tag:blogger.com,1999:blog-73569643878443311412024-03-14T03:40:45.106-06:00Steve Koch ScienceI figure I'll use this blog for posts that aren't clearly related to teaching or research but are still generally related to my professional life as a scientist.Steve Kochhttp://www.blogger.com/profile/09076719001132389463noreply@blogger.comBlogger22125tag:blogger.com,1999:blog-7356964387844331141.post-67254072338318842302011-12-02T15:18:00.000-07:002011-12-02T15:18:25.830-07:00Quick summary ARL / DLF E-Science Institute Capstone -- AtlantaWaiting for flight home from Atlanta from the <a href="http://uchc.libguides.com/content.php?pid=228797&sid=2246588">ARL / DLF E-Science Institute Capstone</a> event. Overall, it was a very productive event, especially for discussions with Rob Olendorf (my collaborator and a data management librarian at UNM) and Dale Hendrickson (head of Library IT at UNM). Almost all of the attendees were library personnel, and I learned a lot from my interactions and the ideas presented. I thought I would jot down some ideas and action items.<br />
<br />
First, action items. We were encouraged to develop "next steps" for when we return to our institutions. Here are some of ours:<br />
<br />
1. Incorporate Library interactions with the undergraduate physics course (PHYC 308L, electronics lab) I am teaching next semester. This is a new course for me, and I won't have time or familiarity to diverge much from the very good plan that prior instructors have developed. But I know enough that Rob, Dale, and I came up with some concrete ideas that will be great for spurring data management at UNM and with these budding scientists:<br />
<br />
<ul><li>Guest lecture by Rob to describe data management and related library services. I think this would be best for the second lecture period in the course. Rob will describe issues of data management and we will announce our intention to integrate library data management into the course (below). Rob will also give an overview of github and a quick "how to."</li>
<li>A substantial part of the course (as I understand from talking to prior instructors and students) involves developing LabVIEW code for circuit design and simulation. I'm guessing (pretty sure) that no source code control or versioning is used. I think this presents a good (not perfect) opportunity to teach the students how to use github for versioning and source code sharing. I'm thinking it will be an integrated requirement for all of the coding during the semester. The reason it's not perfect is because LabVIEW uses binary files, so some of the forking and merging functionality will not be appreciated. Many of the students are experienced in Matlab, though, and where possible I will encourage moving to that platform. Regardless of how this plays out, I think for sure the students will come away from the course with a fundamental knowledge of github and how wonderful it is for protecting and sharing code. I think I will also require LaTeX for their final reports, which will work well with github.</li>
<li>Incorporate data management, using the Library Institutional Repository. Some infrastructure and coordination with the library will be necessary here, because I don't think we've done it before at UNM. Dale's idea is to create a "community" in the d-space IR for our course, e.g. "Junior Lab 308L." The students will be in charge up uploading their final data sets (testing their circuits) into permanent, curated objects in the IR. There may be difficulties with this, but I am confident that the students will come away with a good appreciation of the power of good data management, and, hopefully a real, curated data set as part of their career portfolio.</li>
</ul><div>2. Participation is data management "group meeting." The library currently has some kind of regular meeting like this, and I will visit one of their upcoming meetings.</div><div><br />
</div><div>3. (Mostly for Rob)--"finish" our pilot data management project. Rob has been working on this for a long time and it hasn't been easy. He is working on curating and archiving one of Andy Maloney's complete kinesin gliding assay data sets. The uncurated data can be seen on our <a href="http://kochlab.org/files/Passivation/">server</a>. I don't really understand how Rob is doing this, but he's done a lot of coding and is close to putting a curated version of that data set into our institutional repository. There are 500,000 images in the set, and I think Rob said that involves more than 50 million lines of (XML?) code to describe it. I may be getting terminology and numbers wrong ("schema," etc.) but the point is Rob is writing a lot of code to do it "right." A finished product will serve as a great example to everyone on campus (and even broader), especially researchers as to what the library can provide for data management. I think this will be a huge step for us at UNM and in convincing more researchers to collaborate with the Library for research data management.</div><div><br />
</div><div>There were many more "next steps," but they aren't coming to mind now. More than just next steps, there were a lot of visionary ideas presented by groups at the capstone event. Here are some that stuck in my mind:</div><div><br />
</div><div>1. Graduate students are key to connecting data management librarians with research groups. What seemed the best idea to emerge was that an existing pipeline to graduate students is the general requirement for "ethics / responsible research conduct" courses as part of NIH/NSF training grants. Good data management is often part of these courses, and in my mind is essential for responsible / ethical research. Given how these courses are usually implemented, I think it would be fairly easy for data management librarians to obtain one or more time slots to discuss data management with the graduate students. Best would be "hands-on" coursework, where the students are asked to bring data to the course. This was discussed a bit on a <a href="http://friendfeed.com/stevekoch/fd2dc64a/idea-at-workshop-to-surmount-library">friendfeed thread</a>.</div><div><br />
</div><div>2. Our institutional group and at least one other (can't remember the institution) more than once mentioned a vision for the library providing more than just data curation / preservation / storage. I don't have a good term to capture this area, but it involves capturing / helping with workflow (especially custom software used in labs for data management / processing) and data visualization. In my mind, a ripe area for connecting with researchers is to work backwards from the traditional publication. Currently, many libraries have an institutional repository that allows researchers to post PDFs of research papers. And usually that's about it (from what I can see). Working back upstream, what I think would be very useful is to provide a computational workspace (through the libary) where researchers can process and produce the figures in those papers. As an example, my graduate student logs into the library workspace, and uploads the data needed to produce the final figures. The graduate student and me then use software on that workspace (maybe R, Matlab, Excel) to create the figures for the paper. There is a versioning system to keep track of the code used to process the figures and the many versions created. When the paper is submitted for peer review (the current standard), it is seamless to link each figure to the data sets and the code used to generate those figures, using either permanent URLs or DOIs. For me as a researcher, I would LOVE such a system. And talking with Dale and Rob, it doesn't seem too much of a pipe dream. It's a lot of work, but I think it would be a huge step and improvement in data management and data sharing in research. Successful implementation would also be a really great way to recruit more researchers into data management partnerships with the library. An important component of this I forgot to describe above is that there will be experts in the Library (such as Rob) who can work side-by-side (virtually) with us to develop the data visualization code and figures.</div><div><br />
</div><div>3. Related to item 1 above, I think connections with graduate students could be greatly accelerated by a grants / data management competition. A $1000 dollar research grant prize, directly to graduate students for "the best data management," would I think be very effective. Compared to what we need to accomplish to transform research and the library's involvement, $1000 every so often is not a lot. But it would mean a lot to the graduate students in the competition.</div><div><br />
</div><div>4. The NSF Data Management Plan (DMP) requirement has already done a lot to connect researchers with data management librarians. Rob estimates more than 30 faculty connections have been made for him at UNM because of DMPs. I think this is just one great outcome of the DMP requirement. And it illuminates a huge opportunity that I see for researchers and libraries. In my specific case, if I get tenure at UNM, I want to pursue a couple training grants. One specifically I would like to try for is an "open science" NSF REU program. REU is "research experience for undergraduates," usually involving summer research internships for undergraduates from other institutions around the country. I think an REU proposal with a heavy focus on "open science" and advanced data management would look very appealing to the NSF. Of course I also think it would be very effective in training the next generation of researchers. Importantly, though, I would need a lot of help to write this grant. The Library's experience with DMP's can be extended to this effort and people like Rob and others will be essential in planning, writing, and executing the grant. Moreover, I think other people on campus who are planning other training grants would get a big "broader impacts" boost from this kind of data management or "open science" collaboration with the library. So, hopefully, our Research office can help coordinate these endeavors.</div><div><br />
</div><div>Many, many more ideas but I think I'm out of steam for now. Overall, a great conference and I'm excited for pursuing these ideas!</div>Steve Kochhttp://www.blogger.com/profile/09076719001132389463noreply@blogger.com16tag:blogger.com,1999:blog-7356964387844331141.post-39012266206491402932011-11-22T16:23:00.000-07:002011-11-22T16:23:30.671-07:00An idea for wealthy donors: alternative to direct research funding: fund libraries to help with e-researchNext week, I am attending the <a href="http://uchc.libguides.com/content.php?pid=228797&sid=2246588">E-Science Institute Capstone event</a>, along with Rob Olendorf and Dale Hendrickson from U. New Mexico Libraries. As part of our preparation for this event, we are interviewing several people around the university to capture their views on e-research. Today, Rob and I interviewed <a href="http://elibrary.unm.edu/deansoffice/mbbio.php">Martha Bedard</a>, Dean of the UNM Libraries. Rob and Dale figured it would be good to have me lead the interview, since I'm coming from outside of the library and thus would ask different questions. At least from my perspective, this was a success and I learned a lot in the generous one hour of time that Martha gave us. <br />
<br />
At this point, I can't share the interview notes publicly, but I did want to share one idea that emerged during our discussion (and there were several good ideas!). I'm having trouble getting the idea in writing so maybe by poorly blogging it, someone else can turn it into a good idea, if it's sensible at all. Here's what I'm thinking: wealthy donors, or a group of donors that want to make a big impact on research at their university have at least the following two choices:<br />
<br />
1. Provide substantial money to fund research in a specific field, for example by providing 10's million dollars to fund a nanomedicine research center. Or to build a new biomedical engineering building. Etc.<br />
<br />
2. Provide substantial money (say $10 million) to the university library in order to vastly improve the ability of ALL researchers at the university to conduct e-research. The money would go towards hiring many new library faculty and staff members and procuring and implementing storage and networking infrastructure. The goal would be a completely transformed library that would make it easy and almost automatic for all university researchers to conduct connected, networked, open, archived, discoverable, etc. research.<br />
<br />
Option 1 is common and makes a big impact on specific research fields. Performing research in excellent facilities, with dependable funding is a great thing for researchers. As far as I know, option 2 is less common, and I'm not aware of a good example. But I think there'd be tremendous leverage compared to option 1. The reason there is so much leverage is because currently the huge potential of "e-research" remains almost untapped. There are shining examples of successes. (For an excellent overview of the successes and the vast, untapped potential, read Michael Nielsen's <a href="http://www.amazon.com/Reinventing-Discovery-New-Networked-Science/dp/product-description/0691148902">excellent book</a>.) But in reality, for most researchers it's really difficult to manage data, share data, provide open access publications, etc. And this is true even for researchers like me, who've decided to be as open as possible yet are finding it difficult to do so effectively! So, it's basically true that there are huge technical barriers for most of the researchers to maximize the impact of their research by sharing. Because we're so bad at it and because it's so difficult, I think there's a ton of room to make a huge impact at a university with a medium-sized grant. I think the uinversity library is the natural and only choice to lead the effort. And by doing so, it would impact all of the researchers across all of the disciplines (humanities, science, medicine, etc.). How would they implement option #2? I don't actually know, and that's a big reason why I want the library to do it! Rob Olendorf, my collaborator at UNM on open data projects has a vision for how to make it seamless and almost automatic for researchers like me to connect, archive, and share our research and data. I don't understand how that can work, and I don't have time to understand. But I would LOVE to participate in that system.<br />
<br />
That's the final key to the idea. I think a university would gain a huge competitive advantage by becoming the "e-research leader." There is a perception that most researchers are content with limited sharing and the status quo. This may or may not be true. But regardless, it looks like there is a lot of momentum, driven by the public interest, for funding agencies to go much further with data sharing, data management, open data mandates. These mandates are scary to many researchers. Even if researchers want to have excellent data management and share their data, it's almost impossible to do so now. So, compliance will be a huge and new headache for researchers. If a university could boast that compliance is "seamless and easy" it would be a real and strong recruitment incentive. This probably sounds questionable to some, but I really see it as a huge incentive. It would be just as appealing as the opportunity to work in a fancy new research facility.Steve Kochhttp://www.blogger.com/profile/09076719001132389463noreply@blogger.com24tag:blogger.com,1999:blog-7356964387844331141.post-68973502054811064522011-11-03T11:26:00.000-06:002011-11-03T11:26:49.927-06:00The inevitable spread of open scienceTwo things have happened this week that make me really happy about the research in our lab and the spread of open science. First, we have a new undergraduate REU student, Alex Haddad, who has started her own open notebook science under the mentorship of Anthony Salvagno. Her notebook is on wordpress.com and can be found <a href="http://alexhaddadnm.wordpress.com/">here</a>. This is Alex's first experience in a research lab and she has immediately embraced open notebook science and she is excited about it. One cool thing that I've noticed already is that her notebook entries are automatically linked in Anthony's notebook when she links to them. Some kind of trackback thingy that I don't understand, but is great as far as good notebooks go. An example can be found in <a href="http://research.iheartanthony.com/2011/11/02/repeating-crumley-4-the-setup/">Anthony's notebook entry</a>, which automatically links to Alex's entry providing more information (see the trackback at the bottom of the page). Welcome, Alex, to open notebook science!<br />
<br />
The second thing that happened is that our former PhD student, Andy Maloney, just started a new postdoc at UT-Austin with Hugh Smyth. This is going to be a very productive experience for both Andy and Hugh's lab, I am confident. Most excitingly, though, is that Andy and Hugh have decided to incorporate open science into their projects! I think this is very big news and a success for the spread of open science. Major props to both Andy and Hugh for their willingness to carry out major parts of their research using open science! I had some further thoughts on this and the implications for the spread of open science. Instead of re-writing them, I'll just quote my comments on the <a href="http://friendfeed.com/stevekoch/05cefc7f/andy-maloney-back-to-open-science">FriendFeed thread</a>:<br />
<br />
<blockquote class="tr_bq">I think big factors are Andy's commitment to open science and his new PI's commitment to making an impact in science and medicine. I met Hugh Smyth a few times when he was at UNM and only detected awesomeness, both in his research and in his mentoring and concern for students. Openness is probably going to be more challenging for them, though. One reason is their research is much more applied and medical, and thus IP plays a major role. The field is probably a lot more competitive. And their lab is much more successful with funding. As Nielsen and others have pointed out, the current reward system stacks the cards against openness. So they will have to be careful. But I think they're clever enough to figure out how to do it, and their success will pave a lot of roads for future openness. I've been thinking about it pseudo-mathematically and I think the fact that they're even willing to try is a success. I've had two PhD students graduate so far. One is likely in industry for a long time and unlikely to be open for a long time if ever. The other, Andy, is now at least partially doing open science. The subsequent students in our lab (Anthony, Alex, Nadia, Pranav) are still performing open science. A former intern, Diego Ramallo Pardo is in grad school at Stanford and has a passion for openness, but not able to be open yet. Dozens of undergraduate lab students have performed open notebook science in my lab course, and there have been a few instances of continuing ONS after the course (most do not continue in research careers). So, at first glance it appears that there isn't a high rate of spread of openness from our research and teaching labs. But it occurs to me that it doesn't matter. If we were to model openness as an infection, it's a powerful one. I think it's even a latent infection in almost all scientists. Participating in openness awakens the infection for life and it sheds constantly. The immune reaction is our current system of practicing and rewarding science and it's quite powerful. So it wins in a lot of cases. Nevertheless, openness is slowly winning more often and the immune system is not going to adapt to get stronger. On the contrary, the immune system is going to take major hits in the coming years. Funding agencies are going to change rules. Tenure and Promotion and hiring committees are going to add members who value openness. Closed-access publishing for profit is going to topple precipitously. And at that point, openness will spread and emerge naturally and quickly. It seems plain as day to me. Now, one of you all can translate that into epidemiological mathematics and fiddle with some exponents.</blockquote>Steve Kochhttp://www.blogger.com/profile/09076719001132389463noreply@blogger.com15tag:blogger.com,1999:blog-7356964387844331141.post-74942687690503632102011-10-28T09:33:00.002-06:002011-10-28T09:37:32.809-06:00Open Access Week event at U. Arizona: Reproducibility, Open DataEarlier this week I was lucky to participate in the <a href="http://en.wikipedia.org/wiki/Open_Access_Week">Open Access Week</a> event at the University of Arizona: <a href="http://www.library.arizona.edu/news/entries/view/2634">The Future of Data: Open Access and Reproducibility</a>. The event was hosted by <a href="http://www.linkedin.com/pub/christine-kollen/18/637/13a">Chris Kollen</a> and <a href="http://www.openaccessweek.org/profile/DanLee">Dan Lee</a> of Arizona University Libraries. I am very grateful for the invite and the opportunity to meet them, some active member of the audience, and the other speakers, <a href="http://www.stanford.edu/~vcs/">Victoria Stodden</a> and <a href="http://isd.ischool.berkeley.edu/person/ekansa">Eric Kansa</a>.<br />
<br />
Victoria Stodden gave an excellent talk, framed around the computational sciences, and with the major point: Instead of promoting "open data," we should promote "reproducibility" in science. She argued, very convincingly, that good science requires reproducibility and thus scientists should be easily convinced that we need very high standards for reproducible results. For computational research, the only way to ensure reproducibility is to publish much more open data and open code than is normally done now. If your result is computational, how can anyone hope to replicate and build upon your results if you haven't provided the source code and the data sets? They can't, but publications without code and data are by far the most common these days. It's a failure of science that is probably caused by many factors. One that comes to mind is that computational scientists have been forced to fit their "publications" into standard peer-reviewed articles, where the system is not set up to accept and / or host source code and data. (As an aside, this is clearly a routine failure of peer review, as referees obviously are not ensuring reproducibility of the research, which should be a primary criterion for publication.) Scientists understand that reproducibility is an essential element of research. For example, two years in a row, my undergraduate physics majors identified reproducibility as the most important element of good science (see <a href="http://openwetware.org/wiki/Physics307L:Schedule/Week_2_agenda/Small_group_exercise">brainstorming 2010</a>). Since scientists understand this, then they will naturally practice open publishing of data, code, methods when they realize that reproducibility is missing without those elements. As Victoria argued, demanding "open data" leads to confusion and resistance and ultimately probably lack of compliance. In contrast, demanding "reproducible research" is already a cultural norm and it naturally leads to open data and open code of the most helpful variety for reproducibility. Victoria's slides can be found <a href="http://www.stanford.edu/~vcs/talks/OAuofAOct252011-STODDEN.pdf">here</a>.<br />
<br />
The notes for my presentation can be found on linked mindmaps, starting <a href="http://www.mindmeister.com/119784203/2011-arizona-oa-week-reproducibility-open-data-multiplication-of-data-impact-steve-koch-u-new-mexico-stevekochscience-gmail-com-click-on-arrows-for-links">here</a>. (Click on the tiny right arrows to navigate.) My notes are probably not too meaningful if you weren't at the symposium. In contrast to Victoria's high-level talk about policies that could make a major impact, I told a few stories about open data and open notebook science in our own teaching and research labs, and the successful impact we've had already. I think (hope) it provided concrete example of the benefits of open science. On the one hand, I showed that open science, especially open notebook science strongly promotes reproducibility. This has been seen best in the undergraduate physics lab that I teach. Students read the notebooks of other students from prior weeks and prior years. They build upon these previous results, which allows them to get the experiment working much quicker and have more time to explore new aspects of the experiment, or to develop new data analysis methods. They are doing real science! I showed an example of an <a href="http://www.openwetware.org/wiki/User:Alexandra_S._Andrego/Notebook/Physics_307L/2009/10/12">excellent primary notebook</a> from Alex Andrego and Anastasia Ierides. However, I think I also showed that open data and open science make an impact beyond just reproducibility. This impact is in reuse and repurpose of data. I told <a href="http://www.mindmeister.com/119870361/research-lab-open-data-kinesin-gliding-assay-up">two stories </a>where theory and research groups already have been able to use data we publicly shared on youtube. One group has already used our data in a theory preprint on the arXiv. Both groups expressed <a href="http://www.mindmeister.com/120218834/igor-kulic-cnrs-quotations-from-email-describing-benefit-of-our-open-data">delight and gratitude</a> that our data was freely availalbe. There are two important features of these stories. First, both groups used our data for a purpose that we had not (and probably would not have) imagined! Clearly the impact of our data was multiplied by being public. Secondly, we did the easiest and simplest sharing method we could find: youtube, yet we still made an impact. We are currently working with Rob Olendorf, a data curation librarian at UNM to vastly improve our sharing. This will include permanent citation links, vastly improved metadata (at least 10x more than the data itself), hosting by the institutional repository (much safer than our lab server), and links to other data sets. Reason would have it that if we could make an impact with the imperfect system we tried first, then the impact will be much higher with the data shared via Rob and the institutional repository.<br />
<br />
The final talk was by Eric Kansa, who described the amazing work of him and his colleagues on <a href="http://opencontext.org/">Open Context</a>, a platform for sharing and linking archaeological data. His notes from the event can be found <a href="http://ux.opencontext.org/blog/2011/10/26/open-access-week-presentation/">here</a>. And his slides are available also: <a href="http://alexandriaarchive.org/wp-content/uploads/2011/10/OpenAccessWeek_UofAz_OpenContext_Kansa_Oct2011.pdf">A More Open Future for the Past</a>. Despite being far from the field of archaeology, it was easy for me to see the vast impact that Eric and his colleagues are making via the open context project. A large amount of time, sweat, and money are expended collecting archaeological data. Without opening these data and curating and linking these data, the potential impact is severely limited. The Open Context team has developed a method for collecting these data, archiving them, and linking them to other data sets. The method is very effective, and importantly requires far less work than required to collect the data in the first place. This seemed clearly, to me, a case of the huge power of data reuse and repurpose. In contrast to computational science, the power of data reuse seemed to trump the need for open data for reproducibility. This is not surprising, given how different the two fields are. But it was an interesting and somewhat confusing contrast for me between the needs for open data in computational research versus archaeology.<br />
<br />
There were several engaged audience members. One of them was Nirav Merchant, with the <a href="http://www.iplantcollaborative.org/">iPlant Collaborative</a>. Victoria and I were highly impressed by the computational platform that iPlant has developed already, only three years into the NSF cyberinfrastructure project. I was simply amazed and I couldn't do it justice describing it. The ability to ensure reproducibility of computational research with the iPlant platform is vast. One example is how easy it is to save an image of a virtual machine and then share this image with other users. They demonstrated this for us and it took only a few clicks and less than a minute. I highly recommend reading more about iPlant at their site linked above. The iPlant team that we met was energized, engaged, and collectively brilliant. I'd love to know how they assembled their team as they've clearly done an excellent job. I intend to keep in contact with the iPlant folks and am even hoping that I could introduce the computational platform to my Junior Lab students this year. I think the exposure to these state of the art and "open" tools will be invaluable for their future research.<br />
<br />
Overall, the one-day Open Access Week event was highly successful for me. I met some amazing people and gained a lot of clarity in my thinking about the imperative for much more openness and sharing in science. Incidentally, maybe not coincidentally, during my flights I was able to read Michael Nielsen's fantastic new book on the untapped potential of connected, open science: <a href="http://www.amazon.com/Reinventing-Discovery-New-Networked-Science/dp/product-description/0691148902">Reinventing Discovery</a>. Despite having met Michael and having heard him speak a few times, I still found the book riveting and I learned a lot. I absolutely recommend the book to anyone interested in the practice of science!Steve Kochhttp://www.blogger.com/profile/09076719001132389463noreply@blogger.com9tag:blogger.com,1999:blog-7356964387844331141.post-32144834258090780062011-03-04T17:25:00.004-07:002011-03-04T17:27:34.320-07:00I am maximally-skeptical that there currently exists any evidence that drinking deuterium-depleted water has health benefits or will cure disease.Because of our lab's interest in the biophysical effects of heavy water--both <a href="http://en.wikipedia.org/wiki/Heavy_water">heavy-hydrogen water</a>, D<sub>2</sub>O, and heavy-oxygen water, H<sub>2</sub>O<sup>18</sup>--I received a very friendly email inquiry today. The person suffers from a health problem and currently hopes that drinking deuterium-depleted water will help with that condition. <br />
<br />
As a scientist and a health consumer, I am maximally-skeptical of any medical claims related to drinking deuterium-depleted water. This is despite that fact that I think there's a good chance that cells may behave differently if deprived of deuterium, which exists in all natural water sources. The reasoning for my skepticism is very straightforward. There is a dearth of any published scientific or medical research utilizing deuterium-depleted water. As I will note below, there are less than a dozen research papers on the topic. So we really don't know. There is almost no evidence. We don't know whether drinking large quantities of deuterium-depleted water will be helpful or harmful or negligible. <br />
<br />
There is much more evidence, though, that the quantity of water that would need to be consumed is quite large. Because deuterium is natually-occurring, there's a lot of it in your body! It would take a long time of drinking lots of D-depleted water to have a systemic effect. My interpretation of the existing evidence is that by far the most likely outcome of this therapy is that it will generate profit for whomever is selling the D-depleted therapeutic water.<br />
<br />
Because I think it's a shame that a Google search for "deuterium-depleted water" is overrun by claims of cures for horrible diseases, I asked the person who wrote me if I could send my response on my blog instead of privately. So that perhaps our discussion could benefit more people. The person kindly agreed and so I will post his email:<br />
<br />
<div style="padding-left: 30px;"></div><div class="MsoPlainText"><blockquote>Dear Steve,<br />
I enjoyed reading your blogs and noted that you work with D2O.<br />
I have a medical condition that I want to treat with alternative methods - one of them is drinking "light" water.<br />
Do you know, or can you suggest any resources for the following:<br />
1. how to make "light' water, with D2O concentration of below 50ppm 2. who does D2O concentration testing in the us for water samples 3. who makes light water (for sale) 4. any scholarly literature on this topic...<br />
Any info will be much appreciated and shared with fellow friends who are in need.<br />
Thank you very very much!!</blockquote></div><div class="MsoPlainText"><br />
</div>Here is the reply I would have sent, but instead post publicly:<br />
<br />
<blockquote>Dear ___, </blockquote><blockquote>Thank you for your kind message. I am sorry to hear of your medical condition. I am not an expert on the medical effects of deuterium-depleted water. In fact, I am not aware of any medical experts on this topic. As a scientist, I am maximally-skeptical of any claims of currently-known medical benefits of drinking deuterium-depleted water. I'm not saying it will help or hurt you, I'm saying that I don't think anyone is close to knowing whether it will be helpful, harmful, or negligible. There is almost no published, rigorous research on the subject (your question #4), and thus any claims are probably speculation. I would suggest talking to a medical doctor, which I'd guess you've done plenty of, since they know almost infinitely more about the human body than I do. However, I would think that any medical doctor, or indeed any living person, would merely have to guess, because I do not see any experimental evidence beyond just less than a dozen published reports which have yet to be challenged or supported. </blockquote><blockquote>Below I will put responses to your specific questions, and I wish you the best, </blockquote><blockquote>Sincerely,</blockquote><blockquote>Steve </blockquote><blockquote>1. I don't know of an efficient method for producing mildly-deuterium-depleted water. The deuterium-depleted water we use in our research is much more depleted. We obtain it from Sigma, a chemical supply company, and it is roughly $100 per 100 milliliters (a few ounces). As you may know, you would probably need to drink a lot of water over many days to appreciably deplete deuterium from your body. This would surely be expensive. And like I said above, as far as I can ascertain, it's unknown whether it would be helpful, harmful, or negligible.</blockquote><blockquote>2. I don't know who does D2O testing. I'd be skeptical of anyone offering these services related to this medical purpose. Incidentally, deuterium-rich water is inexpensive. You could easily mix D-rich water with regular water and see if the purported D2O-testing company is able to correctly discern the difference. </blockquote><blockquote>3. We so far have only purchased from <a href="http://sigmaaldrich.com/">Sigma</a>. See for example product <a href="http://www.sigmaaldrich.com/catalog/ProductDetail.do?N4=195294|ALDRICH&N5=Product%20No.|BRAND_KEY&F=SPEC">#195294</a>.</blockquote><blockquote>4. I have read two scholarly papers on the subject, both from a research group out of Hungary. I found both papers very interesting, but I also am highly skeptical of the interpretation of their results. A good place to find scholarly papers related to biology or medicine is on Pub Med. <a href="http://www.ncbi.nlm.nih.gov/pubmed?term=%22deuterium-depletion%22%20OR%20%22deuterium-depleted%22">This link</a> will hopefully take you to a search for articles related to deuterium-depleted water. I can only see one that is freely available. <a href="http://scholar.google.com/">Google Scholar</a> is another place to search, but it will not be limited to biological articles. </blockquote><blockquote>I actually find this topic fascinating, as far as whether life has evolved a beneficial use for naturally-occurring deuterium. We have a side project in our lab to see whether we can notice any effects on tobacco seed growth. We're using tobacco seeds because they are tiny, so we don't need much water to see an effect. We got<a href="http://pubs.acs.org/doi/abs/10.1021/ja01335a509"> this idea</a> from Gilbert N. Lewis, who did the<a href="http://www.sciencemag.org/content/79/2042/151.extract"> initial studies in the 1930's that showed that too much deuterium affects life</a>. One of the reasons I find this side project on deuterium-depletion so fascinating is that I see it as an open mystery. That correlates well with my skepticism of claims related to therapeutic effects of drinking light water.</blockquote><br />
Below, I will embed a comment thread from FriendFeed, and also there are potential comments on the blog itself. I expect them to be a mix of helpful and derisive...hopefully more of the helpful type!<br />
<br />
<iframe frameborder="0" height="400" src="http://friendfeed.com/stevekoch/6048d065/i-am-maximally-skeptical-that-there-currently?embed=1" width="450"></iframe>Steve Kochhttp://www.blogger.com/profile/09076719001132389463noreply@blogger.com49tag:blogger.com,1999:blog-7356964387844331141.post-59931859674133467692011-02-05T17:19:00.001-07:002011-02-05T17:22:34.341-07:00An open data success storyOver the winter break, <a href="http://flavors.me/andy_maloney#871/custom_plain">Andy Maloney</a> and our lab enjoyed an open data success story. Andy shares his data publicly with a CC0 / public domain license. Some scientists ran across the data, I think by Google searching and contacted us to ask if they could use our data to support their research. Since it is CC0, they didn't have to ask, but like most scientists, they were courteous and did contact us. I shared this story at the ScienceOnline2011 "<span class="Apple-style-span" style="font-family: arial, helvetica, sans-serif; font-size: 13px; line-height: 19px;"><a href="http://scio11.wikispaces.com/Program">Data Discoverability: Institutional Support Strategies</a></span>" session and I think people liked the story. Jean-Claude Bradley mentioned it in<a href="http://usefulchem.blogspot.com/2011/01/science-online-2011-thoughts.html"> his blog summary of the conference</a>, and<a href="http://lucypower.com/"> Lucy Power</a> saw this and contacted me for more details. Lucy's is studying e-Research for her Ph.D. dissertation topic. I sent her a reply, and instead of rewording it, I will just past it below. I can answer questions on the FriendFeed thread. Yay Open Data!<br />
<br />
<br />
<blockquote><span style="color: #1f497d; font-family: Calibri, sans-serif; font-size: 11pt;">H</span><span style="font-family: Calibri, sans-serif; font-size: 11pt;">i Lucy – I definitely should write up a blog post about it and I will try to do that soon. I think it’s a great little success story for open data and data reuse. In a nutshell (and I can answer questions): Some people found Andy’s microtubule gliding assay data on youtube and emailed us to say it was very interesting to their theoretical work and could they use our data in a pre-print. We replied “of course!” “woo hoo!” and we told them that it’s all public domain data so they are free to do whatever. As a courtesy, we said we’d like a shout-out. They went further and offered co-authorship, but Andy and I decided an acknowledgment was more appropriate at this time. Andy suggested they acknowledge open notebook science, etc. and they did in their pre-print. You can find the pre-print here: </span><a href="http://arxiv.org/PS_cache/arxiv/pdf/1101/1101.2225v1.pdf">http://arxiv.org/PS_cache/arxiv/pdf/1101/1101.2225v1.pdf</a> <span style="font-family: Calibri, sans-serif; font-size: 11pt;">see Figure 3A for Andy’s data and the acknowledgments section.<br />
<o:p></o:p></span><span style="font-family: Calibri, sans-serif; font-size: 11pt;"><o:p> </o:p></span><span style="font-family: Calibri, sans-serif; font-size: 11pt;">I think it’s a great success story because (A) they never would have known about our data if it weren’t open. It didn’t necessarily have to have an open license, but it needed to be discoverable. (B) we never would have thought to use our data for this purpose. So obviously value was created via openness.</span><span style="font-family: Calibri, sans-serif; font-size: 11pt;"><o:p> </o:p></span><span style="font-family: Calibri, sans-serif; font-size: 11pt;">OK, I’ll try to write up the story in a blog or something soon! (Maybe I should just post the above and not worry about wording it better? </span><span style="font-family: Wingdings; font-size: 11pt;">J</span><span style="font-family: Calibri, sans-serif; font-size: 11pt;"> )<br />
<o:p></o:p></span><span style="font-family: Calibri, sans-serif; font-size: 11pt;"><o:p> </o:p></span><span style="font-family: Calibri, sans-serif; font-size: 11pt;">--Steve</span></blockquote><br />
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">FriendFeed Thread:<br />
<iframe frameborder="0" height="400" src="http://friendfeed.com/stevekoch/6b05727d/open-data-success-story?embed=1" width="450"></iframe></div>Steve Kochhttp://www.blogger.com/profile/09076719001132389463noreply@blogger.com35tag:blogger.com,1999:blog-7356964387844331141.post-36983151141511815072010-09-07T21:38:00.002-06:002010-09-07T21:46:07.097-06:00Thank you, Addgene, for the award!<div xmlns="http://www.w3.org/1999/xhtml">A big "Thank You!" to <a href="http://www.addgene.org/pgvec1?f=a&cmd=showfile&file=services">Addgene</a> for giving <a href="http://openwetware.org/wiki/User:Andy_Maloney">Andy Maloney</a> and our <a href="http://www.openwetware.org/wiki/Koch_Lab">lab</a> a "<a href="http://www.addgene.org/pgvec1?f=a&cmd=showfile&file=labgiving#winners">Resource Sharing Award</a>!" The award is a $5,000 donation to our lab that we can use to further our kinesin research. Very generous and very helpful to our lab. Big props also to Andy for applying for the award with no help from me! One more piece of evidence that the students in the lab are much better at grant writing than I am :) <br />
<br />
The award was given to Andy and our lab for our commitment to open science. This includes open notebook science, open data, sharing protocols, designs, etc. Andy has been a very impressive open scientist. It's just a guess, but I'd say so far, probably his biggest impact has been with the very detailed "do it yourself" biology projects he's contributed. He's absolutely amazing with designing solutions from off-the-shelf components, and equally amazing with using Google Sketchup and photographs to describe the designs to the public. A good example is his <a href="http://openwetware.org/wiki/User:Andy_Maloney/Notebook/Lab_Notebook_of_Andy_Maloney/2010/06/17/Temperature_stabilization">microscope objective heater</a>, which was somewhere around $500 and is working very well for our gliding motility assays.<br />
<br />
There are now many labs around the world deserving of this award, and it feels really good to receive it. And I think it was a great contest for Addgene to sponsor. I actually wasn't aware of Addgene before Andy told me about the contest. So just learning about them made the effort worthwhile. I had a great conversation with Melanie Herscovitch on the phone a few weeks ago and she explained to me Addgene's mission and services. Here's a picture from their website to explain what they do: (used without permission! :) )<br />
<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhQ27gLnzT1WRDCM7osEaLGL28GStRqzKj3ldGtI5OURvm5I34eIzT9nj7MLmy7xx9-fetWOYviGZfk8cpPFo9YBWaHcc0-A8-1tT34lpO7KmOS1uOnMpxc2hx7ewvmRSu1i6_smxILcUdY/s1600/Addgene+plasmid+flow.gif" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="172" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhQ27gLnzT1WRDCM7osEaLGL28GStRqzKj3ldGtI5OURvm5I34eIzT9nj7MLmy7xx9-fetWOYviGZfk8cpPFo9YBWaHcc0-A8-1tT34lpO7KmOS1uOnMpxc2hx7ewvmRSu1i6_smxILcUdY/s400/Addgene+plasmid+flow.gif" width="400" /></a></div><br />
In a nutshell, addgene is a non-profit organization dedicated to making it easier for researchers to share and obtain published plasmids. Authors of papers submit their plasmids to Addgene (either purified DNA or transfected cells, as I understand it). Readers who would like to obtain the plasmid contact Addgene, and Addgene provides the plasmids for just a cost-recovery fee. This works out well for all parties. Without Addgene, it's often a very inconvenient process. The authors are burdened with keeping track of plasmids that may have fallen out of use. And researchers requesting the plasmids often face a long delay in obtaining them. I think Addgene is a wonderful service and I look forward to working with them as we create and publish our own plasmids in the coming years. I also got the feeling from talking with Melanie that Addgene is a really great place to work. I don't know whether or how often they're hiring, but you can take a look <a href="http://www.addgene.org/pgvec1?f=a&cmd=showfile&file=careers">here</a> for current job openings.<br />
<br />
Thanks again, Addgene! If you're reading this, it'd be great to post a little thank you comment (on friendfeed or the blog) or congratulations to Andy!<br />
<br />
FriendFeed Thread:<br />
<iframe frameborder="0" height="400" src="http://friendfeed.com/science-2-0/a331cd48/steve-koch-science-thank-you-addgene-for-award?embed=1" width="450"></iframe></div>Steve Kochhttp://www.blogger.com/profile/09076719001132389463noreply@blogger.com10tag:blogger.com,1999:blog-7356964387844331141.post-63657341292319586852010-02-21T02:27:00.003-07:002010-02-21T02:34:06.140-07:00Science Commons Symposium Pacific Northwest 2010, quick summary #scspn<div xmlns="http://www.w3.org/1999/xhtml">Today I was lucky to attend the amazing <a href="http://sciencecommons.org/events/salon/">Science Commons Symposium</a>. There were back-to-back fascinating presentations by <a href="http://cameronneylon.net/">Cameron Neylon</a>, <a href="http://usefulchem.blogspot.com/">Jean-Claude Bradley</a>, <a href="http://www.chemspider.com/blog/">Antony Williams</a>, <a href="http://wwmm.ch.cam.ac.uk/blogs/murrayrust/">Peter Murray-Rust</a>, <a href="http://www.arl.org/sparc/about/staff/joseph.shtml">Heather Joseph</a>, <a href="http://www.sagebase.org/INTRO/Directors.html">Stephen Friend</a>, <a href="http://friendfeed.com/peterbinfield">Peter Binfield</a>, and <a href="http://scienceblogs.com/commonknowledge/">John Wilbanks</a>. It was wonderful to meet in person a few people that I either did not know before, or whom I'd only know online previously, including <a href="http://friendfeed.com/boudicca">Lisa Green</a> (who went out of her way to invite me to attend this conference, thank you!), <a href="http://friendfeed.com/researchremix">Heather Piwowar</a>, <a href="http://friendfeed.com/grumpator">Anali Perry</a>, and <a href="http://friendfeed.com/brianwestra">Brian Westra</a>. It was also a great pleasure to meet again people whom (with the exception of Cameron) I'd only met in person a few weeks ago at the ScienceOnline2010 conference: Jean-Claude, Cameron, <a href="http://friendfeed.com/hleman">Hope Leman</a> (another tireless organizer of the conference who graciously invited me to attend), <a href="http://friendfeed.com/billhooker">Bill Hooker</a>, Pete Binfield, and Antony Williams. (My apologies if I missed out on name-dropping anyone, it hurts me more than you!)<br />
<br />
I'm off to the Biophysical Society meeting tomorrow morning, and a bit out of steam, so I'm going to cop-out a bit and just embed a mindmap of my notes from the meeting. Before doing that, I'll post a few action items from the meeting, and maybe later I'll come back and link to specific friendfeed or other threads for the items:<br />
<ul><li>Antony and I made some progress discussing our athletic challenge to raise money for asthma research or other charity. I think it's promising we can make it "generative," and successful.</li>
<li>Pete Binfield used Heather Piwowar's PLoS ONE paper as an example. I want to read it and then rate it.</li>
<li>Improve our lab's Open Notebook Science. This is ill-defined, but there are many steps we can begin taking immediately to work towards a system that works for us as well as it does for Jean-Claude Bradley and his students / collaborators.</li>
</ul>OK, Here's the mindmap. I started doing it as an example for Heather, Hope, Bill and others from a discussion at dinner. Too tired to convert it into regular text now...would be interested to know if it's useful at all to you!<br />
<br />
<iframe frameborder="0" height="400" width="400" src="http://www.mindmeister.com/maps/public_map_shell/42518239/steve-s-experience-science-commons-symposium-2010?width=600&height=400&zoom=0&live_update=1" style="overflow: hidden;" width="600">&lt;p&gt;&amp;amp;amp;amp;lt;p&amp;amp;amp;amp;gt;&amp;amp;amp;amp;amp;amp;lt;br /&amp;amp;amp;amp;amp;amp;gt; &amp;amp;amp;amp;amp;amp;lt;br /&amp;amp;amp;amp;amp;amp;gt; &amp;amp;amp;amp;amp;amp;lt;div class='zemanta-pixie'&amp;amp;amp;amp;amp;amp;gt;&amp;amp;amp;amp;amp;amp;lt;img src='http://img.zemanta.com/pixy.gif?x-id=35781fef-0c7f-888e-9137-2b6663e98189' alt='' class='zemanta-pixie-img'/&amp;amp;amp;amp;amp;amp;gt;&amp;amp;amp;amp;amp;amp;lt;/div&amp;amp;amp;amp;amp;amp;gt;&amp;amp;amp;amp;amp;amp;lt;/div&amp;amp;amp;amp;amp;amp;gt;&amp;amp;amp;amp;lt;/p&amp;amp;amp;amp;gt;&lt;/p&gt;</iframe></div><br />
FriendFeed comment thread:<br />
<br />
<iframe width="400" height="400" frameborder="0" src="http://friendfeed.com/science-commons-sympo/df22ead6/steve-koch-science-commons-symposium-pacific?embed=0" ></iframe>Steve Kochhttp://www.blogger.com/profile/09076719001132389463noreply@blogger.com6tag:blogger.com,1999:blog-7356964387844331141.post-62718797397179195732010-01-21T22:56:00.004-07:002010-01-22T15:34:09.572-07:00ScienceOnline2010 -- Top N things I learned and was inspired to do at #scio10<div xmlns="http://www.w3.org/1999/xhtml"><ul><li><a href="http://friendfeed.com/scienceonline2010/a926ef43/steve-koch-science-scienceonline2010-top-n">FriendFeed thread for this post </a><br />
</li>
</ul>I had a blast at <a href="http://www.scienceonline2010.com/index.php/wiki">ScienceOnline2010</a> last weekend! Thank you Anton, Bora and others who spent so much energy organizing it! Approximately 250 people attended and it was a very diverse crowd of scientists, science writers, publishers, librarians, science outreach specialists, high school teachers, even high school students. Much has already been blogged about the conference, including many "Top N" lists. You can find a <a href="http://www.scienceonline2010.com/index.php/wiki/BlogMedia_Coverage/">list of them here</a>. My favorite so far is <a href="http://friendfeed.com/treeoflife">Jonathan Eisen's</a> "<a href="http://phylogenomics.blogspot.com/2010/01/enough-w-good-here-are-top10-problems-w.html">Enough w/ the good: here are the top10 problems w/ the #scio10 meeting</a>." Hilarious! Despite everything having already been done, I hereby present my belated list of things I learned, things I did, and things I've been inspired to do:<br />
<br />
<b><big>1. I had a ton of fun interacting with a bunch of e-friends, old and new.</big></b><br />
I attended as a scientist with an interest in all of the other areas. It was definitely a new feeling to be in a session and have the speaker ask, "how many of you are scientists?" with the answer being a very small fraction of the participants in the room. It was also a very new and thrilling experience to finally meet in person many people I've known only virtually for the past year. I think <a href="http://friendfeed.com/cameronneylon">Cameron Neylon</a> was the only person I'd met in person previously. Despite that fact, it was incredibly easy to have conversations during lunch, between sessions, and of course at the bar. I uniformly enjoyed these people even more in person. An incomplete list of the people I had the pleasure of chatting with include: <a href="http://friendfeed.com/billhooker">Bill Hooker</a>, <a href="http://friendfeed.com/jcbradley">Jean-Claude Bradley</a>, <a href="http://friendfeed.com/freesci">Pawel Szczesny</a>, <a href="http://friendfeed.com/wjjessen">Walter Jessen</a>, <a href="http://friendfeed.com/cpikas">Christina Pikas</a>, <a href="http://friendfeed.com/hleman">Hope Lehman</a>, <a href="http://friendfeed.com/peterbinfield">Peter Binfield</a>, <a href="http://friendfeed.com/habib">... Plus I found some completely new friends at the conference, including </a><a href="http://friendfeed.com/chemspiderman">Antony Williams</a>, <a href="http://scienceblogs.com/cognitivedaily/">Greta Munger</a>, <a href="http://scienceblogs.com/bookoftrogool/">Dorothea Salo</a>, <a href="http://openpaleo.blogspot.com/">Andy Farke</a>, <a href="http://www.natalievillalobos.com/about-me/">Natalie Villalobos</a>, <a href="http://friendfeed.com/habib">Michael Habib</a>, <a href="http://www.diveintoyourimagination.com/">Annie Crawley</a>, ... Now, those previous two sentences could be perceived as egregious name dropping, which I am guilty of, simply because it's quite an amazing list of people, none of whom I knew before I became active in open science. Clicking through those names and reading what they're saying, and you'll realize why I feel so lucky to have met them!<br />
<i>(Note, I forgot: <a href="http://friendfeed.com/kubke">Fabiana Kubke</a>, ...) </i><br />
<br />
<b><big>2. Antony Williams and I made some kind of running challenge.</big></b><br />
I knew of Antony Williams from his <a href="http://www.chemspider.com/">ChemSpider</a> fame. I also had recently read one of his personal blog entries, about <a href="http://1000milesin1year.blogspot.com/2010/01/two-hours-in-emergency-room.html">running 1000 miles in a year</a>, along with his ugly and unfortunate calf injury. I'm not sure I knew these were the same person, though. Nevertheless, he walked passed me in the hotel bar, and I accosted him to inquire about his calf injury. I'm pretty sure he didn't know me at all, but luckily we had on slick name badges and I was surrounded by credible people. It'd be a big challenge for me to recount the conversation (I swear I remember it perfectly, I just don't feel like writing it down). Let's just say that I was happy to learn that he'll be back running again within a week or so and that he has a goal of raising money to fight asthma. I have had an idea mulling in my head that I could raise money and get motivated to get better at running by setting a race time goal. I thought this was a perfect match with Antony's goal, so I quickly challenged him to a running competition. He quickly agreed (fearlessly) and I <a href="http://friendfeed.com/scienceonline2010/adf7cedc/fwd-scio10-antony-williams-i-agreed-on-plan">tweeted/friendfeeded</a> it to lock in the deal. Over the next week, I'll see if I can clarify the challenge and I'll post updates to that thread. I'm thinking I'll setup a Google spreadsheet for me and others to place their pledges and monitor the progress. Antony already knows about Nike+ technology, and I'm looking forward to doing something like that too. It'd be a good way to try out new things in open data, and open notebook science, actually. Suffice to say that I'm going to get better at running, lose a lot of weight, and hopefully we'll raise some money too!<br />
<br />
<b><big>3. I and KochLab are going to get better at doing Open Notebook Science and sharing data & software this year</big></b><br />
I learned a lot at the conference about tools that exist for carrying out open notebook science and sharing data, methods, software, etc. I still have a lot to learn, and indeed many tools still need to be developed. But I know that our lab can make improvements this year. Here's some concrete things that we'll do:<br />
<ul><li>I've sent an email to <a href="http://elibrary.unm.edu/documents/employeedirectory.php">Amy Jackson</a>, Digital Initiatives Librarian at UNM, requesting a meeting. I had briefly spoken to her via email in October and now I'm fully energized to have a meeting with her and see what kinds of first steps we can take towards building a partnership between the library and our lab in terms of sharing data and conducting open science. I'll try to leave <a href="http://friendfeed.com/scienceonline2010/522edaac/inspired-by-conversations-with-dorothea">updates on this FriendFeed thread</a>.</li>
<li>Get better at sharing software. Currently we use LabVIEW, which is a wonderful programming environment. One of the major benefits is that it's a graphical, data flow language. This makes the code a 2-dimensional diagram...so in my opinion, it's exceptionally easy to read other people's code. Unfortunately, it's a proprietary and expensive coding environment. You are allowed to compile .exe and .dll files for others to use freely. But that's not open source. So, there are two routes to go: (1) We could compile virtual machines (VM) and send those to people for exploring our code. For example, referees of papers we submit. This was an idea from <a href="http://friendfeed.com/mndoci">Deepak Singh</a> at the meeting. Licensing is an issue here, and what I'd like to do is find someone at National Instruments (creators of LabVIEW) and discuss what can be done to serve our open source needs. (2) Learn a text-based, freely available language. I think this would be valuable for our students anyway, in terms of building their resumes. While at the meeting, I thought Ruby was a good idea, but now not so sure. I've posted a <a href="http://friendfeed.com/the-life-scientists/c6ea26e0/larry-and-i-want-to-learn-ruby-first-using">FriendFeed message about this</a>, and have received all kinds of very valuable advice.</li>
<li>Adopt techniques to make it easier to capture our workflow in the lab. OpenWetWare has innovations coming up soon and we'll certainly jump on those. Cameron also hinted at something revolutionary coming up this year, but said he'd have to kill Bill if he told him what it is. It wasn't clear that he'd have had to have killed others in the room, so I was disappointed he didn't say what it was. (Just kidding, Bill!) But the fact is, I don't think our current tools are nearly sufficient. I'll put in more effort to make positive steps here, but I'm not sure exactly what yet.</li>
</ul><big><b>4. Improve the state of publishing, one article at a time: Try out some ideas via PLoS ONE.</b></big><br />
I was delighted to have the opportunity to talk with Peter Binfield at the bar and discuss publishing ideas with him. I have a lot of ideas that I'd like to try out, and it hasn't yet been proven that all of them are lousy. I ran many of them past Peter and his general response was, PLoS ONE would love that -- it's just that whatever scientific community you're in may not respect it. Very true. However, I do think many in my community would respect <i>anything</i> that showed how publishing could be better by being different. And I now realize that PLoS ONE is a very good platform for trying out a few things.<br />
<ul><li>At lunch with Bill and Pawel, they mentioned an idea that others had been talking about. Unfortunately, I don't know to whom to attribute the idea. <i>(Note: Bill and Pawel give attribution to Fabiana Kubke, which sounds right to me now.)</i> The idea is that publishing one very good figure would be a good idea. I like this idea enough to think about trying it out. It is related to an idea Larry Herskowitz and I were discussing a few days before the conference: Can we publish a paper without an introduction? Or an introduction that just says, "see such-and-such other paper for introduction?" So much time is wasted rewriting introductions (in my opinion), especially when trying to avoid copying prior written work. Is this necessary? Publishing a single figure takes this even further. I have some interesting data from grad school and postdoc that I have not been able to publish. It pains me that it's just sitting around, useless. Do you think it's worth using this data to test out the "publish one figure" method? If I make progress on this, I'll post updates on <a href="http://friendfeed.com/scienceonline2010/d4d06106/during-lunch-at-scio10-scienceonline2010">this FriendFeed thread</a>. <i>(Note added: Cameron Neylon reminded me that BMC Research Notes may be a better venue than PLoS ONE for this.)</i><br />
</li>
<li>For maybe ten years now, I've thought that the value of anonymous peer review is overstated. During that time, I've heard other people, much more eloquent than me also express this opinion. Just briefly, I think fully-attributed, non-anonymous peer review would solve many problems that exist with today's science, and I discussed this a bit at the meeting. Two of these problems are: (a) good referee work is difficult, and good referees are not credited for the work and the original ideas, and (b) a whole lot of incomplete and sloppy work is submitted and much of it is published due to ineffective referees / editors. The solution I like is for every aspect of the peer-review process to be published, including the original manuscript submitted, all subsequent revisions, and all communication between authors, editor, and referees. Clearly this solves problem (a). As for problem (b), people often say, "but people aren't going to say negative things if their name is on it!" First of all, that's not necessarily true. Secondly, referees have the option to decline without comment. If the editor cannot find someone willing to slam the paper, then it's just returned to the authors. Voila! One less crappy paper published. The arguments get more complicated, especially when considering that grant review is anonymous, providing a lot of opportunity for underhanded retaliation. I can't mathematically prove that it's a good or bad idea, so I'd like to try it out and see what happens. It occurs to me that I could submit a manuscript to PLoS ONE and request that the Academic Editor implement this idea. Why not? Should be OK as far as I understand the rules. I don't expect to submit garbage, so it won't be a complete experiment. But something may be learned, and at least all the referees will get credit. I may update progress on this idea on <a href="http://friendfeed.com/scienceonline2010/3eda5fff/i-also-want-to-try-out-another-idea-discussed-at">this FriendFeed thread</a>.</li>
</ul>OK, That's enough for now. I can always add more later, especially since I aptly named this post. For example, I may talk about the rebranding of our blogs that Walter Jessen recommended. It's a good and valid suggestion, but I'm not adding it yet, because I'm not sure how soon I'll be able to think about that :)<br />
<br />
<div class="zemanta-pixie"><img alt="" class="zemanta-pixie-img" src="http://img.zemanta.com/pixy.gif?x-id=0f7dc9e9-7bd9-8190-9c1c-af94cc5ee4a0" /><br />
</div></div>Steve Kochhttp://www.blogger.com/profile/09076719001132389463noreply@blogger.com8tag:blogger.com,1999:blog-7356964387844331141.post-68205664603753419242009-12-10T00:01:00.001-07:002009-12-10T00:12:56.360-07:00A PLoS ONE Success Story--Taxol Crystals Masquerading as Microtubules<div xmlns="http://www.w3.org/1999/xhtml"><br /><span style="padding: 5px; float: left;"><a href="http://www.researchblogging.org/"><img alt="ResearchBlogging.org" src="http://www.researchblogging.org/public/citation_icons/rb2_large_gray.png" style="border: 0pt none ;" /></a></span><br />Andy Maloney, a Ph.D. student in our lab, recently read and summarized a very interesting paper in <a href="http://openwetware.org/wiki/User:Andy_Maloney/Notebook/Lab_Notebook_of_Andy_Maloney/2009/12/01/Taxol_Crystals_Can_Masquerade_as_Stabilized_Microtubules">his open lab notebook</a>. The paper, "<a href="http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0001476">Taxol Crystals Can Masquerade as Stabilized Microtubules</a>," was published in PLoS ONE in January of 2008 by Margit Foss, Buck W. L. Wilcox, G. Bradley Alsop, and Dahong Zhang<sup>1</sup>. Since our lab is now heavily involved in experiments involving kinesin and microtubules, and because it addresses something that had been a mystery to us, the paper really caught my interest. I'll explain more about that below. But before doing that, I wanted to talk about something probably of more general interest: a success story for publishing in PLoS.<br /><br />Andy noticed that in their methods they defined <a href="http://friendfeed.com/the-life-scientists/59d2ea57/does-anyone-here-know-what-initials-brb80-stand">BRB80</a> as having 4% glycerol. Glycerol is used to promote tubulin polymerization, and I've never seen it included in the BRB80 (aka PEM) definition. It could also affect solubility of Taxol, so it's an important detail whether or not a substantial amount of glycerol was in their standard BRB80 buffer. I strongly suspected that this was just an oversight by the authors...and I could easily have assumed this and moved on. But what about future readers of the article? Was there anyway to correct that article? For most journals today, even in the year 2009, the answer would have been, "no." However, this is no ordinary journal, this is PLoS ONE! All I had to do was select the text in question, and then click to add a note. After adding my note, an icon appeared in the article, allowing any future reader to see the question.<br /><a title="PLoS Comment Image by skoch3, on Flickr" href="http://www.flickr.com/photos/stevekoch/4173728548/"><img alt="PLoS Comment Image" src="http://farm3.static.flickr.com/2741/4173728548_aa235dc89d_o.png" height="63" width="515" /></a><br /><br />I don't know whether authors are notified when their article is commented on. (If not, it would be an important feature for PLoS to add.) So, I sent an email to the corresponding author of the paper (D. Zhang) pointing out the question. In less than a day, D. Zhang wrote back saying that he'd asked M. Foss to look into the issue. And then again in less than a day, Margit wrote me back to say that she'd looked at the original lab notes and indeed they'd made a bit of a typo in how they described BRB80 in their report. She added a very clear response to my note. She also went out of her way to point me to two subsequent papers that have extended their taxol microcrystal research<sup>2,3</sup>. These authors deserve a lot of praise for responding to this question so quickly! A few months ago received a similarly rapid response from authors of <a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0004612">another PLoS article</a>...only two data points, but I wonder if PLoS authors are indeed more likely to respond quickly to questions from readers?<br /><br />Now, why am I so happy and why do I think this is a success story for PLoS? It's because now, for the rest of time, when readers of this excellent paper do look into the methods, they will be able to <a href="http://www.plosone.org/annotation/listThread.action?inReplyTo=info%3Adoi%2F10.1371%2Fannotation%2F17e811a5-583b-4dd0-9bf9-023425757824&root=info%3Adoi%2F10.1371%2Fannotation%2F17e811a5-583b-4dd0-9bf9-023425757824">see the corrected definition of the buffer used</a>. Given how many times I've been burned by incomplete or incorrect methods, I do believe this will save substantial amount of time for at least a couple people down the road. (Will the PDF version of the article ever incorporate this note? As it stands now, I don't think it does...it would be very valuable if technology could be worked out to include links to these comments in future PDF downloads.) One more thing: I just noticed that Margit Foss today also posted a new comment on her article. She links to the two papers she'd told me about in her email, as "<a href="http://www.plosone.org/annotation/listThread.action?inReplyTo=info%3Adoi%2F10.1371%2Fannotation%2Fb87bdb49-d1b9-4f17-a637-1e30648180c6&root=info%3Adoi%2F10.1371%2Fannotation%2Fb87bdb49-d1b9-4f17-a637-1e30648180c6">Relevant references on Taxol crystals.</a>" This is a great service to readers, especially since the newer reports<sup>2,3</sup> support a different mechanism for Taxol microcrystal / fluorescent tubulin binding. In summary, many thanks to PLoS for this wonderful journal and to these authors for their dedication to excellent science!<br /><br />Now, if you're still reading, I'd like to also comment on the very interesting science in their report. Taxol (generic name is <a href="http://en.wikipedia.org/wiki/Paclitaxel">paclitaxel</a>, I think) is a drug used in cancer chemotherapy. It's proposed mechanism of action is to inhibit mitosis by stabilizing microtubules in the spindle apparatus. In vitro, Taxol dramatically reduces the rate of microtubule depolymerization. Many people, including kinesin researchers in our lab, leverage this microtubule-stabilizing effect by adding Taxol to microtubule-containing solutions. What I learned from the Foss et al. paper is that the concentration of Taxol <a href="http://www.cellbio.duke.edu/kinesin/Methods/motility_MT.html">typically used in microtubule gliding assays</a> (10-20 micromolar) is far above the solubility limit of Taxol (somewhere around 0.8 micromolar in aqueous solutions). Furthermore, they show that Taxol forms microcrystals above this solubility limit (even at 0.92 micromolar) and that often these microcrystals form a striking resemblence to microtubule bundles and asters! DIC images of these microcrystals (formed in absence of tublin) are shown in these images from Foss et al.<sup>1</sup>:<br /><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgokF9HYf_bTZGeyi5eM1MRDaVPMAlzbwoPYRLNAzWCz7JQ1QWLH7idrocfCYpRbfvYvNIFpFKQcqWQHdry4joXsdLfcEZz962NcQ4Oj3Y9LRNJ2hzq7w5V2iNsqfUwkrnKC76nuZcIYivz/?imgmax=800" style="max-width: 800px;" /><br />(scale bar 10 microns)<br /><br /><br />The final piece of crucial information provided by this article is: these Taxol microcrystals rapidly bind fluorescently-labeled tubulin! (Later reports indicate that it's the fluorophore, not the tubulin that is binding to Taxol<sup>2,3</sup>.) This means that many kinesin researchers (including me) likely have Taxol microcrystals in their samples, and because they become coated with fluorescent tubulin, there is a huge risk of misidentifying these structures as microtubule structures. Indeed, here is a recent fluorescence microscopy video that Andy took of something that at the time was a mystery but which we now know is likely a Taxol microcrystal decorated with rhodamine-labeled tubulin!<br /><br /><div class="youtube-video"><object height="355" width="425"><param value="http://www.youtube.com/v/2Tn7P957iXU&feature=youtube_gdata" name="movie"> <param value="transparent" name="wmode"> <embed wmode="transparent" type="application/x-shockwave-flash" src="http://www.youtube.com/v/2Tn7P957iXU&feature=youtube_gdata" height="355" width="425"></embed> </object></div><small>Likely Taxol microcrystal in kinesin / microtubule gliding motility assay (using rhodamine-labeled tubulin). Andy Maloney data.<br /></small><br />In my past, I've also often seen these structures which I attributed to "clumpy" or "weird" microtubule structures. For example, I often noticed very bright, thick, and stick-like structures that I called "microtubule logs." It never occurred to me that they were Taxol crystals! (Also I remember that these structures were much less prone to photobleaching. I wonder if that's because (a) there are buried fluorophores inside the crystals, protected from oxygen, or (b) even on the surface of the crystals, Taxol somehow protects fluorophores from photobleaching?)<br /><br />Foss et al., go further and speculate on whether this has important implications in vivo (i.e. in cancer chemotherapy). I can't really comment on that, but it's interesting to think about. What's most important for us is that we now know we have a problem with our buffers (too much Taxol!) and we may be able to fix it. The concentration of tubulin that we typically use is about 0.4 micromolar of tubulin dimers. Thus, for a 1:1 ratio of Taxol to tubulin dimers, we'd need 0.4 micromolar starting concentration of Taxol, which is below the solubility limit. There's at least two things I don't know: (a) What is the binding affinity of Taxol for microtubules? and (b) Do we need a 1:1 ratio to get significant stabilization? If the answer to (a) is something like a few nanomolar, then we may be OK with something around 0.5 micromolar (500 nanomolar) Taxol. If not, then we may have to hope the answer to (b) is "no."<br /><br />A quick search just now yielded a paper from 1994 that says the binding constant for taxol to microtubules in 10 nM. That'd be good, except that they also seem to say that they only get stabilizing effects when the concentration is in the micromolar range<sup>4</sup>. Dang! Well, it shouldn't be too hard to try out 500 nM Taxol and to see whether MTs are reasonably stable. It's possible our MTs may be more stable than those used in the Caplow et al. study. It's also possible that the Taxol microcrystals are not affecting the kinesin activity in our system, and that we can do our studies at high Taxol concentration. Even if so, it's great to know about this issue so we can keep on the lookout for Taxol problems.<br /><br /><big><b>References</b></big><br /><br />1. Foss M, Wilcox BWL, Alsop GB, Zhang D (2008) Taxol Crystals Can Masquerade as Stabilized Microtubules. <a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0001476">PLoS ONE 3(1):e1476.</a> doi:10.1371/journal.pone.0001476<br /><br />2. <hanging-indent>Castro, J. S., Deymier, P. a., Trzaskowski, B., & Bucay, J. (2009). Heterogeneous and homogeneous nucleation of Taxol crystals in aqueous solutions and gels: Effect of tubulin proteins. <i>Colloids and surfaces. B, Biointerfaces</i>. <a href="http://dx.doi.org/10.1016/j.colsurfb.2009.10.033">doi: 10.1016/j.colsurfb.2009.10.033</a>.<br /><br />3. </hanging-indent><hanging-indent>Castro, J. S., Trzaskowski, B., Deymier, P. a., Bucay, J., Adamowicz, L., Hoying, J. B., et al. (2009). Binding affinity of fluorochromes and fluorescent proteins to Taxol™ crystals. <i>Materials Science and Engineering: C</i>, <i>29</i>(5), 1609-1615.</hanging-indent> <a href="http://dx.doi.org/10.1016/j.msec.2008.12.026">doi: 10.1016/j.msec.2008.12.026</a><br /><br />4. <hanging-indent>Caplow, M., Shanks, J., & Ruhlen, R. (1994). How taxol modulates microtubule disassembly. <i>The Journal of biological chemistry</i>, <i>269</i>(38), 23399-402. Retrieved from <a href="http://www.ncbi.nlm.nih.gov/pubmed/7916343">http://www.ncbi.nlm.nih.gov/pubmed/7916343</a>.</hanging-indent><br /><br /><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=PloS+one&rft_id=info%3Apmid%2F18213384&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=Taxol+crystals+can+masquerade+as+stabilized+microtubules.&rft.issn=&rft.date=2008&rft.volume=3&rft.issue=1&rft.spage=&rft.epage=&rft.artnum=&rft.au=Foss+M&rft.au=Wilcox+BW&rft.au=Alsop+GB&rft.au=Zhang+D&rfe_dat=bpr3.included=1;bpr3.tags=Research+%2F+Scholarship">Foss M, Wilcox BW, Alsop GB, & Zhang D (2008). Taxol crystals can masquerade as stabilized microtubules. <span style="font-style: italic;">PloS one, 3</span> (1) PMID: <a rev="review" href="http://www.ncbi.nlm.nih.gov/pubmed/18213384">18213384</a></span><br /><br /><a href="http://friendfeed.com/plosone/f547b00e/plos-one-success-story-taxol-crystals">Link to FriendFeed discussion thread</a>.<br /><div class="zemanta-pixie"><img src="http://img.zemanta.com/pixy.gif?x-id=0f7dc9e9-7bd9-8190-9c1c-af94cc5ee4a0" alt="" class="zemanta-pixie-img" /></div></div>Steve Kochhttp://www.blogger.com/profile/09076719001132389463noreply@blogger.com6tag:blogger.com,1999:blog-7356964387844331141.post-70140269150310530762009-06-09T00:10:00.003-06:002009-06-09T15:06:58.139-06:00My first rating and commenting of a PLoS article in my own field (Scary!)<div xmlns="http://www.w3.org/1999/xhtml"><span style="font-style: italic;">SJK 6/9/09: Here is a </span><a style="font-style: italic;" href="http://friendfeed.com/plosone/9fc5e7dc/my-first-rating-and-commenting-of-plos-article">link to related friendfeed discussion</a><span style="font-style: italic;">.</span><br /><br />I just finished reading and commenting on a <span class="blsp-spelling-error" id="SPELLING_ERROR_0">PLoS</span> One article that is near my own field of research. The article is titled, "<a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0004612">Dissection of <span class="blsp-spelling-error" id="SPELLING_ERROR_1">Kinesin's</span> <span class="blsp-spelling-error" id="SPELLING_ERROR_2">Processivity</span></a>." The authors are: Sarah <span class="blsp-spelling-error" id="SPELLING_ERROR_3">Adio</span>, Johann <span class="blsp-spelling-error" id="SPELLING_ERROR_4">Jaud</span>, Bettina Ebbing, Matthias <span class="blsp-spelling-error" id="SPELLING_ERROR_5">Rief</span>, and <span class="blsp-spelling-error" id="SPELLING_ERROR_6">Günther</span> <span class="blsp-spelling-error" id="SPELLING_ERROR_7">Woehlke</span>. You can see <a href="http://www.plosone.org/rate/getArticleRatings.action?articleURI=info%3Adoi%2F10.1371%2Fjournal.pone.0004612">my rating and overall comments here</a>. (Since I'm not sure if that link will work, I'll also <span class="blsp-spelling-error" id="SPELLING_ERROR_8">repost</span> my comments below.)<br /><br /><span class="blsp-spelling-error" id="SPELLING_ERROR_9">Throughout</span> the process of reading and commenting on this article, I learned a lot more about my fears and barriers to <span class="blsp-spelling-error" id="SPELLING_ERROR_10">PLoS</span> commenting. I discussed some of these in my <a href="http://stevekochscience.blogspot.com/2009/05/my-first-plos-comment-high-rating-of.html">prior post about my first <span class="blsp-spelling-error" id="SPELLING_ERROR_11">PLoS</span> rating</a>. In contrast to my first rating, this article is smack in the middle of my field of interest (the <span class="blsp-spelling-error" id="SPELLING_ERROR_12">kinesin</span> molecular motor). I deliberately chose the most relevant <span class="blsp-spelling-error" id="SPELLING_ERROR_13">PLoS</span> article I could find. I'd estimate that my fear of placing comments was at least 10 times higher than for an article outside my field. I definitely felt like my comments were piping directly into the author's email inbox, ready to enrage them at any misunderstanding or criticism I posted. I still feel this way and am a bit worried. My worries are probably justified to some extent, since I am very new to this field. Thus, I could easily be seen as an ungrateful newcomer who hasn't paid his dues. And of course the people who wrote the article could end up anonymously reviewing my own papers and grants.<br /><br />Given those worries, I came close to deciding not to post my rating. However after much reading and thinking about their results, I felt compelled to make a serious comment about error analysis supporting one of their conclusions (not their major conclusion). I was confident that my criticism was fair, and convinced myself that posting the comment was the right thing to do--perhaps I can save another reader a lot of time, or even help the authors out if they read it. I posted my criticism <a href="http://www.plosone.org/annotation/listThread.action?inReplyTo=info:doi/10.1371/annotation/88d84f47-3d67-4dbf-b0da-84fc8ef63ee1&root=info:doi/10.1371/annotation/88d84f47-3d67-4dbf-b0da-84fc8ef63ee1">directly in the article</a>, along with several typo corrections. After doing that (late last night), I realized that if / when the authors DO see my comments, they'll see a string of petty typo corrections and then this criticism, but nothing positive at all. That's a problem!!! Because of this, I decided to sleep on it, and compose an overall rating with positive comments today. I was busy most of the day, but finally tonight was able to finish my rating. In all honesty, though, without having travelled that slippery slope of commenting, I don't think I would have posted this rating tonight. I would have balked at the risk of angering the authors, sticking my neck out, and possibly being wrong. I probably would have convinced myself that these risks outweighed any meager potential gain that the world of science would get from my remarks.<br /><br />I'm a bit worn out now. Hopefully in the comments here or more likely, on <span class="blsp-spelling-error" id="SPELLING_ERROR_14">FriendFeed</span>, we can talk about these things. I hope in the next couple days to expand on my review of the paper in my research blog, and to include it as my first Research Blogging attempt.<br /><br /><big><span class="blsp-spelling-error" id="SPELLING_ERROR_15">Reposting</span> of my rating and overall comments on the article</big><br /><i><br />This is what I submitted to PLoS as my rating:<br /></i><br />Insight: 4 stars, Reliability 3 stars, Style, 4 stars.<br /><br />The authors recently characterized <span class="blsp-spelling-error" id="SPELLING_ERROR_16">NcKin</span>3, which is the first known,<br />naturally <span class="blsp-spelling-error" id="SPELLING_ERROR_17">dimeric</span> but non-<span class="blsp-spelling-error" id="SPELLING_ERROR_18">processive</span> and plus-end motor. In this<br />report, they are leveraging this discovery to study chimeric constructs<br />between <span class="blsp-spelling-error" id="SPELLING_ERROR_19">NcKin</span> (a <span class="blsp-spelling-error" id="SPELLING_ERROR_20">dimeric</span>, <span class="blsp-spelling-error" id="SPELLING_ERROR_21">processive</span> <span class="blsp-spelling-error" id="SPELLING_ERROR_22">Kinesin</span>-1 motor in the same<br />organism) and <span class="blsp-spelling-error" id="SPELLING_ERROR_23">NcKin</span>3. They make two different chimeric constructs: one<br />with the head of <span class="blsp-spelling-error" id="SPELLING_ERROR_24">NcKin</span> and the neck of <span class="blsp-spelling-error" id="SPELLING_ERROR_25">NcKin</span>3, and the other with head<br />of <span class="blsp-spelling-error" id="SPELLING_ERROR_26">NcKin</span>3 and neck of <span class="blsp-spelling-error" id="SPELLING_ERROR_27">NcKin</span>. Importantly, the head included the core<br />motor domain AND the neck linker region.<br /><br />I congratulate the<br />authors on a lot of very nice work that must have been very difficult!<br />The results they report come from an impressive array of difficult<br />assays spanning single-<span class="blsp-spelling-error" id="SPELLING_ERROR_28">fluorophore</span> position tracking, single-molecule<br />bead motility assays with optical tweezers, gliding assays, and a<br />variety of ensemble biochemical assays.<br /><br />Study of the two<br />chimeric constructs, in comparison with the <span class="blsp-spelling-error" id="SPELLING_ERROR_29">NcKin</span> and <span class="blsp-spelling-error" id="SPELLING_ERROR_30">NcKin</span>3 <span class="blsp-spelling-error" id="SPELLING_ERROR_31">wildtypes</span><br />allowed the authors to gain insight into which parts of the <span class="blsp-spelling-error" id="SPELLING_ERROR_32">kinesin</span><br />motor are important for conferring <span class="blsp-spelling-error" id="SPELLING_ERROR_33">processivity</span> onto <span class="blsp-spelling-error" id="SPELLING_ERROR_34">dimeric</span><br />constructs. (And also, which parts are important in <span class="blsp-spelling-error" id="SPELLING_ERROR_35">NcKin</span>3 for<br />inactivating one of the heads.) As far as I know, these are the very<br />first two chimeras created between these two <span class="blsp-spelling-error" id="SPELLING_ERROR_36">kinesins</span> and thus open the<br />door for many more investigations into how <span class="blsp-spelling-error" id="SPELLING_ERROR_37">processivity</span> is regulated in<br />the motor domain, neck-linker, and neck regions. The results here<br />indicate that many more chimeric structures and site-directed<br /><span class="blsp-spelling-error" id="SPELLING_ERROR_38">mutagenesis</span> studies will be necessary and valuable. Of course, that is<br />a lot of work, but the results here open the door for those further<br />studies.<br /><br />For me, the most fascinating result was point (iii) on<br />page 4. The authors show that the Head3/Neck1 construct seems to get<br />stuck in a "kinetic dead end." As they say, the <span class="blsp-spelling-error" id="SPELLING_ERROR_39">kinesin</span>-1 neck appears<br />to confer some elements of <span class="blsp-spelling-error" id="SPELLING_ERROR_40">processivity</span>, but not all. Combined with the<br />missing elements (which <span class="blsp-spelling-error" id="SPELLING_ERROR_41">kinesin</span>-3 head lacks), the motor is actually a<br />bit more handicapped, as shown by a gradual decrease in gliding<br />velocity as the concentration of motors is increased.<br /><br />I also had a couple questions about the paper that I noted previously (see prior article comments):<br /><br />* Statistical significance of <span class="blsp-spelling-error" id="SPELLING_ERROR_42">processivity</span> measurements.<br /><br />* Lack of discussion and comparison with previous <span class="blsp-spelling-error" id="SPELLING_ERROR_43">Ncd</span>/<span class="blsp-spelling-error" id="SPELLING_ERROR_44">Kinesin</span>-1 chimera results<br /><br />DISCLOSURE:<br />Our lab (http://openwetware.org/wiki/Koch_Lab) has recently obtained<br />major funding to study <span class="blsp-spelling-error" id="SPELLING_ERROR_45">kinesin</span>. I do not think we have competing<br />interests with these authors or the work they've presented here, but I<br />thought it worth mentioning.<br /></div>Steve Kochhttp://www.blogger.com/profile/09076719001132389463noreply@blogger.com4tag:blogger.com,1999:blog-7356964387844331141.post-38573374376367113482009-05-28T23:39:00.001-06:002015-12-31T17:28:45.739-07:00Pondering our Kochlab graduate student compass...how about "Always Contribute?"<div xmlns="http://www.w3.org/1999/xhtml">
Last weekend, my friend <a href="http://filtrate.blogspot.com/">Richard <span class="blsp-spelling-error" id="SPELLING_ERROR_0">Yeh</span></a> posted a couple essays by Paul Graham onto <span class="blsp-spelling-error" id="SPELLING_ERROR_1">Facebook</span>. I loved the essays and <a href="http://friendfeed.com/science-2-0/474666d1/cities-and-ambition-via">linked to one of them on <span class="blsp-spelling-error" id="SPELLING_ERROR_2">friendfeed</span></a>. <a href="http://michaelnielsen.org/blog/?page_id=181">Michael Nielsen</a>, in turn pointed me to another essay by Graham that he thought I'd like, "<a href="http://www.paulgraham.com/love.html">How to Do What You Love</a>." Michael was completely right, I loved the essay. If you have not read that essay, I command you to stop reading my blog and to go read that article! You'll get much more out of his essay than this blog.<br />
<br />
OK, now that I have you defiantly reading my blog, intent on garnering something useful from it, to spite me, let me continue. The "Do What You Love" essay resonated with me very strongly. It reminded me of the discussion of talents in "<a href="http://www.amazon.com/First-Break-All-Rules-Differently/dp/0684852861/ref=pd_bbs_sr_1?ie=UTF8&s=books&qid=1231773579&sr=8-1">First Break All the Rules</a>" by Buckingham and <span class="blsp-spelling-error" id="SPELLING_ERROR_3">Coffman</span>. I think Graham and Buckingham and <span class="blsp-spelling-error" id="SPELLING_ERROR_4">Coffman</span> are talking about the same thing: that finding work you love is a key to happiness (and productivity), but that finding out what you love is a very difficult task worth working very hard on. The language of Buckingham and <span class="blsp-spelling-error" id="SPELLING_ERROR_5">Coffman</span> is to talk about finding one's "talents." I've been talking with my graduate students about this a lot for the past six months. (In fact, it's time for me to have another awkward <a href="http://stevekochscience.blogspot.com/2009/01/talents-in-lab-part-one.html">talent-finding session</a> with them, I do believe!) I also preach to all of my undergraduate students about the importance of finding their talents and I give them an <a href="http://openwetware.org/wiki/User:Steven_J._Koch/Talents_assignment">end-of-semester assignment</a> to think about their talents. I'm delighted to have been shown the Graham essay, because I think it is yet another way of presenting this argument to students, and a very eloquent one.<br />
<br />
Since I loved the essay so much, I sent it to the person who gave me the First Break All the Rules book. He wrote back to me and keyed in on the "always produce" part of the Graham essay:<br />
<br />
<blockquote>
"Always produce" is also a heuristic for finding the work you love. If you subject yourself to that constraint, it will automatically push you away from things you think you're supposed to work on, toward things you actually like. "Always produce" will discover your life's work the way water, with the aid of gravity, finds the hole in your roof.</blockquote>
<br />
While reading the note, the Do What You Love essay finally clicked with another I read by Graham last weekend, "<a href="http://www.paulgraham.com/wealth.html">How to Make Wealth</a>."[1] It's another fantastic essay that I feel like commanding you to read. One premise in that essay is that people in start-up companies can be 20-30 times more productive than they can in an ordinary 9 to 5 job. Thus, a small group of people can create a tremendous amount of wealth by working really hard for a few years. They can also get financially rich as a reward for their production of wealth for the world. The thing that clicked for me is that you cannot make the world a better place without producing. Most people are producing at a rate at least 20 times less than they could be producing, <i>if they found what they loved and were able to do it all the time</i>. I garner great optimism from this fact that we're on average so incredibly inefficient. It means most people are not even close to any absolute point of diminishing returns, and with the right kinds of changes, they could easily multiply their productivity and impact on the world by <span class="blsp-spelling-corrected" id="SPELLING_ERROR_6">manyfold</span>.<br />
<br />
So, then I started thinking about our research lab and the students in our lab. I thought over things that each student has done in the past year that made me profoundly happy. As I thought over all these things, I realized they had a common theme: I was recalling instances of those students being unusually productive. Furthermore, my favorite recollections involved those where the students had shared their work on our public wiki, or our blog, or in some other fashion open to the world. This made me think that it is now very easy for me to summarize my main expectation and goal for my students: "always produce," borrowed from Paul Graham, of course. My students like to make <span class="blsp-spelling-error" id="SPELLING_ERROR_7">Kochlab</span> <span class="blsp-spelling-error" id="SPELLING_ERROR_8">slogans</span>, so I thought of "<span class="blsp-spelling-error" id="SPELLING_ERROR_9">Kochlab</span>: Produce" or "<span class="blsp-spelling-error" id="SPELLING_ERROR_10">Kochlab</span>: Always Produce," but if you <span class="blsp-spelling-corrected" id="SPELLING_ERROR_11">pronounce</span> the "Koch" correctly ("Cook"), then it has the problem of making one think of produce the noun, e.g. apples and bananas. Thus, I am thinking something like "<span class="blsp-spelling-error" id="SPELLING_ERROR_12">Kochlab</span>: Contribute" or "<span class="blsp-spelling-error" id="SPELLING_ERROR_13">Kochlab</span>: Always Contribute."<br />
<br />
In some sense, "always contribute" means the same thing as "always produce." The point of the producing, in regards to Graham's essays is that you're creating wealth, and therefore contributing something to society. However, I like "contribute" much better, because it has much more clarity in the science world. "Contribute" automatically points the way towards open science (aka <a href="http://friendfeed.com/science-2-0">Science 2.0</a>). Whereas, production in the traditional scientific world ("closed science") can be done with a very limited amount of contribution.<br />
<br />
I have mulled it over for a couple days now, and I think I really like this as the main piece of advice and constant guidance to give to our students: "always contribute." Does this work? Let me try it out in a few ways:<br />
<br />
1. By the time the students get their Ph.D.s, I want them to have learned a tremendous amount about what their talents are. I want them to clearly see what the next step in their career should be in order to leverage those talents and help them be successful and happy. A compass of "always contribute" will lead the students towards finding ways of being productive instead of spinning their wheels. These activities will be the means by which the students and I discover what their talents are. This is the point of Graham's "always produce" advice. Check.<br />
<br />
2. By the time the students get their Ph.D.s, I want them to have a strong and large professional network of people that know them and the work they have done. "Always contribute" tells them that <a href="http://en.wikipedia.org/wiki/Open_notebook_science">Open Notebook Science</a> is a good thing to do. Sharing code, design drawings, personal summaries of research papers, tips and tricks on protocols -- these are all ways to contribute. In our limited experience in our lab, we have received validation after validation after validation that open contributions get attention. We can see this vaguely via page views or Google search rank or quite vividly via positive feedback from people that we admire and people whom we've helped. Combined with traditional publishing (also a contribution) and attending scientific meetings (contributing), I think "always contribute" will make building a powerful professional network almost automatic. Check.<br />
<br />
3. I want our lab to produce innovative, exciting, and high-impact scientific results. Will "always contribute" point us in the right direction for this goal? Does it point in any direction? I need to think about this one some more. I feel like it must point in the right direction--for example, innovations are contributions. But there's some risk that focusing on contributing could lead towards a lack in overall production. Basically I am thinking of the standard arguments against open science -- increased likelihood of scooping, which in turn reduces chances of funding and publishing. I fundamentally believe that those arguments are strong enough to tip the balance, but I don't think they've been proven yet. Another example of how "always contribute" may be counter to our lab's scientific productivity: some students may discover that they are wickedly talented at contributing in ways that do not advance their research projects. That's a great thing to discover! An example that hasn't happened in our lab yet would be for a student to discover that they're <span class="blsp-spelling-corrected" id="SPELLING_ERROR_14">fantastically</span> talented at writing popular science articles and want to do so at the expense of doing any research. I want students to discover something like this. It fits perfectly with items 1 and 2 above. However, it is clearly a problem in regards to item 3. This is not a new problem, though. My job as a research professor is to both mentor students as well as ensure production of research results. The way the system is set up those goals are not always aligned, and sometimes in conflict. It's possible to be rewarded with research grants, even by abandoning the best interests of your graduate students. Most people in the system know this and have seen the <span class="blsp-spelling-corrected" id="SPELLING_ERROR_15">devastating</span> results it has for too many <span class="blsp-spelling-error" id="SPELLING_ERROR_16">Ph</span>.D. students. I am absolutely against doing that and despise many people who have chosen that route. On the other hand, I don't have a good idea about what do do if "always contribute" turns into "I can't do my research." That's definitely going to happen eventually. In many cases, it will be possible for the student to discover their true calling in life, but then re-focus on making the research contributions necessary to finish the <span class="blsp-spelling-error" id="SPELLING_ERROR_17">Ph</span>.D. that they've invested so much time in. Will there come a time when the student should rightly choose abandoning the Ph.D.? Ugh, this is a tough one: Item #3 gets an: almost check / need more thinking.<br />
<br />
I've painted myself into a corner now. If I were Paul Graham, I would figure out a way to backtrack. But I'm not, and I don't really know how to end this blog post, so I think I'm going to end it by linking to another Graham essay about writing essays. This one was linked to me by <a href="http://friendfeed.com/akkartik"><span class="blsp-spelling-error" id="SPELLING_ERROR_18">Kartik</span> <span class="blsp-spelling-error" id="SPELLING_ERROR_19">Agaram</span></a> on <span class="blsp-spelling-error" id="SPELLING_ERROR_20">friendfeed</span>. It's an <a href="http://www.paulgraham.com/essay.html">essay that explains why high school and college writing assignments sucked so badly</a>. If you hated those assignments but never quite knew why, you'll love this story. Plus, you'll feel vindicated and it will give you one more reason to trust your gut in the future. For example, if your gut were telling you that "always contribute" is a fantastic compass to present your graduate student <span class="blsp-spelling-error" id="SPELLING_ERROR_21">mentees</span>.<br />
<br />
Footnote:<br />
[1] I'm taking a bunch of liberty here with my own story. It wasn't until I started writing this blog that I realized the two essays had clicked. But I think <span class="blsp-spelling-corrected" id="SPELLING_ERROR_22">subconsciously</span> this is what was happening. Also, I probably had the <a href="http://www.herecomeseverybody.org/2008/04/looking-for-the-mouse.html">Gin, Television, and Social Surplus</a> essay by Clay <span class="blsp-spelling-error" id="SPELLING_ERROR_23">Shirky</span> in my head, as Joelle <span class="blsp-spelling-error" id="SPELLING_ERROR_24">Nebbe</span> had linked to it <a href="http://friendfeed.com/iphigenie/bd442ff0/gin-television-and-social-surplus-here-comes">recently</a>.</div>
Steve Kochhttp://www.blogger.com/profile/09076719001132389463noreply@blogger.com26tag:blogger.com,1999:blog-7356964387844331141.post-55671617017413095212009-05-26T23:19:00.002-06:002009-05-27T07:09:46.221-06:00My first PLoS comment: High rating of an article on TSLP being the cytokine link between eczema and asthma<div xmlns="http://www.w3.org/1999/xhtml"><span style="font-style: italic;"></span><blockquote><span style="font-style: italic;">5/27/2009 SJK Note: After I wrote this, Bora Zivkovic sent me links to the PLoS community blog where he talks about </span><a style="font-style: italic;" href="http://everyone.plos.org/2009/04/07/why-post-comments-on-plos-one/">commenting</a><span style="font-style: italic;"> and </span><a style="font-style: italic;" href="http://everyone.plos.org/2009/04/28/rating-articles-in-plos-one/">rating</a><span style="font-style: italic;"> PLoS articles. Both are very much worth reading! Bora is the Online Discussion Expert for PLoS.</span></blockquote><br /><br />Recently, <strike>William Gunn</strike> Mr. Gunn composed an <a href="http://synthesis.williamgunn.org/2009/05/24/online-engagement-of-scientists-with-the-literature-anonymity-vs-researcherid/">excellent article</a> discussing online identity and the making of public comments in scientific circles. Without immediately spiraling into a stream of ridiculous conversation, I can't really comment on his post, or the ensuing friendfeed thread. Suffice to say that Mr. Gunn and others on friendfeed inspired me to be a lot bolder in commenting on PLoS articles.<br /><br />So, tonight I made <a href="http://www.plosbiology.org/rate/getArticleRatings.action?articleURI=info%3Adoi%2F10.1371%2Fjournal.pbio.1000067">my first comment on a PLoS article</a>. Previously, I had viewed commenting on the actual article site as a very formal procedure that required attaining the highest level of understanding of the article before submitting a comment. Essentially, I was viewing commenting on an online article the same way I viewed submitting an official comment to an article published in Science or Nature (or other journals). Published comments in those journals are almost always refutations of the article that seemingly without fail lead to concomitantly published rebuttals by the original article authors. Thus, the culture of commenting on articles is fraught with nastiness and putting one's scientific reputation on the line. This could be the reason that so far "official" online commenting on peer-reviewed articles has been very limited, whereas "unofficial" or off-site commenting has been more common. By "unofficial," I am loosely referring to comments made anywhere that is at least one link removed from the actual published article site. For example, an external blog, friendfeed discussion, or notes left on article managing services such as citeulike.<br /><br />It occurred to me while laughing and crying my way through the recent friendfeed discussions (OK, fine, <a href="http://friendfeed.com/mrgunn/b752969d/online-engagement-of-scientists-with">here's a link</a> to perpetuate the madness) that this culture may be relatively easy to change. (Aside from any questions of whether it's necessary to change.) In my opinion, PLoS has already made one innovation that vastly increases the odds of a user making a public "comment." They have separated the article ratings into three categories: Insight, Reliability, and Style. From my personal experience, that opens the door almost all the way in terms of inviting some kind of reader feedback. Rating an article on "Style" does not carry much professional risk from my viewpoint. Rating on "Insight" requires understanding of the possible impact of the article, and is thus much more weighty than the "Style" rating. However, I personally feel I can rate an article on "Insight" without assessing the quality or reliability of the methods and data. I recently did this with a PLoS ONE article I saw on <a href="http://www.plosone.org/rate/getArticleRatings.action?articleURI=info%3Adoi%2F10.1371%2Fjournal.pone.0005299">single-cell sequencing of uncultured organisms</a>. To rate an article on "Reliability," I feel requires the kind of in-depth understanding that would be required for me to send a formal letter into the editor of Science or Nature that could be published. Thus, the barrier for me to rate on "Reliability" is quite high. Especially since if I'm going to put in enough effort to feel completely justified in rating, it's likely to be less than a 5-star rating. (I guess I'm feeling like I spend more time reading articles that I disbelieve than those I do believe?)<br /><br />Another reason that placing online comments does not have to be as formal and negative as with traditional published comments is that the comments are published without a delay waiting for the original authors to compose a response. This then reduces the expectation that the publishing authors must respond and therefore takes the formality down a bunch of notches in my opinion. Also, in terms of PLoS the whole mission of the journal is to make research more broadly and rapidly available--and thus I think there is an expectation that the comments should also come from a broader base of readers.<br /><br />So, that is what inspired me to take the time to read a <a href="http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000067">PLoS Biology article</a> and compose my first online comment tonight. I was also inspired by the belief that we're still very early in the process of dictating the culture of online discussions of peer-reviewed research--and thus a concerted effort can make impact in what ends up happening. This inspiration was combined with the coincidence that my wife sent me <a href="http://www.babycenter.com/204_molecule-in-skin-may-link-eczema-and-asthma_10313951.bc">an article from BabyCenter today</a> that caught my interest because it was discussing the recent PLoS Biology article. Finally, the thing that finally tipped the balance and convinced me to take the leap and make my first PLoS comment was a healthy dose of "<a href="http://en.wikiquote.org/wiki/Risky_Business#Dialogue">WTF</a>" So I stopped worrying and took the leap. :)<br /></div>Steve Kochhttp://www.blogger.com/profile/09076719001132389463noreply@blogger.com6tag:blogger.com,1999:blog-7356964387844331141.post-24878367885968189932009-05-25T23:58:00.000-06:002009-05-25T23:58:31.558-06:00Time for more blogging! Warming up... You can't believe what you see...<div xmlns='http://www.w3.org/1999/xhtml'>I'm just now coming out of the end-of-semester fog. I've been through three academic years so far as an assistant professor. That's six semesters, five in which I've taught a course. In all five of those semesters, I ran out of steam and could not keep up with all the things I'd have liked to have done in my areas of research, mentoring, teaching, and family. In my opinion, 16 weeks is too long for a semester...I notice myself and my students beginning to burn out after 8 weeks. <br/><br/>It's a pattern for me that I take on too much at the beginnings of semesters and then have to cast things aside as I get overwhelmed. Before this semester I took a big leap into communicating with scientists on the internet, via blogging and discussions with a bunch of new friends on friendfeed. As the semester engulfed me, I ended up casting aside blogging, but actually was able to maintain a lot of dialogue on friendfeed (e.g. in the <a href='http://friendfeed.com/science-2-0'>Science 2.0</a> and <a href='http://friendfeed.com/the-life-scientists'>The Life Scientists room</a>). So, even though I was disappointed to not keep up the blogging, I can look back and see that overall I made a huge amount of progress in terms of scientific communication and meeting (virtually) many great people around the globe. I'm very happy with that, and I'm even happier that a couple of my graduate students came along with me. They have made their own connections with other scientists and made substantial progress in open science and open scientific communication.<br/><br/>I've been excited for the last week or two to ramp up the blogs again. In particular, I'm excited about a couple things. One is to try out <a href='http://researchblogging.org/static/index/page/help'>Research Blogging</a>. This was suggested to me by Michael Nielsen in a <a href='http://friendfeed.com/science-2-0/7011705b/faculty-of-1000-interview-with-richard-grant'>friendfeed thread</a> in which I learned a lot, but which I started by spouting off way too ignorantly. My apologies to Richard once again! As I understand it, the service will allow me to write up blog reviews of specific research papers and then label my posts as suitable for listing in Research Blogging. For me, it will be a step up from what I started doing this semester, which is trying to make a few notes on every paper that I add to citeulike. You can see my citeulike RSS feed, with my comments added, on this <a href='http://pipes.yahoo.com/pipes/pipe.info?_id=NHLMoeXk3RGVOmisbbsjiw'>Yahoo pipe</a>. It will be a lot more work to write what I think is a worthy blog report about a paper, but I'm excited about testing the waters. The way citeulike is set up, I feel like my comments there are pretty much wasted as far as benefit to others goes. In the future, I'm expecting my group to communicate more via citeulike (or another service) as a form of "journal watch." But as it stands now, I'm pretty sure nobody reads the comments I add to my citeulike library.<br/><br/>The other thing that should be exciting is to write a guest blog for Lisa Green at <a href='http://www.nextbio.com'>NextBio</a>. We've talked about this a bit, and I think it may happen in the next few weeks. What I will blog about that is worthy of a "guest blog," I don't know...but it should be a fun experience!<br/><br/>Finally, I needed some inspiration to come in here and start dusting off my blogs. I had been a bit depressed at their dormancy, which was a postive feedback loop preventing me from blogging. A blog warm-up idea came to me earlier tonight as I was staring at the ceiling fan. I recalled something I'd noticed maybe 6-10 years ago in graduate school, which made me recall something else I'd noticed at the same time. They're two "illusion" kind of things that I think are fun, and which I'm going to describe here without actually researching them scientifically. Hopefully someone who knows something will pipe in and tell us something about them!<br/><big><big><br/>1. Blurry motion seems slower with peripheral vision</big></big><br/><br/>I first noticed this illusion when I was trying to make large graphs in Origin back in graduate school. Whenever I made the mistaking of clicking on very large matrix plots, the graph would flash for like a minute before opening the graphing preferences window. I would look aside in frustration each time. And then I noticed that when I looked at the flashing graph (which was more like quick vertical scrolling of a dark patch), it seemed to scroll much slower in my peripheral vision. A few years later, I noticed the same thing when looking at a ceiling fan, an experiment much easier to reproduce.<br/><br/><i><big>Here is the experiment you can try</big></i><br/><br/>Find a ceiling fan that's not too far away, and spinning at about 2 hertz. When you look at it directly, if you're like me, the default image is to ignore the individual fan blades, and perceive a blur. You can change the image dramatically by following an individual blade with your eyes. For me, that motion seems "slower" than the blurry motion, but it's not the illusion I'm talking about here. The illusion that I see is when you quickly switch from looking at the fan with your central vision and instead use your peripheral vision. When doing that, the motion seems to slow down substantially. For me, it is substantial and repeatable.<br/><br/>I couldn't resist checking into this a bit on wikipedia, and I found something called "<a href='http://en.wikipedia.org/wiki/Flicker_fusion_threshold'>flicker fusion threshold</a>" in this <a href='http://en.wikipedia.org/wiki/Peripheral_vision'>wikipedia article on peripheral vision</a>. In the flicker fusion article, it is said, "so flicker can be sensed in peripheral vision at higher frequencies than in foveal vision." Given this, I wonder if the effect I am seeing has to do with some part of the visual system normalizing a given flicker relative to the maximum possible perceived flicker? The fan produces a constant rate of flicker...but it is a larger percentage of the fastest possible flicker when looked at with foveal vision?<br/><br/><big><big>2. I think you can hear individual splashes in the roar of a waterfall.</big></big><br/><a href='http://www.flickr.com/photos/37176420@N00/3000288249'><img src='http://farm4.static.flickr.com/3295/3000288249_44a29c99fe.jpg'/></a> (Photo by Ant J on Flickr.)<br/>This is an experiment I can't replicate easily now that I live in Albuquerque. We do have waterfalls in the mountains, but it's nothing like when I lived in Ithaca, NY during graduate school. Almost every day, I would cross the bridge over the waterfall at the end of <a href='http://www.cornell.edu/tours/scene66d4.html'>Beebe Lake</a>. This was on my way between Clark Hall (the physics building) and A-Lot, the parking lot the bus dropped off at. I would often stop and stare at the falling water. I noticed one day that if I followed with my eyes a particular part of the broken stream from the lake to the point at which it hit the rocks, I could audibly hear it "splash" within the "blurry" roar of the waterfall.<br/><br/><i><big>Here is the experiment you can try</big></i><br/><br/>If you have access to a waterfall, this experiment isn't too difficult to try. As I mentioned above in item 1, you can track the blades of a ceiling fan with your eyes, and this is the same thing you need to do with the waterfall. Track a "patch" of water all the way from the point at which it starts falling to when it hits the rocks or water below. Keep doing this repeatedly in a cycle, and you should "hear" the individual splashes--or at least I do. It's also fascinating to just look at the water as it breaks into pieces on the way down.<br/><br/>I just attempted 30 seconds of lazy google research for this phenomenon and was not successful at uncovering a wikipedia article to give insight into this effect. I am 50% sure it's an auditory illusion, and the other 50% of me thinks, "why not...maybe the sound isn't as 'blurry' as it seems?" It would be possible to check this with an objective audio/visual recording system.<br/><br/><big><big>3. The Blue Field Entoptic Effect -- Mystery Solved!</big></big><br/><br/>Also known as <a href='http://en.wikipedia.org/wiki/Blue_field_entoptic_phenomenon'>Scheerer's phenomenon</a>. As opposed to the above two illusions, this one I now know what it is. I first noticed it on airplanes when flying in a really bright sky. In Albuquerque, we have bright blue skies frequently, and I can see the effect. According to wikipedia, most people can see what I see in these conditions: counteless point-like bright white things that travel in squiggly paths in the field of vision. It turns out that these are white blood cells flowing through the capillaries that cover the non-foveal parts of the retina. On a blue background (e.g. the sky), those capillaries produce very dark lines all across the field of vision--due to red blood cells absorbing blue light very well. Somewhere in the visual processing system, these dark lines are "edited" out, so we don't perceive them. However, when a white blood cell travels through, it is mostly transparent, and the increased light is perceived as a tiny white thing in the field of view (which it is, I guess). One of the most fascinating things to me is that it allows you to actually visualize your own blood cells flowing. According to the article, some doctors have tried to leverage this as a diagnostic technique.<br/><br/><i><big>How to try out the experiment:</big></i><br/><br/>This one is easy. Wait for a nice sunny day. Pick a big blue patch of the sky and stare at it for a couple minutes. Keep your attention focused on looking for bright dots appearing and traveling in squiggly paths. You won't be able to follow individual ones, but by trying to use your peripheral vision, you can see hundreds or thousands of them. They are quite different than "floaters." They are smaller (point-like), quicker, and more fleeting.<br/><br/><big><big>4. The McCollough Effect -- An amazing optical illusion</big></big><br/><br/>I'm including this one because I realized that I ended up having a common theme of "can you believe your eyes?" The answer is "no!" apparently. So, I'm including this final, amazing illusion that is well worth trying out.<br/><br/><i><big>How to try out the experiment:</big></i><br/><br/>If you have 10 minutes, you should go try out this optical illusion: <a href='http://www.cheswick.com/ches/projects/me/index.html'>The McCollough Effect</a>. Spend the 5 minutes they recommend and then test it out for yourself. You can read a <a href='http://en.wikipedia.org/wiki/McCollough_effect'>description of it on wikipedia</a>. I found this illusion mind boggling, because for me it persisted for DAYS after I'd spent the five minutes training whatever part of my visual system that is being trained. Just an amazing demonstration of an ability to unwillingly and semi-permanently "program" part of your brain (or visual system at least) just by staring at some images for a few minutes.</div>Steve Kochhttp://www.blogger.com/profile/09076719001132389463noreply@blogger.com10tag:blogger.com,1999:blog-7356964387844331141.post-57443628670117387972009-03-27T11:06:00.001-06:002009-03-27T11:24:28.994-06:00The value of an open-access publication record for an academic job search and tenure & promotion.<div xmlns="http://www.w3.org/1999/xhtml"><br /><blockquote><br />11:22 am update<br /><br />Steve says: I just read <a href="http://www.academicevolution.com/2009/03/intellectual-apartheid.html">Gideon Burton's excellent post about "Intellectual Apartheid."</a> One of his recommended steps for administrators is "Update promotion and tenure policies to favor open access publications and to accommodate evolving scholarly genres (such as data sets, software, and scholarly tools that build the cyberinfrastructure)."<br /></blockquote><br /><br />Earlier this week, my department chair sent our department a link to an <a href="http://chronicle.com/news/index.php?id=6173">article in The Chronicle of Higher Education about MIT's open-access policy</a> announcement. (I believe there is the standard irony that the article from the Chronicle is limited-access, but you <a href="http://news.google.com/news?pz=1&ned=us&cf=all&ncl=1319189978">may be able to find freely available stories on Google news</a>.)<br /><br />Without being an expert on open-access or doing much background research, I decided to send the following email to my department. I'll let you know what happens (if anything)!<br /><br />Email to Physics & Astronomy faculty:<br /><blockquote><br />This got me to thinking. Our department could adopt a simple & public policy, such as: "Regarding new faculty hires and promotion & tenure decisions, we highly value an open access publication record. We place a value on open access publishing comparable to the value we place on publishing in top-tier scholarly journals which may have limited access." I don't know whether we could agree on such a statement, but if we could, I think it would place a positive light on our department, similar to how the MIT and Harvard statements below do for those universities.<br /><br />As a tenure-track faculty in our department, I do feel that open-access publishing will be viewed positively by the voting faculty. It would be good to know that more formally, but I'm not worried. A much more worrisome thing for me is how open-access publishing will affect my <span class="blsp-spelling-error" id="SPELLING_ERROR_0">Ph</span>.D. students.<br />Will they lose out in job searches or will they stand out? Our own department's stand on this issue won't help our own students. But maybe by taking a public stand, we can set an example that other departments can follow.<br /><br />I think it'd be worth spending a bit of time discussing at an upcoming faculty meeting.<br /><br />--Steve<br /></blockquote></div>Steve Kochhttp://www.blogger.com/profile/09076719001132389463noreply@blogger.com7tag:blogger.com,1999:blog-7356964387844331141.post-70574660234939237312009-02-24T01:16:00.003-07:002010-09-17T21:53:00.825-06:00Assistant to Robot, Promoted to RobotI was telling my grad students this story last week, and they liked mocking me so much as "assistant to a robot" that I thought I should post the story on here so more people can mock me. My first job in a research lab was the summer before starting my undergraduate career at the University of Michigan as a physics major--1992. I was really lucky get a summer job in one of Francis Collins' labs at UM. Yes, I am name dropping. The name I just dropped was that of <a href="http://en.wikipedia.org/wiki/Francis_Collins_%28geneticist%29">Francis Collins</a>, who was leader of the NHGRI from 1994-ish to 2008. Prior to that he was at the University of Michigan, with primary roles of hiring me as a work-study student and also leading teams that found the genes for cystic fibrosis, Huntington's disease, neurofibromatosis, and other diseases.<br />
<br />
I have been lucky so often in my life, and in particular in my career "planning." I'll tell you some other day how lucky I got in obtaining my current job at UNM. This is how I obtained my first job in a research lab: I was friends with Dr. Collins' daughter, and I liked science. I knew he had a research lab because he had visited our classroom in Junior High to tell us about cystic fibrosis and genetics. So, I asked my friend if I could work in her Dad's lab. A few days later, she told me, "he says yes," or something along those lines. I was 17 years old at the time. But when writing this story, it seems like I was younger, as I recognize this strategy as the same one I used for obtaining a rollerskating "skate" with a girl in the 6th grade. I think the song was "Manic Monday."<br />
<br />
I actually worked in a lab led by Chandra Sekharappa, who I think now has <a href="http://www.genome.gov/10000442">this lab</a>. He was such a great guy and I am eternally grateful to him, Dr. Collins, and the other people in that lab who welcomed the unusual physics undergraduate to their lab. As I am writing this blog entry, a flood of memories are coming back to me. I learned so many things from working in this lab, and now, 17 years later, they are still coming back to me and helping me in my research (which coincidentally, or probably not coincidentally is tending towards genomics applications). In this lab is where I learned to pipette. I learned what PCR was. I unfolded paper towels for Northern blots. I "stuffed tips" (FYI: I could use each hand independently on two different boxes). I helped with "rows and columns." I washed dishes. Wow, did I wash dishes. I became obsessed with: -80 freezers; dry ice; vacuum-bake ovens; centrifuges; liquinox; reverse-osmosis water; latex gloves; latex gloves filled with water and frozen in the -80C freezer; and latex gloves in the vacuum-bake oven.<br />
<br />
I cannot even come close to expressing how important this experience was to my career. Being immersed in this environment was so valuable -- whether I knew it at the time or not. The lab was focused on cloning the gene for early-onset familial breast cancer. (I believe another lab ultimately beat them by identifying BRCA1, but I'm not sure.) There was such a palpable excitement about the race to find this gene and I loved watching it. I distinctly remember that Dr. Collins welcomed me into group meetings, where the postdocs or grad students (I'm not sure what they were) would pass around these developed images of gels with the faintest of bands that proved something about their PCR reaction. I distinctly remember that they'd let the ignorant physics undergraduate stare at the film and then tolerate it when I said, "I think you're crazy, there's no band there." Somehow they kept inviting me, and they kept trying to explain to me "gene jumping" or "chimerisms" or "FISH" or other topics. The collaborative atmosphere in Chandra and Francis's lab is something I'm striving to replicate in our lab at UNM.<br />
<br />
OK, now onto the good part. Of course, being the undergraduate in the lab made me a target for the grunt work. More than that, I wasn't even a biologist! So, it happened that the lab (or someone on the floor) had gotten their hands on a robotic system that could essentially print microarrays on filter paper. Or perhaps the predecessor to microrrays. The "robot" could print media from sixteen 96-welled plates onto a single filter paper. Then, these 4x4 arrays could be used for some kind of hybridization assays. This was a big deal, and the robot cost something in the 100's of thousands of dollars. Basically, you'd put a stack of 16 microtiter plates in the holder next to the robot. You'd set up the filter paper, and then the robot would proceed to: grab a plate; take lid off plate; put plate down; stick pins in plate; stick pins on filter paper; clean pins; put lid on plate; put plate away; repeat with new plate.<br />
<br />
The problem was, the robot was controlled by some kind of SGI machine that nobody knew how to program. It cost a whole bunch of money to have the tech rep come out and program the thing. Everything about the robotic system worked well. Except, after taking the lid off the plate, it accelerated too fast, and media would splash from one well to another. This was terrible. I know what you're thinking: ask the physics undergrad to reprogram the robot! This is what I was thinking too when the grad students (or postdocs) explained to me the problem. I'm pretty sure I could have figured this out, no matter how obscure and proprietary the programming language. But, this was not my fortune. Instead, what they had figured out was that my $5.50 / hour salary was a perfect solution. I could perform the first part of the robotic sequence (grab plate; take off lid) and then at the appropriate time, hand the plate to the robot. So, this is when I took on my esteemed position as "assistant to the robot." I don't know how many days this lasted ... probably not too many, I think maybe for a few hundred plates or so. I do remember how utterly boring it was. I actually tried to read a book in 20 second increments while I tag-teamed with the robot.<br />
<br />
Perhaps during my time as <a href="http://en.wikipedia.org/wiki/Dwight_Schrute">Assistant to the Robot</a>, I impressed people enough to get my first promotion in the lab: to actual robot. (I previously mentioned my prowess at stuffing tips and unfolding paper towels, which probably factored into this promotion.) This job took most of a summer (1993 maybe?) and actually I'm pretty proud of it. My task was to copy the Washington University YAC (yeast artificial chromosome) library. I think it was about 200 96-welled plates and it took me most of a summer to make two copies. I became the most efficient plate-pourer of all time (in my own mind), and discovered that you can actually pour them so thin that even yeast can't grow. I wonder if these YAC libraries are still around nowadays?<br />
<br />
Well, that's the anti-climactic ending to my story. I don't have a coherent point, and I know this goes against all of the how-to-be-a-good-blogger advice. My points are: (1) I collaborated with a robot in the past because it was cheaper than fixing the robot and (2) I had an awesome undergraduate research experience that has profoundly impacted my career. In regards to (2), there are so many lessons I can learn to help me in my current position as a research mentor. The main thing I have been thinking is that undergraduate research can be valuable for the lab, and incredibly valuable for the undergraduate. I feel like we're not even coming close to achieving what we could at UNM in regards to undergraduate research, and I would like to change this over the next couple years. I routinely meet Junior-level physics majors who are interested in research, but haven't yet been in a lab. We are next door to Sandia National Labs, and only 2 hours away from Los Alamos National Lab...both of which have amazing resources and opportunities for undergraduate scientists. And of course, we have plenty of our own labs at UNM. One of my goals over the next few years is to help our students find research jobs earlier in their careers...perhaps even before they start at UNM. Whether their jobs can be as prestigious as my own assistant to robot jobs, I don't know, but I can definitely strive for that!<br />
<span style="font-style: italic;"><br />
SJK Note 4/2/09: I found a picture in my garage of the completed robot project. That's me admiring my 400? or so microtiter plates, all nicely stacked and labeled.</span><br />
<br />
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhOMpOJBINq3hfCgCLTQZiemnbXaCsii_jN1RlpUD0ZdLn_hls_SQPEFO_keO7BlWQBWLRhcH8A0VFnq0hESUkZjgXEqH29A7qN6vpyWkHrY4Yhxf_kyEUyWIXO_ddi6vjPrIsQL7-LyyjR/s1600-h/Wash+U+Human+YAC+Library,+1993.JPG" onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"><img alt="" border="0" id="BLOGGER_PHOTO_ID_5320334860191396034" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhOMpOJBINq3hfCgCLTQZiemnbXaCsii_jN1RlpUD0ZdLn_hls_SQPEFO_keO7BlWQBWLRhcH8A0VFnq0hESUkZjgXEqH29A7qN6vpyWkHrY4Yhxf_kyEUyWIXO_ddi6vjPrIsQL7-LyyjR/s320/Wash+U+Human+YAC+Library,+1993.JPG" style="cursor: pointer; display: block; height: 213px; margin: 0px auto 10px; text-align: center; width: 320px;" /></a>Steve Kochhttp://www.blogger.com/profile/09076719001132389463noreply@blogger.com10tag:blogger.com,1999:blog-7356964387844331141.post-53251730405067574312009-02-11T00:40:00.001-07:002009-02-11T00:40:00.316-07:00A science outreach idea, what do you think?I live on a cul-de-sac where we are lucky enough to know and enjoy hanging out with many of our neighbors. Many have kids who play with our kids. It's like when I was a kid, and I thought those days had passed, but they haven't. (As an aside, I love hyphen-ating words, but it bothers me that cul-de-sac is hyphen-ated.)<br /><br />Many of my neighbors really enjoy hearing about the science we're doing in the lab, and I really enjoy talking about it with them. This actually led to a very fun event we did during Winter Break where I brought in some neighbors to our Junior Physics lab course so they could get hands-on experience with some very cool physics. You can check out our <a href="http://openwetware.org/wiki/Physics307L:Winter_Break_Lab_Fest">OpenWetWare page (unfinished)</a> for the event (sorry the<a href="http://www.facebook.com/album.php?aid=8656&id=1577513688&ref=nf#/event.php?eid=56767847558&ref=mf"> facebook page</a> seems to be private). A brief summary is that I only had to invest a few hours of time, and I think the attendees really enjoyed it. I know I did.<br /><br />Recently I had an idea for science outreach that I'd like your opinion on. The idea is that I (or a student) will explain our research to one of our biggest neighbor fans. Then, we'll record an interview with him describing our science, what we do, it's importance, etc., from his point of view. Or we could do it with a couple neighbors talking. But the main point is that the non-scientists will be explaining the science to the (mostly) non-scientist audience on youtube.<br /><br />There are a few reasons I think this may be useful and fun. First, I always find it informative and fun to hear people "re-describe" our research to someone else after I've described it (unless it's printed in a magazine). Second, I have an inkling that it would be effective for communicating to non-scientists. Third, the people I have in mind for this project are very good at picking out the essence of what I'm telling them, and distilling it down to the exciting parts in layman's terms.<br /><br />So, do you think this is a good idea? Maybe it's been tried before many times, and if so, please send me the links. If we do give this a whirl, there is one thing I'd like to figure out how to do:<br /><ul><li>Record video with two cameras (for example, one on me, one on him)</li><li>Splice and edit the video to make a good video for posting to youtube</li></ul>I'd really appreciate advice on software and hardware to use for those purposes. Thanks!Steve Kochhttp://www.blogger.com/profile/09076719001132389463noreply@blogger.com5tag:blogger.com,1999:blog-7356964387844331141.post-3256793428866357632009-02-07T23:20:00.002-07:002009-02-07T23:31:19.711-07:00Personal open science challengesThere was recently <a href="http://friendfeed.com/e/7a496210-affe-4220-8844-31ac9a230d6f/Open-notebook-quantum-information/">a very interesting thread</a> regarding open notebook science in the <a href="http://friendfeed.com/rooms/science-2-0">Science 2.0 friendfeed room</a>. This was in response to <a href="http://michaelnielsen.org/blog/?p=552">Michael Nielson announcing</a> that Tobias Osborne had begun <a href="http://tjoresearchnotes.wordpress.com/">doing open notebook quantum information theory</a>. I think this is fantastic, and my kudos go to Tobias (whom I don't know). The friendfeed debate had to do with whether Tobias's work can be called open notebook science, which has <a href="http://en.wikipedia.org/wiki/Open_notebook_science">a specific definition</a>.<br /><br />The debate got me thinking again about something that's been bothering me recently. I've been having a hard time getting my thoughts straight, and that's still true. I'll quote myself and then try to clarify:<br /><blockquote><br />A really good motto for a scientist who wants to be open could be this: "Be as open as I personally want to be." This is very different than "be as open as possible." What I am specifically thinking is that young scientists (i.e., not yet beaten-down) seem to usually have very natural tendencies towards open science. But the overall level of natural talent for openness may vary enough that "open notebook science" may just not be the best method of openness for some people. But everyone can strive to "be as open as they want to be", and resist pressure to be closed coming from outside (fear of scooping; lack of technical means; resistance from colleagues). In contrast to these external pressures, I think it may be legitimate for someone to want to be open, but also maintain some privacy so they can get a personal reward of doing something all by themselves, for example. Perhaps posting all of their electronic notes 6 months or a year down the line.<br /></blockquote><br />"Be as open as I want to be." I don't know if that has value for anyone else, but it a very powerful mission statement for me right now. It's powerful, because I really believe in it, but I am not achieving it. I'll talk about that later in the post. But, first I want to talk about it in a more positive light.<br /><span style="font-size:130%;"><br />What kind of openness should be required?</span><br /><br />I am starting to decide that I'm not going to try to force my lab members to do specific kinds of open science. I am thinking instead that my goal will be to remove as many barriers as possible so that my lab members can achieve the level of openness they desire. I believe that adults have unchangeable natural talents, and I think that scientists will be cutout for different kinds of openness. For example, Anthony in our lab has recently <a href="http://openwetware.org/wiki/User:Anthony_Salvagno/Notebook/Research">started doing open notebook science</a>, true to its definition. I am really excited about this. He is a natural for ONS. I don't think that he has any problem writing anything in public. In fact, I think his notebook being open is a motivator for him to make it even better than he would a private notebook. This is the way he's wired, and it's not surprising if you know him. In contrast, I think some people would find that their creativity and drive are seriously hampered by doing ONS. For example, me as a graduate student. I don't know whether doing ONS would have worked or not. I actually kept what I think is a very good electronic lab notebook. But it was private, and I don't know whether I would have taken as many notes (and dropped as many F-bombs) if I knew it was public. I also don't know if I would have reacted well to someone posting a suggestion to me when I was immersed in trying to figure out something by myself. I do know that I would have been fine posting my notebook in public with some time delay. In fact, if anyone posts a comment to this blog asking me to post my grad school notebook in public, I'll go ahead and do that...f-bombs and all.<br /><br />So, while I don't think I'll require ONS for all lab members, I may have other requirements, such as delayed notebook publishing. What I am worried about is hampering creativity and productivity of young scientists by striving for inappropriately selected open science goals. I do want my students (and postdocs in the future) to strive for open science, but I want them to do it in the way that best leverages their talents.<br /><br /><span style="font-size:130%;">I am failing at my own principles</span><br /><br />"Be as open as I want to be." I and our lab have <a href="http://stevekochscience.blogspot.com/2009/01/update-on-our-new-open-science.html">made some great strides in the past few months </a>towards this principle. For me, I think the transformation was fueled by a strong belief in the power and even morality of open science. But it did take a heavy dose of "<a href="http://en.wikiquote.org/wiki/Risky_Business#Dialogue">what the fuck</a>" to spark the flurry of steps I took this past winter break. (I think that may be my first f-bomb while blogging; I feel alive.) I'm happy and excited about what we're doing. But I'm also not achieving openness as much as I'd like. And I'm confused. Two themes dominate my struggles with openness:<br /><ul><li>The students in my labs and their scientific careers</li><li>My collaborators, their careers, and my gratitude for their assistance and mentoring<br /></li></ul>I'm not trying to sound altruistic here. One of my talents is that I get genuine happiness out of feeling like I've helped other people succeed. You can see that both of those items above feed that desire in me. I do think those two items are what is confusing me. In contrast, the issue of being scooped, in itself does not impact my thinking. I do worry about being scooped, but I have already concluded that being open does not increase the chances of being scooped. I believe being open <span style="font-style: italic;">decreases</span> the chances of being accidentally scooped substantially. Furthermore, I even believe that being completely open would reduce the chances of being purposefully scooped. This is because the published track record would make it easier to shame the person who did the scooping.<br /><br />Being scooped would be emotionally devastating. This is true. And it would have an impact on my lab and my students. This is what my students and I have been discussing the past couple years, and I think we've developed a collective (perhaps unspoken) understanding that we'll be OK even if that does happen. I think I can protect and rescue my students from that scenario. The collaborator issue is so much more complicated.<br /><br />The collaborator issue is what is bothering me quite a bit now, and I really don't have any answer. Most of the scientists I know personally are "traditional." The ones I am trying to collaborate with are outstanding and highly respected by everyone, including me. The ones I am thinking about right now have put in a huge amount of effort helping me throughout various stages of my career. These traditional scientists, of course, are not Scientists 2.0, but they are fantastic scientists. I suspect, and in some cases directly know, that they would not approve of my science openness. So, I don't know how to deal with this external pressure towards closed science. The "what the fuck" strategy seems so disrespectful to people who've put energy into my career. But the "try to convince" them strategy is futile. "Showing them the way" will work...but at the risk of looking like "what the fuck" along the way and angering them. If we do get scooped, my students and I will be OK. But our mentors may never forgive us? <br /><br />OK, I'm going to stop now...those are the challenges that are really bothering me this weekend.Steve Kochhttp://www.blogger.com/profile/09076719001132389463noreply@blogger.com12tag:blogger.com,1999:blog-7356964387844331141.post-2063137468397835022009-01-26T22:54:00.000-07:002009-01-26T22:54:00.306-07:00Update on Our New Open Science ActivitiesI think it's been about a month since I started these blogs and joined <a href="http://friendfeed.com/stevekoch">friendfeed</a>. It's been a whirlwind, really. I've e-met dozens of scientists around the globe in that short time, most of them much farther along than I and my lab are in terms of open science. The community of scientists out "here" is incredibly welcoming and helpful, and I want to send a thank you out to whomever of you read this post.<br /><br />It's also been a time of huge change in terms of our lab's open science activities. We have started a lot of new open activities, and I thought I would make a list of them here. I'll only list those things that are new since mid-December, and I think it's quite a lot.<br /><br /><span style="font-size:130%;">Blogging</span><br /><br />Of course, I started blogging. We also started<a href="http://kochlab.blogspot.com/"> a blog that I and our lab members to contribute to</a>. So far, only <a href="http://www.blogger.com/profile/13721683514085788985">Anthony</a> and I have contributed to it, but that will evolve over the year, I think. So far for me, blogging is a treat and I've been able to rationalize doing it based on potential synergies with the activities I'm supposed to be doing :)<br /><span style="font-size:130%;"><br />Posting grants in public</span><br /><br />We started posting our grants on Scribd. I chose this site from advice from Jean-Claude Bradley and Cameron Neylon. So far, I've liked the site as a place for sharing grants and other documents and it seems to work well. As an example, <a href="http://www.scribd.com/doc/11333168/2009-ACS-IRG-Proposal-Submitted-Research-Plan">here is the grant we submitted last week</a>. Posting grants has been really helpful so far and I expect it to continue to be helpful. We've received helpful comments from a couple people, and also made some science connections because of it. For example, Cameron and I realized we have a lot of science interests in common!<br /><br /><span style="font-size:130%;">Paper preprint</span><br /><br />A big step we took is we drafted our first paper out of our lab and we <a href="http://precedings.nature.com/documents/2808/version/1">posted it on Nature Precedings</a>. Larry Herskowitz is the lead author on this paper. We posted it a week ago, and we immediately received very helpful comments, questions, and suggestions from Richard Yeh. We're <a href="http://openwetware.org/wiki/Koch_Lab:Publications/Proof_of_principle_for_shotgun_DNA_mapping_by_unzipping">using OpenWetWare to talk about the paper</a> with Richard and any others who want to join. My opinion right now is that OpenWetWare is a better place for these kinds of detailed lists of questions and suggestions, because we'll easily be able to break it into different topics, create sub-pages, and post supporting data, figures, etc. (In contrast, we found that trying to write the paper on a wiki just did not work for us at all.)<br /><br /><span style="font-size:130%;">Open research projects</span><br /><br />We have also taken some big steps towards "open notebook science" in the past month. We've been using a private wiki for about two years now, hosted by OpenWetWare. As I understand it, providing us with a private wiki was part of an experiment to see if it could draw in more users and lead them towards open science. You can't scientifically extrapolate from our experience, but then again, you don't have to approach it scientifically...so, my opinion is that providing the private wiki worked out beautifully for OWW's mission. I think they should continue to provide private wikis, including for select new users on a trial basis. It's quite possible (impossible to prove, though) that none of the open science activities I'm describing in this post would have been started had not Jason Kelly offered me the private wiki two years ago. Thank you Jason & all the OWW founders! I'd also like to thank Bill Flanagan who has helped me tremendously in many areas of the public and private wikis. <br /><br />Having prepared via our "warmup time" with the private wiki, many of the students in my lab have begun to take open notebook steps in the past few weeks. You can find links to these on our <a href="http://openwetware.org/wiki/Koch_Lab:Research#Open-Research_Projects">open-research projects section</a>. Anthony Salvagno has started doing real <a href="http://openwetware.org/wiki/User:Antonio/Notebook/Research">open-notebook science</a>, keeping his daily notes on OWW, using the Lab Notebook system that Ricardo and others developed. Anthony is about to start learning molecular biology in our collaborator's lab, with guidance from Kelly Trujillo. The lab is not accustomed to e-notebooks, so it's going to be really tough for Anthony to not be driven to use a paper notebook. We'll see how it goes, I'm hoping he can show them the way!<br /><br />Caleb Morse is embarking on some <a href="http://openwetware.org/wiki/Koch_Lab:Research/MediaWiki_for_Open_Science">MediaWiki projects</a> and we're trying to do our communication via OWW. There are many interesting things he might pursue this semester, many of them improvements to OWW and / or MediaWiki that can make the conduction of open research much easier. For example, he's currently working on modifying an extension to MW that uses cookies to prevent data loss when the browser crashes or closes while editing a page. This would be a huge plus for OWW.<br /><br />Finally, Andy Maloney joined our lab in October and has learned to use the wiki very quickly. He recently took his first leap into the public wiki by posting his incredible<a href="http://openwetware.org/wiki/Koch_Lab:Research/How_to_build_your_own_laser_diode"> instructions on how to build a laser diode control system from OEM parts</a>. I'm also pushing him to post some of his earlier research accomplishments on OWW, including a custom microscope he built for imaging ultrasonic fields via the sonoluminescence. His Google SketchUp drawings and fly-by animations of the thing are amazing and I want you all to see them! <br /><br /><span style="font-size:130%;">Open teaching</span><br /><br />I've also started posting teaching material on Scribd. I'm trying to be careful about copyrighted material, so I'm not sure whether I can keep that up. One of the things I try to do after lecturing is to "debrief" to help with next year's lecture. So, combining blogging with Scribd is a good way to do that.<br /><br /><span style="font-size:130%;">Back Pat</span><br /><br />Looking back over that list of new things we started doing only recently has made me feel great about our lab. Obviously that rate of science "opening" can't continue. But I really do think we'll be able to keep up most of the things we've started, and I'm excited about that. On our private wiki, use a template that Anthony wrote for giving yourself a pat on the back. You just add {{BP}} to a page to use the template, and then you get an electronic pat on the back and feel good about yourself. Or at least some of use do. So, I'm going to put {{BP}} on this article and it's for me and all the students in our lab for these accomplishments. It's also a {{BP}} for all of the scientists I've been talking to recently and who have helped us take all these steps. They've provided very valuable advice and examples about how to do it, as well as encouragement and feedback for the steps we've taken. Thank you!Steve Kochhttp://www.blogger.com/profile/09076719001132389463noreply@blogger.com9tag:blogger.com,1999:blog-7356964387844331141.post-23748910281289587232009-01-16T00:18:00.001-07:002009-01-16T00:18:30.776-07:00Talents in the LabSo, I just got back from a vacation--no internet access for a week! Ugh--I think some people find getting away from it all rejuvenating, but that is not me at all. In fact, this would be a complete non-talent for me. "Non-talent" is terminology from a book that I re-read while on vacation: "<a href="http://www.amazon.com/First-Break-All-Rules-Differently/dp/0684852861/ref=pd_bbs_sr_1?ie=UTF8&s=books&qid=1231773579&sr=8-1">First Break All the Rules...</a>" by Buckingham and Coffman. I first read this book several years ago, when I was immersed in the misery of being mismanaged. The concepts in this book are not complicated and to me even seem obvious (now that I've thought about them), but it still seems to be true that most managers ignore these concepts. Re-reading the book last week was even more illuminating, now that I've had a couple years of being a manager myself and can reflect on my own strengths and weaknesses as a lab manager and plan small changes that may have a big effect on outcomes for our students and the science we're doing.<br /><br />One of my talents is the ability to read these kinds of management and leadership books without getting too hung up on the fact that they're not perfect science. Though, I do like this one especially because it is founded in a whole bunch of research (the authors are out of Gallup Consulting) and objective analysis. Via hundreds of thousands of interviews with employees and managers across all types of industries they tried to determine common qualities of managers whose groups far outperform the others. Thus, they tried to find out what great managers do differently than good and bad managers. The main points they found out ring very true for me, and really, THE main point is that great managers recognize the following things:<br /><br /><ul><li>By the time people are grownups, their brains have been "wired" in unique ways because of their genetics and their experiences growing up. These genetics and experiences produce a set of talents and "non-talents" for any individual. The authors refer to this as the unique "filter" each individual uses for their everyday experiences. The key point is that these talents are not teachable to grownups and great managers recognize this. Skills and knowledge contrast with talents, in that they are teachable. Learning skills and knowledge is easy for someone with underlying talent in that area. Learning skills and knowledge without the underlying talent is a constant uphill battle.</li></ul><ul><li>In order to succeed and be happy in a particular job, a person needs certain talents. Great managers figure out what those talents are, and try to assess those talents when hiring people. Contrast this with the system most of us are familiar with, where people are assessed based on resumes and interviews which focus on skills and knowledge. Determining what talents a job requires is not easy. It's even more difficult for a manager to assess someone's talents. And possibly, for many people, the most difficult thing is for an individual to assess their own personal talents--I know it is very difficult for me.</li></ul><ul><li>A great manager spends time helping his people discover their own talents and helps them make career decisions based on those talents.</li></ul><br />I think while reading this book in graduate school was the first time I'd consciously considered talents existing for things besides athletics, music, acting. I think I easily accepted, for example, that professional musicians had innate "hard-wired" abilities that enabled them to enjoy the hard work it took them to achieve that kind of excellence. I knew I didn't have those talents and didn't entertain any notion that I could just "work really hard" to become a professional musician or athlete. But I don't think I ever considered the vast array of other ways people could be talented, or non-talented, and I think I was probably a subscriber to the popular notion that I could succeed at any kind of job I landed just by forcing myself to work hard. And if I was failing it was my own fault for not working hard or smartly.<br /><br />While considering that last paragraph, I think it's not quite correct. Back then, I probably did recognize the existence of many talents, but I had not sensibly defined them. For example, I may have thought I had a "talent for science," since from 1st grade through graduate school I had received good grades and succeeded in science "things." Therefore, I would have deduced that I have a talent for any kind of career related to science: graduate student, professor, R&D, science writer, elementary school science teacher, science policy advisor, etc. In fact, I think I entertained the notion of all of those careers at some point. I probably made the reasonable step of considering whether I'd like those careers, but I did not even come close to considering that it was my own talents and non-talents that would determine whether those careers would be thrilling or miserable.<br /><br />Ever since reading that book, I've been wondering about my own talents. Ironically, I'm untalented at discovering my own talents. I suppose some people are very talented in this. When I preach to my students about this topic, I'm often asked, "What are your talents?" I know that I have many talents, and some I know specifically. For example, I know that I absolutely love computer programming. I can work on data analysis applications for 16 hours straight days at a time and love it. This is a talent for me, and considering that I was spending 10 hours a day in 3rd grade playing around with BASIC on my Commodore 64 this is not a surprising talent. But it's one I don't get to use very much any more, due to my career choice. I also know that I have a lot of non-talents. I think it's just as important to discover these, and for me these are easier to find. I'm still not quite sure what it's called, but I have at least one non-talent that would be required for easy writing of scientific papers and grant applications. In contrast, I find these blogs fun and fairly easy to spew out--I enjoy this kind of writing, and I probably have some kind of talent that is being used by blogging. But there is something about the precision or brevity or efficiency or whatever about formal papers and in particular grant writing that give me serious writer's block. I have been writing grants for two years now and it is always unpleasant and very difficult. I feel like I produce good documents, but it is very far from easy.<br /><br />That last point is the key: it's not easy. (And I don't enjoy most parts of it.) This is a great way of discovering talents. In the book, they cite a manager (anonymously, unfortunately) who developed the "Sunday Night Blues Test." He asked his employees to stop and think on a Sunday night whether they were happy the weekend was over, or whether they were a little depressed. (Assuming a five day work week.) The employees then were to consider what specific things they had planned to do the next day. Their level of happiness / unhappiness about their activities the next day would be a way of understanding what talents or non-talents they possessed. I like this test, and it's helped me quite a bit in assessing myself.<br /><br />I've used a variation of the test in the courses I've taught, in the hopes that my students will learn something about themselves far earlier than I ever did. On the last day of class in the four semesters I've taught, I've presented them this last un-graded homework assignment. You can <a href="http://openwetware.org/wiki/User:Steven_J._Koch/Talents_assignment">view it on this openwetware page</a>. I ask them to reflect back on the semester that's ended and to ask themselves which courses they're most sad are ending and which they are elated to be done with. I ask them to think about specific assignments that were fun or others that were dreaded. I don't have any kind of evidence, but I feel like there's enough variety of things students are asked to do that they may be able to discover talents and non-talents this way. A few of my students "turn in" this assignment via email or WebCT, and I always find it fascinating and pleasurable to read what they have to say. Usually these are students that I've come to know a bit, so I can give them a little feedback on it too, which I enjoy. (This probably indicates a talent I have for getting true pleasure out of students' successes.)<br /><br />I realize this blog is getting long. I think I did say above that brevity is a non-talent of mine. I'm considering breaking this into two posts, but instead, I think I'm going to leave it as one post glued together by this added paragraph.<br /><br />So, as I mentioned above, I re-read this book a couple weeks ago, and I must have marked up every other page and wrote down several dozen ideas it gave me for how to better teach, manage our lab, and be a better person. One of those ideas which I've followed through on is to work on identifying talents of the students in our lab. I have a few reasons for wanting to do this. The most important reason is that I want to maximize the success of every student that comes through our lab. I really believe that the more they can understand about themselves and their talents, the happier and more successful they will be in their next career step. The next reason is that I can manage the lab much more effectively if I know what talents and non-talents my students have. I'm not sure I have the talent to do this, but I am sure that it can't hurt for me to know more.<br /><br />Believe it or not, I actually had a "talents" meeting with all three of my graduate students this week...between 2 and 3 hours with each person. I even went so far as to use the interviewing questions from the book. This was really cheesy, but my students trust me enough to have followed through honestly with the process. The questions are designed to reveal talents. I left the book in my office, so I can't quote any of them directly now, but some of the questions I found most revealing were:<br /><br /><ul><li>What keeps you working here? (in the lab)</li></ul><ul><li>What is the best kind of praise you have ever received? What made it so good? </li></ul><ul><li>What is a productive partnership or mentorship you've had? Why did it work so well?</li></ul><ul><li>What are your current goals and what is your timeline for achieving them?</li></ul><ul><li>How often do you want to meet with me to discuss your progress?</li></ul><br />All the questions are good, but those are coming to mind now as having elicited responses that pointed towards talents or non-talents.<br /><br />I don't want to get into any specific results here, because my students and I didn't really discuss yet whether this process would be open or not. Actually, what I'm hoping is that through this continuing dialog, it will become a habit of our lab to point out to each other obvious talents and even non-talents. I think we have a lot of respect and trust in each other, so it's likely we can achieve this kind of productive openness. In any case, without being too specific, I can tell you that I was really surprised at how much I learned from these meetings. Even considering that I already expected them to be productive meetings. Again, I think I am lucky to have very good and trusting students, so our dialog was very open. In addition to the questions from the book, I also asked each student to talk about their most productive time(s) in the lab so far. (Another variation on the Sunday Night Blues Test.) I found this incredibly useful.<br /><br />One of the most humorous, surprising, and potentially useful result was what I learned about the students' and my own talent for competitiveness. If someone has this talent, they are driven to compete and win against other people. A different kind of talent is a need for achievement. This is different, because it is not relative to other people, but an internal measuring stick and a desire to constantly improve. It turns out I and one of my students have a strong competitiveness quality. This didn't surprise me too much. What did surprise me was that the other students did not have this quality. One common flaw of managers is to follow the golden rule of treating others the way you'd like to be treated. I have this flaw too. Up until this week, I think I'd pretty much assumed that everyone was competitive. But what I discovered is that's completely not true. I had also down-played my own competitiveness, and I now realize it's an important part of me and my motivations. So, what can I do with this information? I'm not sure, but given how surprising some of it was, I don't see how it can make me a worse manager. Just a simple example is that if you try to motivate an achiever and a competitor by having them compete against each other it's not going to work well. I don't think I've tried do that, but as a manager I'm always doing <span style="font-style: italic;">something </span>, whether or not I'm trying to.<br /><br />I'm going to try to wrap up this wandering post now. If you have a talent for reading management or self-help books, I strongly recommend you read the book I've linked above, "First Break All the Rules." If you don't have that talent, I do recommend trying out different ways of discovering your own talents. During the few weeks I've been on FriendFeed, I've already seen a few people making or considering career moves. I think talents are the number one thing that will determine whether these moves produce success and happiness. A perfect example is the ineffective way in which university faculty are chosen. Successful graduate students and postdocs are evaluated for professorships based upon their achievements, skills, and knowledge as researchers in the lab. The job, however, is not at all similar. I am now a manager, teacher, grant-writer, leader, and I don't know what else...but I'm not doing research in the lab very often if at all. In light of the selection process (and the utter lack of training), it's not surprising that there is so much struggle seen in this career path. Luckily, I think I do have enough of the talents required for my job, and I can ultimately succeed.Steve Kochhttp://www.blogger.com/profile/09076719001132389463noreply@blogger.com5tag:blogger.com,1999:blog-7356964387844331141.post-51048800082160074352008-12-28T21:49:00.002-07:002008-12-28T23:07:58.513-07:00Tenure dossier: expanded statement of goals and achievements<div style="text-align: center;"><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhjFp-IeGsRmvZSv36lZIGDfoRZIwTbZMrgMTEL4qqkEu1ecc-Hsm6_AbzoshsP03S0ZzK8UfaI1ILegLxMyf7oF8uZTPiTq8X0evrCerQsEDMai_DU2mFKaFfFR7faDu9o3Nj9LAhNrTcP/s1600-h/expanded+statement.bmp"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer; width: 320px; height: 151px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhjFp-IeGsRmvZSv36lZIGDfoRZIwTbZMrgMTEL4qqkEu1ecc-Hsm6_AbzoshsP03S0ZzK8UfaI1ILegLxMyf7oF8uZTPiTq8X0evrCerQsEDMai_DU2mFKaFfFR7faDu9o3Nj9LAhNrTcP/s320/expanded+statement.bmp" alt="" id="BLOGGER_PHOTO_ID_5285089148127608642" border="0" /></a><a href="http://http://www.wordle.net/gallery/wrdl/410839/Mid-probationary_tenure_review%3A_goals_and_accomplishments"><span style="font-size:85%;">Image from wordle.net</span></a><br /></div><br /><div class="Section1"><span style="font-size:100%;">I'm currently midway through my 3rd year as an assistant professor at the U. New Mexico in Albuquerque. I'm on a six year <a href="http://www.colorado.edu/facultyaffairs/deskref/part5tenure_clock.htm">tenure clock</a>, which is pretty typical here (though some also do 4 years). During that 6th year will be the decision whether to promote me to associate professor (with tenure), and during this 3rd year is "mid-probationary review," which I tend to think of as "practice tenure." I don't want to get into the whole process right now (though there are many amusing parts), but I'm happy to provide details and / or links I can find in the comments or a future post.<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi9sCVh-Nhk76paK_KKGES_0vfDZ9rRhdcO0btWlEdH74q8Mn-eFZulkvPkhC4VTJsWCcKFuj7npFoPUOBHuXh2HV9SJBxLO_vWZfCxRPtfXyO83MRycih9_jAZLgUrUDtBTqzC7JjcfytI/s1600-h/dossier.bmp"><img style="margin: 0pt 0pt 10px 10px; float: right; cursor: pointer; width: 320px; height: 202px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi9sCVh-Nhk76paK_KKGES_0vfDZ9rRhdcO0btWlEdH74q8Mn-eFZulkvPkhC4VTJsWCcKFuj7npFoPUOBHuXh2HV9SJBxLO_vWZfCxRPtfXyO83MRycih9_jAZLgUrUDtBTqzC7JjcfytI/s320/dossier.bmp" alt="" id="BLOGGER_PHOTO_ID_5285068790303118386" border="0" /></a> Part of the tenure review process here (and I suspect at other universities) is to collect a whole slew of documents that you know nobody is going to read and assemble them into a tenure dossier.<br /><br />One requirement for the dossier is the "expanded statement of scholarly professional achievements and future goals." I deduced from the outset that most people weren't going to look at my dossier, and those that did would look at this section (as opposed to the interminable appendices). So, I knew the smart thing was to spend most of my time on this statement. I didn't do the smart thing, however, so I ran out of time to revise my statement as much as I would have liked. This is a common occurrence with me, and is part of my lame time management "strategies." I don't think my statement was too bad, though, and I think if people read it they'll get a good impression of my real goals over the next couple years as a professor here. I figured I would post it here on my blog, so I'm posting it below. The only changes I'm going to make are a few minor changes and insertion of some hyperlinks here and there (we submit the dossier on paper still!!!) if I think they're helpful. I really welcome any comments, questions, and critcisms!<br /><br />Here is the statement (converted from Word format):<br /></span><br /><div style="text-align: center;"><b><span style="font-size:180%;">Research</span></b><br /></div><p class="MsoNormal"><b>Science goals</b>: Our lab's research area is in experimental single-molecule biophysics. To us, that means that we are primarily physicists by training, and we are applying our physics skills (building instruments, data analysis, automation, nanoscale physics) to problems in molecular cell biology. In order to maximize our impact, we seek collaborations with outstanding biologists with whom we can identify key open problems and design new experiments. Currently, our research focus is on the molecular aspects of DNA damage repair and gene transcription—two important research areas for understanding and developing treatments for all types of cancer. For example, we are using biophysical tools such as <a href="http://www2.physics.umd.edu/%7Ealaporta/ALPTech.html">optical tweezers</a> (an instrument that can apply and measure tiny forces on single biomolecules) to develop methods for mapping DNA by unzipping single DNA molecules extracted from living cells.</p> <p class="MsoNormal"><b>People goals</b>: Young scientists will be the key to our lab’s success and to the long-term impact of our research. We seek to recruit diverse people with strong talents for experimental research and a passion for biophysics. Mentoring in ethical science and professional development of young scientists in the lab is a key goal and will be partially achieved by open communication and involvement of lab members in all aspects of lab operations, including funding, teaching, and outreach. </p> <p class="MsoNormal"><b>Funding goals</b>: Our research requires people, instruments, and supplies, and thus substantial ongoing funding is essential. My goal is to obtain multi-year renewable funding that is sufficient to fund a lab of several graduate and undergraduate students and all necessary supplies. An NIH R01 grant ($200K / year direct for 5 years) is a major goal and is an ideal funding level. An NSF CAREER award ($100K / year direct for 5 years) would be a significant achievement and sufficient in combination with student fellowships. Numerous other sources of funding for our type of research are available (particularly shorter-term “idea” grants), both from public and private sources and we will pursue all of these, including after obtaining a big NSF or NIH grant. Graduate students and postdocs will also be encouraged to apply for fellowships from NSF, NIH, and other sources. </p> <p class="MsoNormal" style="margin-bottom: 0.0001pt;"><b>Impact Goals</b>: First, we believe that open sharing of our plans, methods, data, results, software, etc. is the best way to speed the progress of science, the understanding of our results, and adoption of our methods. Thus, “open science” is a major goal, and one aspect of this is the traditional goal of publishing in high-impact peer-reviewed scientific journals and presenting regularly at national meetings. Second, we strive to leverage our exciting research in our teaching and service goals (below). Third, we will maximize impact through training and mentoring of students and postdocs who will make further innovations in their future careers beyond our laboratory.</p> <p class="MsoNormal"><b>Research accomplishments</b>:</p> <ul style="margin-top: 0in;" type="disc"><li class="MsoNormal" style="margin-bottom: 0.0001pt;"><b>Interdisciplinary collaboration</b>. We have established several valuable collaborations. </li><ul style="margin-top: 0in;" type="circle"><li class="MsoNormal" style="margin-bottom: 0.0001pt;">Our collaboration with the Mary Ann Osley lab (UNM Dept. Molecular Genetics and Microbiology) has resulted in generation of key biological materials (such as DNA constructs), some preliminary data, letters of support for grant applications, student fellowships, and two conference presentations. </li><li class="MsoNormal" style="margin-bottom: 0.0001pt;">Collaboration with the Steve Brueck lab (UNM CHTM) has resulted in a NanoLetters publication, letters of support and preliminary data for grant applications, and student fellowships. </li><li class="MsoNormal" style="margin-bottom: 0.0001pt;">Collaboration with Evan Evans (Physics, U. British Columbia; Biomedical Engineering Boston U.; Adjunct Chemical Engineering UNM) has resulted in Evans bringing two state-of-the-art single-molecule manipulation systems to the CHTM, joint recruitment of a postdoctoral researcher to UNM (funded by Evans NIH grant), and initiation of a joint research project.</li><li class="MsoNormal" style="margin-bottom: 0.0001pt;">Collaboration with Karen Adelman lab (NIH National Institute of Environmental Health Sciences) has led to letters of support for grant applications and agreements to share biological materials for upcoming single-molecule research.</li><li class="MsoNormal" style="margin-bottom: 0.0001pt;">We are planning collaboration with Susan Atlas lab (UNM Physics and Cancer Center) and Chris Lorenz Lab (Mechanical Engineering, King’s College London) and have submitted proposals with each lab as co-PIs as well as obtained letters of support for other grants.</li></ul><li class="MsoNormal" style="margin-bottom: 0.0001pt;"><b>Instrumentation</b>. Graduate and undergraduate students have played major roles in all aspects of lab start-up—providing valuable fundamental knowledge at the expense of slowing down construction. We have currently built prototype low-power optical tweezers (OT) and stretched single-DNA molecules using DNA constructs we have produced at UNM. Construction and calibration of a high-power OT system will be completed in Spring 2009. Also, partnership with Evans lab and student knowledge of OT has resulted in access to Evans’ state-of-the-art and fully calibrated OT system that he has recently (November 2008) completed transferring to a lab we share at the CHTM.</li><li class="MsoNormal" style="margin-bottom: 0.0001pt;"><b>Lab IT infrastructure</b>. We have in place very successful hardware and software that will serve all of our needs in data storage and backup, global sharing of data and methods, and collaboration. One key to this is a 2 terabyte RAID-5 server with VPN firewall running Windows Server 2003, Exchange Server 2003, and Internet Information Services (IIS) that was setup by a talented UNM ECE undergraduate (Caleb Morse). Another key component is a MediaWiki-based lab wiki (courtesy of <a href="http://openwetware.org/wiki/Koch_Lab">OpenWetWare</a>) that we use for all lab notebooks, lab communication, and some communication with collaborators and grant writing.</li><li class="MsoNormal" style="margin-bottom: 0.0001pt;"><b>Major results and preliminary data</b>. Our most major research achievement has been proof-of-principle for “shotgun DNA mapping,” led by Ph.D. student Larry Herskowitz. Larry is currently writing a paper for submission to Biophysical Journal, will present a poster at the 2009 Biophysical Society meeting, and we have submitted a patent disclosure to the STC. Our collaboration with the Brueck lab has resulted in a 2008 NanoLetters publication. We have also developed two fully-functioning software applications for stochastic simulation of eukaryotic gene transcription that we hope to publish in 2009. All of these results will provide key preliminary data to strengthen grant applications in 2009 and beyond.</li><li class="MsoNormal" style="margin-bottom: 0.0001pt;"><b>Student recruitment.</b> We currently have three physics Ph.D. candidates in the lab, all funded by fellowships--two have NSF IGERTs (two years of funding) and one has a CHTM / Emcore fellowship (8 months of funding). Two of these students have been in the lab from their second semester (spring 2007), while one student (R. Maloney) passed all of his exams and carried out significant research in the Thomas lab before transferring to our lab in late 2008. A “post-bacc” student, Diego Ramallo Pardo, performed research in our lab for over a year as part of the UNM PREP program and he is now at Stanford biophysics graduate school. An undergraduate physics major (Linh Le) is currently carrying out honors thesis research in our lab. We hosted an NNIN REU student summer of 2008. Finally, an ECE undergraduate and a biochemistry undergraduate student have carried out research for credit in our lab since early 2007.<b> </b></li><li class="MsoNormal" style="margin-bottom: 0.0001pt;"><b>Funding</b>. We obtained an American Cancer Society (ACS) starter grant for $22,500<b>—</b>this is an institutional research grant led by Janet Oliver in UNM Pathology. This is an important foothold in cancer research funding and is seeding preliminary results for NIH, NSF, DoD and other applications. Numerous national peer-reviewed grant applications have been submitted—none have been funded so far, but we have received much positive feedback. </li><ul style="margin-top: 0in;" type="circle"><li class="MsoNormal" style="margin-bottom: 0.0001pt;">I have also participated in a number of grant writing workshops, including a year-long monthly NIH grant writing workshop (led by Laurie Hudson, UNM College of Pharmacy), a one-day NSF grant workshop (led by UNM Chem. Eng.), and an NIH NIGMS mock review panel at the Biophysical Society Annual Meeting 2008.</li></ul><li class="MsoNormal" style="margin-bottom: 0.0001pt;"><b>Open Science</b>. We have implemented mechanisms for carrying out open science: OpenWetWare lab site with numerous protocols published; Optical tweezers control software project on Sourceforge; Lab server with Windows Server applications for sharing data over internet. I was also mentioned in an article about Open Science published by the Howard Hughes Medical Institute (HHMI). (12/27/08 Note: I don't like the way I was quoted, though!).<b><br /></b></li></ul> <p class="MsoNormal"><b>Upcoming Research Goals</b>:</p> <ul style="margin-top: 0in;" type="disc"><li class="MsoNormal" style="margin-bottom: 0.0001pt;"><b>Funding</b></li><ul style="margin-top: 0in;" type="circle"><li class="MsoNormal" style="margin-bottom: 0.0001pt;">Continued attempts to obtain major multi-year funding. (Maybe get lucky with a pending grant!) In 2009, planning NIH R01 to National Human Genome Research Institute, American Cancer Society (national) Research Scholar Grant, resubmission of NSF CAREER, resubmission of Human Frontier Science Program (HFSP), DoD Breast Cancer Research Program Idea, and other opportunities that develop.</li><li class="MsoNormal" style="margin-bottom: 0.0001pt;">Improved networking with program managers in Washington—face to face meetings when possible.</li><li class="MsoNormal" style="margin-bottom: 0.0001pt;">Mentoring graduate students in obtaining NIH NRSA (fellowship) and other funding.</li></ul><li class="MsoNormal" style="margin-bottom: 0.0001pt;"><b>Science</b></li><ul style="margin-top: 0in;" type="circle"><li class="MsoNormal" style="margin-bottom: 0.0001pt;">In 2009, we hope to achieve major progress and publications in three areas: shotgun DNA mapping; unzipping analysis of chromatin and RNA Polymerase II transcription complexes; nanochannels analysis of DNA and chromatin. These projects will be led by the three graduate students as major focuses of their dissertations and will be in collaboration with the Osley, Brueck, Adelman, and Evans labs.</li><li class="MsoNormal" style="margin-bottom: 0.0001pt;">Also in 2009, we hope to initiate research and obtain preliminary data to initiate the collaborations with Atlas and Lorenz labs.</li></ul><li class="MsoNormal" style="margin-bottom: 0.0001pt;"><b>People</b></li><ul style="margin-top: 0in;" type="circle"><li class="MsoNormal" style="margin-bottom: 0.0001pt;">I do not plan on soon expanding beyond the three graduate students plus the shared postdoc with Evans. I do plan on maintaining the level of undergraduate involvement in research by recruiting REU students, undergraduates from outside physics department, and future honors thesis candidates in physics.</li></ul></ul><br /><p style="text-align: center;" class="MsoNormal"><b><span style="font-size:180%;">Teaching</span><br /></b></p><p class="MsoNormal"><b>Teaching Goals: </b></p> <p class="MsoNormal">My primary mission in any course is to help students achieve goals that will benefit them in their future careers. These goals will differ depending on the course, level, and target population. Some goals will be specific learning outcomes (e.g. physics concepts) whereas others will be a broader foundation of the students’ careers (e.g. attitudes towards science; general research skills). I also strive to enhance my courses by leveraging exciting results from my research group and implementing educational innovations. While setting these goals is important, so is measuring progress—thus I intend on implementing assessment (pre- and post-testing) that is backed by education research. Finally, in any course I teach, I am a role model, leader, and motivator for the students in their university careers. Thus, I seek to maximize my accessibility to the students by facilitating many modes of interaction, particularly by leveraging modern communication, including email and messaging on WebCT and wikis.</p> <p class="MsoNormal"><b>Teaching Accomplishments:</b></p> <ul style="margin-top: 0in;" type="disc"><li class="MsoNormal" style="margin-bottom: 0.0001pt;">Two courses developed (Physics 102 “Intro Physics” and Physics 307L “Junior Lab”) with above average ICES scores.</li><li class="MsoNormal" style="margin-bottom: 0.0001pt;">27 PowerPoint lectures, hundreds of quiz and exam questions, and dozens of clicker questions and homework puzzles developed for Physics 102. Implementation of Just in Time Teaching (JiTT), peer instruction, and interactive lecture demos. Use of WebCT Vista for quizzes, homework, and communication with students. (12/27/08 Note: please let me know if you would like these materials, I am happy to share!)<br /></li><li class="MsoNormal" style="margin-bottom: 0.0001pt;">Wiki-based TA / instructor collaboration system developed for Physics 102. Mentored TA and two graduate RAs through process of developing and presenting one lecture.</li><li class="MsoNormal" style="margin-bottom: 0.0001pt;">Innovative “open science” <a href="http://openwetware.org/wiki/Physics307L">wiki system implemented for Physics 307L</a>—completely electronic and public lab notebooks, lab summaries, formal reports, and instructor feedback.</li><li class="MsoNormal" style="margin-bottom: 0.0001pt;">Attended American Association of Physics Teachers (AAPT) “New Faculty Workshop” in November 2008. Learned about a variety of research-proven physics instructions methods and where to find further information and teaching resources. </li></ul><b><span style="line-height: 115%;font-family:";font-size:11;" ></span></b> <p class="MsoNormal"><b>Upcoming Teaching Goals:</b></p> <ul style="margin-top: 0in;" type="disc"><li class="MsoNormal" style="margin-bottom: 0.0001pt;">Implementation of research-proven assessment in all courses (pre- and post-testing).</li><li class="MsoNormal" style="margin-bottom: 0.0001pt;">Refinement of teaching strategies, based on published physics education research that I learned about at AAPT workshop.</li><li class="MsoNormal" style="margin-bottom: 0.0001pt;">Presentation at UNM teaching conference and possible publication of innovative teaching strategies I’ve implemented so far. (12/27/08 Note: I am starting to do this with my new <a href="http://stevekochteaching.blogspot.com/">teaching blog</a>.)<br /></li><li class="MsoNormal" style="margin-bottom: 0.0001pt;">Teaching a third course in P&A department (probably calculus-based intro physics).</li></ul><br /><p style="text-align: center;" class="MsoNormal"><b><span style="font-size:180%;">Service</span><br /></b></p><p class="MsoNormal"><b>Service Goals:</b></p> <p class="MsoNormal"><b>University</b>: My goal for university service is to help guide and improve research and education in the department, college, and university through active participation in a few committees. <b>Local community</b>: My goals for service in Albuquerque and New Mexico are (a) to improve science education, (b) recruit minorities to the university sciences, and (c) improve the understanding and enjoyment of science by non-scientists. <b>Nation:</b> My goal is to make an impact on biophysics at the national and international level by committee service in the Biophysical Society, journal referee and grant reviewing service, “open science” leadership, and recruitment and mentoring of young scientists, including minorities.</p> <p class="MsoNormal"><b>Service Accomplishments:</b></p> <ul style="margin-top: 0in;" type="disc"><li class="MsoNormal" style="margin-bottom: 0.0001pt;">Participation in numerous committees in department, CHTM, and university-wide.</li><li class="MsoNormal" style="margin-bottom: 0.0001pt;">Minor committee member for two Ph.D. students outside my lab. </li><li class="MsoNormal" style="margin-bottom: 0.0001pt;">Several outreach activities with students and teachers in NM at middle and high school levels.</li><li class="MsoNormal" style="margin-bottom: 0.0001pt;">OpenWetWare leadership—especially electronic lab notebooks.</li></ul> <p class="MsoNormal"><b> </b></p> <p class="MsoNormal"><b>Upcoming Service Goals:</b></p> <ul style="margin-top: 0in;" type="disc"><li class="MsoNormal" style="margin-bottom: 0.0001pt;">Participation in another P&A committee within the next couple years– graduate recruitment desirable.</li><li class="MsoNormal" style="margin-bottom: 0.0001pt;">Service on Biophysical Society national committee ( I have volunteered and expect to be appointed in 2009).</li><li class="MsoNormal" style="margin-bottom: 0.0001pt;">Continued leadership in Open Science via involvement with OpenWetWare.</li><li class="MsoNormal" style="margin-bottom: 0.0001pt;">Expanded journal referee and grant review service.</li><li class="MsoNormal" style="margin-bottom: 0.0001pt;">Expanded local community outreach. I want to continue my lab’s involvement in local science fairs and I would like to develop partnerships with local science teachers as part of likely NSF CAREER award resubmission in 2009. I would also like to expand UNM’s role in local Habitat for Humanity projects, based on what I learned via participation in Sandia National Labs’ successful Habitat for Humanity program—but this will likely have to wait a few years.</li></ul> </div>Steve Kochhttp://www.blogger.com/profile/09076719001132389463noreply@blogger.com7tag:blogger.com,1999:blog-7356964387844331141.post-1008107791283621172008-12-26T11:08:00.010-07:002008-12-26T13:45:41.849-07:00My first blog post (at least as a scientist)Today I set up three blogs that I am going to start using soon:<a href="http://stevekochscience.blogspot.com/"> Steve Koch Science</a> (this blog),<a href="http://stevekochresearch.blogspot.com/"> Steve Koch Research</a>, and <a href="http://stevekochteaching.blogspot.com/">Steve Koch Teaching</a>.<a href="http://stevekochresearch.blogspot.com/"></a> I'm planning to use this science blog for posts about open science (aka Science 2.0), lab management, or other science professional issues which don't fall in the teaching or research areas. The research blog will be about our research, grant writing, etc. That leaves teaching for the teaching blog. I'm still not sure whether it will make sense for me to have three separate blogs, but I think it may...I'm modeling this after <a href="http://www.blogger.com/profile/06807912674127645263">Rosie <span class="blsp-spelling-error" id="SPELLING_ERROR_0">Redfield's</span></a> <a href="http://rrresearch.blogspot.com/">research</a> and <a href="http://rrteaching.blogspot.com/">teaching</a> blogs. In addition to her blogs, I'm also inspired by some other people such as Maureen <span class="blsp-spelling-error" id="SPELLING_ERROR_1">Hoatlin's</span> <a href="http://twitter.com/HoatlinLab">lab twitter</a> and <span class="blsp-spelling-error" id="SPELLING_ERROR_2">friendfeed</span>, Cameron <span class="blsp-spelling-error" id="SPELLING_ERROR_3">Neylon's</span> "<a href="http://blog.openwetware.org/scienceintheopen/">Science in the ope</a><a href="http://blog.openwetware.org/scienceintheopen/">n</a>" blog, The Science Commons <a href="http://sciencecommons.org/weblog/">blog</a>, <span class="entry-author-name">Pedro <span class="blsp-spelling-error" id="SPELLING_ERROR_4">Beltrão's</span> <a href="http://pbeltrao.blogspot.com/">Public Rambling</a>, and many friends at <a href="http://openwetware.org"><span class="blsp-spelling-error" id="SPELLING_ERROR_5">OpenWetWare</span></a>.<br /><br />What are my goals with these blogs? Well, first, I hope that my opinions and ideas here will have a positive impact on science and issues facing scientists nowadays. Second, I'm looking forward to feedback and ideas from others who read and comment on this blog and making more connections with scientists and others. Finally, I think it will be fun and rewarding (I enjoy this kind of writing compared to, say, grant writing or tenure dossier preparation). I believe it's an amazing time to be a scientist, with the ability to rapidly and efficiently communicate and collaborate with anyone around the globe. As others have noted, scientists on average have tended to be very slow to adopt the new web tools that are available. I firmly believe that Science 2.0 and Open Science (I'm not exactly sure of any definitions of these terms) are by far the best way for science to impact humanity, but I too have been slow to adopt. Blogging is one of these tools, so I'm looking forward to finally taking this step!<br /><br />I have a lot more to say, and much, much more to learn about open science. For now, I'll just mention that my lab participates in <span class="blsp-spelling-error" id="SPELLING_ERROR_6">OpenWetWare</span>, we're big fans of open science, and I think we're moving in the right direction to someday be truly open. Here are some of our <a href="http://openwetware.org/wiki/Koch_Lab:Protocols">shared protocols on <span class="blsp-spelling-error" id="SPELLING_ERROR_7">OpenWetWare</span></a>. Another thing I am very excited about on <span class="blsp-spelling-error" id="SPELLING_ERROR_8">OpenWetWare</span> is a course I teach at <span class="blsp-spelling-error" id="SPELLING_ERROR_9">UNM</span>: <a href="http://openwetware.org/wiki/Physics307L:People">Junior Lab</a>. When I first started teaching this in Fall of 2007, I took a (perceived) gamble and decided to teach the modern physics lab course almost 100% on the wiki. I'll talk more about this on the teaching blog, but I think it's been very successful, and has been a terrific introduction to open science for the young scientists in my course.<br /><br />Finally, I'll just note a couple tools I've been shown in the past few days that are helping me get my s together, professionally speaking:<br /></span><ul><li><span class="entry-author-name"><a href="http://facebook.com"><span class="blsp-spelling-error" id="SPELLING_ERROR_10">Facebook</span></a>. OK, I've known about this for more than a few days. <span class="blsp-spelling-error" id="SPELLING_ERROR_11">Facebook</span>, obviously, is great for reconnecting with people from kindergarten. That alone is worth it. But I'm lately realizing how useful it is for <span class="blsp-spelling-error" id="SPELLING_ERROR_12">communicting</span> with other scientists and / or about science. For example, I made a "page" for our lab, which we can use to communicate exciting results and events with our fans (aka groupies). I've also discovered the "event" tool for coordinating an <a href="http://www.facebook.com/pages/Koch-Lab/38244807238?ref=ts#/event.php?eid=56767847558&ref=mf">outreach event</a>.</span><br /></li></ul><span class="entry-author-name"></span><ul><li><span class="entry-author-name"><a href="http://friendfeed.com"><span class="blsp-spelling-error" id="SPELLING_ERROR_13">Friendfeed</span></a>. I just found out about this the other day. So far I love it, especially as far as science goes. I'm still confused, though, as to why <span class="blsp-spelling-error" id="SPELLING_ERROR_14">friendfeed</span> and <span class="blsp-spelling-error" id="SPELLING_ERROR_15">facebook</span> are separate applications, or whether they're converging to the same thing? They have the same little "f" logo...I suppose I'll figure it out someday.</span><br /></li></ul><span class="entry-author-name"></span><ul><li><span class="entry-author-name"><a href="http://www.google.com/reader/">Google Reader</a>. Previously, I'd tried out <span class="blsp-spelling-error" id="SPELLING_ERROR_16">RSS</span> readers in browsers or in my email and just didn't succeeded in keeping up. I also tried some <span class="blsp-spelling-error" id="SPELLING_ERROR_17">facebook</span> apps which weren't what I needed. Google reader so far seems perfect for me. But on the other hand, I've had a bit more free time than normal, so we'll see how it goes. The key things for me about Google Reader are the abilities to tag and share (which is tied in with <span class="blsp-spelling-error" id="SPELLING_ERROR_18">facebook</span> and <span class="blsp-spelling-error" id="SPELLING_ERROR_19">friendfeed</span>).</span><br /></li></ul><span class="entry-author-name"></span><ul><li><span class="entry-author-name">Oh, and also Blogger (<span class="blsp-spelling-corrected" id="SPELLING_ERROR_20">which</span> I already knew about). This is a really great application. It's funny, though, that the <span class="blsp-spelling-error" id="SPELLING_ERROR_21">wysiwyg</span> editor is really tough for me to use, having grown so accustomed to editing <span class="blsp-spelling-error" id="SPELLING_ERROR_22">MediaWiki</span>. Is there a way to use <span class="blsp-spelling-error" id="SPELLING_ERROR_23">MediaWiki</span> style code on blogger (I'm not good at pure html)? </span></li></ul><span class="entry-author-name"><br /></span>Steve Kochhttp://www.blogger.com/profile/09076719001132389463noreply@blogger.com6