A workaround for WordPress.com users

By Dave Munger | May 12, 2008

I've been in contact with the folks at WordPress.com about the problems users of their system have had getting ResearchBlogging.org's citation code to display properly. WordPress has acknowledged that the problem is due to a bug in their system and has initiated a ticket to repair the problem.

Unfortunately there's no telling how soon they'll get to fixing the problem so I spent a little time seeing if I could come up with a workaround. Based on my testing, I think I've come up with a solution. It's not perfect, but it's better than the blank citations we're getting now.

Here's what you need to do (applies only to WordPress.com users):

1. Generate the citation using our system.

2. Copy and paste it into your blog post, making sure you're in the "code" view.

3. Delete the following text from the first <span> tag in the post:

info:

[make sure the colon is deleted! That's what causes the problem. Leave the "DOI" text and everything following]

4. Publish your post. That's it!

You don't need to worry about re-entering the "visual" mode after making your post. This takes care of that problem as well.

A side-effect of this workaround is that the citation on ResearchBlogging.org doesn't include the DOI. However, the DOI is still intact on your post, and it's much better than a blank citation. Let me know if the workaround works for you.

Topics: Administration | 5 Comments »

Suggest topics/categories for version 2.0 of ResearchBlogging.org

By Dave Munger | April 28, 2008

We're hard at work on version 2.0 of ResearchBlogging.org. Though we can't say for sure when the site will be publicly available, we'll start internal testing of the new system next week, so it shouldn't be too much longer!

We had promised to revisit the topics (Biology, Chemistry, etc.) for this new version of the site, so this post will be a place where we can collect feedback. Here is the current list of topics:

Anthropology
Astronomy
Biology
Chemistry
Clinical Research
Computer Science
Earth / Environmental
0 - Economics
0 - Engineering
0 - Mathematics
4 - Philosophy
5 - Physics
4 - Political Science
Psychology
8 - Sociology
6 - Research / Scholarship
Other

I've put numbers indicating total number of posts next to the topics with fewer than 10 posts. We might want to consider eliminating some of these topics. Other very popular topics, such as Biology and Clinical Research, might warrant splitting into more than one topic.

So, please make suggestions for what primary topics to include in the next version of the system. We like the current number of topics, but we want them to be as descriptive as possible of the interests of the bloggers actually using the system.

The new system will also have the option of including secondary topics, or tags (like developmental biology or ecology). We'll discuss those  in a separate post.

Update: One suggestion. Since psychology and clinical research are two of the busiest topics, we might try this: Add a new "health" category that would include medicine, psychiatry, public health, and so on. That would limit both psychology and clinical trials both to primary research and give medicine and psychiatry a more comfortable home. What do you think?

Also, maybe combine economics, political science, and sociology into "social science"?

Topics: Administration | 15 Comments »

Development starting on German-language ResearchBlogging.org community

By Dave Munger | April 11, 2008

Tobias Maier of the German science blog WieterGen has initiated development of a German-language community of ResearchBlogging.org. This will be our first experiment in admitting non-English language blogs into our system. There's already a blog devoted to organizing bloggers, enlisting volunteers to help moderate blog posts, and translating and adapting our guidelines for a German audience.

Tobias and other volunteers will be working in parallel with us as we develop version 2.0 of the ResearchBlogging.org system. Our vision is to have a system where users can select the languages they'd like to see (German only, English only, or both languages). A German-speaking community of bloggers will ensure that all posts in German meet the same standards as the English language system. Below is Tobias' announcement. If you're interested in participating as we develop this new community, then make a comment on this post.

If the German community is as successful as we hope it will be, we'll add other languages, one by one, following the German model.

Neues Qualitätssiegel für wissenschaftliche Blogposts

 

blogging on peer-reviewed research white.pngIn Zusammenarbeit mit researchblogging.org und scienceblogs.de hat WeiterGen die Übernahme eines Gütesiegels für deutschsprachige Blogeinträge über wissenschaftliche Publikationen initiiert.

Wer bloggt über Wissenschaft?

Bloggen über Wissenschaft ist das Thema von ScienceBlogs.de. Wie das geht und was gutes Bloggen über Wissenschaft ist, wurde in den letzten Wochen ja auch schon in einigen Blogs diskutiert, unter anderem natürlich in der Wissenswerkstatt (in einer dreiteiligen Serie), von Monika Armand mit einem kompletten Blog zu dem Thema, im Fisch-Blog, im Basic Thinking Blog, zuletzt hier auf SB.de bei Stefan Jacobasch und bei etlichen anderen, die ich jetzt nicht mehr finde (gerne als Kommentar hier darauf hinweisen). Sogar auf der re:publika08 gab es einen Workshop zu dem Thema.

Die authentischsten Quellen für Blogeinträge zu wissenschaftlichen Themen sind wissenschaftliche Publikationen. Subjektiv wahrgenommen sind es aber eher Pressemeldungen, die von Bloggern aufgegriffen weden (mein Blog eingeschlossen).
Blogeinträge zu Papern haben meiner Meinung nach leider nicht die Resonanz, die sie verdienen, und fachfremden Lesern fällt es schwer zu beurteilen, ob ein entsprechender Blogpost der zitierten Veröffentlichung gerecht wird.

Das soll sich jetzt ändern.

In Zusammenarbeit mit researchblogging.org und scienceblogs.de hat WeiterGen die Übernahme eines Gütesiegels für deutschsprachige Blogeinträge über wissenschaftliche Publikationen initiiert. Auf german.researchblogging.org kann man sich anmelden

Blogautoren, die auf deutsch über wissenschaftliche Publikationen schreiben, können jetzt durch Einbinden des "Blogging on Peer-Reviewed Research" Logos (siehe hier oben links) in ihre Einträgen deutlich machen, dass sie über Artikel aus anerkannten Wissenschaftsmagazinen schreiben.

Die Vorteile

Für den Leser ist mit diesem Gütesiegel sofort erkennbar, dass der Eintrag sich fundiert mit rezensierten Quellen aus anerkannten Magazinen auseinandersetzt, und trotzdem eine individuelle Leistung des Blogautors ist, also nicht nur wiedergegeben wird, was sowieso schon in der Originalveröffentlichung steht.

Auch für Blogautoren ergeben sich Vorteile:
-Eigene Blogeinträge werden bei researchblogging.org zusätzlich gelistet und haben daher eine höhere Präsenz, was wiederum die Anzahl der Leser erhöht.
-Wissenschaftler, die höchstens sporadisch bloggen, dann aber über ihr Fachgebiet (oder darüber nachgedacht haben), haben nicht das Gefühl "ins Nirvana" zu schreiben, sondern werden sofort von einer wissenschaftlich interessierten Lesergemeinde wahrgenommen.

Das Qualitätssiegel wird bereits von vielen englischsprachigen Wissenschaftsblogs genutzt. Eine aktuelle Übersicht der jüngsten, englischsprachigen Artikel findet man hier.
Hier einige Beispielposts:
Can grammar be sexist?, Ice-free arctic by the year 2030, You can learn to be nice, Elephants are not ethnic blind

Wie komme ich an das Logo?

Um das ganze auf Deutsch zum laufen zu kriegen brauchen wir ein paar deutsche Blogs, die - regelmäßig oder sporadisch - über wissenschaftliche Veröffentlichungen schreiben, und sich bei german.researchblogging.org registrieren. Dort finden Blogautoren weitere Informationen und regelmäßige Updates zu dem Projekt.

In der aktuellen Aufbauphase ist es vor allem wichtig, dass sich Blogger dort registrieren. ResearchBlogging.org wird derzeit komplett überarbeitet. Deutsch wird die erste Sprache sein, die neben Englisch in das System integriert wird, sobald die Seite fertig ist, und sich einige Blogs registriert haben.

Also Kollegen, schmeißt das Answers Research Journal in die Ecke, greift zu peer-reviewten Veröffentlichung, und vor allem:

Registrieren und weitersagen!

Topics: Administration | No Comments »

Guidelines for registering with ResearchBlogging.org

By Dave Munger | April 8, 2008

ResearchBlogging.org receives anywhere from two to five applications from bloggers hoping to register each day. In order to ensure that the blog isn't spam, and to forestall any potential problems down the line, a human reviews each application before approving.

Typically this involves visiting the blog to make sure it's being actively updated, to see if there are any posts that meet our guidelines, and generally to see if the blogger seems to understand the type of thoughtful posts we are looking for. In about half the cases, it's obvious that the blog qualifies, and the blog is approved without any further effort. About half the remaining cases are obviously spam and are rejected.

When it's unclear whether a blog is really right for ResearchBlogging.org, we usually send an email that reads something like this:

Dear Blogger,

I have just had a chance to review your request for your blog to be included in ResearchBlogging.org. I looked briefly at your blog and did not find any posts about peer-reviewed research. Could you show me some examples of posts that meet our guidelines for inclusion? Here's a link to the web page with our guidelines:

http://bpr3.org/?p=53

Thanks!

Most bloggers never respond to these queries -- once they realize what our organization is all about, they just "go away." Sometimes examples are provided, and then the blog is approved.

This weekend,  a blogger with no posts about peer-reviewed research attempted to register with us, I sent an email like the one above, and the blogger responded that our guidelines did not require bloggers to have previously posted about peer-reviewed research. Such posts are a lot of work, and so we should approve the blog now so that the blogger's efforts will be rewarded when they do write such a post.

This doesn't seem like a prudent approach to me, but the blogger does have a point. We should have some guidelines for registering with ResearchBlogging.org.  Here's a first pass at a set of guidelines. We welcome suggestions for additional guidelines or revisions to these guidelines in the comments.

Guidelines for registering with ResearchBlogging.org
To be included in our database and aggregation system, blogs must:

  1. Contain at least one post meeting our guidelines and at least five total posts.
  2. Have been updated within the past six months.
  3. Be well-maintained by the blogger (e.g. relatively free from spam comments, bad code, etc.).
  4. Include original work by the blogger and link or cite materials taken from other sources.
  5. Meet community-established standards for decency (e.g. free from pornography, hate speech, etc.).
  6. Have some means of contacting the blogger (e.g. email address, "contact" form, comments, etc.).
  7. Be freely available to all readers.
  8. Be written in a supported language. (Currently English is the only supported language, but we plan on adding additional languages in the future.)

I think that's a pretty good start. Any additional suggestions or comments?

Topics: Administration | 38 Comments »

Tips for WordPress bloggers

By Dave Munger | March 31, 2008

We're hard at work on version 2.0 of our system, but until the new system is implemented, we'll have to live with some of the quirks of the old system. One of the most pernicious problems is the appearance of blank citations, such as this one:

The problem with this post is that WordPress has mangled the information our aggregator needs to "see" the citation. The code on Guadalupe Storm-Petrel begins like this:

<span class="Z3988" title="DOI/10.1051%2Fgse%3A2002039"></span>Mariat

 
But it should look like this:

<span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi
%2Ffmt%3Akev%3Amtx%3Ajournal&rft.aulast=Mariat&rft.aufirst=Denis&rft.
au=Denis+ Mariat&rft.au=Sead+Taourit&rft.au=G%C3%A9rard+Gu%C3%A9rin&
rft.title=Genetics+Selection+Evolution&rft.atitle=&rft.date=2003&rft.
volume=35&rft.issue=1&rft.spage=119&rft.epage=133&rft.genre=article&
rft.id=info:DOI/10.1051%2Fgse%3A2002039"></span>Mariat, D., Taourit,
S., Guérin, G. (2003). . <span style="font-style: italic;">Genetics
Selection Evolution, 35</span>(1), 119-133. DOI: <a rev="review" href=
"http://dx.doi.org/10.1051/gse:2002039">10.1051/gse:2002039</a>

 
See the difference? There are two ways to fix the problem.

  1. Put the citation into your post  using the "code" view rather than "visual" view. As long as you save your post in this view and don't return to the "visual" view, WordPress won't change the code.
  2. If you prefer the visual view, you can modify the tag somewhat so that WordPress doesn't alter it. All that you need to do is add a space between the opening <span> tag and the closing </span> tag (in this case, it would go right after id=info:DOI/10.1051%2Fgse%3A2002039">). Once the space is inserted, you can safely edit in "visual" mode.

A second way that a blank citation can be generated is if you enter an incorrect DOI into our citation generator. This affects all blogging platforms, not just WordPress. Make sure you look at the Output area to verify that your DOI has been correctly registered by the system.

Enhancements are on the way, but in the meantime these tips should streamline your experience using ResearchBlogging.org.

Topics: Administration | 5 Comments »

Interesting issues in the forums

By Dave Munger | March 12, 2008

ResearchBlogging.org users may not be aware that we have a growing community in our forums. There you can find help with problems with the site, discussions about the future of the site, and a space to talk about whatever you'd like.

If you haven't checked them out yet, I'd encourage you to visit and join the conversation. I'd like to highlight a few particularly relevant threads that have been brought up in the past couple of days:

If you haven't yet signed up for the forums, now's a great time to make your voice heard -- you can respond to these threads, or start a new one of your own. It's a great way to help shape the future of ResearchBlogging.org, or just to connect with others who are doing research, or would like to learn more about research.

Topics: Administration | 2 Comments »

What should science blogging be?

By Dave Munger | February 27, 2008

There's an interesting discussion going on over at Bayblab about what science blogging should be. The basic complaint is this:

Now there are thousands of blogs dedicated to science, yet only a few are popular. And strangely the popular ones are only loosely related to science. Just take a look at the top 5 science blogs (according to postgenomic):

1 Pharyngula (mostly about creationism)
2 Cognitive Daily (psychology research)
3 Living the Scientific Life (personal journal)
4 Sandwalk (some evolutionary genetics, and creationism)
5 Aetiology (pop science)

Of those only Cognitive daily is consistently talking about peer-reviewed research. Why is that? Perhaps there is less appeal in discussing recent papers than bashing creationists. But bashing creationists is almost too easy, and not very constructive.

I'm pretty sure PostGenomic's stats are off -- I happen to know, for example, that Cognitive Daily is not one of the five most popular science blogs, since it's not usually one of the top five on ScienceBlogs.com. Some huge science blogs, like Cosmic Variance, Real Climate, Bad Astronomy, and Cocktail Party Physics, aren't even on the list. But taking the list as it's printed, all of the blogs do discuss science quite regularly. They just happen to talk about lots of other stuff too.

For most bloggers, that's what blogging is supposed to be. A blog is a very personal space, where a poster might put pictures of her trip to Valencia in one post and an analysis of a paper appearing in a peer-reviewed journal in the next.

ScienceBlogs.com could have exerted much more editorial control over the bloggers it recruited, for example demanding that all their posts be about peer-reviewed research. It chose not to take that approach for a couple reasons. First, they probably would have had a difficult time recruiting bloggers. Second, they probably would have had to pay the bloggers substantially more, because instead of blogging for themselves, the bloggers would be writing to meet the standards of the organization. Third, and possibly most importantly, they might have compromised the scientific content of what the bloggers were posting. Once you're monitoring the content of an entire blog, you're encouraging bloggers to play it safe. With an editor looking over her shoulder, maybe a blogger will decide not to cover an issue for fear it's not "sciencey" enough.

But if that's the case, then why should there be any attempt to control the content of blogs? Isn't that what ResearchBlogging.org does? I'd submit that there's a critical difference: Bloggers are under no obligation to write posts that meet our guidelines. They are free to submit posts that they believe do meet the guidelines, but they aren't required to. You can sign up for an account at ResearchBlogging.org and never write a post that meets our standards. As long as you don't attempt to get your post aggregated, you can maintain your account indefinitely.

ScienceBloggers are actually required to produce a certain number of posts per week, and ScienceBlogs has the (rarely invoked) right to shut down blogs that don't meet that requirement. But ScienceBlogs has no restrictions on the type of posts its members write, which makes the first requirement less onerous

I think both commercial sites like ScienceBlogs and independent blogs are critical to the online dissemination of science. Independent bloggers are free from the restrictions of a commercial site, but they might not attract as large an audience. A large audience for science blogging is important not only because of the potential for bloggers to make money, but also because of the public service the science blogging represents. If commercial blogs can expand the readership of science on the internet (even if it also increases the number of political/religious rants), isn't that, on the balance, a good thing?

And isn't it also good that we have sites like ResearchBlogging.org, where readers who are only interested in science can find what they're looking for as well?

Topics: Opinion | 5 Comments »

Are you seeing noticeable traffic gains when you post?

By Dave Munger | February 15, 2008

ResearchBlogging.org is still quite a young site, but it's beginning to have an impact on the blogosphere. Perhaps the greatest form of flattery for a web site is imitation, and we've already got a really great site that's clearly playing off of our idea: bpsdb.org. That stands for "Blogging on PseudoScientific DoucheBags," and it covers just about exactly what you might expect. But it's a well-done site that definitely fills a slightly different niche from ResearchBlogging.org, so it's probably a good addition to the blogosphere.

But I'm also interested to know the impact our users are noticing after registering and posting with ResearchBlogging.org. Whenever a Cognitive Daily post is aggregated, we definitely see a noticeable bump in traffic, but we're just one data point. If your posts are aggregated, do you notice a difference in site visitors? Have you found that more blogs link to you? Do you have more RSS subscribers?

Use the comment thread to let us know the impact ResearchBlogging.org has had on your site.

Topics: Administration | 20 Comments »

Great new posts on peer-reviewed research

By Dave Munger | February 7, 2008

ResearchBlogging.org has seen a surge of new registrations over the past week. We now have over 200 registered blogs, and so far this week we've been averaging about 15 new posts per day. The posts cover 12 different topics from across the disciplines, from anthropology to chemistry to clinical research. Here are just a few of my favorites:

Topics: News | No Comments »

The Luskin situation: A summary, analysis and decision

By Dave Munger | February 6, 2008

This week's episode dealing with the Casey Luskin's post Leslie Orgel: Metabolic Origin of Life 'Unlikely'; Complexity Requires 'A Skilled Synthetic Chemist' has highlighted some important issues for the future of our organization. I'll address those in a separate post. In this post, I'd like to focus in on this particular case, and what I believe we should do about it.

First, the background: Several readers pointed this post out to me as an example of a post that violates the ResearchBlogging guidelines -- before Luskin had even applied for an account with ResearchBlogging.org. Luskin has since removed the icon from his post and applied for an account, but we still need to resolve two questions.

  1. Should we allow Luskin to register his blog Evolution News & Views with ResearchBlogging.org?
  2. Does this specific post qualify for aggregation and use of the icon should Luskin wish to add the icon again in the future?

The first question is in many ways dependent on the second. In the future we plan on having several administrators with the authority to approve new accounts at ResearchBlogging.org, but now, although all members of our team have administrative access, I'm the only person actively managing the registrations, so let me take you through the process I use to approve an account.

When I see a new registration application, I'm looking primarily for two things. First, is the information on the registration form accurate? An incorrect URL or feed address means that a blog's posts won't be aggregated. So I visit the site and verify the feed address. Second, does the blog appear to have posts that meet our guidelines? Do any of the posts cite peer-reviewed research, and are those posts making substantive comments on the research? If the site meets those two requirements, I approve the registration. I don't look too closely at the content of the blog -- I figure if the blog later turns out to be a problem, we can always temporarily suspend the account and discuss what further action to take in the forums.

Using this process, it might seem that we should probably approve Evolution News & Views, but there's a hitch: my prior knowledge that several readers had already objected to a post. Why should I approve an account when I know a post is problematic? One possibility is that these readers' objections were unfounded. Another is that this post is anomalous -- that there are many other posts on the blog which follow the guidelines.

Let's consider the first possibility. The discussion thread I posted on February 4 was supposed to address whether Luskin's post met our guidelines, but the 88 comments that thread has received so far range far beyond the scope I had intended. There have also been some incisive posts on other blogs. I'm going to attempt to summarize that discussion here. I'm also going to offer my own opinions about the issues. I had wanted to stay a bit removed from the fray, but emotions are running so high in this debate that it now seems important to bring the discussion back down to a restrained level.

Some commenters suggested that the post violated Guidelines #1 and 2 -- that it wasn't actually referencing peer-reviewed research, because the article in question was an essay, not a report on "real" research. I disagree with this contention. The term "research" on our site was meant to cover all scientific and scholarly discourse, not just experiments.

Some commenters also contended that the article wasn't peer-reviewed, perhaps due to some confusion over an acknowledgement of a colleague who commented on a draft of the manuscript. I contacted the editor of this section of PLoS - Biology, Liza Gross, and she assured me that this article, like all articles published in that journal, was indeed peer-reviewed.

The real issue, then, is whether the post adheres to Guidelines #4 and 5. We'll have to take Luskin's word on #4 (which requires that the blogger read and understand the article cited), and he assures us that he does meet this guideline. So we're left with Guideline #5: Does the post report accurately and thoughtfully on the research it cites?

Commenter Doc Bill gets to the heart of the matter:

Clearly, Luskin doesn’t understand the purpose of Orgel’s essay, that is, to discuss the plausibility of hypothetical nonenzymatic cycles.

Instead Luskin just makes stuff up, like this: “Again, Orgel essentially assumes that cyclic metabolic pathways are irreducibly complex systems that require a large number of parts in order to function”

Luskin replies:

Orgel states, “At the very least, six different catalytic activities would have been needed to complete the reverse citric acid cycle. It could be argued, but with questionable plausibility, that different sites on the primitive Earth offered an enormous combinatorial library of mineral assemblies, and that among them a collection of the six or more required catalysts could have coexisted.” That seems to meet the definition of irreducible complexity.

Doc Bill then points out that Orgel doesn't specifically state that his objections to these processes means they are irreducibly complex, and that Orgel in fact never uses the term. I might add that Orgel's essay only addresses a few possible mechanism for these cycles; it doesn't argue that no other mechanism could possibly work, only that these proposed mechanisms probably wouldn't.

DiGz discusses another portion of the post:

“Just like the case of the ribosome, the evidence shows that the complexity of life requires an intelligent cause.”

That’s a conclusion based on his own pre-conceived notions and is not mentioned anywhere in the paper, nor could it be extrapolated scientifically from its contents. That’s simply Casey making something up and as such it misrepresents the content and conclusions of the paper.

Luskin contends that that's his own opinion and not relevant to his accurate reporting on the facts of the article. He is correct in pointing out that the guidelines do allow bloggers to state their own opinions -- we don't restrict bloggers to a bland reporting of the facts. However, I'm troubled by the statement DiGz quotes because it's unclear that it in fact represents only Luskin's opinion.

I talked privately with science ethicist Janet Stemwedel, and she agrees that the blurring of the distinction between what's supported by the article itself and what constitutes the blogger's personal opinion is problematic. In this case, when Luskin refers to "the evidence," what evidence could he be referring to, if not the evidence supposedly offered in Orgel's article? Yet Orgel does not present any evidence that "the complexity of life requires an intelligent cause." The blog post itself should make it clear that this final assertion is Casey's alone, not Orgel's. We shouldn't have to wait for Luskin's assertion that this was only his personal opinion, especially when he still hasn't modified his original post to make that clear.

Moving on to the second possibility, it's also possible that this post is an anomaly and that in general Luskin does report accurately on peer-reviewed research. Unfortunately, based on the comments in Monday's thread, that doesn't seem likely either. Many commenters point to Luskin's frequent "quote mining" of articles, taking statements out of context in order to make his case. It doesn't seem to me that Luskin is making an honest attempt to accurately discuss peer-reviewed research. Indeed, many of Luskin's posts argue that the peer-reviewed research system is itself flawed. While we acknowledge that peer review isn't perfect, why should we accept as a participant in our organization someone who doesn't believe that one of our founding principles -- the peer review process -- is worthwhile?

Some commenters have argued that we should give Luskin the benefit of the doubt, and that even if he abuses our guidelines, other blogs will respond to his arguments and that open discussion will win out. I, along with most commenters, disagree. The point of our organization is to promote peer-reviewed research and add credibility to serious research blogs. We don't need to prop up sites that don't live up to our guidelines.

For now, therefore, I'm not approving Luskin's request to be included in the ResearchBlogging.org site.

This decision is not final; I'd still like your input, but I was a little disappointed with the quality of the discussion on Monday's post, so I'd like to try something new here. I'm asking commenters on this post to focus on the substance of Luskin's case for inclusion on our site, and the case for denying his request. I'm going to delete comments that are unprofessional, rude, ad-hominem, unsubstantive, or otherwise uncivil. This is an experimental approach which I hope will keep responses focused on the question of whether or not to include Luskin in our aggregation system.

Topics: Administration | 46 Comments »

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