Tag Archives: ons success

Open notebook science thoughts inspired by the biomedical research symposium

First let me say that my presentation went amazingly. I spoke for ten minutes with a five minute Q&A session after. The audience was comprised of IMSD students, their faculty advisors, and their friends and family. It was also easily the largest audience I’ve spoken in front of. I estimate about 70-100 people.

The Q&A was quite exciting. I received questions from every audience group: students, faculty, and nontechnical attendees. This is very important to me because it tells me that my presentation was engaging and impactful. The questions used the entire allotted time and it spilled over into break period.

During the break I spoke with students interested in open notebook science, participating in it, and reaching out to others who could be interested in it. I also spoke with nontechnical audience members (the friends and family) about the core values of ONS. This was very exciting to me because it shows me that taxpayers and the general public care much more about science and information more than we give them credit for. I always say ONS is more than just data provenance, but is also scientific outreach, and the conversations I had today demonstrate that.

I also received some interesting comments from faculty. I always receive comments from this crowd regarding two things: 1) information signal to noise and 2) data protection. Here are my thoughts regarding these two issues:

1) Scientists already publish a ton, and there is already a decent amount of bad science. Open notebook science does not add to this perceived signal to noise ratio. In this case signal to noise refers to the amount of relevant scientific information (for your interests) in the sea of all publications. By providing open access to your data and keeping a complete account of your research you are actually making it easier to find the information you want and need.

If you are reading a journal article, you have to sift through the document and spend time trying to understand what the author is proposing with their conclusions. With open notebooks that information is laid out for you in plain english with minimal effort required. You need a protocol? Here are my steps. You want the raw data? Here you go.

While it is true that open notebooks will increase the amount of published scientific information in the world, in this case that overload enhances the discovery process and minimizes the time required to follow up on prior experiments. I can’t count the number of times I’ve saved oodles of time by finding information in my notebook and the informally published documentation of others.

2)  When it comes to data protection, I will admit that I don’t know everything there is to know about this. I also have never been a victim of data theft (scooping) myself. But I don’t see how open notebooks can increase the frequency of data thievery.

Firstly, bad scientists are trained to be that way. There aren’t many people that want to be a bad or ethically incompetent scientist. Those that are trained to be that way. In graduate school you are prepared to lead the next generation of science and you learn from those around you. If your PI follows a negative code of ethics you wont have all the necessary tools for success upon graduation. Luckily even those who are raised in this environment, like my advisor Steve, have the choice to follow those guides or choose a different path. In the case of Steve, he was so uncomfortable in his environment he chose to be an open scientist. This decision ultimately led me to becoming an open notebook science evangelist, a career path that has led me on a wonderful adventure.

Aside: I really hope I can convince Steve to air his grievances publicly because his experiences are something that all scientists can learn from.

Secondly, data thievery already occurs in a closed environment. I’m sure someone one day will be a victim of these circumstances in an open environment (if it hasn’t already happened), but being open won’t open the flood gates on scooping and unethical science. In fact, I believe that open science can help minimize it.

By being open you are essentially prepublishing and staling claim on your research domain. In the event of catastrophe, you can point to the fact that you have been working on this project and that your information is valuable and full of integrity (integrous?). Peers may also be able to back you up and essentially police the situation accordingly. Being open makes your research transparent and could help prevent tragedy. Why would you choose to steal information that others already know exist?

And to that point, why would you choose to steal information that is encouraging reuse? By participating in open science and open notebook science and publishing your data with open access you are encouraging data sharing and reuse. You can’t steal information that is being given away.

I think the issue is that scientists who work in the closed environment think their research is theirs and the protect it like it is an extension of themselves. Open scientists, on the other hand, view their data as that to be shared with the world. Their data is not theirs but something that they produced and should be consumed and developed by others in ways they can’t imagine. Traditional scientists who think about open science continue to view their data as theirs in the open environment. The truth is the two systems are fundamentally different and require a mental reprogramming in order to go from closed to open science.

As I always say, education is the required mental reprogramming and when this happens we will see a much faster shift from one system to the other. I envision a world that is based on the quality of research you produce, not the quantity or the perceived impact of that research.

Personally speaking, I feel that younger scientists can embrace open science much better than the older more established generation. The older generation was scientifically raised in a system that embraced a different set of core values. New scientists haven’t been influenced as much by the current system and are more open to change because of this lack of influence.

With regard to data theft, I want to add that I wouldn’t mind being scooped. This may sound strange to invite unethical conduct, but how can anyone understand the negative aspects of the system without experiencing it themselves. Unfortunately all my data is public domain so data theft is essentially impossible. Perhaps I don’t get a credit or a citation if someone reuses my data, and that would basically be the most unethical thing that could happen to me. And if that is in fact the worst case scenario then I would say the system works pretty well.

Mini-win for open science

I’m currently at the Biomedical research symposium that I am scheduled to speak at in less than one hour. I’m currently practicing my talk via slideshare by way of my phone. I thought that was so cool that I should share that with the world. If I wasn’t open I would never be able to have this opportunity. Just another reason you should consider going open.

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.

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!

IGERT Limited Competition Results

I just received word that the UNM limited competition results are in. Our IGERT proposal has been selected by UNM to proceed to the NSF letter of intent phase! That’s great news! Open science is finally being recognized by UNM as a major innovation and key for scientific development and they are going to help us push this forward to the NSF.

The letter of intent is due June 4. Any feedback I receive from the limited competition committee will be posted online.

In the meantime follow the next phase on the document which can be found here.

Shameful self promotion

Everyone always says shameless, so I’m going to begrudgingly promote myself and do it very shamefully (in case you can’t be full of shame and be grudged).

Anyways, a couple weeks ago Mark Hahnel asked me if I had any kind words to say about figshare, and if I did would I mind speaking them aloud. I said sure, and then proceeded to talk to the empty lab about how great figshare was. I reported back the results of the empty conversation, and Mark explained that he meant that I write a post about them for the SoapBox Science Blog over at Nature.

So I got in touch with Laura Wheeler, and I started a Google Doc so she could real-time review my post. I wrote and she told me it was all wrong (actually she was very supportive!) and I wrote some more. The real-time collaboration would have been awesome if I didn’t go days between edits. But nonetheless, eventually the post was finished and she published it to SoapBox Science. Here is the link:

Woohoo! I’m published in Nature bitches!

And so that completes my story. I regretfully inform you that my boasting did not fill me with joy in the slightest bit, and I wish I hadn’t even mentioned this post at all. Nor do I wish I had mentioned it on Twitter a couple times, and I especially wish no one had tweeted my story either. But what’s done is done, and I can’t change the past, nor can I tell people to stop doing it in the future. I’ll just have to live with the repercussions.

Take that UNM administration who thinks that online science is useless, and see no merit or value in open science.

Again I apologize for burdening you with the post…


IhateAnthony, do you?

Preparing LB Media in Different Water Types

Yesterday it occurred to me that I couldn’t autoclave LB media made with DDW or D2O because of D-exchange. So I had to come up with a solution which prompted me to ask the world (thank you internet). Through the power of open science (victory for ONS!) I was able to get some comments that said I should use a 0.2 micron filter:

Well that is what I did and here is my protocol:

  •  I have this easy mix stuff that dissolves pretty rapidly (see Experiments’ Products Page), and it requires 20g/L
  • I want to make 100ml amounts for each water type (99% DDW and 99% D2O), so I need 2g of LB media.
  • Add 2 g to the 100ml of water and stir.
  • Suck up in a sterile syringe.
  • Add 0.2 micron filter to syringe and pump into autoclaved glassware.