Category Archives: Blog

Call for Editors!

As you know, we have a fantastic group of editors who make our site what it is.

James Montgomery Flagg / CC

Our editors are responsible for making weekly Editor’s Selections within their scientific areas of interest and expertise. These selections appear daily on the ScienceSeeker homepage. It’s this personal touch that makes ScienceSeeker so unique and personalized among other science news aggregators.

We are on the hunt for some fresh, enthusiastic faces to join our team. Currently, we are looking for individuals who enjoy reading science news in the following topic areas:

  • Academic Life
  • Chemistry
  • Climate & Earth Science
  • Physics
  • Psychology

If you or someone you know reads or writes on these topics, WE WANT YOU! Please e-mail contact AT scienceseeker DOT org if you’re interested or have any questions.

Since ScienceSeeker is a project of ScienceOnline, our editors also get priority registration for the annual SciO conference in Raleigh. Just another fun perk of being part of an incredible team!

Meet the Editors: Jordan Gaines Lewis

In the coming weeks, we’ll be featuring short interviews with each of our editors, so that you can get to know those folks who are responsible for highlighting your posts each week as editors’ selections. First, meet Jordan Gaines Lewis.

Hello! Let’s start with first things first. Where are you from, what do you do how did you get into science?

Hi all! I’m originally from Maryland and graduated from St. Mary’s College of Maryland in 2011 with my bachelor’s degree in biology. I’m now in my third year of the Neuroscience Ph.D. program at Penn State College of Medicine in Hershey, Pennsylvania. (Yes, living in the chocolate capital of the U.S. is as great as it sounds.) You can connect with me on Twitter, Google+, and my website is here.

I used to want to be some sort of counselor; this was back in 8th grade, when my friends would tell me their deep, dark secrets over AOL Instant Messenger after school. Somehow this all transitioned into a fascination of the brain and, in college, the study of neuroscience as a whole. I work in a sleep research lab, which captivated me after a lecture in my introductory neuroscience class two years ago. On the side, I write neuroscience/psychology blogs for Scitable by Nature Education, Psychology Today magazine, and NBC News Health. I also started up a blog written by the graduate students at Penn State College of Medicine called ”Lions Talk Science” (‘cause we’re Nittany lions, and I like assonance!). And, of course, I’m your Social Media Editor here with ScienceSeeker!

What is the name of your blog and why did you choose that name – what does it mean?

My blog is called “Gaines, on Brains,” and I thought of it while…well, taking a shower one day. It is what it is: me, Jordan Gaines, discussing brains. It just seemed fitting that my last name would rhyme with the organ of interest. (I’ve since gotten married, so my last name is now actually Lewis, but nothing in neuroscience rhymes with Lewis. Trust me, I’ve racked my brains). You can check out “Gaines, on Brains” here.

How did you get into science blogging and science writing? What were the early influences on you regarding your blogging style and topics?

I’d had the Scientific American gadget on my iGoogle homepage for years (RIP iGoogle) and always enjoyed reading the articles on there. It took me awhile to realize that half of the pieces I was enjoying were actually blog posts by writers in the SciAm blog network. SUPER cool. That, combined with my lifelong love of writing (and the impending fear of beginning my doctoral program and being out of work after attaining my degree), inspired me to start up my own blog. I can’t believe how much my blog has evolved and how many different types of people I’ve reached since starting it up.

What is your blog about? Who is your target audience, and why do you think people should read your blog?

“Gaines, on Brains” is pretty much about anything remotely brain-related that I think will be interesting. Ah, I just had a deja vu episode…hey, I bet people are curious about what’s going on there. Better blog about it! I also take suggestions from readers and am constantly jotting ideas down in my planner. I also write about current research and hot topics in the news in an effort to “set the record straight,” so to speak. My target audience is the general lay community. Neuroscience is a ubiquitous and highly-misconstrued field, and dopamine is more than just the “happiness chemical” that “makes your brain light up,” as the TV doctors would say.

How do you spend your time when you’re not doing science or science blogging? Any interesting hobbies?

I dabble in all sorts of things. (I get bored easily.) I like working out (just ran my first half-marathon two weeks ago), reading, knitting, painting, binge-watching shows on Netflix, and eating delicious food (not hard when I live in Hershey). I’m a huge trivia nerd when it comes to The Beatles, Harry Potter, and Titanic (the actual ship, not the movie). I also like to volunteer my time walking and socializing dogs at the local shelter.

Why did you decide to become an editor at ScienceSeeker?

I’d actually applied to be ScienceSeeker’s Photo Editor last year. When Dave Munger saw my application, he thought I’d be well-suited to being some sort of Social Media Editor; and thus the position was created. So when you see a Facebook post (“Like” our page here!) or Tweet link to our Twitter), that’s me!

Next steps for the new site

We’re now beginning work on the new version of the Science Blogging Aggregated site.

We’d like to have a working prototype of the site ready for the ScienceOnline conference in January.

Realistically, by then we’ll probably be able to implement the following features:

  • Users login and register blogs
  • Some sort of administrative check-off on registration, with anti-spam measures
  • Aggregator compiles entries from registered blogs, displays on home page
  • No tagging of individual posts, but blogs are categorized by user-specified “themes”
  • Visitors can filter posts appearing on home page by theme

We may also add a language filter allowing users to specify their preferred languages. (This may be difficult to implement because it would require having curators in each language we support) Over the long term, we would like a multi-lingual interface, so all users can experience the site fully in their native language.

We are leaning towards a dense, information-rich layout for the home page, much like the existing home page, but with additional tools for users to filter posts, login, register, and so on.

In order to maximize the site’s utility, we are thinking about pre-populating the database. This would probably be a manual process, based on the existing feeds for ScienceBlogging.org. This would require an additional feature so that users could “claim” their blog and personalize their account. However, we’re not sure that’s doable by the January deadline. If readers can suggest models for how claiming a blog could work, with a minimum of fuss, we’d appreciate suggestions.

We are also considering a a new domain name for the site—we’d like it to be a truly notable name, one that’s memorable, says something about the site, and isn’t easily confused with some of the other science sites currently out there.

So here’s our plan for the next steps. We’ll keep you up to date as we continue to work on the project:

  1. Develop a schema for a database that can handle the trimmed-down version of the site that we’re planning for January, but is flexible enough to meet our long-term goals
  2. Arrange for site hosting. We can work on our existing personal server space for now but we’ll need a permanent home, and the sooner we find it the better.
  3. Wireframe the first (limited-feature) version of the site: Create a template that developers can use to build the system, indicating what information will go on each page. Again, we may want to do this in anticipation of the higher-functionality site to come, so we don’t have to constantly reinvent the wheel.
  4. Explore the process of creating a non-profit organization. This may be a larger non-profit that also includes ScienceOnline.
  5. Create a schedule for the process of developing the site up through the conference.
  6. Recruit additional help. We’re really short on programmers and designers. Any volunteers?

An outline for version 2.0 of the site

A few weeks ago I wrote up a tentative outline for the next generation of Science Blogging Aggregated. I’ve been sharing bits and pieces of it with you over the past week, but now I’d like to share the whole thing. It’s still a work in progress, a Google Doc that reflects our current thinking on the project—but of course, something that will continue to be refined as we move forward with the project.

Click here to view the document.

I’ve already tried to incorporate as many as possible comments from readers as I’ve shared the plans with you, but of course we continue to be open to additional suggestions. I think this is enough for us to use to get started, but there’s obviously much work still to be done. If you’d like to help out, you can either email us directly at contact@scienceblogging.org, or add a comment below and we’ll get in touch with you via the (hidden) email link you provide in the comment form. Particularly useful at this stage are people with CSS / web design experience, developers, and sysadmins.

We’re hoping to present a working prototype of the site at Science Online 2011. I’ve suggested a session on the conference wiki here.

We’ll continue to keep you posted and ask for your advice and suggestions as work progresses.

Tagging strategies

Dave’s earlier posts sparked some good conversation about tagging. Here is my proposal for how tagging could work on the new version of the site. This proposal isn’t necessarily what we will do; I’m putting it out there to get feedback from the community about whether it’s the right approach.

First, an overview. There are two ways to approach tagging:

  • Folksonomy: all the users use their own tagging schemes. There are tools to let users discover tags already in use.
  • Ontology: the owners of the site describe exactly what tags people can use, and expect people to use them.

Our goals are also twofold:

  • To help  readers of science blogs more easily find the content they are looking for, and
  • To do so without imposing constraints on the authors of science blogs

I believe that folksonomies are the best solution to the above dilemma: they impose no constraints on authors; and, if things are done right, hopefully many of the tags will start to come together. My suspicion is that if we specified a strict list of tags, users would not want to use them.

But how to make the folksonomy chaos into something useful? We will maintain adatabase of tags. Each tag’s entry in the database will have (at a minimum — this can be expanded later):

  • Name of tag (e.g., “tamarin”)
  • List of synonymous tags (“Saguinus”, maybe “tamarind” if we want to support common mistakes)
  • List of children tags (“cotton top tamarind”, “cotton top”, “Saguinus oedipus”, etc — may be very long)
  • List of parent tags (“New World monkeys” — may be multiple)

Bloggers may tag with any of the synonymous tags. Let’s say we do decide to support mistakes. Someone may tag “tamarin” or “tamarind”. Those are different tags, but our system understands that they are synonymous.

Someone searches for “tamarin.” They get a list of posts tagged with either “tamarin” or any of the synonymous tags (so “tamarind” or “Saguinus”).

So what are some problems which might arise?

What if one tag is used for two entirely separate things?

A physics blogger uses “charm” to describe a kind of quark. An anthropologist uses “charm” to describe something used medicinally by a tribe of primitive people. A user searching for “charm” will get both.

I submit that this isn’t a huge problem. It isn’t going to happen all that often. When it does, in almost all cases, the user will be able to refine their search to say “I am only interested in ‘charm’ tags used on blogs with a ‘physics’ theme.” It will be annoying to the people who want to see what the parent/children tags are for “charm,” because they’ll get a weird mix of physics and anthropology subjects. But I think it is not going to happen often enough to really be annoying (and it is better than the alternative of trying too hard to control things).

Sounds like a lot of work to input parent/children/synonym relationships!

Yes. We will have to start with no relationships at all — just a big flat list of tags. Eventually, each subject area will have one or more curators who help manage it. Part of their jobs may be to input relationships for tags in their areas. We will have to make a user interface to make this very easy. Perhaps we will build a user interface to allow users to suggest the addition of new relationships, as well.

The point is that we can do this very gradually. The system will start working immediately, and then be improved with time.

What about brand new tags (“pepsi-gate” vs “pepsigate”)? How can curators possibly keep up with that?

In that case, I believe that the crowd will start to converge, if a) we provide incentives to use the same tags — “if you use the most popular tags, your post will be more discoverable and you’ll get more readers” — and b) we make it very easy for bloggers to find out what the relevant tags are.

Of course, we will provide a list of available tags, organized for readability once we have parent/child relationships. Additionally, we will need a tool to provide tagging suggestions to bloggers while they are writing blog posts. Again, that can be something to do a little ways down the road.

We can also provide a page on the site which offers lists of the currently most popular tags, maybe even the most popular new tags. If it’s clear to someone that they are about to browse “pepsigate” posts, then if they want to write a followup, they are likely to remember that that’s the tag they are responding to, and tag their post appropriately.

Won’t this list of tags become so long that any tool which auto-suggests tags to users will become too slow to use?

This problem can be at least partly alleviated by letting users specify that they are only interested in tag suggestions from particular categories. Once parent/child relationships are in place in the tag database, tag suggestions can be filtered that way. We can also learn from other tools that offer auto-complete over large spaces to see how they solve this problem.

Have folksonomies been successfully used in the past? What are good examples?

Obviously, Flickr is the best example of a site which has completely user-generated tagging. Their mission is somewhat different from ours, though! Do you have examples of folksonomies that work or that have failed?

This post is intended to start discussion, so please, weigh in! What do you think about this approach to handling the huge number and variety of tags in use on science blogs? Is it clear, and do you have questions?

Building a better network: Identifying trends/posts of interest

When you build a network of blogging networks, the problem quickly escalates from “how do I collect as much data as possible?” to “how do I manage all this data?”

Take a look at the Science Blogging Aggregated home page. There’s lots of great stuff there — too much for the typical reader to handle. Even if you visit several times a day, the information rushes by too quickly to discern any trends, and it’s hard to know which posts are really well thought out and which are just one-off posts that hardly merit your attention at all.

We talked yesterday about one way of sorting through the data — tags. However, this method alone probably won’t satisfy all users. A person might be interested in all posts tagged “psychology,” but they might just want to see the highlights of what’s going on in other fields, and tagging won’t help them identify the most interesting, thoughtful posts.

We see at least four possible ways of sifting through the posts to find the most interesting ones.

1. Crowd-sourced ranking. Users rate or recommend posts they like, so others can sort by rating or number of recommendations to find the posts they want to see. An advantage is that there is no central authority telling readers what to like. A disadvantage is that blogs that are already very popular are perhaps most likely to be recommended, so this system might not help users identify up-and-coming blogs that are very high quality.

2. Self-promotion. Bloggers could promote a small number of their posts, indicating these are their best work (one per week? one per month?). This overcomes the “up-and-comer” problem, but a blogger whose work is mediocre could exploit the system by promoting posts that aren’t very interesting or useful to others.

3. Active curation. Editors could be chosen for each field (physics, biology, etc.) and actively promote one or two posts each day. That way readers would know that an expert has read all the posts on a topic and selected the most interesting or relevant. Advantages are that editors may be able to identify trends that more automated systems don’t catch, and that editors may be less swayed by the most popular blogs. Disadvantages include possible bias of editors, and variable editor quality. It would also require coming up with a system for selecting editors. Would a central person be in charge of that, or would we need to create some sort of a system for nominating/voting for editors?

4. Social networking. We could create a truly social network where users are only shown the “likes” of their friends. However, this requires a significant programming effort, and people are reluctant to join new social networks when they already participate actively in one or more networks. I think we might be better off using the social features of other networks, rather than building our own. If we could make it really easy for people to post their “likes” to Twitter and Facebook, then we could leverage those networks to perform the social function.

There is, of course, no reason that we shouldn’t do all of these things over the long run. But we have limited resources. Which of these approaches is most useful? Are there any other approaches that would work better? Do you have any specific suggestions for how to implement any of these ideas? Let us know in the comments.

Building a better aggregator: Goals, Tagging

The ScienceBlogging site you see now was always intended to be a temporary solution. What we really need is a site that not only aggregates blog posts, but also allows users to classify them, search them, highlight their favorites, point their friends to them, and do many other things we haven’t even imagined yet.

Behind the scenes, Bora, Anton, Jessica, Mark, and I have been discussing how to do that, but we realized that limiting the discussion to just ourselves is depriving us of a valuable resource: The people who’ll be using and contributing to the new site.

So, over the next few days, I’ll be offering some thoughts about how to proceed and inviting your comments. Our plan is to have at least a partially functional, working prototype of the new site by the ScienceOnline conference in January 2011. Let’s get that started right now by discussing the goals for the site.

Goals
Here are the goals we came up with for the site:

  • To be a central site where scientists, media, other experts, and laypeople see what scientific topics are being discussed on blogs, in real time
  • To be a resource for locating past discussions
  • To promote science blogging and other online discussion of science
  • To promote scientific accuracy and avoid pseudoscience and crackpottery
  • To be encyclopedic and inclusive
  • To be searchable and filterable
  • To have a system (or multiple systems) for highlighting discussions and posts that are especially topical / high quality
  • To have a means of removing or hiding posts that are not scientific (e.g. vacation photos, political rants unrelated to science, etc.)
  • To be multilingual
  • To be open source / open access

Should anything be added, changed, or removed?

Tags
One of the first considerations will be how to keep track of all this information, and a huge key to that will be classifying it. That’s why we think it will be essential to have a unified tagging system in place. If bloggers don’t select their primary tags from a central list, then it will be difficult for users to find posts on the topics that interest them. On the other hand, if bloggers must visit our site to choose primary categories, then usage will suffer. We can allow bloggers to set default tags for their posts using their registration page, but there should be some way to override those settings for individual posts, still using our list of preferred tags.

Could we create a WordPress plugin for this? Or adapt an existing plugin? What about other blogging platforms? What about templates that don’t support tags? One possibility is using a bookmarklet, which would be platform neutral but not ideal. Any other ideas on how to implement a tagging system?

That’s just the first bit — there’s a lot more to discuss, but we thought this would be a good way to get the conversation started. So please, let us know what you think in the comments.

Finding people to aggregate with

Aggregating blogs is not technically difficult. (See previous posts: How to create an aggregated feed and Feed aggregator choices.) Finding other people to aggregate with can be a challenge, however. Feel free to comment here in order to find other people to aggregate with. One way to start is to suggest a topic (neuroscience? medicine? new bloggers? meta-science blogging? students? faculty? physics? astronomy? anthropology?) that you blog about, and ask if others want to aggregate posts on that topic.

Remember, if you are an independent blogger who wants to be listed on scienceblogging.org, putting together an aggregated feed is currently the only way.

Also, remember that you can choose to aggregate only selected posts if you want, using tags as filters. Or you could aggregate your entire blog.

Feed aggregator choices

There are a bunch of feed aggregators out there. However, I haven’t used any of them, so I don’t know which ones work well and which ones work poorly. I encourage people to try them and comment here with their experiences. I can edit this post with useful information from the comments.

Web services

Below is a list of web services which will allow you to set up a feed aggregation.

  • Yahoo Pipes. Widely used. Pipes has a blog where you can learn more about it. Some people seem to find it hard to use. Others complain that it edits the RSS feeds that it passes along (for example, changing whether the links open a new window or not). The Scienceblogs Diaspora Feed runs on Pipes; you can clone and edit that feed (this may be a good way to get started if you find Pipes confusing). There is a review of Pipes which might be interesting.
  • FriendFeed. Another widely used one, and seems to be a better bet than Pipes (but comment here and say why or why not!). FieldOfScience uses this one. Commenter Edward says: “FWIW, I’ve done the grunt work with the Yahoo Pipes. You’ll need a Yahoo account, but once you have one you can simply Clone this pipe: http://pipes.yahoo.com/fieldofscience/full. With your Clone, go to Edit Source, then change the feeds in the Feed Fetch module to yours, and in the Simple Math module put the number of feeds you are combining.”
  • XFruits. Seems to be very feature-rich. I don’t know of anyone who is using it.
  • Dapper
  • FeedWeaver
  • FeedStitch
  • FeedKiller. Looks very easy to use; doesn’t require a login; which means, I think, that the feed won’t be editable later; puts a feedkiller ad on each post.
  • Feed Informer. Also looks really easy to use.

Software packages

If you have access to a web server and are able to set up a software package on it, you can run your own feed aggregator. Benefits: no ads inserted into the feed; you are in charge of the server and whether it is stable. Down side: you have to have some knowledge and a server.

Other tools

  • Feedburner. Once you have a feed, you can use Feedburner to make a new URL for it. This can be nice a) because Feedburner provides usage statistics, and b) in case your new aggregated feed has an ugly URL.
  • Feed Rinse. Filters feeds for you: “You can rinse your feeds by keyword, author, tag, etc, or filter profanity and more.”

Did I miss anything? I’m sure I did, but I’m happy to add more if you let me know what I left out.

How to create an aggregated feed

Hi. You don’t know me, but I’m here to try to help out with some of the technical aspects of science blog aggregation. I’m going to start by writing about how some bloggers might get together to set up a blog aggregation.

So: you are an independent blogger, and you want to aggregate your blog with some friends’ blogs, and then you want scienceblogging.org to aggregate that aggregation. What does that mean, and how do you go about it?

The people

The first step is to find a group of people who blog about similar topics at least some of the time.

You sometimes post about cognition, sometimes meta thoughts about science blogging, and sometimes personal ramblings, at ramblingscienceblogger.blogspot.com. Your friend Jane writes about neuroanatomy, addiction, and her young daughter at janesaddictionneuro.blogspot.com. Your friend Bob writes about behavior, neurotransmitters, and his dogs at bobsbehavior.wordpress.com. The three of you would like to create a “Brain and Behavior” aggregated feed. You agree that any posts in any of your three blogs tagged “neuroanatomy” or “behavior” should be included in the new aggregated feed. Posts that don’t have either of these tags won’t be included, although posts that have one or both of these tags and some other tags will be included.

For example, when Jane writes a post about the hippocampus, she tags it “hippocampus” and “neuroanatomy.” This post will be included in the aggregated feed. When she writes a post about her daughter, she tags it “kidblogging” only. It will not be included in the aggregated feed. Bob writes a post about a funny thing his dog did yesterday and tags it “ginger”; it is not included. Then Bob writes a post about how his dog’s behavior during thunderstorms reminds him of a recent article he read about fear conditioning in rats, and he might tag that “ginger” and “behavior.” That post would be included.

My examples assume that all the bloggers in this group are independent bloggers, but of course they could just as easily be bloggers on a network of some sort.

The aggregation

You choose an aggregator service to manage your new aggregated feed. You tell this aggregator service to aggregate the following feeds:

http://janesaddictionneuro.blogspot.com/feeds/posts/default/-/neuroanatomy

http://janesaddictionneuro.blogspot.com/feeds/posts/default/-/behavior


http://bobsbehavior.wordpress.com/tag/neuroanatomy/feed/


http://bobsbehavior.wordpress.com/tag/behavior/feed/


http://ramblingscienceblogger.blogspot.com/feeds/posts/default/-/neuroanatomy


http://ramblingscienceblogger.blogspot.com/feeds/posts/default/-/behavior

In other words, you are telling the aggregator service to pull in RSS feeds for Jane’s, Bob’s, and your blogs, but only the posts with the tags that you care about. You must include a separate URL for each tag and each feed — so for two blogs and two tags, you include four URLs. For three blogs and two tags, you include six URLs, and so on. The patterns demonstrated above will work for all blogspot and wordpress blogs.

The aggregator service then provides you with a new RSS feed which contains all the posts from Jane’s, Bob’s, and your blogs tagged “neuroanatomy” or “behavior.” You publicize that RSS feed however you want — you may just blog about it, or you may create a web page as a home site for it. You definitely let scienceblogging.org know to aggregate it (contact@scienceblogging.org).

If you later decide that you want to aggregate your meta science blogging thoughts with some other people who also like to write about science blogging in general, there’s nothing to stop you from having a second aggregated feed on an entirely different topic, with entirely different people, using your same blog. Just use different tags. In fact, one post could show up in both aggregated feeds, if it used the right tags.

What is a tag?

Tagging is a way of noting the subject matter of a particular blog entry. Most blogging platforms will provide a way for you to tag each blog entry.

What tags should I use?

That’s for you and your co-bloggers to decide. It would be nice if bloggers started coming to a consensus on tag names for particular topics, so that aggregating different blogs by tag was easier. We’ll see if this happens.

What if my blog is not a Blogspot blog or a WordPress blog? How do I find out what the right format is for a feed for a particular tag?

Try doing a web search for “tag RSS” and the name of your blogging platform. Or comment here and I will try to help you figure it out.

What’s the point of this, anyway?

Subject aggregations are convenient for readers — a way to get an overview of blog posts by topic, rather than by author. They are also a way to build community, with several different authors working together to generate related content.

What aggregator services are out there and which are the best ones to use?

There seem to be several to choose from, but I don’t have experience with them to know which are better. If you have found particular ones that you like or don’t like, comment here and let people know. Yahoo Pipes seems to be widely used, but there are others.