Synthesis

Real innovation in scientific publishing

Mr. Gunn — Mon, 10 May 2010 17:02:47 +0000

Many attempts have been made to re-imagine a scientific article, but just adding semantic markup or visualizing the document in a different way has never quite felt right. Previous efforts have felt like they’re just trying to prop up a print idiom whose usefulness is limited in the new medium of the web. Cameron Neylon has come up with a re-imagining that’s truly useful and truly innovative. The idea is to break down a publication into its component parts, so that the smallest unit of publication is no longer a document. This allows publication to move beyond the limitations of the print era and enables the info overload management practices that work best online to be applied to research output.

For me, a paper is an aggregation of objects. It contains, text, divided up into sections, often with references to other pieces of work. Some of these references are internal, to figures and tables, which are representations of data in some form or another. The paper world of journals has led us to think about these as images but a much better mental model for figures on the web is of an embedded object, perhaps a visualisation from a service like Many Eyes, Swivel, and Tableau Public. Why is this better? It is better because it maps more effectively onto what we want to do with the figure. We want to use it to absorb the data it represents, and to do this we might want to zoom, pan, re-colour, or re-draw the data. But we want to know if we do this that we are using the same underlying data, so the data needs a home, an address somewhere on the web, perhaps with the journal, or perhaps somewhere else entirely, that we can refer to with confidence.cameronneylon.net, Science in the Open » Blog Archive » The future of research communication is aggregation, May 2010

This post is about research, scientific publishing

Public anywhere is public everywhere.

Mr. Gunn — Sat, 08 May 2010 23:30:26 +0000

There are three parallel stories flowing past me via Tweetdeck and on Friendfeed right now: One story is about Facebook and their hubristic attempt to declare everyone’s personal information public. Another story is a librarian debating whether it’s OK to write a blog post containing tweets from library users with public accounts. Third is this story about the poor student who had a harsh appraisal of her posted to the internet by her pseudonymous advisor. This blog, named Synthesis, exists precisely to synthesize meaning from these seemingly unconnected events.

About a year ago, I wrote a post about what I had learned in my previous job. It was a thoughtful post where I wrote about some great experiences I had and some rather disappointing ones, and my purpose in writing it was to update my small community of friends and professional acquaintances about the changes in my life and professional status. When Genomeweb linked to my post, I was surprised and delighted. After all, the whole point of keeping a weblog instead of a diary is for other people to read it. I’ve begun to notice a concerning trend, however, of people assuming that content they post to the small community of people they know on social networks is like a whisper – that there’s an implicit assumption that the intended audience will keep the content to themselves and not talk about it to others. This is entirely the wrong way to think about this, and failure to understand this point is setting yourself up for serious trouble later on.

Let’s take the case of BittersweetGirl first. She became upset when Inside Higher Ed linked to her blog. She wrote:

I don’t think IHE knows what it is like to be one of those linked blogs — and it can be disconcerting and sometimes quite upsetting. If you have a humble little blog like mine, to suddenly see a dramatic spike in readers — in numbers that far outstrip the usual blog traffic — is unsettling. There are some bloggers who cultivate a big readership and crave celebrity status, but not everyone strives for that.

This I can understand. The feeling is similar to the feeling you get when you suddenly notice the room has gotten quiet and everyone is looking at you. Instead of taking this as a lesson, however, BittersweetGirl (whose real name is probably not that hard to find) blames IHE for linking to her.

But, what’s worse is that IHE doesn’t seem to recognize that there are some blog posts on topics appropriate for general consumption but some on topics that are deeply personal, maybe even painful…I think IHE may need to be informed of the consequence of their practice and encouraged to be more discerning about what posts they link for their readers.

This is really unfortunate, because if she had learned from her experience instead of trying to blame someone, perhaps she wouldn’t have subsequently posted the following about how she doesn’t think a graduate student she’s advising will be successful:

Jane is not making the progress she needs to make — I can no longer say with any confidence that she can finish her degree in the time frame we had planned — and, obviously, there are serious consequences for the next stage of her career.

Now that this particular opinion of hers has been published not just here, and at Dr. Isis’s blog, but at Technorati and Google and ten thousand other web spiders, it’s part of Jane’s permanent record. BittersweetGirl may blame the people who linked to her if or when her negative public appraisal of Jane affects Jane’s career, but she’s seriously misled to think that posting that on the public web was ok in the first place, pseudonym or not. I’m pointing this out because it’s clear that BittersweetGirl doesn’t understand the ramifications of what she’s done. As a further sign of her apparent cluelessness, she’s disabled comments on the IHE-linked post. If she hadn’t, I might have just left a comment instead of writing a whole blog post about it, but this post needed to be written.

The musings of the non-pseudonymous librarian, Aaron Tay, are a much more benign case. He wondered on Twitter if he needed to ask permission of the people showing up in search results to write a blog post in which their status updates were featured:

Twitter / Aaron Tay: To be exact, what about a … via kwout

The link he posted was to the Booshaka service, which aggregates public Facebook updates. Below is a screenshot taken shortly after his tweet:

Booshaka – Search public Facebook updates… via kwout

Social mores are different in Singapore and they’re more concerned with “saving face”, so I can understand his wondering if he should ask them first, but it’s worth noting that the next major feature coming from twitter is designed to make it easier to do exactly this. When you make something public on the internet, you no longer have any control over it. The social conventions which hold sway in your part of the world are irrelevant because the web is worldwide and there are news stories containing embedded tweets quite often in the US. In the US, we have a saying that it’s better to ask forgiveness than permission. Implicit in this is the idea that opportunities are lost when you spend too much time coming to consensus and trying to please everyone. Aaron Tay lost an opportunity to write a blog post, perhaps not a very important thing, but if writing blog posts is a part of his career advancement strategy, not writing them is a lost opportunity.

Finally we come to Facebook. It will be no surprise to anyone who’s been following me on Twitter that I’m not a fan and I do not like what they’ve been doing. The tragic thing about what Facebook is doing is that it’s going to bring regulation down on the heads of everyone working in social media. Unless you think Senators have a nuanced understanding of social media and can appreciate why it’s not OK for Facebook to make status updates or location public yet it is OK for Twitter or Flickr to do so, then you’ll recognize that any regulation of social media is going to be a bad thing. One could argue here that no one should have posted anything that they didn’t want to whole world to see, but that argument fails when you consider that Facebook offered to manage their privacy for them and then shirked that responsibility when it became clear that the path to riches lay in exposing that userdata. Now the whole industry will suffer from reduced trust and governmental regulation due to their failure. Furthermore, they really missed a trick. There’s a great demand for a trustworthy and easy to use service that gives people control over their online profile, and they would have been a shoe-in for such a provider. That would have been the route to even greater ubiquity than Facebook Connect. Instead, Facebook is raining hot wax all over us like a malevolent Icarus.

The thread that ties all of this together is expectations of privacy. Simple expecting your wishes to be honored isn’t enough. The content will be around longer than you will, the content will be seen by people you couldn’t even imagine seeing it, and even if you’re told that it’ll only be shown to a limited audience, that can change, leaving you with little recourse.

I propose three things to ease the pain of future events like the above. First, understand that anything you put on the public web can and will be used in ways you couldn’t imagine. It will outlast you and any legal regime that might currently exist. Second, understand that you don’t have any right to blame anyone for any use they make of data you’ve made public. If you make your desires known, people will generally obey them, but there’s no guarantee they will or recourse if they don’t. Taking an active role in presenting and maintaining your public web profile helps ensures that what people see is what you want them to see. Third, give people the benefit of the doubt. Many people have made mistakes and exposed stuff publicly about themselves or others that they didn’t intend, so give ‘em a break. Don’t come down hard on people posting pictures of themselves doing things that are legal and accepted in their social group, even if they’re disapproved of in yours.

_{I remain convinced there’s much more upside than downside to having a public presence on the web. I got more job offers extended to me after writing my blog post about moving on than I would have gotten had I not written it, and the linkage from Genome Web’s horde of readers certainly didn’t hurt. LinkedIn remains a great source of opportunities for me. My former employer, on the other hand, didn’t like how my blog post was the top link on Google for their name. I later removed their name when they asked. Also, if I were single and female, I might feel differently about exposing so much information, but if I were and did, I would be my responsibility to not expose that information.}

This post is about archiving, career, culture, facebook, mentorship, privacy

If I published in or reviewed for PLoS, I’d be pissed off too.

Mr. Gunn — Fri, 30 Apr 2010 22:50:43 +0000

Cameron Neylon responds to the allegations that PLoS is a pay-to-play vanity press:

That an author pays model has the potential to create a conflict of interest is clear. That is why, within reputable publishers, structures are put in place to reduce that risk as far as is possible, divorcing the financial side from editorial decision making, creating Chinese walls between editorial and financial staff within the publisher. The suggestion that my editorial decisions are influenced by the fact the authors will pay is, to be frank, offensive, calling into serious question my professional integrity and that of the other AEs. It is also a slightly strange suggestion. I have no financial stake in PLoS. If it were to go under tomorrow it would make no difference to my take home pay and no difference to my finances. I would be disappointed, but not poorer.cameronneylon.net, Science in the Open » Blog Archive » In defence of author-pays business models, Apr 2010

You should read the whole thing.

This post is about open access, PLoS, publishing

No Twitter at ASCB

Mr. Gunn — Sun, 06 Dec 2009 22:38:02 +0000

An anonymous source has informed me that the ASCB has banned “replication of data” by visitors, but has presented Twitter as the poster child of conference data leaks. No word on whether ASCB attendees will be subjected to memory scans upon exit. The sign says:

Twittering and other forms of communication involving replication of data are strictly prohibited at all sessions, in the exhibit hall, and all poster sessions.

This post is about ASCB, conferences, fail, twitter

An open letter to the medical community.

Mr. Gunn — Tue, 03 Nov 2009 22:47:37 +0000

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:

Where Dr. Murphy and I differ is in the regulation of medical tests, diagnostic or otherwise. Why should diagnosis (the test + the interpretation thereof, sans recommendations) be considered to be treatment? Certainly insurance companies shouldn’t pay for quack treatments, but getting a test, even having the result of the test explained to you, isn’t a treatment for anything.

The laws were written back when people didn’t necessarily want to see the raw data because they wouldn’t have known what to do with it if they had it, and the tests were inaccurate enough that they didn’t mean much on their own anyways. That was a good reason to make doctors the gatekeepers, but that’s all changed now.

People neither want nor need a gatekeeper now. It’s not about self-treatment, it’s about empowerment. Patients should be empowered to understand what’s going on with their disease or condition or lack thereof, and they should be empowered to ask better questions. Every good doctor wants their patients to be empowered like this. The only thing total release of all information and interpretive notes, medical or otherwise, would do is reveal which doctors are the good ones who stay up-to-date and which are the slackers.

Patients might get together and discuss their tests and decide as a group that they’re going to undertake some quack treatment, but they might also get together and discuss their tests, bring their concerns to a good doctor, and he might realize that “Gee, maybe we should tell myeloma patients undergoing treatment with Zometa to avoid invasive procedures on their jaw.”

There’s upside and downside risks to these kind of patient rights, but Gilles Frydman at ACOR is an example of how to do this in a way to minimize the downsides while maximizing the upsides. They’ve published a study of how this works here. In short, an informed patient is a healthier patient when they’ve got a community like that. Take a look at what they’ve done at ACOR and you might realize the assumed or historical risks of self-treatment pale in comparison to the benefits that tens of thousands of patients are seeing today.

Things have changed and the medical establishment needs to get ahead of the curve on this one, or they risk losing the trust and respect they’ve been afforded for so long. In fact, it’s this loss of trust that has provided an opportunity for the dangerous quack treatments you see today among autistic parents, for example.

Please, in your advocacy of personalized medicine, abandon the paternalistic model. Seek to empower patients and regain the trust our profession has deserved for so long. Don’t let mistrust and arrogance leads patients away into the arms of the quacks.

Sincerely Yours,

William Gunn

Further reading:
In Iran and in the US Health Care System, Citizens’ Access to Computable Data Frees Everything!
It’s my genome: should researchers be obliged to return genetic data to research participants?
A Mom Brokers Treatment for Her Twins’ Fatal Illness
Participatory Medicine

I’m officially looking for another job.

Mr. Gunn — Mon, 07 Sep 2009 21:07:55 +0000

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.

The opportunity was a unique one because my whole lab was moving to another state, and I was done with experiments, so it didn’t make sense to move with the lab just to finish writing things up. Although there were tremendous social ties holding me to New Orleans, I was preparing to leave for a post-doc anyways when they invited me out to San Diego. I figured it would be just as easy to finish writing my dissertation in San Diego as in New Orleans, so I jumped at the chance.

Where I went

The situation when I arrived was interesting. They had moved out of the garage I last saw them in to a real lab, with chemicals on the shelves and pipettes on the benches. More importantly, they had some working prototypes running. My job was going to be to take charge of the assay development and to manage the lab. Now, at a small company, the hierarchies are essentially flat, because everyone needs the expertise of everyone else pretty much at all times. The team wasn’t so big that we couldn’t all gather together in the meeting room and discuss whatever we needed to.

I loved the freedom of being able to come up with a plan and pursue it, and it was great knowing that I was working on important problems. It was also very cool being surrounded by fantastically talented people from fields quite different from mine. In fact, the first challenge I faced was getting the respect of the others. At a small startup, it becomes very obvious when someone isn’t pulling their weight. However, because the problems you’re solving are always changing, the needs of the company are always slightly shifting as well. My joining the team was part of an overall re-organization of the company to refocus now that the needs had shifted away from their starting point. I didn’t realize this immediately, but I was actually replacing someone in some capacities, with the hope that the tasks which were tangential proficiencies of the existing employees were more direct competencies of mine.

This being my first professional job in biotech, (not my first non-academic job, but I’ll spare you that part of my biography) there was a lot to adjust to. I learned that there are many differences in how groups communicate in academic and industrial settings. The other team members need to feel that you’re confident, because they don’t always have the background that your lab mates may have had to dig into your science and ask critical questions. Additionally, they don’t expect the level of criticism that’s common in a meeting with your lab mates. Of course, the goals of a company are to get to something serviceable as fast as possible, not to find The Truth™, and that’s actually not unappealing to me. As much as I remain committed to The Truth™, I also like doing things which are technical and applied. At a startup or small company, it’s possible to both have a relatively short-term impact on how science is done or how care is provided, yet at the same time be part of the infrastructure for more fundamental contributions. Being quite used to the graduate school schedule, I immersed myself in the work and comfortably worked 12 hour days and weekends and even pulled an all-nighter or two before an important meeting. Perhaps obviously for those reading along, I became so immersed that 5 months later, I hadn’t so much as looked at my dissertation.

I don’t know what sort of schedules my readers work on, but 4-5 months is when I entered a reflective phase. I was somewhat satisfied with what I had been able to contribute, I felt like I had achieved the respect of many of the team members, and I was particularly happy to have been able to bridge the engineer-biologist gap that existed prior to my arrival. Getting the whole team to speak the same language remains one of the accomplishments I’m most proud of. Teaching the language and concepts of a empirically-based science like molecular biology to a bunch of engineers with physics and computer science backgrounds is not easy, let me tell you!

This time was also a sort of breakpoint we had discussed internally in terms of my stake in the company, so it was time to make some decisions. When my wife delivered the happy news that our first child was due towards the end of the year, it became even more clear that all the loose ends in my life needed to be tied down. I had the following issues to deal with: I needed to finally finish writing up and defend, I needed to find us a living situation more conducive to raising a child, and I needed to have a serious discussion with the company founders about my future. I began working more normal hours, so I could finish writing up and defend. Writing for a couple hours here and there on nights and weekends just wasn’t getting me anywhere. Even as the pace began to pick up at work, I finished my dissertation and prepared for my defense, dropping essentially everything else. If it wasn’t for the selfless support provided by my wife during this time, our life would have probably unraveled entirely. Next, we moved from the loud, noisy, and somewhat juvenile neighborhood where we first landed in San Diego to a quieter neighborhood. Finally, I tried to get some clarity and commitment from the company regarding my long term prospects for advancement and career development. They assured me that I was a valued member of the team, and promised that as soon as they closed this next deal, which was practically a sure thing, everyone would get raises and bonuses and options and all that.

What happened when I got there

As I mentioned above, the needs of a small startup are ever-changing. I found myself spending more and more time doing things where I couldn’t draw from my background, experience, and training. I think I’m a pretty smart guy and a quick study, and I love learning new things, so always having to learn something new wasn’t a problem for me. However, when I stepped back and looked at where things were going, it just wasn’t where I wanted to go. It wasn’t where I could bring my knowledge and skills to bear most effectively, so I wasn’t setting myself up for success. Nor was I setting myself up for failure, but irrelevance? – perhaps. As fun as it was being in that diverse environment, it was also a little isolating. As each sure thing materialized and then evaporated again, I considered applying for a postdoc just to have colleagues again, but I’ve known some 30-something post-docs with children, and there was always a slight whiff of desperation coming from them.

I still believe that the company will do very well, but I had to make a decision between staying with the company, drifting further away from my optimal career path, and possibly showing up one day to find the doors closed or starting now to look for another position in a very tough job market. I picked the second choice because that at least put my fate in my own hands. My leaving was in no way a vote of no confidence in the company. If I was still a single unmarried guy with no kids, I’d probably still be there.

I had been a part of the San Diego Biotech Network since shortly after I came to town, thanks to Mary’s engaging twitter presence and inclusive and generous demeanor, so I knew how hard it was going to be to find another job. I had seen many of the same people at the SDBN meetings, month after month. I began actively applying for positions, but at the same time I started thinking about other possible opportunities, and now I find myself with a variety of loose ends again.

Where to now?

I enjoy working a few hours a week with Mendeley, helping to make introductions between the academic community members who are looking for some solutions that Mendeley provides, and the Mendeley team who want to know what are the as-yet unmet needs of the academic community. As I’ve said before, I think these guys have the potential to transform how research is communicated and how scientists collaborate and there’s a good chance they’ll do just that.

I also enjoy writing about scientific and social issues, particularly ones brought up as the cultures of traditional publishing and the online open access web collide. I’ve had some offers to blog at various outlets and although I would love to take them all up, I can’t yet find a way to do that as more than just a hobby. There’s certainly enough interesting stuff going on around here that I could keep myself busy, though.

Last but certainly not least, I really enjoy doing research, and there’s a local company(should I say?) who has just started a project doing almost exactly what I did for my dissertation. I’ve spoken to people at the company and am currently trying to convince them they’d be crazy not to at least have me in for a talk. They’re large enough that they’re probably not going anywhere soon, yet small enough to give me the chance to be involved in some really groundbreaking work. Not to mention, they’ve assembled a fantastically talented team that I would love to be a part of.

So that’s where things lie at the moment. I have a PhD, I have two years of biotech industry experience, I write fairly well, I have a good number of connections in academia, in publishing, in research, and I’ll have a daughter pretty soon. Hopefully I’ll have a new job soon, too. It’s been quite a year.

This post is about career, job, me, mendeley, sdbn, work

The effect (on one person) of pulling tweets into friendfeed.

Mr. Gunn — Wed, 02 Sep 2009 06:52:14 +0000

Does adding tweets to friendfeed affect twitter followers?

With the announcement of Facebook’s acquisition of Friendfeed, I decided to start pulling my tweets into friendfeed. The results were interesting.

Why did I do this?

I did this because Facebook bought Friendfeed and everyone I read expected this to pretty much mean the end of Friendfeed as we knew it (and I still think it does), so I wanted to advertise the new focus of my social network activity. I had not done this in the past because I found that it made for a very noisy friendfeed and because I rather expected an @reply to a tweet than a comment on it in friendfeed. I expected this to shift a small number of subscribers from friendfeed to twitter followers, however what I actually found was a very weak effect on both sites.

How did I analyze the effects?

First, I used Twittercounter to get a graph of my twitter follower history and I compared it with the follower history of Neil Saunders, another person in my network with a similar number of followers and approximate level of activity. Referencing my follower trends to a related person helps indicate which are twitter-wide events (or twittercounter hiccups) and which are specific to me.
Next, I got my Friendfeed subscriber number trends via Feedburner. Because I hadn’t written a post in a few months, my feedburner stats reflected almost exclusively my friendfeed subscriber trends. I couldn’t get a reference graph for FF subscriber numbers like I did for twitter followers, but if you’d like to take my data and overlay it with yours you can download the .csv.

The results

The friendfeed-facebook announcement was made on August 10th, and I added twitter as a service on that day.

You can see that there’s a very slight dip on that day, but there was essentially no change. You can also see that both Neil and I are fairly aggressive about weeding out our spam followers, looking back at the Great Twitter Spam Attack of July.

The friendfeed subscriber trend remained basically unchanged as well. There’s a sizeable dip a couple days after the 11th, long enough for people to get annoyed and unsubscribe, but the numbers bounced right back with a couple days. I don’t know what the two previous spikes were, but in my experience with Feedburner it’s not unusual for your subscriber numbers to be abnormally low for a day or two and then recover.

What does this all mean?

Not a whole heck of a lot, I don’t think. While it confirms my hypothesis that it would annoy some of my friendfeed subscribers and drive them away, the effect, purely based on numbers, wasn’t very large. Checking my email for new subscriber emails since the 11th confirms that the recovery was from new subscriptions on friendfeed (from good people, too!) not feedburner weirdness or a sudden unexplained bump in RSS subscribers. The blip on the very end of the friendfeed graph could have come from some recent messing around I’ve done with my google profile, or it could be from some emailed-but-not-yet-blogged-about stuff that I’ve been doing. I’ve now removed twitter as a service again.

This post is about analysis, friendfeed, stats, twitter

Protected: Fate and Stemgent SDBN Video

Mr. Gunn — Thu, 27 Aug 2009 05:36:25 +0000

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

Mr. Gunn — Sun, 24 May 2009 20:21:52 +0000

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.

1) Online participation depends on lowering the barriers to participation, and unlogged anonymous comments lower the bar to the absolute floor.
2) Online participation depends on a functioning ResearcherID system so commenters can actually get credit for taking the time to write a comment.(Related Blog posts from neilfws, Martin Fenner, Deepak, Peter Murray, and others on friendfeed)
3) Some people don’t want to sign their name to a critical comment, so they just refrain when they don’t have the anonymous option.
4) People comment where there’s a community in which their comment will get exposure and contribute to a discussion.
5) Comments attached to scientific articles aren’t for the purpose of stimulating discussion, but for aiding interpretation of the paper in subsequent years.

It’s apparent that there’s a little bit of talking past one another regarding these points, which is why I’ve collected and laid out the arguments here where they can each be commented upon. My initial impression is that comments as part of a discussion will mostly be made wherever there is community, which isn’t PLoS at the moment. However, comments intended to be interpretive aids for the paper will be made on the PLoS site, and registration won’t be much of a barrier for someone sufficiently motivated to write such a comment in the first place.

In the first thread, which developed more subsequent to the discussion on the second, Ian York (FriendFeed) (LinkedIn) commented that he felt it was rude to take his throwaway comment on friendfeed and re-post it on PLoS. Björn Brembs (FriendFeed) (LinkedIn), Bill Hooker (FriendFeed) (LinkedIn), and Cameron Neylon then pointed out that anything posted on a public site is pretty much free for the taking whether anyone likes it or not. The issues I’ve identified here are as follows:

1) Don’t make a public comment if you don’t want the whole world to hear it. This is especially true for comments to the media, which none of the members of this thread are (or are they?)
2) People will comment in different ways in different places, and, while linking to one from the other is always possible and always within the rights of anyone to do, it may occasionally be rude.
3) Deliberately taking someone’s comments out of context is rude.
4) You get the broadest view of reactions to an article if you don’t limit yourself to comments posted directly on the site, but rather go and find comments in the communities where they’re being made.
5) PLoS could have more comments if it went and found the comments in their communities, instead of expecting the comments to come to them.
6) It’s not technologically feasible to get permission to index every tweet or friendfeed comment made by everyone.

It’s apparent that some of these ideas are also in conflict with one another. To resolve some of these issues, perhaps it would be helpful to view them in light of yet more general issues.

1) Technology should adapt to people, not the other way around.
2) Online, your identity is your content, not your Real Name™.
3) Free and open sharing provides the greatest good for the greatest number.

I don’t believe these ideals are in conflict with one another. All we have to do to make this work is to find a way to aggregate things and re-share them such that context is preserved. As the friendfeed redesign made clear to most of us, tweets are totally different items than blog posts. I think it’s a UI issue. On the right, you’ll see a sidebar containing my most recent tweets. Would a sidebar on the article containing “aggregated commentary about this article” with short snippets and a link out sufficiently respect the need for maintaining context while also respecting that viewers of the article want to see the broadest picture of the engagement with the content as possible?

What is most fair and logical is rarely what happens. The system promoted by the guy with the greatest motivation or most money is generally the one that wins out, so perhaps that can lend some perspective to this discussion.

This post is about commentary, friendfeed, open access, PLoS, ResearcherID

Science Blogging Benefits Everyone

Mr. Gunn — Wed, 25 Mar 2009 07:12:45 +0000

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.

When I hear people complaining about blogger bias or twitter banality, my response is that they’re reading/following the wrong people, so let me help him out here:
Steve Koch is pioneering the field of Single-molecule genetics and has interesting stuff to say about the life of a young assistant professor.
Cosma Shalizi has been blogging since before the term was coined about complex systems.
Mark Chu-Carroll makes math and programming fascinating, and he works for Google.
Ben Goldacre certainly fills a niche that mainstream journalists either can’t or wont fill – that of debunking pseudoscience.
Michael Nielsen‘s post on Statistical Machine Translation was written as he’s learning, making it a perfect intro for someone else wanting to learn about the area.
Though certainly not free of opinion, Bart Laws has one of the best and most accessible explanations of sensitivity and specificity I’ve ever read, and lots more about health policy.
Blake Stacey writes entertainingly about string theory (no mean feat) in his blag.
Sean Carroll got 241 comments on his short post about Garrett Lisi’s Theory of Everything, including active participation from the author of the paper under discussion, and also wrote this post about why scientists should blog back in 2006.
Just about everything Ian York writes (not including the pictures of his kids) is not only accessible, but fascinating and relevant to my own work, as well.
Then there’s the Bayblab, who may be just a bunch of degenerate graduate students, but cover science news better and more in depth than all of the mainstream media science writers put together.

I’m going to have to stop here before I repost my whole blogroll, but I think you get the point. Stop whining, start reading.

Now, I can’t speak towards Nature’s motivations for encouraging blogging, but I do think they have something to gain from a more efficient peer-review process, and are sufficiently incentivized to encourage anything that looks like it might help. I made a comment on one of the Nature blogs regarding peer-review reform and someone found it and emailed me to ask if they could put it in the print issue as a correspondence, which is suggestive, at least, that someone there agrees with that sentiment. At any rate, Sean Carroll’s post had plenty of company when he wrote it back in 2006, so I trust he’s clear of the aspersions Mr. Crotty is casting.

Dispassionate and accurate journalism from people who studied journalism is all well and good, but as they’ve mostly abdicated their responsibility to educate the public on scientific issues (vaccines, evolution, and global warming are but recent examples), someone needs to step up, and if actual scientists can’t fill that gap, I don’t know who will.

This post is about journalism, publishing, science blogging

I’ve joined Mendeley as Community Liaison.

Mr. Gunn — Wed, 18 Mar 2009 14:00:57 +0000

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.

Needless to say, the more I tried to do it right, the further and further away I got from having the manuscript completed. I ended up with a enormous Reference Manager library, only some of which was relevant to the paper or the section I was currently composing in Word. At some point in my Googling for solutions for the the myriad little annoyances I had during this process of knowledge (mis)management, I stumbled upon Alf Eaton’s Hubmed. Not only did it free me from the propellerhead search interface of Pubmed at that time and reduce the amount of clicking required to get a reference, but it turned me onto his blog, his parallel, but far more sophisticated, approach to the same problems I was having, other people who were also trying to do it right, and eventually Connotea. In short, they showed me that there was a better way. Now I could build a library, tagged by keyword, and thus only download the particular set of papers I needed at the time into a new Reference Manager library, which was still necessary for the actual writing and formatting of the bibliography in Word. Now things were looking up. I had found something that allowed me to leverage one of my strengths, lateral thinking, and still achieve the order necessary to find a specific item when I needed it.

The idea that there is a better way is an insidious one, though, and once I realized that it might actually be possible to use open source software for the whole process, I no longer had that excuse for using Reference Manager/MS Word. I learned about LaTeX, Zotero, metadata, and the semantic web. After more work requested by the reviewers, the paper eventually came out in 2006, and was submitted from my brother’s computer while I was evacuated from New Orleans for Hurricane Katrina. It was entirely written using MS Word and Reference Manager, because the journal required Word, and because Zotero couldn’t pick up cleanly from where Reference Manager had begun. The different version of Word and the lack of Reference Manager on my brother’s computer caused much difficulty in the edits needed to incorporate the additional experiments asked for by the reviewers. Knowing there was almost a better way that would actually work for me and the publishers made it all the more painful.

Subsequent papers and grant proposals were written using Connotea + Zotero, but as Zotero became more useable, Connotea became less. I attempted to share what I was learning about these new tools for doing and communicating science with my colleagues in the lab who were having the same issues and solving them in their own ways, but the activation energy to get them going with Connotea² was too high for something that was still missing that bit of UI polish a mass appeal app needs. Citeulike just had too embarrassing of a name for me to recommend. 2collab was an interesting development, but wasn’t quite good enough for me to switch from Connotea. Less people used it and it wasn’t becoming part of the ecosystem like Connotea and Citeulike. The missing link was still integration with Word, because while Zotero’s word integration became better, the moving of information from the online services to Zotero was fraught with difficulty. A particular problem was that although these programs had been designed with tagging specifically in mind, the data exchange formats(.ris) were from the pre-tagging era and there wasn’t agreement on in which field tags should be put/found. Where URLs should be stored was another issue. Connotea had an API, but none of the other citation managers used it. My efforts dealing with this can be seen in the comments below my post on Connotea. Because by this point I had drunk deeply of the Semantic Web Big Data Open Access Collaborative Filtering Kool-aid, served in large glasses by the likes of Deepak, Peter Suber, Cameron Neylon, and JC Bradley, I was no longer content with online bookmarking of stuff; I wanted a dataset that I could do something with. I wanted recommendations and discovery and cool visualizations. I wanted serendipity.

Mendeley may not be open source, and it might not get everything just right, right now, but I think they’re heading the right way. I think Victor and Jan get it, and I asked them, subsequent to the discussion around my last post on a killer app to drive adoption of social networking among scientists, how I could help drive the adoption of their approach. I see this as taking market share away from Endnote, and promoting use of tools which help generate Big Data among people for whom social bookmarking is a total non-starter. I’m excited about the pace of developments in this space and more optimistic than ever that we’re finally starting to get some traction, moving towards a new way of collaboration that will finally start to transform the way collaboration, research, and publishing is done for the whole field.

Please remember that this is still my blog, and my opinions are still my own. Not only that, but my opinions are attained through reading and interacting with the group of early adopters than I’ve come to know and depend on ever since that first irritation-induced foray into this space, so long ago¹. Then read this short and fantastic story by Hari Kunzru.

1. Centuries ago, in internet time
2. Switch to Firefox – easy, incorporate Connotea into their workflow – hard

This post is about big data, citation management, citeulike, connotea, mendeley, open access, publishing, reference manager, science20, semantic web, social networking, Zotero

Twitter Weekly Updates for 2009-02-22

admin — Sun, 22 Feb 2009 18:12:00 +0000

If it’s just hosting you need, I’ve got way excess capacity in my dreamhost account. I’d be happy to set you up… re: http://ff.im/ZB7T #
Twitter Updates for 2009-02-15 http://ff.im/14tNd #
Nice summary! re: http://ff.im/14eMe #
Wow. I understand wanting to avoid eye-strain and all that, but it is an electronic device after all. How hard… re: http://ff.im/12PKx #
The main difference is that a quiche is made from egg custard, whereas a fritatta is usually just egg, without… re: http://ff.im/14kHk #
Liked “Genetic Future : The 1000 Genomes Project is holding back genetics!” http://ff.im/14cTx #
Will it take the media as long to realize they lost the speed battle as it did record co’s to realize they lost the digital content battle? #
Surely a switch to turn on a backlight for those times when you don’t have natural daylight wouldn’t have been… re: http://ff.im/12PKx #
Hopefully this doesn’t get too recursive. I’ve already got double entries showing up on twitter for some… re: http://ff.im/14tNd #
Liked “In the rain shadow of Big Science” http://ff.im/14trG #
RT @NobelIntent: Science gleans 60TB of behavior data from Everquest 2 logs – http://ping.fm/81ud8 (mrgunn:to glean, that is.) #
The problem with Digg-style interfaces to science literature is that I don’t care what’s hot “in science” I care what’s happening in my area #
See http://tinyurl.com/dm37xv Good for journalists, not for researchers. #
Not exactly, vellino. I was thinking of something more along the lines of a recommendation engine. re: http://ff.im/14sDx #
I’ve tried Synthese, and it’s a serious effort, but it seems the interface is missing some key components. For… re: http://ff.im/14sDx #
10,000 maybe? re: http://ff.im/14xMq in reply to attilacsordas #
How many of the GOP desired amendments were there explicitly to be “poison pills”? Likely story they want… re: http://ff.im/14pSF #
I’m not sure where you’re misunderstanding lies, Wobbler. Yes, it is just a tool for digitally signing stuff on… re: http://ff.im/ZuN4 #
That’s right, Cameron. To put things a different way, “What can we learn about the two approaches applied to… re: http://ff.im/12Ud1 #
Liked “The need for a clear identity to aggregate contributions – openid, researcherid etc” http://ff.im/v6aF #
Judgmental heuristics — Knowledge beyond words http://ff.im/14Bcb #
I’ve mentioned to Victor/Mendeley that this would be a cool direction to go, and it’s exactly the kind of thing… re: http://ff.im/12Ud1 #
FUCK! My flickr login has expired, I have no clue what garbage I gave yahoo, and I can’t simply get a password reset email #
I don’t know if it’s the new firefox or what, but my logins are expiring all the time now. #
Ah, found an old email with the ID in it. Still sucks that you can’t just give the email to get a pw reset. #
Yesterday some guys tried to sell us steak from a delivery van. Went around knocking on everyone’s door. No… re: http://ff.im/14Lua in reply to neilfws #
FYI – If you get held up by the registration prompt, enter the URL(just up to, not including, the ?) into a… re: http://ff.im/15oey #
RT @NextGenScience: Synthesis http://twurl.nl/djeih6 (me) Xythos – Online Document Management http://twurl.nl/awowuv #
This is perhaps going to sound perverse, but I’m actually starting to *like* MS Project. #
Liked “A human-scored research paper recommendation engine?” http://ff.im/15hdD #
I left my comments on your blog, Victor, but basically I think the “paper pages” idea is spot on. The kind of… re: http://ff.im/15hdD #
Rating, in the sense of giving a numerical score to, never seems like it gets much use at the sites where I’ve… re: http://ff.im/15uCR #
Liked “We Will Become Silhouettes by The Postal Service” http://ff.im/15u9M #
“As such, this information measure identifies and quantifies those protein concentrations that render the… re: http://ff.im/15ulZ #
Liked “The miners strike again – but these are text miners… | Professor Douglas Kell’s blog” http://ff.im/15ulB #
What an amazing collection of links! Particularly http://celldesigner.org/payao/ re: http://ff.im/15ulB #
http://tinyurl.com/aw6pt6. looks promising, but I don’t use… re: http://ff.im/14Gcz #
Paging Roubini, Mr. Nouriel Roubini, to the thread, please. re: http://ff.im/13Z7d #
Liked “Facebook Change of Policy: Why You Should Care « Pixel Bits” http://ff.im/15rb2 #
Liked “Bill Clinton: I should have better regulated derivatives – CNN.com” http://ff.im/15iTi #
bash him if you must, but do you think we’ll ever see the most recent past president say something like, “You… re: http://ff.im/15iTi #
Strange that photography becomes a terrorist act precisely when they’re installing CCTV cameras everywhere. re: http://ff.im/154kz #
40-50 votes doesn’t quite seem like enough, but if it’s restricted to people who share a common interest… re: http://ff.im/13DCE #
Liked “open access: (too) much emphasis on text, not enough on data?…” http://ff.im/152rC in reply to tlemberger #
Is anyone really surprised about this from the company that brought you Beacon? re: http://ff.im/15rb2 #
Liked “Google Health, IBM: real-time, vital medical data stream” http://ff.im/UsAg #
RT @RickyWhy: Citizen ideas to cut the San Diego city budget (sell beach drinking permits, etc)) http://tinyurl.com/c6zohv #
There are some developing standards for reporting data on many kinds of experiments…. re: http://ff.im/152rC in reply to tlemberger #
Liked “In which I ramp up – Mind the Gap – Jennifer Rohn’s blog on Nature Network” http://ff.im/15Dfj #
Liked “The quest for a definition of the term ‘consciousness’ (page 94) Nature Network” http://ff.im/15uuj #
Everything depends on a red wheelbarrow re: http://ff.im/15uuj #
There’s no way with today’s level of audience that a blogger could make the same amount of money, but if we’re… re: http://ff.im/15xHJ #
I read through all this just to make sure no one said, “The Secret”. re: http://ff.im/15gYd #
sent re: http://ff.im/15K0g #
Liked “AIDS: ‘Major advance’ seen in revolutionary gene therapy – Yahoo!7 News” http://ff.im/15Kd4 #
Amazingly, Yahoo even gave the names of the people and the journal the article was published in. re: http://ff.im/15Kd4 #
Dr. Centeno certainly doesn’t sound like a crackpot, but if he can do what he’s doing, any crackpot can too, and… re: http://ff.im/15LvH #
Time for dinner: http://www.joeyssmokinbbq.com/ where they have SWEET TEA!!1!!!1!!one!!!WTFBBQ!!! #
Funny to hear people out here talk about tickets for Mardi Gras. By Mardi Gras, they apparently mean “Gay Parade”. I miss New Orleans. #
Finally have my RSS reader back up and running(just can’t do google reader) and suddenly feeling like blogging again – funny how that works. #
You know what I REALLY love? When a long multi-field form interprets “Enter” as “submit the whole page” instead of go to next field. #
Float position river side – float 18 – on top. Holler “Throw me something Mister Gunn!” on Sunday!! #
Claim for Mr. Gunn aka William Gunn http://ff.im/15Se1 #
Finally! OpenID doing what it’s supposed to do. Check out http://williamgunn.pip.verisignlabs.com #
Personal Identity Portal (PIP) – OpenID page for William Gunn http://ff.im/15TOL #
Liked “Shirley Wu has to be one of the coolest people I have yet to meet. Her FriendFeed says it all:…” http://ff.im/16oTV in reply to gotgenes #
Liked “Heavy Atoms, Heavy Profits?. In the Pipeline:” http://ff.im/16gxK #
Thanks for the update. I look forward to your post. re: http://ff.im/MoYx #
Liked “Please let me know if you are aware / could recommend / want to be a mentor of any bio-related project which…” http://ff.im/165rz #
Liked “It happened _again_: tried to login on a site (i.c. ensembl) and can’t because it username is my old email…” http://ff.im/16o04 in reply to jandot #
Liked “Does the Journalist’s Creed need to be updated for the 21st Century?” http://ff.im/16sVx #
Liked “Is academic research a bubble?” http://ff.im/16sWd #
There’s a lot that felt really wrong about this, until I noticed that someone was actually just complaining… re: http://ff.im/16sWd #
Liked “Some Datasets Available on the Web » Data Wrangling Blog” http://ff.im/16nfV #
Liked “How to fund investigative digging: huge issue. But http://is.gd/jhfJ says much of the banking meltdown was…” http://ff.im/16p2w in reply to jayrosen_nyu #
A couple people were calling it, but they weren’t listened to. How to overcome bad news anti-bias? re: http://ff.im/16p2w in reply to jayrosen_nyu #
Well, yeah, biomed isn’t without it’s crap, but the argument that a result is valuable only because it’s… re: http://ff.im/16sWd #
Liked “Scientific workflow design for mere mortals” http://ff.im/16u51 #
Mere mortal with access to the article, that it. re: http://ff.im/16u51 #
Beyond the Impact Factor: a new, multifaceted view of journal performance http://ff.im/16vOT #
Oh look! Someone (@Adam4004) has turned down the AM talk radio, quit harassing PZ for a sec, and learned, kinda, how to use twitter. #
RT @shwen: Nice! Have bn waiting for this – RT @Zee: Tweetdeck adds a killer feature: username auto-complete http://ff.im/-16Bvq #
Liked “Modern Collaboration” http://ff.im/16Cf5 #
We’ll have to disagree on this one, dekay. re: http://ff.im/16vVJ #
RT @ernieattorney “_______ seems like a good idea, too bad there are so many legal hurdles to surmount.” #
RT @RickyWhy: “Browsing a newspaper is rewarding and serendipitous, and doing it online should be even better.” http://tinyurl.com/dnycfc #
RT @drkiki: Enjoying this: http://booksthatmakeyoudumb.virgil.gr/ (mrgunn: this was made before “the secret”) #
Getting ready to head over to the SDBN networking event: http://tinyurl.com/c9a6uy #
Deepak’s on to something here. Digg kinds sucks for science, and it has a lot to do with the readership as… re: http://ff.im/13DCE #
Liked “Digg-style biotech news site” http://ff.im/13DCE #
Trying, again, to explain to engineers the mysterious concept of a negative control. #
He spends a lot of time making the argument that domains are in general untrustworthy and subject to change to… re: http://ff.im/16BBg #
Liked “Interview with Geoffrey Bilder – Gobbledygook – Martin Fenner’s blog on Nature Network” http://ff.im/16BBg #
I am coming around to his way of thinking regarding random string (opaque) identifiers as opposed to human… re: http://ff.im/16BBg #
Oh the stuff we still don’t know. re: http://ff.im/16IDw #
Liked “Paper writing and online tools – a test – A(frican) Blog of Ecology – Raf Aerts’ blog on Nature Network” http://ff.im/154xY #
RT @JeffHoard: Breaking…. Mahalo Answers to offer money for every best answer…. http://is.gd/k0Xj #
That’s a useful development. Identifiers and authentication rears its head again! re: http://ff.im/17ql8 #
RT @seriouseats: Truly awful seafood display at Whole Foods: http://is.gd/k1Mn [Via http://tinyurl.com/dxjyvc #
Yes, you're right there's a disconnect and where something is published does make a big difference re: funding.... re: http://ff.im/16sWd #
I talked to more than a few people in drug discovery last night, and they all seemed to know someone how has or... re: http://ff.im/16gxK #
I've wanted to do this, because it's quieter and faster, so let me know what you find, Andrew. re: http://ff.im/17DMR #
Liked "Widespread bidirectional promoters are the major source of cryptic transcripts in yeast" http://ff.im/17BMa #
Wow, Brian Bernstein is getting hosed. re:http://www.idontcare.com/acs/ re: http://ff.im/15VuI #
Liked "Is boycott best? :The Scientist [18th February 2009]” http://ff.im/17DXH #
Moving it I can understand, but to Utah? Don’t they know the mormons are fundie’s too?… re: http://ff.im/17DXH #
BTW, The Scientist – compulsory registration sucks. I’ve too many accounts already, I’m well tired of new… re: http://ff.im/17DXH #
UK only? ah, boo! re: http://ff.im/17xgz #
Seriously, it’s like moving from China to North Korea in a civil rights protest. re: http://ff.im/17DXH #
RT @Barbarellaf: Me, being a GEEK: http://tinyurl.com/ddaonp (mrgunn: Have you seen http://is.gd/k2D5 #
Liked “BBC NEWS | Technology | Facebook ‘withdraws’ data changes” http://ff.im/17F5X #
Liked “The Blog That Ignited a Privacy Debate on Facebook – Bits Blog – NYTimes.com” http://ff.im/17EWp #
They really do have a bully pulpit there, but so far have used their powers only for good, nevermind the… re: http://ff.im/17EWp #
Liked “More on financial outlook for CIRM” http://ff.im/17Fqo #
Just got a Twine connection request from someone with “market on twitter” and holy roller twines. Dude, you’re doing it wrong. #
Liked “Patients’ genetic profiles can help avoid incorrect dosing of a common, dangerous drug, say Stanford scientists” http://ff.im/17FAr #
Yes, more like this! re: http://ff.im/17FAr #
I think there’s an inherent resistance. Popularity contests aren’t good for recommending unpopular things, like… re: http://ff.im/13DCE #
Liked “If You Build It, They Will Fly Away” http://ff.im/17Gyk #
I don’t know, Bill, but if find one, let me know! re: http://ff.im/16sWd #
Liked “Chefs Gone Wild: Thai Red Curry-Coconut Soup with Grilled Shrimp & Sticky Rice” http://ff.im/17IU7 #
Liked “The Bitten Word: Perfect French Omelets” http://ff.im/17J0F #
Liked “Muffuletta Recipe Inspired by New Orleans’s Napoleon House YumSugar” http://ff.im/17HmX #
greatest @woot item writeup EVAR! #
Disney + Doctorow + media sharing = awesome good jorb @woot #
RT @Comprendia: Wonder why some people’s twitter avatars are black squares? http://is.gd/jNwg #
OK @tweetdeck y’all gotta fix that memory leak issue #
Chris, if you need anyone with frickin’ shark laser beam installation experience, drop me a encrypted note on… re: http://ff.im/17Gkp #
Piggy Bank + the Solvent Extension allows you to write a custom scraper, which can get whatever can be specified… re: http://ff.im/17Q9E in reply to freesci #
RT @NOLAMardiGras: Song ‘If Ever I Cease to Love’ is synonymous with Mardi Gras http://tinyurl.com/ct4xhe #
for the next couple days, it’s #mardigras all the time. We will return to our regularly scheduled programming Wednesday #
Watch my flickr photostream, or better, Maitri: http://is.gd/keVI or skeletonkrewe: http://is.gd/keVt #
This is an ideal use scenario for some @qik streaming video with my N95, but no phone has enough battery for that #
In honor of our float’s theme: http://twitpic.com/1lamv #mardigras FYI: the #mardigras tag is occasionally, but not usually, #nsfw #
RT @NOLAMardiGras: Live from the street: The Times-Picayune ‘Twitters’ Mardi Gras http://tinyurl.com/cyosoj #mardigras #
Getting preparade cajunburger at fat harry’s #mardigras #
#mardigras works where other massive fests fail because of a shared understanding among the crowd. #
Under #mardigras conditions your scope of actions is limited #
You can’t run a tab during #mardigras. #
you can’t drive many places during #mardigras. #
You’ll be elated and let down at almost audible hertz during #mardigras #
You will leave someone or get left at some point during #mardigras #
Hark! I doth hear the sounds of distant drums! #mardigras #
Another gorgeous parade from Hermes #
How the hell can this many people have this good a time? Selection for people who are survivors. #mardigras takes survivorship, hardcore. #
Endymion at girod #mardigras #
Part of the magic of costumes is the free pass it provides to check others out. #mardigras #
Overheard: “I don’t even like fucking hot dogs, but i’m about to eat one.” That’s the spirit of #mardigras #
Y’all is a fucking great word. Everyone should use it. #mardigras #

This post is about tweets, twitter

Twitter Updates for 2009-02-15

admin — Sun, 15 Feb 2009 18:12:00 +0000

Twitter Updates for 2009-02-14 http://ff.im/13I0x #
Liked “Econbrowser: Tribune reports that 28% San Diego County owe more on their mortgage than the house is worth;” http://ff.im/13IqJ #
I’m only surprised the number isn’t higher. re: http://ff.im/13IqJ #
Richard, doesn’t the WSJ logic, as you explain it, only work under zero-sum conditions? To get a smaller… re: http://ff.im/13EsR #
@sdbn Digg for medicine has been tried: http://tinyurl.com/b7crd6 in reply to sdbn #
That’s only sometimes, and xp had the same behavior. It is annoying. #
@kejames I don’t know of a client that threads replies, but Troy’s Twitter Script for greasemonkey works if you click through from client in reply to kejames #
RT @sdbn: Protip: you can quickly look up San Diego Biotech companies by typing the SDBN URL followed by the first letter: http://sdbn.org/c #
RT @sciam: Now up: Steven Benner. LiveScience’s on his talk yesterday on 8-nucleotide (rather than 4) genetic code http://is.gd/jB6M #AAAS09 #
RT @psiquo: Science news in crisis http://ff.im/-14ec9 (mrgunn:Throwing down the gauntlet for @sciam @alexismadrigal @BoraZ to get audience) #
@Pontchartrain Always “the fly” around my friends. in reply to Pontchartrain #
The most common fixable error in ad science writing is not giving the lit. citation, study author name, drug name, or other pertinent info. #
RT @kejames: Goodness gracious great balls of fire! Debris from satellite collision raining down in #texas http://is.gd/jBTl #
@sdbn Got your email, getting approval to put it on company tab. Monday OK? #
@marycanady What definition of “working hard” involves ICHC retweets? in reply to marycanady #
Liked “If both sides are mad at your reporting, it’s due to all can see that you are doing it wrong. Make the good…” http://ff.im/13Iet in reply to BoraZ #
@BoraZ Including an editorial from Maxine, whose editorial raises the question: To what extent does blogging about your own research, wh … in reply to BoraZ #
Including an editorial from Maxine, whose editorial raises the question: To what extent does blogging about your… re: http://ff.im/13Iet in reply to BoraZ #
@BoraZ Maxine suggests a comparison between the “as submitted” and “as published” versions of a manuscript would reveal the value of the … in reply to BoraZ #
Maxine suggests a comparison between the “as submitted” and “as published” versions of a manuscript would reveal… re: http://ff.im/13Iet in reply to BoraZ #
@BoraZ Michael Gross bemoans the loss of depth in science coverage, ascribing it to the “fast food” culture. Here’s an idea: If you’re p … in reply to BoraZ #
Michael Gross bemoans the loss of depth in science coverage, ascribing it to the “fast food” culture. Here’s an… re: http://ff.im/13Iet in reply to BoraZ #
Liked “Excellent column on the Times adaptation to the web from its public editor http://is.gd/jBp6 Word of Hudson…” http://ff.im/14iDr in reply to jayrosen_nyu #
@jayrosen_nyu Thanks, Bora. No printing press in the world is as fast as twitter, and if you’re shallow, you’re just opening yourself up … in reply to jayrosen_nyu #
Thanks, Bora. No printing press in the world is as fast as twitter, and if you’re shallow, you’re just opening… re: http://ff.im/14iDr in reply to jayrosen_nyu #
@BoraZ Bud Ward argues that it’s not practical for an individual reporter to remain absolutely unengaged and impartial. Rather, one shou … in reply to BoraZ #
Bud Ward argues that it’s not practical for an individual reporter to remain absolutely unengaged and impartial…. re: http://ff.im/13Iet in reply to BoraZ #
Thanks for the re-share. There are pandora-like and last.fm-like approaches, where the recommendations are from… re: http://ff.im/14sDx #
Did I read correctly that the Kindle can’t be read in the dark? re: http://ff.im/12PKx #
@jhpincus Another dumb list because it doesn’t have “say interesting and timely things” at the very top in bigger type. in reply to jhpincus #
Another dumb list because it doesn’t have “say interesting and timely things” at the very top in bigger type. re: http://ff.im/14sY3 in reply to jhpincus #
Liked “What’s the Matter With Teen Sexting? | The American Prospect” http://ff.im/14pJI #
“…the harm we do trying to protect teenagers from themselves.” The problem is one of their own creation. re: http://ff.im/14pJI #
@BoraZ Thanks for the suggestions, Bob. What percentage of total submissions do you reckon are on Precedings? What kind of sample bias … in reply to BoraZ #
Thanks for the suggestions, Bob. What percentage of total submissions do you reckon are on Precedings? What kind… re: http://ff.im/13Iet in reply to BoraZ #
Liked “My story on “weird” life from #aaas09 is now up: http://is.gd/jC8c” http://ff.im/14p6D in reply to alexismadrigal #
Thanks for your continued coverage of the interesting bits of science. re: http://ff.im/14p6D in reply to alexismadrigal #

This post is about tweets, twitter

Twitter Updates for 2009-02-14

admin — Sat, 14 Feb 2009 18:12:00 +0000

I hope you don’t have an EPOCH FAIL today! http://xkcd.com/376/ re: http://ff.im/12U0Y #
Liked “It works. I put “resisting salty snack chips” into http://gopproblemsolver.com/ “The solution to your…” http://ff.im/12U5B in reply to jayrosen_nyu #
Could this be the Science Social Networking killer app? http://ff.im/12Ud1 #
@Barbarellaf If you use Tweetdeck, you can do the categorization yourself. in reply to Barbarellaf #
@gregaustin1 You as well, Greg. in reply to gregaustin1 #
@GregorMacdonald Shall we call them the Globe and Fail? in reply to GregorMacdonald #
I just ask them, very politely, if they could follow me out to my car, and I keep on walking. re: http://ff.im/12UHy in reply to davemunger #
@davemunger I just ask them, very politely, if they could follow me out to my car, and I keep on walking. in reply to davemunger #
Liked “Transform our Economy with Science and Technology” http://ff.im/12VdG #
Especially down here in dry San Diego! re: http://ff.im/12WGs in reply to DanielleFong #
@DanielleFong Especially down here in dry San Diego! in reply to DanielleFong #
F1000 is very similar, but it’s not a seedable recommendation engine. You’re at the mercy of what is made… re: http://ff.im/12Ud1 #
Liked “NSF looking OK in revised stimulus bill” http://ff.im/12XmG #
Luis von Blog: Academic Publications 2.0 http://ff.im/12Zp7 #
Related articles is similar, and I don’t actually know how they come up with the suggestions. I was thinking of… re: http://ff.im/12Ud1 #
Liked “Why are modern scientists so dull? How science selects for perseverance and sociability at the expense of…” http://ff.im/131w0 #
I tend to agree with the quote, because you do have to be unusually obsessed with finding the truth and there… re: http://ff.im/131w0 #
Thanks, Joe! re: http://ff.im/12Ud1 #
Having read it, it seems that it’s a combination of word frequencies and MeSH terms(which are human supplied). I… re: http://ff.im/12Ud1 #
@vicka You got that right. I noted, as did you I’m sure, that it was the editor of the journal that published said essay. in reply to vicka #
Resurrecting the ancient desktop from storage. I wonder how much stuff is gonna break. #
Liked “Mobile Websites – Cantoni.mobi” http://ff.im/13aGJ #
Quite the list! re: http://ff.im/13aGJ #
Checking Ebay for a monitor power cord. FrankenPC will not wake tonight. #
Liked “Programming the Semantic Web, 1st Edition” http://ff.im/13fZY #
Yeah, it didn’t escape my notice that the author was also the editor. Funny, not entirely untrue, but not… re: http://ff.im/131w0 #
@jayrosen_nyu Looks like someone did. I’m ready for her to retire already. in reply to jayrosen_nyu #
Looks like someone did. I’m ready for her to retire already. re: http://ff.im/13yxa in reply to jayrosen_nyu #
Liked “TiPS: now with option to normalize to total publications” http://ff.im/13ydr #
yeah, like rebranding your semi-automatic ass. ed. to half-automatic. Think you’ll get that done by Apr 1? re: http://ff.im/13ydr #
Liked “Cell Therapy Blog: Cell Therapy Industry HiLites 2009-02-13″ http://ff.im/13tjy #
Why wouldn’t you want to know if someone you’re not following has a comment for you? Maybe if you were making a… re: http://ff.im/13pjS #
Liked “Genetic Future : Routine whole-genome sequencing of babies by 2019?” http://ff.im/136hw #
Someone, I think it may have been either Dave Munger or Bora, had a series of posts on risk aversion behavior,… re: http://ff.im/136hw #
Liked “Le Creuset Cast Iron Heart: Love It or Hate It? | poll, Love It or Hate It, le creuset | YumSugar” http://ff.im/13sWk #
Liked “How I failed the Turing test” http://ff.im/11EyX #
@neilfws That’s a pretty cool screenshot, where is that? #
@zerojinx as if @wtsi_pipe wasn’t evidence enough! in reply to zerojinx #
There’s also an XML-RPC posting interface, if you’d rather that. For files, http://mosh.nokia.com is handy, if… re: http://ff.im/13fs6 #
RT @longbead: I’m finding @parades one of the best to follow for #mardigras (mrgunn: parade progress, status updates via twitter!) #
Liked “Why Wikipedia’s Policy to Blacklist Blogs is Outdated and Wrong” http://ff.im/13sBn #
I’m not holding out hope that anything will change soon, either, because of the ideology behind the decision. re: http://ff.im/13sBn #
RT @sdbn: Digg-style biotech news exchange http://is.gd/jxna #
@Comprendia value upfront. What would “digging” do for them immediately? #

This post is about tweets, twitter

Could this be the Science Social Networking killer app?

Mr. Gunn — Fri, 13 Feb 2009 21:02:27 +0000

There are tons of social tools for scientists online, and the somewhat lukewarm adoption is a subject of occasional discussion on friendfeed. The general consensus is that the online social tools, in general, which have seen explosive growth are the ones that immediately add value to an existing collection. Some good examples of this are Flickr for pictures and Youtube for video. I think there’s an opportunity to similarly add value to scientists’ existing collections of papers, without requiring any work from them in tagging their collections or anything like that. The application I’m talking about is a curated discovery engine.

There are two basic ways to find information on the web – searches via search engines and content found via recommendation engines. Recommendation engines become increasingly important where the volume of information is high, and there are two basic types of these: human-curated and algorithmic. Last.fm is an example of a algorithmic recommendation system, where artists or tracks are recommended to you based on correlations in “people who like the same things as you also like this” data. Pandora.com is an example of the other kind of recommendation system, where human experts have scored artists and tracks according to various components and this data feeds an algorithm which recommends tracks which score similarly. Having used both, I find Pandora to do a much better job with recommendations. The reason it does a better job is that it’s useful immediately. You can give it one song, and it will immediately use what’s known about that song to queue up similar songs, based on the back-end score of the song by experts. Even the most technology-averse person can type a song in the box and get good music played back to them, with no need to install anything.

Since the reason for the variable degree of success of online social tools for scientists is largely attributed to the lack of participation, I think a great way to pull in participation by scientists would be to offer that kind of value up-front. You give it a paper or set of papers, and it tells you the ones you need to read next, or perhaps the ones you’ve missed. My crazy idea was that a recommendation system for the scientific literature, using expert-scored literature to find relevant related papers, could do for papers what Flickr has done for photos. It would also be exactly the kind of thing one could do without necessarily having to hire a stable of employees. Just look at what Euan did with PLoS comments and results.

Science social bookmarking services such as Mendeley, or perhaps search engines such as NextBio, are perfectly positioned to do something like this for papers, and I think it would truly be the killer app in this space.

This post is about last.fm, pandora, publishing, recommendation, science

Claiming my blog on the new Nature Blogs.

Mr. Gunn — Wed, 05 Nov 2008 18:31:28 +0000

Great work, guys! More on Friendfeed’s Life Scientists room .

This post is about 3f264daad619f7d46c331c14e0a2cb26

Thompson Scientific has a closed science search engine.

Mr. Gunn — Tue, 24 Jun 2008 18:35:55 +0000

They sent me a survey and asked me some simple questions, but I don’t think they asked me the right ones, so I’m going to give a free-form review here. I think it’s a great idea, and presents some features not available anywhere else, but it’s missing some important content, and like everything Thompson does, it suffers from some useability issues.

The search engine is called Thompson Scientific WebPlus, and you can only access it through their Web of Knowledge service, which they should really link to from the page telling you so. It’s also closed in the sense of being a somewhat curated list, with Thompson-selected authoritative sources ranked highest, but to their credit they do have a “suggest a site” button.

If you can get to it, it’s actually a pretty standard Google-like interface, but with Tabs for Topic, Author/Person, Organism, Drug, and Gene, instead of the normal Web, Images, Maps, News tabs at google.com. The search results returned are then presented as normal search results, with separate tabs for only News articles, Blog posts, or Repository links. I really like the idea of institutional repositories having their own tab, so you can search for a gene and get only links pointing to pages in a repository. I also like the idea of blogs having their own tab, so you can see what people are talking about, and having the News on a separate tab helps you scan for press releases and see how (badly) science is covered in major media. Once you’ve executed the search, you can narrow it by TLD, to pick out only results from .com, .org, .net, etc.

I tried a sample search that I’m familiar with in each one, just to see how this would work in practice.

A topic search for “multiple myeloma” has multiplemyeloma.org and myeloma.org at the top of the list, as with a standard Google search for the same. The notable difference is that wikipedia is dead last in the WebPlus results. News and Blog tabs are present, but no repository tab is available.

A Person/Author search for “William Gunn” looks much like it does on regular Google, again with Wikipedia being conspicuously absent. I’m pleased to see that my blog is the first in the results, as it should be for my name, and other results from the same domain are grouped. There’s even a link, which is dead, to my Nature Precedings account on the repository tab. Where things get strange are on the blog tab. They only list my other, infrequently updated, nonscience blogs, including a link to a development site on which I had a robots.txt containing User-agent: * Disallow: /, but no link to Synthesis. Certainly not expected behavior. They’re just as bad as Google Scholar always was with author searches, too, because they aren’t able to figure out that results for William and Wallace Gunn should be shown in a search for W Gunn. WG Gunn is even worse. Pubmed remains best at handling this.

An organism search for “mus musculus” gives results similar to standard Google’s results, again trashing wikipedia, but it’s the repository tab fails this time, not including links to Jackson’s MPD or MGI, though they are in the regular web results.

A drug search for Velcade works like the organism search, presenting some good links up front and strangely lacking a repository tab. The blog tab works more or less as expected.

A gene search for DKK1 works similarly as well. If there’s anywhere I would have expected a repository tab, it would be here, but no such luck. However, this is where the blog tab really comes in handy, allowing you to see who’s talking about your favorite gene. Given the incompleteness of the results in the blog tab, I’m concerned about coverage here, but they do have scientificblogging.org, scienceblogs.com, blogs.nature.com, and even friendfeed, as well as some really weird french splog results.

So let’s summarize:
Topic – Works as expected
Person/Author – OK for finding people, even if the tabs don’t exactly work, but for finding authors it gets a FAIL.
Organism/Drug/Gene – Works as expected, but tabs fail.

Overall, it’s a strong first effort, and I expect the results to improve as they tweak things. I do think it’s a mistake to all but exclude wikipedia from results. For all it’s flaws, wikipedia still does a decent job on most things, and usually provides authoritative links for further reading.

As I was finishing the survey about the service, they asked some questions about ResearcherID.com and about something that seemed to be referring to a search portal. I wouldn’t be surprised in the slightest if someone at Thompson thinks a 90′s Yahoo style search portal would be a good idea, but search isn’t about being a portal anymore. It’s about helping people find the best information from the millions of results for any given term. I would not like to see an igoogle or yahoo search portal, but rather a open search that widely syndicates results so existing filtering systems such as social networks can help promote the more relevant results.

Other improvements I’d like to see:

I’d like to see “share this” links to automatically save links to my bookmarking sites such as Connotea, del.icio.us and friendfeed.

I’d like to see RSS feeds for search results.

I’d like to see a search API that returns results in a variety of structured formats including RDF and json.

I’d like a search widget so I can display search results in other pages.

and, of course …

I’d like to see representatives from Thompson’s search team participating in online discussions at social networking sites such as Nature Network and Friendfeed.

This post is about ISI, publishing, search, Thompson, WebPlus

Great news for the Louisiana research community – Charity Hospital to be converted to University Medical Center

Mr. Gunn — Thu, 19 Jun 2008 15:09:21 +0000

Maybe there’s a chance I could end up back in this wonderful city and have a career, too.

In a monumental announcement made late this afternoon, Department of Health and Hospitals Secretary Alan Levine said he will recommend that the state build a 424-bed, $1.2 billion academic teaching hospital in Downtown New Orleans that will serve as the hub of a rebuilt medical corridor.

Referring to the DHH proposal, the head of Louisiana State University’s health care division, Dr. Fred Cerise, said, “They revised the business plan a bit based on population and some shift in the makeup of the population, but overall (they) agreed that if we’re going to change the model to more of an academic medical center then we’re going to need the capacity to not only fulfill the charitable mission but also have space for our faculty to see their private pay patients there as well.”

The new hospital will be instrumental in the revitalization of not only the health care industry, but also the entire medical district and Downtown New Orleans. It will serve as the main teaching hub for medical students, nurses, post-graduate residents and other allied health students from LSU and Tulane University. The new facility will be instrumental in developing the DDD’s “industries of the mind” initiative. Attracting members of the creative class, such as leading medical researchers, technicians, and practitioners, is critical for shaping Downtown’s economic future.

The HPS consulting firm’s assessment is less sanguine, but overall deems the success of the center “likely”. Just to help paint the picture of things, the projected patient mix is:

13-21% Medicare
33-35% Medicaid
39-52% indigent

This post is about development, louisiana, New Orleans

I told you he was a Trojan horse

Mr. Gunn — Tue, 17 Jun 2008 16:32:13 +0000

Way back when he was running for Governor of my fine state, I told everyone I could that Bobby Jindal was a Trojan horse for the religious right. I predicted that he was going to get right on the legislation they wanted. I thought he was going to go after stem cell research instead of evolution first, but I didn’t know what was going to happen with iPS cells in the meantime. Now look: Louisiana has a “protect the teaching of creationism” bill and he’s being considered as a VP candidate for McCain.

Quid pro quo, no?

This post is about creationism, GOP, jindal, louisiana, Politics

Connotea, you’ve been good to me

Mr. Gunn — Mon, 16 Jun 2008 23:05:44 +0000

Despite all that, you’ve been a little slow lately, and I found my thoughts wandering. Earlier today, I noticed a 2collab link, and, without thinking about it, clicked over to see what has changed since last time we met. Before I knew it, I was pulling in my publications via Scopus ID, tagging papers, and joining interest groups. I’m sorry, Connotea, but the speed was just so intoxicating that I went and exported my whole library from you and went to import it to 2collab. It seems my affections weren’t returned, however, as I was slapped with the following message:

Unable to import bookmarks: org.hibernate.exception.ConstraintViolationException: Could not execute JDBC batch update

Like a bucket of cold water, that returned me to my senses, and I came back to you, ol’ Buggotea.

This post is about 2collab, connotea, fail

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