Category Archives: Open Notebook

Defense Outline

Just over a week away now…

  1. Introduction
    1. What is D2O?
    2. The history of D2O
      1. Gilbert Lewis:
        1. purification
        2. biological effects
        3. The hypothesis
      2. Joseph Katz
        1. various experiments
    3. Uses of D2O
      1. NMR, mass spec
      2. The need for a D2O adapted organism
    4. Experiments in DDW
      1. use for space travel
      2. cure for cancer?
  2. The effects on life
    1. Tobacco Seeds
      1. The Crumley experiment and repeating the experiment
      2. Tobacco seed germination rate
      3. tobacco seed growth rate in low deuterium concentration
    2. Arabidopsis
      1. arabidopsis growth rate
      2. arabidopsis morphology
    3. E. coli
      1. growth rates
      2. adaptation and adapted growth
      3. morphology
    4. Yeast
      1. growth rates
      2. adaptation – can’t adapt
      3. morphology
        1. stall during cell division
        2. microtubule stabilization in D2O
  3. Molecular effects
    1. Stabilization of biomacromolecules
      1. DLS experiments
        1. Catalase
        2. Ovalbumin
      2. YPD longevity
    2. Investigation of HD exchange
      1. mechanism and exploitation for protein struture studies
      2. FT-IR analysis
      3. Cavity ring-down analysis
        1. low cost measurement of local atmosphere isotopic composition
    3. Effect on DNA
      1. The pursuit of shotgun DNA mapping
      2. optical tweezers
      3. methods
      4. overstretching data
  4. Future Work
    1. Arabidopsis
      1. adaptation
      2. seed growth in low deuterium
    2. Tobacco growth in low D2O
    3. Yeast morphology in taxol
    4. E coli protein expression in D2O and protein structure analysis
    5. DNA
      1. overstretching in D2O with intercalators

Well there is my idea of how to present my dissertation. I’m not sure if/where I should put my discussion on open notebook science. Also there are a couple things that I could see going elsewhere. I could describe the yeast and e. coli stuff in parallel instead of one after another. Also the HD exchange stuff could easily go right after the yeast, e. coli, or even the tobacco seed stuff. What to do…

Otherwise I think the story is pretty compelling: history of D2O and the unanswered question by Lewis. Investigations into D2O effects and trying to understand low D2O concentration effects, effects on macromolecules, and the understanding of large volume/long-term HD exchange.

Any feedback you may have would be GREATLY appreciated. I’ll send you a figshare t-shirt, or if you are XL, I’ll send you a hoodie (but I only have one).

Chapter 1: Open Notebook Science

View in Google Drive.

The link above should give you access to the chapter in all it’s glory. Currently it is pretty much done barring revisions, the addition of figures, and moving the references from side comments to an end of chapter reference section. I’m providing an embed below in case you don’t care about all the cool references enclosed and just want to read. If you are reading via mobile, click the link.

The entire story of my scientific career

This article is actually the introduction to my dissertation and I thought I’d share it with the world officially rather than let it die in an electronic archive somewhere. I’ve shared this story in some form or another several times already, but I’ve never provided the entire account like this. And so, it is with great pleasure that I share with you, the story of how I became the scientist that I am today…

I joined the KochLab in the Spring of 2007. It was a brand new lab that, at the time, was comprised of Dr. Koch, myself, and my best friend Larry Herskowitz (who is now Dr. Herskowitz). In our first lab meeting, Dr. Koch discussed his scientific endeavors up to that point (some of which are continued in this dissertation) and introduced the concept of open science.

Open science was, and still is, an emerging paradigm, and is not to be confused with a particular field of science. The core concept of open science is providing access information and it is through the opening of scientific research that many new endeavors have become possible. Many of these endeavors have changed the way scientists approach research and acquire data. Citizen science, for instance, has brought a mass scale of human analysis to previously unsolvable problems. Even sharing data has led to new forms of collaboration. Data repositories have allowed scientists to share data with the world in hopes of finding new uses for the shared data. Tools like DataOne have emerged to provide some organization to the new data. Meanwhile, open notebook science has emerged to open the entire scientific process and practitioners make every stage of research accessible including protocols, raw data, data analysis, and much more open to scrutiny.
Continue reading The entire story of my scientific career

The value of open research

This post is written to supplement the P2PU Open Science Education Module, and in particular is meant to be an introduction to open research education.

My name is Anthony Salvagno and I’m an open notebook scientist. That basically means that I publish ALL of my research in real-time on the web. All of that research is attributed under a Creative Commons Attribution ShareAlike (CC BY-SA) license, so the information is free for anyone to use.

If the foundation of science is the pursuit of knowledge and to share that knowledge, then why is it acceptable for scientists to hide their research? Why is it ok for publishers to make you pay for that information? Why is it scientific culture to protect data like it is a commodity to be sold?

In truth, that system worked in the past because the technology was limited. Now the technology exists to instill a new culture. But what are the driving forces that would push someone to make this change? Simply put, I was fed up!

I was originally pushed into open science for one simple reason: my advisor was trained in an extremely closed system. In my first year of graduate school (and his lab), I was presented with the concept of open science, which then was barely taking hold. I was surprised to learn that scientific culture wasn’t a naturally open system, and in fact was surprisingly opposed to that concept.

Early in my graduate program, I became frustrated with the way scientific publications were written. I could only understand a small percentage of the articles I was reading, articles that were written by my peers. I knew most graduate students felt the same way. If we are producing the data and writing the papers, then why would we continue to perpetuate the cycle? So I decided that all of my research would be as accessible as possible.

At times, I would need to understand an experimental process, so I would scan the literature and try to repeat experiments to gain a foothold. I became frustrated with the content contained in the methods sections of scholarly work. Often, the methods would be vague, condensed, or just incomplete, and it would cost me time and money trying and failing to repeat experiments. So I began to document my protocols completely, including minor details that could potentially save other scientists a lot of time.

I have also come across scientific results of a questionable nature. Most of the time the results seemed incongruent with my own research, or even just based on my own expertise I knew there was no way to achieve those results. But the scientific process lacked transparency, so there was no way to understand how the researchers obtained their data. So I made sure that my analysis was entirely transparent, and I provide the data during every phase of analysis including the raw data.

In essence, I have become the scientist that I am because of the experiences that I’ve had. Instead of perpetuating the problems that exist in modern scholarly work, I work toward making a change.

I know I’m not the only scientist who has come across the same issues, in addition to other ones. There are a lot of open scientists who work toward the same goals. We hope to bring about a new culture to enhance the speed of science, to improve our collective knowledge, and to make discoveries that would be impossible in the old system. That is why open research practices are important to me, and that is why every scientist should be an open scientist.

The Open IGERT: Review of the Reviews – Grant Declined

Sorry for the weird title, I wanted to describe as much about this post as possible in the title without making it super huge. Long story short, the IGERT Grant that my peers and I submitted in August has been reviewed and the reviews are in.

The Open IGERT has been declined.

I’m not at all surprised. I knew we were a long shot. And I knew that we weren’t focusing on issues that, while not required or mentioned by the NSF, would be things they would want us to focus on. But, I thought we put together a powerful program. Unfortunately the NSF and their army of anonymous peer reviewers thought otherwise.

So in an effort to improve upon the program I am going to share the reviews with you all, and comment on the reviews. The reviews and the review summary can be found in my Google Drive Folder. Feel free to poke around. For reference, here is the original NSF call for proposals. And so you can skip the link, here is the main objectives of the IGERT call:

  • …NSF recognizes the need to educate and support a next generation of researchers able to address fundamental challenges in
    1. core techniques and technologies for advancing big data science and engineering;
    2. analyzing and dealing with challenging computational and data enabled science and engineering (CDS&E) problems, and
    3. researching, providing, and using the cyberinfrastructure that makes cutting-edge CDS&E research possible in any and all disciplines.

On to the reviews:
Continue reading The Open IGERT: Review of the Reviews – Grant Declined

Impact of Electronic Notebooks on Science