also that you all saw those experiments in real-time and their use in future experiments has been realized. That’s a major win for ONS.

Preparing for the future…

I have super high aspirations for myself and I’m pretty sure everyone around me has those same aspirations for me as well. A lot of people that I’ve met here at UNM call me a rebel. Mostly because it seems that everything I do is against the grain, but effectively so. Last week someone called me a renaissance man.

But I’m not here to brag. Nor do I particularly like doing so.

But I did want to say how high I want to set the bar for myself and I think by posting it in my notebook I’m holding myself pre-accountable (and by that I mean to expect results). So here is what I hope to accomplish in the next few months leading up to my graduation and what I intend to do to get there:

  1. Present at TED/TEDx ABQ: After my open notebook talk yesterday, I got a ton of great feedback. All of it was of the variety of people saying how great of a concept ONS and open science is. They all said I gave a great presentation too, but I know I can always improve in this area. My aim is to present this at TEDx and maybe eventually TED. I mean I definitely want to present at TED, but realistically they may not accept it because of how similar it is to Michael Nielsen’s talk. So in order to accomplish this I’m going to do B things:
    1. I’m going to check out the ABQ Toastmasters to work on my presentation skills!
    2. I’m going to give and organize lots of talks here at UNM and hopefully elsewhere as I expand my network. I’ll also be presenting at SACNAS in October, but that will be a poster presentation.
  2. Fund an ONS educational experience: I’m dead set on getting an IGERT/REU (or both really) for students here at UNM. Steve not getting tenure is really a huge missed opportunity for UNM to be well ahead of the curve in terms of the future of scientific publishing, outreach, and forward progress. But I realize that I can become the catalyst at the university level. So I’m meeting people and meeting with people who can help me get the funding I need to educate students and professors here at UNM. I don’t want this educational opportunity to be just for STEM students. I want open science to be ALL research, but education is key and right now there is none (that I know of) besides whatever gets posted online.
    1. I’ll need a tenured faculty member I suppose. Has anyone ever heard of an interuniversity IGERT?
    2. I was recently put in touch with people here who deal with NSF grant writing, so hopefully she is very helpful and can introduce me to the right people.
    3. Also I was given the contact information for the VP of Research here at UNM, and was told he would be really interested in my open notebook science stuff. Hopefully he can help out too.
    4. Finally I think maybe I could talk to Rob Olendorf about spearheading this, or getting me in touch with someone who would.
    5. Honestly I would love to do all of this myself and be considered the lead PI, but I don’t think NSF would logistically like that.
  3. Graduate: This seems to be the easiest task since I am currently doing research, but I just need to keep kicking ass and getting results. I’ll be working on the D2O/DDW experiments with E. coli and yeast, more tobacco seed stuff, introducing arabidopsis again, and I’ll also be redoing all the shotgun DNA mapping stuff which will hopefully work this time.

I realized a while ago that I can’t imagine doing design without science, and science without design. I do love research, but I love open science and open notebook science much more than standard experiments and results, and so it would make me very happy if I could spend the rest of my life spearheading a movement to change research forever. And I think the path that I’m on will help get me there. And trust me, the design will be forever part of this work.

Yeast and E. coli Day 2

First off, how come yeast has a common  name but E. coli doesn’t? Can we call it shitus?

Anyways yesterday Alex and I did some follow up work after starting some cultures. She did a good job notebooking the experience so I won’t double up on her thoughts. Check that out here.

We took some pictures of the e.coli and the yeast which turned out pretty bad. I’ll have to try and take some better images today or something. In general though it looks like the yeast we have isn’t what we thought it was. It may not be a mutant of S. cerevisiae but may be some version of Schizosaccaramyces pombe (I hope I spelled that right, I like the first name a lot) because it looked nothing like budding yeast.

The result of this is that I will be ordering some new yeast straight up from atcc.org that is of some variety that I commented on in Alex’s notebook (hopefully).

Grant writing for open science/open notebook science

How on earth do I write a grant?

How on earth do I write a grant to host a fellowship program?

How on earth do I write a grant to host a fellowship program that teaches undergraduate (and graduate) students to utilize open science as a mandatory aspect of their education?

I have no expertise in this, but it seems like a very logical step in my pursuit of busting science open. In order for labs to adopt this principle they would need incentive, and what better incentive than free students/money? And what better way to train future scientists to do future science then to give them money? And who better to teach those future scientists than those leading the way in the field?

So who’s with me? I’m assuming I would need a PI on the grant, or maybe not. I would love to be in charge of this project, but understand the necessities that may exist otherwise. Perhaps we could do a inter-university program? Some kind of IGERT program, or REU program would be ideal I think.

The opportunities about this venture completely excite me and I want to get on this now.

But how do I go about it? Please help…

Should I write a formal peer reviewed article on the plant-ddw experiments?

I guess the real question is: Should I submit a paper for peer review? I’m 100% going to write up the findings of these experiments and I’ll write it in the open, but should I submit the paper to an open access publication like PLoS for peer review?

Personally I could go either way. I know that it is useful for my career because current measures heavily favor peer review publications. And I know that it would benefit Koch in his career, but he has given me the freedom to choose what we do with these studies.

And honestly I don’t care about how the current system rewards peer reviewed publications. If this was the year 2030 I could probably just leave a copy of the paper here in my notebook and submit it to Google Scholar search results (which I should make a short post about). At that time (hopefully) the scientific community won’t be afraid to openly critique a publication, but now there is some kind of invisible barrier that prevents this kind of interaction.

If I did this now it wouldn’t be peer reviewed by anonymous reviewers, but I could say send it out to various colleagues and have them review and comment and self publish the comments.

I actually would like to do it this way. I think it would be a worthwhile experiment in open science publication. I’m not afraid of the criticism that I may receive from peers. I’m also not afraid of the impact it could have on my career, if indeed this is not well received. Eventually someone is going to have to make a bold leap, why can’t it be now, and why shouldn’t I make that leap?

On the other side of the coin, I’m not afraid of the current model either. I’m not opposed to publishing in an open access journal like PLoSOne, but I don’t see the value in a closed access journal. With an open access journal I would receive the benefits of open access and the benefits of peer review, the best of both worlds, so why shouldn’t I publish this way? I would get the career benefit that everyone expects to see on your resume and the joy of having shared my knowledge openly with all the world.

So then why do I feel inclined to go against the grain? Why do I feel like it would be a worthwhile risk to publish in an unorthodox way?

Am I crazy?


Experimental Ideas for Effects of D2O on Life

Reading some papers by Lewis and others at the time got me thinking about cool experiments. There is one that I want to replicate where it was stated that plant cells become hypertonic (cell shrivels up) in the presence of D2O (Brooks et al, 1937 which I need to find). This leads me to want to test red blood cells and human cheek cells (because they are easy to get a hold of) for similar effects.

Reading the paper by Lewis revealed some funny results when dealing with mice (he reports an intoxication effect when one mouse drinks heavy water) that intrigue me. But also gave me an idea. I would like to test the effects of D2O on the Tardigrade which is  a microorganism in the animal kingdom. This thing (nicknamed the water bear) is known to survive the most extreme conditions. From Wikipedia:

Some can survive temperatures of close to absolute zero (−273 °C (−459 °F)), temperatures as high as 151 °C (304 °F), 1,000 times more radiation than other animals, and almost a decade without water. In September 2007, tardigrades were taken into low Earth orbit on the FOTON-M3 mission and for 10 days were exposed to the vacuum of space. After they were returned to Earth, it was discovered that many of them survived and laid eggs that hatched normally.

So you can see why I’d want to put this thing in D2O and see what’s up. I found one place that sells them, but I get the impression they sell only one per order and I would like to grow them (which requires two surprisingly, because of the egg thing). I have read that they grow on moss and lichens so maybe I can get some live samples over at the Rio Grande.

In an email correspondence, Koch pointed out that testing with paramecia might be a worthwhile venture as well. They may exhibit visible response in the presence of toxins or at least will definitely slow down and die quickly.

As an aside, in biology class in 9th grade we were given some paramecia to examine and I watched as mine spontaneously exploded in front of my eyes. I told the teacher about this and she couldn’t care less. Thanks a lot Mrs. Cuesta (here’s a Google link for you).

Bill Hooker on friendfeed also suggested an interesting experiment:

You can D-replace prokaryotes… what would happen if you did that for 100, or 100 million, generations, then switched ’em back to regular water? Can you H-replace ’em using D-depleted water? I’m trying to come up with ways to adapt some enzyme or other to D, wondering if you could get it sensitive enough that adding D to a system using that enzyme would act as a switch…

Which got me thinking that maybe I could get these creatures to live in D2O by slowly integrating more deuterium to regular water over time. I read a paper by Keith Hobson where they analyzed the source of hydrogen in quail tissues by feeding a group water with D2O mixed in. By combining their results (which I’ll need to reread) with what Bill says, maybe I can get a species (of anything really) to live in D2O and analyze the effects of regular water on them. Could be fun.

Wow I can get carried away. I started this post as an aside where I was just going to list some quick thoughts and then started rambling. It’s all good.

Also if anyone has read to the end of this post, can you tweet this post? I want to check the ability of Disqus to search tweets and include them in the comments (the Reactions section). Also try sharing via facebook, or whatever other social media that you may use these days. Thanks in advance.