I’m currently updating our website to use some new technology that I’ve come up with to improve our readers’ experiences: Xomment.
Comments will now be panelized.
Comment preview and response will be done on the same page. No more refreshes needed.
There will also be a bathroom wall hosted on this site, already linked to above.
I’ve made some changes to our custom javascripts and some of our backend code. I’ve also enabled compression of the webpages. Hopefully, things will be more responsive.
Our biggest change was the migration from the Prototype javascript library to the jQuery library. Most of the behavior is the same, although some bugs have been fixed.
Our most noticeable change was replacing the existing spellchecker with a new one: GoogieSpell.
Sometime late this week, I’m going to do some maintenance on the server and this website. I’m going to experiment with enabling compression again. Last time it broke page caching on IE 6. So if you see that this page doesn’t update any next week, then try cleaning out your cache (or use ctlr-r) and see if that fixes the problem. Hopefully, it won’t occur again.
Well Bora and I and our 30+ judges managed to sort through the nearly 500 submissions and find our 53 winners. Some of use used the stairs methods to assign grades and others programed complex random number machines, while a few decided to read the 400+ submissions.
I am happy to announce that Ian Musgrave will represent the Panda’s Thumb again this year in The Open Laboratory with an essay that fuses two excellent articles:
Stuck on you, biological Velcro and the evolution of adaptive immunity
Let’s congratulate Ian for his contributions to science blogging.
We are at the submission deadline for The Open Laboratory: The Best Writing on Science Blogs 2007, edited by Bora and myself. Go here to submit quality science blog posts from 2007 before the deadline, Thursday, Dec 20th. Bora has a list of the current submissions, so if you seen any good posts not represented go ahead and submit them.
We are also looking for a good poem and comic to go along with the anthology.
Judging is already underway and it is going to be a tight fit, but I think that we will get the book out before the 2008 Science Blogging Conference.
We are nearing the end of the year and and the submission deadline for The Open Laboratory: The Best Writing on Science Blogs 2007, edited by Bora and myself. Go here to submit quality science blog posts before the deadline ends, Dec 20th. Bora has a list of the current submissions, so if you seen any good posts not represented go ahead and submit them.
Now comes the hard part. I need 20-25 science bloggers and science blog readers to volunteer to judge the quality of the submissions. You won’t have to read hundreds of entries, just the ones in the categories that you are assigned. I’m planning on using the following categories (subject to change):
Life Science: Biology, Evolution, Health, Medicine, Neuroscience
Physical Science: Physics, Chemistry, Math, Astronomy
Environment: Climate change, Pollution, Sustainability, Green living, Alternative energy, Geoscience
Humanities & Social Science: Anthropology, Sociology, Archaeology, Psychology, History and Philosophy of Science, Ethics, Arts & Culture
Education & Careers: Science education, Teaching, Curricula, Lab Life, Grad School, Funding, Evolution in schools
Politics: Politics, Elections, Government, Public policy, Culture wars, Creationism, Antiscience
Medicine & Health: Public health, Epidemiology, Pharmaceuticals, Health care, Medical training
Technology: Computers, Software, Hardware, Engineering, Consumer Electronics, Fuel and energy technology
So if you are willing to judge a couple of these categories, please send me an email at [Enable javascript to see this email address.] with a short message about why you think you could be a good judge.
I think that I’ve fixed most of the encoding issues that I am aware of. I had to edit a few lines of MT code and add some new logic to my MT-Dispatcher.
Parts of the database are still “corrupted” because of the bug. I can fix most of it, but I won’t do it right away.
I will begin to upgrade this site today. Recent comments may be lost, so I am disabling comments until I have finished the change over.
Sometime early this week, we will be upgrading the server software, transitioning to PostgreSQL, and deploying a new site design. Service may get spotty, but enjoy a sample of our new look:
Constraints surround us. One of the constraints we have running a popular and well-received weblog is the fact that our CPU cycles and especially our bandwidth are finite commodities on the server. Earlier this year we upgraded the server hardware (with the aid of readers here and at the After the Bar Closes Forum who donated to the TalkOrigins Archive Foundation), which gave us a lot more CPU cycles to play with than we had before. However, just like other popular web sites, there are people who want to profit off of our popularity on the cheap: spammers. They seek to subvert comments and trackbacks for the purpose of advertising their tawdry and/or fraudulent products and services.
A couple of weeks ago, we made the decision to pull the plug on the trackback facility. We were getting upwards of 200 simultaneous connections on the server, the vast majority of those hitting the trackback script, and the overwhelming majority of those were spammers trying to register thousands upon thousands of fake trackbacks. In the interest of keeping up with real users, trackbacks had to go.
We hope to be able to restore trackback functionality soon. Movable Type has released version 4.0 of their weblog software, and there are improvements in the way spam comments and trackbacks are handled. PT will be upgrading soon. We may be using a default template for a while, but we hope to minimize the disruption to posting and commenting.
As some of you may know, I’m working on a new layout for the Panda’s Thumb and updating our backend at the same time. I’ve decided that this might be a good opportunity to delegate my work load to other experienced programmers.
I have a list of several projects that I’d like to complete before the role out of PT 2.0. So if you are interested in helping, send me a email at [Enable javascript to see this email address.]. I am looking for people who have lots of experience with Perl, MoveableType, MySQL, PostgreSQL, AJAX, JSON, Prototype, and/or Javascript.
For dinner this evening RPM over at evolgen organized a science bloggers dinner. Prof. Steve Steve and I managed to make it. (Of course, Steve Steve is just happy that he is not stuck in the AA system anymore.) On the suggestion (direction?) of John Logsdon we headed to il Mercato for some lovely Italian food. I had seafood spaghettini, and it was mm—mm—good.
At the end of dinner the waitress was nice enough to take a group picture.
Back: John Logsdon Jason Stajich RPM Julius Lucks Reed Cartwright Prof. Steve Steve Rosie Redfield ?
Front: Jacob Tennessen ? ?
I’ll post names and urls of people as people claim themselves in comments.
We’re back from the dead, having pressed our new server into action earlier than expected. The back end is now running again after we handled having the existing PT site and the new site—it’s still secret—running on the same server.
See Wesley’s note on ATBC about what happened and what changes we’ve made.
Here is a teaser of the new site:
The slowdown seen today was the result of a DDOS “attack” on PT. I’ve banned nearly 50 IP addresses that I think were the cause of it. Let me know if there is any collateral damage.
Over at After the Bar Closes, Steve Story has set up a poll asking for educational background from PT/AtBC participants. With 90 responses in, the results so far are:
Check it out.
A researcher at the University of Florida and his colleagues have used game theory, which is important to evolution and economics, to show that net neutrality encourages internet service providers (ISPs), companies that offer dial-up, cable modem, DSL, or similar access to the internet, to increase their bandwidth. The ISP industry is currently pressing congress to pass legislation ending net neutrality.
Under the current, net neutrality law, ISPs are required to partition their bandwidth based on the size of a site and how much their customers access a site. However, if net neutrality is ended then ISPs will be allowed to partition their bandwidth based not on their customers needs but on which websites can pay the most money. If net neutrality is ended, then ISPs will be able to extort money from content providers like Yahoo, Google, or even small fry like us, by offering to increase (or threatening to decrease) the speed at which the customers of said ISP can access the content provider’s sites.
According to an article in ScienceDaily, the researchers showed that customers lose out if net neutrality is ended, for the simple fact that ending net neutrality encourages ISPs to decrease the bandwidth available to their customers.
More important, the researchers found that the incentive for broadband service providers to expand and upgrade their service actually declines if net neutrality ends. Improving the infrastructure reduces the need for online content providers to pay for preferential treatment, Bandyopadhyay said.
“The whole purpose of charging for preferential treatment to content providers is that one content provider gains some edge over the other,” he said. “But when the capacity is expanded, this advantage becomes negligible.”
He gave the analogy of the expansion of a two-lane highway where drivers willing to pay a toll to subsidize road improvements are rewarded with exclusive use of a faster lane.
“If the road is upgraded from two to four lanes, with one express lane, these drivers might say ‘Three lanes are good enough for me. I don’t want to have to pay a toll any longer,’” he said. “So the desire to pay a toll when the road is expanded gets lesser.”
The experience of other countries also suggests that better service – up to three times faster – results when there is greater competition, Cheng said.
“In Japan and Korea, where there is net neutrality and much greater competition among broadband providers than in the United States, there are also higher broadband speeds,” he said.”
I find it interesting that despite several articles on the confluence of science and blogs in science magazines and journals and the establishment of blogs by many mainstream science news outlets, the AAAS’s EurekAlert! refuses to grant embargo credentials to bloggers. As Dr. Hsien Hsien Lei of Genetics and Health was recently told:
I appreciate your email, Hsien, but unfortunately, the decision must stand. Our eligibility criterion does not include writing blogs of any kind. Feel free to re-register in the future, should your writing outlets expand.
Did you get that? Blogging is a narrow outlet. I guess AAAS doesn’t think that thousands of daily readers is a broad enough audience to promote their articles. I guess such an derision of Web 2.0 might explain why PLoS has been successfully cutting into Science’s market.
How about we show EurekAlert! that there is a market out there for blog-based science news? I suggest that all the science bloggers out there, who read this, go apply for journalist access to EurekAlert!. Just fill out this form and mention your position as a blogger. Don’t forget to leave a comment here about your experience.
In the comments, Ginger Pinholster, AAAS’s director of public programs, has clarified their position. It looks like those of us with dual affiliations, e.g. scientist-bloggers, are out of luck.
John Dupuis at Confessions of a Science Librarian has good things to say about The Open Laboratory (2006).
At first glance it seems that [Bora] Zivkovic set himself an impossible task trying to pull something decent together, both in terms of the presentation and the quality of the content, in such a short period of time. We can probably only expect something shoddy and half-assed—right? Well, I’m happy to say that all fears of disaster were certainly not justified—anyone that pays attention to Zivkovic’s blog knows that he’s smart, capable, dedicated and without a doubt energetcic and that he wouldn’t let something unworthy out the door.
This review is just in time for Bora’s announcement that we are now taking submissions for the 2007 anthology. Unlike last year, we will begin to compile a list of worthy posts in March instead of at the last minute in December. Any original blog entry made between 12-20-06 and 12-20-07 is eligible.
If you want to spread the word, I have put together a badge that you can use to link to the submission form.
Also for all you 2006 winners, I have made a badge honoring your achievement. Go ahead, place it on your blog so everyone can know how great of a science blogger you are. Note that you can see a demo over in our sidebar.
Are any of our readers interested in meeting up for lunch in Raleigh next Saturday? Prof. Steve Steve will be there. You can have your picture taken with him.
Some of you may have noticed that the Talk.Origins Archive was not accessible today. Its hosting company changed the IP address for the server that the Archive is on. The new IP address is currently propagating through the DNS network and you will be able to access the site again as soon as your ISP updates its records.
Also we’ve ordered a new server for PT and will have access to more bandwidth soon.
Current plans have us switching to the new connection tonight. This means that PT may go offline for you until your ISP picks up the new IP.
If you haven’t voted for us today, now is the time to do it.
Have you voted today for the Panda’s Thumb as the best science blog of 2006? Remember that you can vote every 24 hours.
Right now we are in a race for third place with In the Pipeline.
Well, our server upgrade didn’t go as planned. As a consolation prize, we’ve added another gig of memory to the existing server, and made changes to the server to take advantage of it. We are still planning to upgrade our server and our bandwidth connection. We have enough funds for a new server, but if you feel like donating for the future, give to the Talk.Origins Foundation.
I’ve also reenabled compression for Microsoft Internet Explorer. My tests show me that the previous pt-msie interaction problem has been fixed, probably when I finally fixed the time zone two weeks ago. Let me know if you are having problems with pages not updating correctly.
We have ordered a new server, and if everything goes according to plan, we will make the switch this weekend. Be prepared for PT to go offline this weekend. We are still exploring our options for improving our bandwidth.
When we switched to our new server software, it appears to have screwed up how some browsers manage their cache. This means that some browsers are stuck on outdated pages.
To fix this issue, you need to clean out your cache (or temporary internet files).
I’ve made some layout changes to my personal blog. Why am I telling PT readers about it?
Well, depending on how the new layout works on my blog, I’m going to update the layout of PT. So let me know what you think about the new layout on De Rerum Natura.
We’re making some changes to the server to increase performance and decrease downtime. We’ve migrated from Apache to Lighty. We’re still tuning things so expect random behavior of the server for a bit.
Long term goals involve getting a more powerful server and getting a fatter connection to the internet.
If you are motivated to donate, there is a link on the sidebar.
Hi All,
Wesley and I are working on fixing the server issues that this website has been having. We switched to a new connection a month or so ago and PT’s popularity is overwealming it. We’re working to optimize the server for short term solutions and looking at solutions for the long haul.
Nature, one of the top journals for scientific research, published an article today about the most popular science blogs. The Panda’s Thumb came out number two, and Jack Krebs was quoted about our success:
Being a group blog is key, says contributor Jack Krebs, president of Kansas Citizens for Science. “We have some of the most well-informed observers and critics of the ‘intelligent design’ and creationist movements.” The nature of the topic helps too, he adds. “There is an interest, a hunger even, for thoughtful analysis of the issues related to evolution and creationism.”
In addition, PT contributor, PZ Myers, found his personal blog, Pharyngula as the most popular science blog.
Over all, six of the top fifty science blogs were personal blogs of PT contributors.
| Rank | Authorship | Blog |
|---|---|---|
| 1 | Paul Myers | Pharyngula |
| 2 | Group Blog | The Panda’s Thumb |
| 7 | Tara Smith | Aetiology |
| 18 | John Lynch | Stranger Fruit |
| 21 | Jason Rosenhouse | EvolutionBlog |
| 26 | Mike Dunford | The Questionable Authority |
| 30 | John Wilkins | Evolving Thoughts |
Those of you who use Google News Alerts for phrases like “intelligent design” and “evolutionary biology” have probably noticed that the Discovery Institute’s Media Complaints Division (aka “Evolution News and Views”) turns up with depressing regularity. More recently, I was amazed to find that “Uncommon Descent” weblog posts were also being treated as news sources.
So, it seemed to me that it couldn’t be so difficult to get a source listed in Google News. And it wasn’t. It is in the Google News FAQ:
What if I don’t see my favorite news source in Google News?
We’re as shocked as you are! If we’re missing a publisher that we should be covering, please send us your ideas. While we can’t guarantee that we’ll heed your recommendation, we do promise to review all the suggestions we receive without regard to political viewpoint or ideology.
I sent in a suggestion that they pick up the National Center for Science Education main page as a news source, and within a week got notice that they were adding it to their list. Recent News Alerts have included NCSE front page items, so that particular suggestion is complete.
Now that you know how it is done and that it works, I’d like to ask the PT readership to take a moment to nominate various pro-science sources to the fine folks at Google News. You may find the list here on the PT right-hand sidebar useful to find candidates. Check out the links at the TalkOrigins Archive, too. Please leave a message in the comments for each site that you do nominate.
