An open letter to the medical community.

I’ve been following the DTC genomics and personalized medicine discussions for years now. I’ve learned that there are diverse and well-reasoned arguments by capable spokepeople proposing many possible futures for the doctor-patient relationship. Discussions during this weekend’s BIL:PIL conference and a recent exchange with Dr. Steven Murphy, with whom I’ve disagreed, occasionally vigorously, for years prompted me to put down my thoughts here. Actual meeting notes will follow in a separate post.

I believe, as does pretty much everyone, that medicine is on the cusp of great changes and that personalized medicine holds great promise. I believe that an informed patient is an empowered patient, and ultimately a healthier one. Every good doctor should want this, and every below-average doctor should pray this day never comes.

Email transcript follows:
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I’m officially looking for another job.

Where I came from

Over a year ago I made one of the biggest decisions of my life. I packed up all my worldly belongings and moved to San Diego to begin working full-time for a small biotech startup. This was a unique opportunity for me because it was a friend who was starting the company, he and I had been speaking over the past couple years about his ideas for a company, they had had me out several years ago during their prototype phase to show me the technology and get a biologists perspective on what a successful product should look like, and I had been doing some consulting projects for them over the past year. At the time, they displayed little understanding of basic molecular biology concepts, but I didn’t think that would be a big deal because they were just starting up and not coming from a biology background, rather an electrical engineering one. I’ve now made another big decision, and that’s to end my relationship with them and move on. Below, I discuss what I’ve learned and what I might like to do in the future. Continue reading

Online Engagement of Scientists with the literature: anonymity vs. ResearcherID

A discussion broke out recently on Friendfeed about online commentary on scientific articles. The discussions were interesting because, for the first time in recent memory, there was disagreement about something fundamental. I view this as an extremely positive sign that out community is starting to grow and incorporate people outside of our core group. In fact, if there’s no disagreement, it’s probably a sign you’re doing something wrong.

The disagreement went in two ways in the two different comment threads. In the second one, genereg promoted the idea that PLoS comments would be more abundant if there was true anonymity afforded to commenters. The other side of the argument, argued by Cameron Neylon(Friendfeed) (LinkedIn), Deepak Singh(FriendFeed) (LinkedIn), and Neil Saunders (FriendFeed) (LinkedIn), was that Real Names™ are important and desirable for online comments. The threads of so many different tangential discussions are running through here that I needed to take a second to write out the background ideologies in play. Continue reading

Science Blogging Benefits Everyone

My colleague David Crotty has a rant at Bench Marks wherein he suggests that Nature’s blogging advocacy is just a shallow attempt to get more content for Nature Blogs, and that scientists blogging is just a fad that can’t replace mainstream media coverage of science and won’t amount to much otherwise. He’s certainly entitled to his opinion, but I think there’s another way to see things and I’d like to present a counterpoint to his Nicholas Carr-ying on.
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I’ve joined Mendeley as Community Liaison.

'Taft in a wet t-shirt contest is the key image here.Reference managers and I have a long history. All the way back in 20041, when I was writing my first paper, my workflow went something like this:
“I need to cite Drs. A, B, and C here. Now, where did I put that paper from Dr. A?” I’d search through various folders of PDFs, organized according to a series of evolving categorization schemes and rifle through ambiguously labeled folders in my desk drawers, pulling out things I knew I’d need handy later. If I found the exact paper I was looking for, I’d then open Reference Manager (v6, I think) and enter the citation details, each in their respective fields. Finding the article, I’d the select it and add it to the group of papers I was accumulating. If it didn’t find it, I’d then go to Pubmed and search for the paper, again entering each citation detail in its field, and then do the required clicking to get the .ris file, download that, then import that into Reference Manager. Then I’d move the reference from the “imported files” library to my library, clicking away the 4 or 5 confirmation dialogs that occurred during this process. On to the next one, which I wouldn’t be able to find a copy of, and would have to search Pubmed for, whereupon I’d find more recent papers from that author, if I was searching by author, or other relevant papers from other authors, if I was searching by subject. Not wanting to cite outdated info, I’d click through from Pubmed to my school’s online catalog, re-enter the search details to find the article in my library’s system, browse through the until I found a link to the paper online, download the PDF and .ris file(if available), or actually get off my ass and go to the library to make a copy of the paper. As I was reading the new paper from the Dr. B, I’d find some interesting new assertion, follow that trail for a bit to see how good the evidence was, get distracted by a new idea relevant to an experiment I wanted to do, and emerge a couple hours later with an experiment partially planned and wanting to re-structure the outline for my introduction to incorporate the new perspective I had achieved. Of course, I’d want to check that I wouldn’t be raising the ire of a likely reviewer of the paper by not citing the person who first came up with the idea, so I’d have some background reading to do on a couple of likely reviewers. The whole process, from the endless clicking away of confirmation prompts to the fairly specific Pubmed searches which nonetheless pulled up thousands of results, many of which I wasn’t yet aware, made for extraordinarily slow going. It was XKCD’s wikipedia problem writ large. Continue reading