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.

When Dr. Koch first introduced open science, he described a world of collaboration and transparency. As a lab, and as individuals, we had nothing to hide. We would let the quality of our experiments stand for themselves. The transparent approach was going to be the mechanism that set us apart from the rest of the world. It would distinguish our research.

As Koch described the real world, and compared it to our future practices, I was surprised to find out that labs weren’t naturally like this. While there are plenty of labs that produce high quality research, there are also a number of labs that exploit the traditional system to falsify their claims, perform sloppy experiments, or stretch data for the sake of publication rights. In fact, Koch’s scientific development was from this particular environment.

He spent some time as a postdoc at Sandia National Labs (SNL). Some of his research at SNL was classified, if not only for it’s governmental affiliation. Even the research that wasn’t classified wasn’t necessarily encouraged to be shared. Before his time at Sandia, he was a graduate student at Cornell and the lab he worked in was a strictly closed environment. After the time he spent in graduate school and in a national lab, he felt it was time for a change. If not for his shift in perspective, I would not be the scientist I am today.

Back in 2007, the lab focus was on developing a technology called Shotgun DNA Mapping (detailed in Appendix A), which was an expansion on the research Koch had undertaken at Cornell. He had come in contact with the developers of a (then new) website known as (OWW), and they were willing to give us access to private space on the site. Since we were one of the first groups to join their fold, we would be the experiment to see how the site could be used for scientific collaboration. We could use the site however we saw fit, but the main purpose was to maintain electronic notebooks that could be accessed and edited from anywhere.

In the Spring of 2009, our collaborator, Dr. Mary Ann Osley graciously hosted me in her lab so I could be trained to undertake the molecular biology portion of the Shotgun DNA Mapping project. At the time, the lab was operating solely via the private site OWW provided, but we also had public space. In one meeting, to prepare me for my time in a wetlab, Koch had mentioned that I should put some work in the public space. My first few days in the lab, I happily obliged, but quickly ran into a roadblock. I was spending so much time writing information on the public site, while also maintaining my private notebook that I had stopped being efficient. So I made the smartest decision I have ever made in my scientific career: I stopped working on the private site and moved all of my research to the public site in my open notebook.

That was the beginning of my journey.

I began learning the HTML and CSS web languages to build a better notebook. I began learning about cloud technology to expand the capabilities of my notebook. I began experimenting with various web software and incorporating them into my notebook. Slowly I had developed a decent knowledge of available tools and how to make the most efficient and powerful notebook. And the knowledge was expanding by the day.

In 2010, the lab received grant money from DTRA to study how heavy water interacts with kinesin, a molecular motor that processes along microtubules. Larry had finished developing the software necessary for Shotgun DNA Mapping and started working on a simulation to study various aspects of kinesin processivity. Andy Maloney, a dear friend, veteran graduate student, and now PhD, had joined the lab and began work developing the gliding motility assay to experimentally study kinesin processivity. Eventually new students, Nadia Fernandez-Oropeza and Pranav Rathi joined the lab to fill out the team. Nadia would continue the work Andy pioneered, and Pranav began work on the optical tweezers that would be used for DNA experiments and hopefully kinesin studies.

I, unsuccessfully, continued my research with the molecular biology behind Shotgun DNA Mapping, while the lab switched gears to D2O-kinesin interaction. Every effort had resulted in a dead-end or failure, and finally in the Summer of 2011, I began to investigate the role of deuterium in life.

During literature searches into the background of the group’s experiments, Koch had stumbled upon the very basic research of Gilbert Lewis, who was an extremely decorated scientist, but was also the first person to purify D2O from natural water. Lewis had performed some simple experiments growing tobacco seeds in 99% pure D2O and found that the plants didn’t germinate in the “heavy” water. Lewis’ work sparked a new field of studies, and many other scientists began to study how heavy water affects living organisms.

Unfortunately in the 1960’s, the investigations into the effects of heavy water slowed down and virtually ceased. Many of the questions that Lewis and others proposed would remain unanswered and unacknowledged until that summer in 2011, when Dr. Koch proposed that I investigate the questions initially asked by Dr. Gilbert Lewis in 1932. He also gave me a challenge:

I should strive to keep the best open notebook in the world.

Repeating and expanding upon the experiments of Lewis, Crumley, and many others was a perfect application for open notebook science. First, the record between the past and the present had been severed and there should be some connection made between the two time periods. Second, the experiments performed at that time were crude and poorly documented. Any potential future work could be made much simpler if only there was some bridge.

It is my hope that the research documented here, all of which can be accessed via my newer open notebook, is the connection between the past and the future. I have gone through the experiments of the past and re-documented their findings. I’ve also repeated their experiments and documented every step of the process. In doing so, I hope to insure that no one will ever need to spend time to decipher my methods. The objective with my research through open notebook science, is that someone down the line (if not myself) can pick up from where I left off without the painstaking effort that was required from me.

When I began my first open notebook, I had no idea the impact this simple idea could have. The impact of the simple notion of sharing one’s research has been amazing. The initial reaction to my approach wasn’t knee jerk, condescending, or negative in any way. In fact when presented with open notebook science initially, Koch had warned me that there would be scientists who would oppose our philosophy and methods. And while I have met just a few of those, for the most part the response has been overwhelmingly positive. To encourage the positive reception, I began documenting everything that I had learned about open notebook science: best tools, incentives, benefits with regard to copyright and patent law, and the uses it can have in scientific culture.

I don’t know if I ever fulfilled the challenge set forth by Dr. Koch in 2011, but I can’t argue that I certainly arose to it. By creating and curating educational resources for open notebook science, I hope that I have enabled scientists around the world to share their research for the benefit of science. And by documenting and sharing my research in full detail, I hope I’ve demonstrated that this practice can be taken seriously and that many others can follow suit in whatever capacity they tolerate. I hope in the years to come, that we can look back at the work of myself and my fellow open notebook scientists and realize this was the tipping point in scientific culture.