Plausible Accuracy

I already linked this story over on the shiny new microblog, but I can’t resist reposting here.

PZ Myers, writer of (probably) the most popular science-related blog on the internet and outspoken Atheist, attempted to go see the Intelligent Design-pushing movie Expelled last night in Minneapolis.

He was turned away from the theater by security.

The end of his tale, however, is so delicious that I can’t spoil it for you.  Just read his post.

I’ve got a “Tumblelog” over at Tumblr.com as well as a Twitter account. I wanted to somehow include both of these in this blog without directly integrating them with the Wordpress blog itself. I decided that this should be possible to accomplish by using a Wordpress Page with a customized template.

Googling didn’t turn up any pre-made solutions, so I decided to hack something together myself. I’m posting it here in case anyone else might find it of use. (more…)

anything is hilarious when paired with the proper track from the discography of Queen

Myself and others have written about the problems PLoS has been having with site performance recently.  I haven’t seen any performance improvements, but the PLoS IT head assures us that things are getting better:

Performance of the websites hosted on Topaz has increased over the last two weeks with a variety of patches ported to the production servers. We still have an outstanding memory problem that requires a restart of the Topaz applications three times a day (these restarts usually occur around midnight, 8am and 4pm with a duration of less than 10 minutes). I feel that we’re close to diagnosing the memory problem which is the last performance hurdle.

The words ring a bit hollow, since as of this writing search is still disabled.  My own non-rigorous test (clicking around the site a bit, loading articles and the like) was still met with long page load times, mainly when actually trying to access an article as opposed to navigating around.  After clicking on a figure, it took well over a minute for the page to load.

Obviously, they still have some major work to do in optimizing their code.  Apparently a new release candidate of Topaz should be ready soon, and one can only hope that this brings some important bug fixes.

I also find it a bit ironic that earlier in the week there was a post on the PLoS blog entitled “If it Ain’t Broke, Don’t Break It“.   Sage advice indeed.

Viruses are really interesting.  We all know about them, mostly as those things that make us sick.  In fact, only a very small percentage of viruses lead to illness in humans.  This is a good thing, because there are lots and lots of viruses.  I’ve been told that there are about 10,000,000 in a single milliliter of ocean water.

Viruses are, generally speaking, composed of two main parts.  The capsid, or outer “skin” if you will, is made up of proteins.  Inside of the capsid is the genetic material (this can be RNA or DNA).  Scientists are interested in examining how these particles are constructed, both as a way to learn methods of combating viruses, as well as to attempt to “reverse engineer” them to do our evil bidding.

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I’m an admitted NPR junkie.  I will listen to just about anything on the local station, although the quasi-religiosity of A Prairie Home Companion is starting to wear on me quite a bit.  My favorite show, however, is This American Life.  It’s pretty much a straight human interest show, with several stories each week based around some common theme.

This week’s episode, #352, was a bit different in that the entire episode concerned a single story; that of a kidnapping from 1912.  I don’t consider it one of their stronger episodes (the story itself didn’t interest me that much), but what did interest me was their choice for some of the music.

You see, I recognized it, because I had just bought the album - it was off of the NIN Ghosts set that I blogged about last week.  Now, I’m not 100% familiar with how these things work, but I do know that the album is governed by a Creative Commons BY NC SA license, which in plain English means that the work must be attributed, used non-commercially, and any derivatives must also use the same license.  This American Life, to the best of my knowledge, did not comply with these restrictions.

They don’t attribute the music (relying on their standard tagline: “Musical help this week provided by [staffers]“).  It’s a “commercial” work (debatably, considering it’s NPR), and although I’m not sure of what copyright the show employs, I doubts that it’s the CC-BY-NC-SA variety.

There are rules governing the usage of music in radio and advertising (a Google search turned up this book result).  The crux of the matter as it relates to the album is whether or not the radio show is a derivative work of the music.  What is interesting to me are the implications of the Creative Commons license/freedom of the original music and the interplay with the rules governing its use as music on a radio show.  Because the license permits remixes into an audio track, presumably this also includes something like a radio show.  This would seem to indicate (to me) that the show should then also be bound by the CC-BY-NC-SA license.  If, on the other hand, the producers of This American Life licensed the recording in the standard way for radio show music, then the issue isn’t relavant and I’m writing this all for nothing.

To me, the non-commercial section of the license is also critical.  If indeed the show producers licensed the music through the typical channels and then incorporated it into a commercial work, does that place their use of the album under a completely different copyright scheme?  Once NIN has released it under a CC license, are they allowed to selectively permit people to use their product in ways which do not adhere to the license?

All of these things will become more important as more and more artists release their work in a similar manner.  It may seem like pedantic nitpicking now, but that doesn’t mean that it won’t matter down the line.

I enter a few online image manipulation competitions from time to time. It’s fun, and I’ve learned a lot about Photoshop that has come in handy for other work, such as making graphics for presentations or the web.

I thought today I’d do a bit of a liveblog while I worked on an entry. Hope you enjoy

I’ll be doing an entry for the Woot weekly contest. They usually provide a theme, and the rest is up to the entrant. The theme this week is:

Show us a past or present woot brought down by scandal.

Let’s get this liveblog started.

8:00 - Brainstorming: This actually probably really started right after I saw the theme yesterday. This morning, however, I start sort of thinking a bit harder. At this time I think I want to do a play on the Teapot Dome scandal.

8:20 - Go back to contest description, look at already posted entries: Here I like to read the contest listing again, to make sure that I haven’t missed anything. Sometimes this gives me new inspiration or perhaps makes an idea I’ve come up with sound dumb. Not so much today. Also, I flip through the entries that are already posted to make sure that someone hasn’t already done something similar to mine. Thankfully, most of the entries so far are some play on drugs, Elvis, or both.

8:25 - Look up the Teapot Dome Scandal

8:27 - Start trying to figure out how to implement this cockamamie idea

8:33 - Look for source images: A source image can make or break a photoshop entry. I want to do an old newspaper, so off we go to the magical Flickr to search for them. After a bit of searching, I found a series of Yorkshire Evening Post snapshots from the 1940s, by Flickr user Mig_R. I really like the look of these, so let’s choose one as our starting point.

8:40 - Find the Font(s): Since I need to change the headline of the paper to a U.S. city, I’ll need that font. I use WhatTheFont along with a cropped image of the headline to identify a close match. It turns up Fette Gotisch, which is a fine font which unfortunately costs cash money. Time to do more searching. Finally I took the easy way out: since I only need a few words, I simply put those into one of the “try this font” boxes on a site trying to sell me the package. Nab a screenshot of the “test” and we are good to go. I used the clone stamp tool to erase “Yorkshire”, pasted the new city name in, and set the blending mode to “multiply” to remove the white background. After that I played with the hue/saturation, curves (drop in red, raise the green), and opacity to get it to match the rest of the text as much as possible. Finally I applied a layer mask and used a “grunge” brush in black to knock out little specks of the text.

To do the other bits of the masthead, I simply matched fonts from my machine and typed in what I wanted.

9:16 - Text work: Replacing all the text of the paper is quite a chore. You have to do a lot of careful work with the clone stamp tool so that the erased text doesn’t look too fake, then of course generate the replacement stuff. Here I decided that the scandal would be “Craps for wine”, in which people who wanted to get a Bag of Crap (Woot’s most famous offering probably) were required to send bottles of wine to the staffers, which they would then use to run Wine.woot.

10:00 - The image: To create the Bag of Crap image, I used the poster edges filter in order to get nice dark lines on the edges of the source. I set the blending mode to multiply again, dropped the opacity a tad, and played with the hue/saturation once again to get it to blend in with the vintage newspaper feel.

10:15 - More text work: Finally I did some ancillary text stuff to tie it in with the Teapot dome scandal (a minor occurrence in this paper’s reporting) and sort of wrap the whole thing up.

10:30 - I think I’m done, time to step away. Click the image for the full version:

Sometimes I’ll go back and make more edits later.  More often I’m sick of looking at the entry, and tend to purposefully delete the PSD file so I can’t fall prey to the endless tweaks.  I think we’ll go with the latter this week.  2 hours is about my limit for one entry.

I tend to talk a lot about Open Access science because it’s the field I work in and the place I feel like I personally can make the most difference. To be fair, however, I really want *everything* to be open.

That’s why I also like the sort of simmering groundswell of musical artists taking their work into more liberal copyright regimes. The ones who “get it” realize that they can’t fight their fans tooth and nail and still get those same fans to spend money on their work. Radiohead got a lot of press for releasing “In Rainbows” as a digital download with an opt-in price, but unfortunately it seems like this may have been more of a marketing maneuver than a real embrace of copyright freedom.

I discovered Jonathan Coulton some time back, sort of because his name kept popping up around other things that I liked. Something about his DIY nature - running his own website, writing and recording the music in his apartment - really make him a likable guy. It helps that his music is catchy and fun. He puts all of his songs up for sale on his website (as well as a few other places around the web, but buy from him and pass along all the profits why don’t you) as 192 kbps MP3s (oh and he has FLAC now as well) with no DRM at all.

Of course I have heard about Trent Reznor (of Nine Inch Nails) and his bile towards the traditional labels. I also knew that they released their latest album, Ghosts, as a $5 download without DRM under a Creative Commons license. What I hadn’t done until today was actually listen to it. I remembered the NIN from my high school days and assumed that it would be the same sort of stuff. I was wrong. Check some of this stuff out:

It’s sort of ambient instrumental, but with a good mix of sounds and beats that keeps it from getting dull.  I’m really loving what I’ve heard so far, and I’ll be buying this as soon as I’m sitting in front of my media machine.

Comment time (please, so far there are a whopping zero comments here): What is your favorite source of DRM free music? Amazon MP3 store? eMusic? Direct from artists? Other (indie) websites?

I really like PLoS.  That’s not entirely true, I love PLoS.  They seem to be doing almost everything right: Open Access scientific publishing, serious web integration, and a devoted and dedicated team of people making it all happen.  There are two things they are doing wrong, however.  The least important of these (in the grand scheme of things) is not giving me a job.  The second, and fairly critical issue, is the recent major performance struggle they have been wrestling with.

According to Richard Crave, the head of the IT/web team at PLoS:

We’ve gone to DefCon 5 at PLoS to resolve the performance issues. It’s time to lock everybody into a conference room, order a bunch of pizza and fix every performance problem on the websites.

That post was 10 days ago… I don’t want to imagine what the conference room smells like by now.
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I spent the first 4 years of my graduate program working on the NK1 receptor.  This is one of the very large and important family of G Protein-coupled Receptors which are a poorly understood and pharmaceutically interesting set of signaling proteins.

In the March 14 issue of Science, George et al report the use of NK1 antagonists - that is to say small molecules which block the signaling that normally takes place through NK1 - to treat alcohol cravings.

Before using the small molecule antagonist, they first looked at mice that were mutated to remove the gene for NK1.  These mice tended to drink a lot less booze than normal mice, or even mice which were missing the NK1 gene on only one chromosome.  Based on these results, they then decided to examine the antagonist treatment in humans.

It’s a bit surprising that the authors move so quickly from animal to human experiments, but they point out that the antagonist they chose is not effective in binding to the mouse or rat versions of NK1.  There is one line in the paper that is a bit frightening:

Preclinical pharmacology, safety, and human pharmacokinetics of LY686017 will be reported separately

I hope this is only for reasons of space constraints in Science…

Regardless, the authors found that treatment with the antagonist tended to decrease alcohol cravings in the patients (who were classified as “anxious alcoholics).  It’s an interesting result, and I think merits further investigation in the form of an expanded clinical trial.

George, D.T., Gilman, J., Hersh, J., Thorsell, A., Herion, D., Geyer, C., Peng, X., Kielbasa, W., Rawlings, R., Brandt, J.E., Gehlert, D.R., Tauscher, J.T., Hunt, S.P., Hommer, D., Heilig, M. (2008). Neurokinin 1 Receptor Antagonism as a Possible Therapy for Alcoholism. Science DOI: 10.1126/science.1153813