User talk:Andy Maloney

Open Dissertation Discussions

Below will be the open discussions relevant for my open dissertation. If you do not have an account with Open Wet Ware, you can obtain one from here. I would like to have people format their questions and comments in the following manner:

1. Make a subheading with your name by typing in the following to the wiki:
   • ===Your Name=== This subheading will be your area where you can post new comments to or, update any comments that you may have previously posted.
2. To make new comments, please use the following wiki markup to sign the new comment with a time stamp.
   • '''~~~~:''' The output of this looks like: Andy Maloney 12:19, 7 February 2011 (EST):.

If you are unfamiliar with how to use media wiki markup, please take a look at the following formatting article. If for some reason you are not willing to join the wiki, you can email me by following the link below.

• Click here to email me.

In the email, please let me know if you would like to be anonymous or not. I would like to give attribution to those that comment but if you would like to remain anonymous, I will respect your wishes.

As much as I would like to keep my dissertation completely open and in the media wiki format, I will have to at some point format it to the guidelines dictated by my university. This will necessitate putting a final "snap shot" of the dissertation in a book format of which, all comments will have their own special appendix in each chapter.

Thanks for looking at my open dissertation!

Add comments below

Cesar A. Rodriguez-Rosario

• Cesar's Blog.
• Cesar's Lab Page.

I have some suggestions for the process of the Open Dissertation itself. After all, this is not only new scientific research experiments, but an experiment on Open Science itself at the same time.

1. Have MAIN area called "Dissertation". I guess it should be this one. Here, explaining the idea of an open dissertation, linking to all the chapters, numbered. Have an area where discussion about Open Dissertations can happen in general, and to your own in particular. Things like formatting, questions about its relationship to the old-style dissertations, etc could go here.
   • Andy Maloney 12:29, 7 February 2011 (EST): Done.
2. In this area where you explain why you are doing the open dissertation, explain also what you need from the community. Some simple instructions, links, etc would attract more people to help you out with this Open Science experiment.
   • Andy Maloney 12:29, 7 February 2011 (EST): Done.
3. Most of the time I don't want to edit the dissertation, I prefer to write comments and question about your dissertation, kind of like the red markings. Do you suggest any mechanisms for this? Any specific formatting recommended? Please, let me know what is the best for you.
   • Andy Maloney 12:29, 7 February 2011 (EST): I have setup talk pages for the chapters. As new chapters are written, I will make sure that the talk pages are clearly linked to so that anyone can post their comments there.

All these would help many people in the Open Science community to make this open dissertation the way to do dissertations.

Committee's response to 1st draft of dissertation and Andy's presentation

Steve Koch 18:26, 30 March 2011 (EDT) CONGRATULATIONS!!! Andy passed the exam. Only minor revisions required on dissertation. In the spirit of this open dissertation, I will try to record some of the main points from the dissertation committee during the talk and the private disucssion afterwards. I won't give attribution to specific members because I don't have their involvement or permission. I also won't organize this because I just want to get the information down before I forget.

• I think everyone enjoyed the presentation. I personally really love the heavy ice demo because it's just cool to see the heavy ice float on the layer of cold heavy water that is created below the warmer light water. Andy did a very good job on the presentation and the audience was engaged. I think at least one committee member wanted to see more of an introduction to "why we care about kinesin" and I probably would agree with that. But I definitely think it came across that he built a really nice platform for studying kinesin and has begun to extract biophysical science out of it.
  • Andy Maloney 18:00, 1 April 2011 (EDT): Done.
• The committee as a whole was uncomfortable with the style of the dissertation. Not the fact that it was open but the (for lack of better phrase) "less formal" style of writing. We agreed that the most likely reason this could matter was the risk that potential future professional connections (e.g. postdoc advisors) may be turned off by the unusual style and discount Andy as a scientist. I agree that's a risk. I was really pleased, though, that the committee respected Andy as an individual and that this is his work and we should be careful not to impose our own "style" on him too much. One committee member besides me in particular was strong about that.
  • Andy Maloney 18:00, 1 April 2011 (EDT): I also feel strongly about this. Yes, I'm a scientist. Yes, I use jargon and have the capability to describe everything I've done, and can do, in the most obtuse manner possible. As physicists, we place a lot of weight on being able to have conversations about science. We even hold weekly meetings called colloquiums in order to spark up conversations about science. Why then do we insist on writing in an archaic manner in which we actively attempt to confuse people and fellow scientists? This is illogical and as a logical person, I find it unnecessary. I will not compromise my principles about writing in a manner that is clear and easy to understand.
• The entire committee was very impressed by the open notebook science, the open data, the open dissertation and everytyhing about that. One member besides me explicitly said that Andy should be commended for his efforts in changing the way science is carried out. During the private session with the committee, we looked at various online contributions of Andy (e.g. the Instructables site), and it was clear to me that everyon on the committee, whether "old-school" or not put a lot of value behind these contributions by Andy. So that is all very good. Also, one committee member specifically commented that he liked Chapter 1 (the methods) and found it very very easy to read. This member said that he often finds journal articles difficult to understand right away, but because of Andy's style he found Chapter 1 really easy to follow, and he thought that was a good thing.
• One committee member thought of a very interesting collaboration that Andy could easily carry out before he leaves in a few weeks. Not sure whether it will be open (I think so), but I definitely think Andy should pursue it.
• Main required revision:
  • Because of the nature of this project (i.e., starting from absolute scratch two years ago), Andy did not get very far into the "science." He got to the point of taking exceptionally high quality gliding motility assay data for heavy-hydrogen and heavy-oxygen water. And he has nice preliminary data for osmotic stress. He demonstrated a lot about the passivation requirements for the GMA. But I think it's a fair opinion that I share that we've yet to get to far into the heavy-duty biophysics of the system. For example, we have a good guess that the heavy water results are due to the viscous changes in the water. Frankly, we don't know what is going on yet, and that is the exciting part.
  • If Andy were a 2nd year graduate student, it would make perfect sense to stay a couple more years and pursue those experiments while we learn new things about kinesin and figure out what is going on in collaboration with theoretical people on our project. But that's not practical now and definitely not reasonable or fair for me to strong-arm or even ask Andy to stick around to do that. He clearly did "enough" work for a very solid Ph.D. This is most easily seen by the fact that whoever lands him as a postdoc is going to be extraordinarily lucky to have him in the lab. Andy worked really hard to build an excellent platform for our studies of kinesin, and that is only just one project that he did during his time at UNM.
  • So, as one committee member pointed out, and we others agreed, the dissertation overall does not currently describe the science behind his work very well. There are two components required to fix this. One would be to amend the title to put more stress on the fact that he did very nice instrumentation and wet lab work and that is a big part of the dissertation. I.e., readers of the dissertation will learn a ton about how to do these experiments and get intriguing data about the effects of water and passivation (but not an explanation as of yet). The more difficult task, but should be quite do-0able by Andy, is to write an additional chapter. This should be an introductory chapter that talks about the science of kinesin. Giving an introduction to kinesin and why it's important. Then getting into more of the questions our collaboration is looking into, and specifically explaining why we thought water isotope and osmotic stress may be a good knob to turn, in order to learn about the mechanochemistry of kinesin in collaboration with the theoretical and molecular modeling group. I agree this will make the dissertation much better and more useful. I also think Andy shouldn't have much trouble doing it, because we have talked about this a lot, and a number of our publications and talks published on Nature Precedings and elsewhere talk about this.
• Well, that's my mind dump for now. CONGRATULATIONS ANDY!!!