Tag Archives: Notable

Copyright and the Internet: A Personal Example

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I don’t normally watch SNL. Occasionally, Sadie and I will flip it on randomly and watch a skit, but I can’t tell you the last time I watched all (or even most) of an episode. I follow @davidsiegel (a software developer) on Twitter, and he tweeted a link to a YouTube video of a recent SNL musical performance by a group I’d never heard of called Fleet Foxes. I liked the song (Mykonos) so much that I had to hear more by them. I checked out Sadie’s cousin Chris’ blog, Flickin’ Spit, for a review, and he listed the newest Fleet Foxes album as one of the Top 50 Albums of 2008. So, I decided to buy the album from Amazon MP3. I went back to the video a few days later to find that it had been removed from YouTube per NBC’s request due to a violation of their copyright.

Without that video, I wouldn’t even know who Fleet Foxes were. I liked their performance so much that I bought one of their albums. You would think this is the point of NBC inviting them onto the show. But now I can’t share the same performance with others so that they might also buy the album. The performance is not available on Hulu or the NBC website. Whose copyright is NBC protecting here? Is it “for the artists’ own good” that the clip has been removed? Obviously not. Who exactly was it hurting to have that clip on YouTube? The answer is exactly no one. This is a perfect example of good advertisement, both for SNL picking a good artist and the artists themselves, squandered by malicious use of copyright power. Gimme a friggin’ break NBC. The online world would be a better place if companies started to see the importance of adopting a pragmatic approach to copyright enforcement.

EDIT: For those wanting to hear the song, you can hear the album version on YouTube.

Making Mistakes

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Making Mistakes | iface thoughts.  This was a great realization by Mr. Nadgouda.  Making mistakes (and learning from them) is the key to true innovation in any field.  Unfortunately, mistakes are not so “affordable” in medical treatment.

What can we do to continue to advance our field without endangering the lives of patients?  Is the only way to innovate in medicine through approved research?  Or is there a place for innovating and learning from mistakes in every medical practice that will not harm our patients?  What about the efficiency of your office and its dynamics?  What about innovation in the economics of the health care industry?

It’s something to think about.  Unfortunately, I think the threat of being slapped with a lawsuit has stifled a lot of potential innovation in medicine.  There is a fear of making mistakes, and a desire to maintain the status quo.  No doubt we want to reduce the number of negative patient outcomes, but that should not be done at the expense of the future of medicine and its practice.

Ubuntu Review: One Year In

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After a somewhat belated New Year’s resolution last year, I did manage to complete my goal much more easily than I previously thought possible. In the last 9 months, I can probably count on my two hands then number of times I’ve booted into Vista or XP. I’ve been using Ubuntu on a regular basis since at least February. Now you may ask why I made the switch to Linux. I intend to answer that by giving a summary, including the ups and downs, of my first year with Linux.

I had heard of Linux in the past, but it always seemed like something that was beyond my ability to comprehend. I had become a huge fan of WordPress and Firefox, and I love the ideals of free software. As I sat there and thought about it, I couldn’t believe that I was still using a proprietary system like Windows when a free operating system like Linux was out there. I did some research on Linux and found Ubuntu to be exactly what I was looking for. It’s self-proclaimed as “Linux for Human Beings.” It’s got the best support for hardware of any Linux distribution and a very welcoming community for newcomers. Since I was a new medical student, the last thing I wanted was something I had to pore over for hours and hours in the command line just to use it.

Ubuntu is everything a person could want being new to Linux. You can download it for free and burn it to CD to install it. It’s a LiveCD, so you can run the entire operating system from the CD to test it out without changing anything on your current system. Just restart your computer with the CD in your CD-ROM drive, and you will boot into Ubuntu. In order to install it, you just run through the installer on the LiveCD, which asks a few fairly easy questions, and after installing for about 45 minutes, you’ll be booting into Ubuntu. If you’re not ready to completely ditch your current system just yet, you can shrink your installation of Windows. If you’d rather not mess with Windows at all (just in case you don’t like Linux), you can install Ubuntu just like a program right inside of Windows using the wubi installer. Using the wubi installer is a great idea for someone who just wants to try Linux, since it is a little bit tougher to uninstall Linux after installing via the LiveCD, which changes the partitions on your computer.

My first few weeks with Ubuntu were great. I couldn’t believe how much this free operating system could do. Nearly any type of application you could think of was either built-in or easily installed right from inside Ubuntu. It came with Firefox, the OpenOffice.org office suite, Evolution Email, Pidgin (for multi-protocol instant messaging), and the GIMP Image editor. Plus the “eye candy” was easily enabled to check out Compiz-Fusion’s desktop effects and the Avant Window Navigator, a dock similar to that found in Mac OS X.

My friend Usama and my dad were both interested enough to try it out for themselves. They played with Ubuntu for a few weeks, but neither of them took to using it full-time. They’re both “power users” on Windows, and getting used to new applications and setting up a completely different type of system might have been too much trouble for them. I don’t think either of them have given up on it completely, but I think they probably needed a little bit of direction in setting things up effectively. I couldn’t see what the problem was since I had very little trouble with my hardware and I didn’t have any pressing software needs. One of the things that helped ease my transition to Ubuntu was that I forced myself to use the system every day and only boot into Windows if I couldn’t do something in Ubuntu that I absolutely needed to. I quickly realized that there was almost nothing that I couldn’t do in Ubuntu. My new webcam worked after an upgrade to Ubuntu 8.04 (the Hardy Heron) and Amazon MP3 released a Linux client so I could buy full DRM-free mp3 albums.

With the release of Ubuntu 8.04 (the Hardy Heron), GNU/Linux seemed better than ever to me. I began to wonder how there could be so few people using it. I mean, sure it’s not for everyone (notably computer gamers, since few computer games were released on Linux). Around this time, I heard about the Linux Hater’s blog, which was causing somewhat of a ruckus in the Linux community. This is mainly because his rants, though crude, were strikingly poignant. He obviously had an in-depth knowledge of the various Linux communities and software, and he loved to point out their flaws. After a few months, he threw in the towel, but not before opening my eyes to some of the shortcomings of GNU/Linux. I think reading this blog was important for me. Although it often depressed me, it helped me see where Linux is strong and where it needs improvement. I knew all the software wasn’t perfect, but I thought it was just a matter of time before this was fixed. The blog helped me see some of the discordance and problems in the communities themselves that are, in some instances, preventing their own success. Yet as I continue to read about the progress that’s being made in all of these areas, I am hopeful that this problems will solve themselves. There are a lot of developers doing great work who understand the problems, and with the rise of netbooks more companies are contributing resources and manpower to solve some of these issues.

With the release of Ubuntu 8.10 (the Intrepid Ibex), some of Ubuntu’s warts began to show. My webcam no longer worked. One of my favorite new productivity applications, Gnome-Do, started showing some significant bugs that make it unusable at times. My wireless card, which was already a little bit buggy, started causing some more issues. My desktop’s CD/DVD-ROM drives no longer functioned correctly. All-in-all the release brought some great new features, but broke some of my confidence in Ubuntu’s stability. Some of these issues have been resolved and some have not. Some of these issues are specific to Ubuntu and some are not. My problem was that these issues were known prior to release time. I know releases can’t be held up for just anything, but when all CD/DVD drives fail to function properly, it seems like a show-stopper. Unfortunately, Canonical seems to value their time-based release schedule a bit too highly over quality, which is really, really going to hurt them in getting people to try and stick with Linux. I would much rather have had them do what Automattic did with WordPress 2.7 and delay the release date for a month so that all the bugs could be ironed out.

Now, I don’t want you to get the idea that I’m growing weary of Linux. Despite some flaws, I’m confident that things will be resolved in future releases, and I have no intention of giving up on an operating system that I love using. It’s just that flaws like these (along with some usability issues and a lack of centralized documentation) make me understand why adopting Linux might be harder than I first envisioned. I do hope that some of the higher-ups understand these issues, since it’s a major barrier to adoption. Ubuntu tends to do a better job at handling these sorts of issues, but as they continue to push for more users, I hope they continually readdress how to keep their current users happy while still progressing their system.

One of the things I like best about using GNU/Linux is how much I learn while doing using it. I’ve learned a lot about security and operating systems in general, and I’ve done it all using free software. I’ve discovered a number of free software applications that I probably never would’ve even heard of. By using free software, I began paying attention to its development to find out about great ideas and features in upcoming versions. I’ve also been keen on helping to test new software and report bugs. I’ve installed both new versions of Ubuntu while they were still in beta to help with bug reporting.

Since one of the cornerstones of Linux is its variety of distributions, or “distros,” I’ve also started using VirtualBox to test some of them in virtual machines inside Ubuntu. One of the things about Linux that really interests me is its versatility to run on a wide variety of hardware and using a variety of software. It’s used to run super-computers at big companies and to resurrect ancient hardware that’s not capable of running any modern version of Windows. Linux can also be used as a “green” operating system both in its own right and through the LTSP. LTSP can be used to connect many low-power, lightweight computers to a single workhorse machine, so an entire computer lab can be run on minimal power. Linux can be used to power your home media center and your cell phone. The versatility of Linux allows it to underlie many great technologies of today and tomorrow.

So how would I summarize my first year with Ubuntu? I think it’s exactly what I needed. It has helped me plan for the future in medicine and my life and better understand some technology along the way. It’s definitely not for everyone, but I do think Ubuntu and Linux is a viable operating system for a majority of users who have never given it a chance. Besides addressing some of the underlying issues in development (as highlighted by The Linux Hater’s blog) and preventing regressions, the Ubuntu community could use a effort to implement or improve a centralized, up-to-date set of documentation for new users. Far too many problems and issues are only addressed in random blog posts or on online forums, both of which tend to be outdated or doing things in an overly complicated manner. Ubuntu would be greatly improved by including some significant “Getting Started” documentation for new adopters and finding a way to point directly toward an up-to-date official wiki with more complicated tasks. The Linux community is continuing to lower the barriers to adoption, and addressing some key usability issues might be just the thing they need to attract the swarms of users leaving Windows and even catch a fed-up Apple user or two. Great strides have been made already and more are planned for the coming months and years. I’m excited to keep participating and to see what’s in store in my free software world. If you’re interested, try out Ubuntu. It’s simple to burn and try. The risks are pretty minimal, and you’ve got a lot to gain. You’ll never have to pay for any computer software again, you’ll learn a lot, and you’ll be ensuring the future of your digital life. Just don’t forget that Linux is different and for the most part you should try to enjoy it.

(Also, this is my sort-of convoluted thoughts on Jono Bacon’s meme)

Windows 7 finally catching Ubuntu?

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There’s been a lot of talk since Microsoft’s PDC about what to expect from Windows 7. It’s due out in late 2009 or 2010, but MS gave a taste of what’s to come at their PDC. Gina Trapani over at Lifehacker posted a good list of the new features they’re working on for Windows 7. Usama and I have talked a little bit about some of the new stuff since he’s very excited about the next product out of Redmond. I’m not trying to be cynical, but as I read through the list of their “latest and greatest” improvements for Windows, I kept thinking to myself, “Sounds like they’re playing catch-up with Ubuntu and Linux.”

10. Ding-dong, the Sidebar is dead.
Windows is losing Vista’s “sidebar” in favor of a desktop-wide “Gadgets“. Doesn’t this sound strikingly similar to Screenlets? I mean there’s no optional hidden “widget layer” in Aero, but at least they’re trying.

9. Calculator, WordPad, and Paint got overhauled.
They stripped out “useless” built-in programs like a photo gallery, movie maker, and calendar. I guess if you can’t make worthwhile programs, you should probably just quit trying. Oh, but they added “useful” features to the Calculator and added their famous “Ribbon” view to many of their built-in programs. Many people love this “Ribbon” view that debuted in Office 2007, which explains its further incorporation into Windows programs. I can’t say much about it because I haven’t used it. Maybe it’s great. I just don’t think many average users appreciate them trimming down their built-in software when adding interesting new features.

8. Windows 7 will run longer on your notebook’s battery power.
Improved battery life. Apparently Windows 7 is making it easier to control the power usage for your laptop. Hmm, I bet something like powertop would really help you pinpoint what’s eating your power. Of course, if Windows was fully customizable, I’d be able to do things like disable my dvd drive, bluetooth, USB ports, and PCMCIA port whenever I’m on battery like I do in Linux.

7. You can switch between Wi-Fi networks in one click from the system tray.
Clicking on the “wireless icon” brings up a list of available wireless networks. Wow, I can’t believe they didn’t already have something like this. This has been available in every version of Ubuntu I’ve used, and now with NetworkManager 0.7 they’ve even added things like Mobile Broadband and VPN connections to the “wireless icon.” Maybe Windows will get there some day. While we’re on the subject of networking, shouldn’t you have proper Zero-Configuration Networking for all types of devices like Linux has with Avahi and Apple has with Bonjour?

6. You can decide what you do and don’t want to see in the system tray.
This one cracks me up. When I first read it, I thought, “Well that’s not such a bad idea.” Of course, I’m able to customize panels in Gnome and tell it what stuff I want on there and where I want it. Yet, if I’ve got the “Notification Area” applet displayed on my Gnome Panel, I can’t pick and choose what programs I want it to display. I don’t ever normally have more than 3 or 4 things on there at once. Then I started wondering why I’d want to hide the 2 programs I currently have running that show up in the Notification Area. Isn’t that its whole purpose? That’s when I remembered the Windows system tray and all the crap-tastic applications that put icons in there that you can’t get rid of, and this all seemed much more reasonable. I guess I just got used to programs that actually gave me an option on whether I’d like an icon in my tray (like gnome-do) and an OS that let me easily customize what applications start when I boot into my system. Of course, there’s also no need to have 50 different icons telling me I have updates for my PDF viewer, printer, and antivirus. I just get the 1 icon from Update Manager telling me that all these things need to be upgraded. But the real kicker here is that Windows isn’t actually disabling these programs from running. It’s just hiding them. That sounds like a great way to fool people into clogging up system resources with a bunch of applications running in the background so they never see them.

5. You get more control of User Account Control.
Let’s admit the UAC was just a really bad implementation of sudo/gksudo that incessantly nagged people trying to do even some simple tasks. Well it looks like Windows 7 has “fixed” that issue. Of course, instead of implementing a proper sudo knock-off and opting to make users understand the importance security, they let you customize how much UAC nags you. Many people will say, “Don’t ever bug me” instead of giving proper credence to the warnings. It doesn’t matter how many security features you add if people just disable them all.

4. Libraries group similar content; Homegroups to make sharing libraries easier.
I see now that Windows has given some thought to networking. If I’m understanding “Libraries” correctly, they will be able to dynamically scan multiple folders for certain types of files (like music), which can then be shared on a network. I’m not able to tell whether this dynamic scanning would have to be manually set up (I would assume) or if it would automatically scan your entire User directory for music files. That’s actually a pretty good idea (assuming it’s manually configured). Of course, none of that does you any good if you can’t easily connect to other computers on your network, which is where Windows drop the ball. Instead of implementing a proper Zero Configuration Network utility, it looks like “Homegroups” replaces the useless “Workgroups” with “Zero Config Windows 7 only networking.” So that sucks if you have other devices, Mac or Linux systems, a network printer, or even an “old school” Vista computer on your network. Networking will still be a pain in the ass. I guess you’d better be ready to shell out some cash to upgrade everything you own to Windows 7 so your networking works better.

3. You can instantly snap your windows to size, and clear the desktop in one motion.
This one kind of leaves me at a loss. Clear the desktop by shaking a window? So does that mean that every time I start moving a Window around, Windows will think I’m “shaking” and minimize everything? Sounds great… Why not just implement something like Compiz’s ADD Helper, where I can press Win+p to activate it? That way I don’t have to worry that every time I move my window I’m going to minimize everything behind it. Then, there’s the “instantly snap your windows to size” feature. It’s actually not a bad idea if you’ve got a big enough screen where having multiple tiled windows open at the same time might be beneficial. I don’t think I’d use this feature much on my laptop, but if I ever get that 24″ HD monitor I’ve been after, maybe this would come in handy. I’d also worry that someone just meaning to drag a window would accidentally have it’s size and position changed without meaning too. Talk about something to confuse novice users. With more and more users on laptops whose screen sizes are shrinking, I wonder how much use it will get. I think a much better idea would be to implement multiple virtual workspaces, but I’ll touch on that more in a minute.

2. Windows 7 starts up faster.
Whoa, faster boot time? Sounds an awful lot like what I’m going to be getting in 6 months. “Let’s see if we can make booting or resuming Ubuntu blindingly quick.” And as a recent proof of concept demonstrates, I think Linux will be winning the “boot time” battle in a few months.

1. You can do MUCH more from the Windows 7 taskbar.
We finally come to the Windows 7 topic of the week: a reworked taskbar. This definitely has been the hottest topic in news about Windows 7. There are at least 2 big features under this heading. First, they’ve made the task bar much more “Dock-like” by combining the quicklaunch icons with a traditional window list. It’s obvious that Windows needs a feature to compete with the Mac OS X Dock, which is beautifully emulated in Avant Window Navigator for Linux. It’s also obvious that they want something of their own, not just a Dock for Windows. The new task bar shows “live previews” of windows, like can be achieved with Compiz and even using Aero with Vista. One nice feature is that you can close windows using the live preview. It’s also interesting that when having multiple windows open for the same application, they get condensed down into one icon that has multiple “live previews” when you hover over it. Both of those seem like worthwhile ideas.

The second big feature is called Peek. Basically whenever you hover the mouse over an application in the new task bar, all other windows will turn temporarily transparent. It’s meant to be non-interactive, just if you need to glance at another window. There is also a built-in Desktop button so that you can peek at the desktop with all your Gadgets on it. This also seems like an interesting feature. I’m not convinced it could replace the quickness of Alt+Tab for me, but for the point-and-click crowd, this could be a time-saver.

It looks like the new Windows 7 task bar is adding some interesting new features to the Windows desktop. My question is, “Is it enough for Windows to save face?” They’re working on making more efficient use of desktop space. Linux and Mac OS X are already doing an OK job of that with their Dock applications, but they’re also giving the option to have multiple virtual desktops for people who want to separate their applications. On my Ubuntu installation, I can have up to 32 virtual desktops. Of course, I normally have only have 4. This makes it easy for me to keep a word processor open on one desktop and my instant messaging client and web browser open on another.

If it makes the Windows fans happy, though, I’ll give them that the new taskbar design in Windows 7 has some potential to be a good new feature. The rest of its new features still make me feel like the folks at Microsoft are trying to catch up with some of the innovation taking place in Linux and Mac OS. With the rapid progression of Linux in the past 2 years, how will the comparison look when Window 7 is released (theoretically) in late 2009? By that point, Gnome should be well on its way to the transition to version 3.0. That will mean a significant change to the user experience by attempting to rework the idea of the desktop, including making the desktop more task-based and less application-specific. For example, imagine having desktop-wide “contacts” that you could email, instant message, chat via video, follow on RSS feeds, and more. With that information built into the desktop, it wouldn’t matter what application you used for a feed reader or email client. Plus, there are other ideas floating around, like Long Term Vision. With the amount of development and innovation going on with Linux, Gnome, and Ubuntu combined with an aggressive 6 month release schedule, I think it’s going to be hard for Windows to keep up!

Of Freedom and Trademarks

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I read an article this past weekend that brought up some interesting issues that I tend to forget about concerning free software. Most people these days are familiar with Firefox. While Firefox is open-source and “essentially” free software, the key area that makes it non-free is in its trademark and copyright. The brand name “Firefox” is a trademark of the Mozilla Foundation, as is the Firefox logo. Since the logo is artwork, it also falls under copyright restrictions.

Trademarks are a funny business. Unlike copyright, which is inherent from the minute that pen touches paper, a quotation is voiced, or a blog post is published, a trademark is not inherent. As such, copyright is enforceable in general. If you find a person violating that copyright, you are empowered to make them stop, but if you choose to ignore it, that’s your decision. Trademarks on the other hand are a “branding” and are not inherent. If you find someone in violation of your trademark, you must act to stop them (or help them to comply). Otherwise, you are forfeiting your right to the trademark.

In general, this is thought to be a good thing because trademarks are “branding” used to ensure quality. I probably don’t want to install just any piece of software on my computer, but if it’s “Mozilla Firefox” then I will. This is especially important when discussing open-source software. With proprietary software, it would be difficult to distribute a “fake” copy without people noticing a difference. But with open-source software, everyone has access to the application’s source code. This means that anyone could build it, modify it, and tell it to collect all of your private information for them. If they can convince you to install “their version” of your favorite program, that’s a major security threat. Sharing code is also the hallmark of free and open-source software, and users are encouraged to modify it. But it doesn’t mean that after doing that, they deserve to still call it “Firefox”. Of course, Firefox should be credited as the basis for the work. It’s good to know when something has been stamped “Mozilla Firefox” because it tells you that it’s endorsed by the Mozilla Foundation and you can trust it.

Now you might be sitting there, scratching your head, and asking, “What’s the big deal? Can’t I just assume that anything I get from mozilla.com is what I want?” For many people, the answer to that is “Yes, you can.” But according to its license, Firefox is free to distribute under its brand name as long as any changes to it have been approved by the developers. This is something that many GNU/Linux distributions take advantage of so that they can package “Firefox” as the official web browser of their operating system. This helps user-friendly distributions like Ubuntu because potential users instantly recognize the brand Firefox and are comfortable with it. This works well for just about everyone involved.

Debian is another GNU/Linux distribution. It has roots as one of the first GNU/Linux distributions, and it defines itself by its commitment to being free. You may have developed a great program that a lot of people like, but if it’s not free software, it’s not good enough to be called “Debian” and included in their operating systems. They would like to be able to use Firefox as their default web browser like other, less “freedom-oriented” distributions do. If it were just a trademark issue, there would be no problem. Debian could easily show Mozilla exactly what changes (if any) are in their version of Firefox. Since the Firefox logo is also under restrictive copyright protection, however, Debian can’t include it. They also can’t just exchange the logo for a non-copyrighted one because the Firefox logo is part of the trademark. This copyright could be changed to a more permissive license by Mozilla, but it looks like their theory is that Debian could just as easily bend their rules. This is where Debian has taken a stand. Since they’re committed to providing a completely free operating system, they do not include Firefox as their browser.

Firefox is a good browser, and Debian doesn’t want to try to code another browser or use a less popular alternative. Since the only real problem they have is with the trademark and artwork, they’d much rather keep the rest of the Firefox code intact. Plus, with the number of Firefox plug-ins available, a lot of users want to use it. So what does Debian do? Since Firefox is open-source, they just strip out the copyrighted logo and come up with their own. This means that they lose the “Firefox” branding, so they chose the name IceWeasel (and a free logo) to replace it.

Now it may seem like kind of a moot point in the long run, but it makes me proud to see that a distribution like Debian will stick to their guns in a situation like this. It may not be for everyone (I’m still using Firefox on Ubuntu), but they chose not to back down on the ideals of their organization and their users when it would have been very easy to do so. So kudos to Debian and IceWeasel.

The “truth” behind Wikipedia

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I’ve heard a lot talk recently about how Wikipedia is bad because “anyone can change anything they want” in an article. A friend of the family has said it, and even one of my teachers said it. I actually become very frustrated by this every time I hear it. It’s mainly because I find Wikipedia to be an incredibly powerful tool and one of the strongest pieces of evidence for the “success” of the Internet. And I’m not alone. I know a number of students and young people who feel the same way. The problem with this mistrust seems to be stemming from some adults who have lived without Wikipedia for much of their lives. I’ve been pondering this over the past few weeks, and then I came across an article today in Technology Review about this very subject.

It was an interesting read for sure, and it brings up some interesting issues about citations. I think the avid nay-sayers generally do not fully understand Wikipedia and the fact-checking that’s involved with the website. I think they generally believe that some 15 year old kid is sitting there filling what he knows about argumentum ad populum (thanks /.) or some crazy person is injecting extreme ideas into a serious article. The fact is simply that this isn’t the case. If an article is found to have something disreputable in it, it’s tagged as such (which is clearly visible to the reader). Since Wikipedia is not willing or able to judge truth from fiction, they rely on the verifiability of questionable statements. As the article notes, this can cause problems because even if a Wikipedia entry is about you, a verifiable reference must be found that can corroborate your claim. They have no way of proving that you are who you say you are, and thus they need evidence. A significant point for the scientific community is that trustworthy evidence is largely based on journal articles, university publications, and university-level textbooks before things like fact-checked sections of newspapers and magazines.

Even with citations, however, things can be wrong or misrepresented, so of course it’s always necessary to take you read on Wikipedia (or anywhere) with a grain of salt. Still, I find that Wikipedia articles tend to be more accurate and less biased than some news agencies’ work. References even act as a way to remove bias by limiting your assertions to something with verifiable proof. Then people can base judgment on the quality of the proof, not on the persuasiveness of the Wikipedia writer.

I guess the underlying point of this post is that you shouldn’t judge something unless you fully understand it. Wikipedia is highly accurate, and the proof that it’s based on is one of its strongest qualities. Question it. Critique it. But, please, don’t just dismiss it because “it can be edited by anybody.” “Anybody” still needs to have verifiable proof of their statements. Wikipedia has made a more profound impact on my life than probably anything else on the Internet. Knowledge should be free, and Wikipedia has aggregated mountains of knowledge that is both easy to access and free for the taking. Gone are the days of lugging out a 20 volume set of Encyclopaedia Britannica only to find out that your version is out-dated. Typing a simple wp Reyes Syndrome into my Firefox address bar brings up most of the latest information instantly. I have gathered immense knowledge over the past half-decade from the giant brain that is Wikipedia. I am (and will be) indebted to it forever, and I hope it never goes away. I have made a promise to myself that once I’ve graduated from school, I will make a significant financial donation to the Wikimedia Foundation and probably another one once I’ve finished residency. The world needs Wikipedia. Go read a few of its articles on something you’d like to know more about. You’re bound to catch a glimpse of how wide its berth of knowledge is. Wikipedia is not just some little tool that can be brushed aside and ignored. It’s a “Google”; it’s a game-changer. And it deserves to be. Please, don’t take it for granted.

Learning to Love Linux?

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I noticed an interesting article on ifacethoughts stating “Linux Education Is The Key To Popularity.” I agree to an extent, but there are some caveats. This started off as a comment on his blog, but I decided it was long enough to merit its own post here.

I agree that Linux should be sold on being different than Windows, but I disagree that it’s entirely an education problem. I think there are 2 large issues that make things difficult for new users, and they’re quasi-related. First is that 99.9% of user’s tasks (even complicated ones) need to be GUI-fied for a Windows migrant to feel comfortable. This is quickly gaining momentum (for example, xorg.conf is all but eliminated in Ubuntu Intrepid Ibex), but it’s still not quite there.

The second, and even more important, piece of the puzzle is the need for a central, well-maintained, well-written set of instructions for how to do anything and everything imaginable in Linux. I think one of the hardest things for new users is when they don’t know how to do something, they don’t know where to go next. They can do a quick Google search or a forum search, but these are often filled with outdated information and they can be hard to sift through, especially when you don’t know what you’re doing. Plus, when you don’t really know what you’re doing, you might just go with the first thing you read, which many times is not a good idea. I also think it’s important for the OS itself to be integrated with these instructions and “Help” should point directly toward them.

I say the 2 issues of GUI and documentation are quasi-related because many times there are GUI options available for something, but instructions are given by old-school experts who find terminal commands quicker and easier. While that may be, to most Windows and Mac users, it’s intimidating. A good example would be adding Medibuntu repositories in Ubuntu. The wiki guide is all command-line, despite the fact that things are basically just as easy in the GUI to complete the same task. Even better might be to just supply repository and GPG key links and then link to a fuller article about how to install external repositories and what their advantages and disadvantages are.

I also feel like proper documentation could help users learn a lot more while they’re doing this stuff. Interspersed with the instructions could be brief descriptions about some of the inner-workings and why things are the way they are. In the previous example, maybe mentioning GPG keys and why they’re used or a link to learn more about external repositories. Some of this has been done with Ubuntu, but it needs to be more comprehensive, clear, and up-to-date. It also needs to be written for lay people and not by developers unless they’re very effective communicators.

It’s one thing to say that people need to “learn Linux” if they’re going to use it. It’s another to expect them to do it without the proper tools and guidance, especially since many aspects are non-intuitive to non-native users.

Taking Back The Power of Science

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I read an article on Ars Technica [via /.]the other day that made me very worried about the future of scientific discovery in the US. With our currently failing economy, I don’t understand how we can still be making such idiotic decisions about the future of some of our most innovative industries.

The scientific research industry is fueled by governmentally funded programs like the NIH and NSF. As a taxpayer and citizen, I cannot believe the idiocy of some of statments against open access in Congress. There is a particularly poignant response on the /. article demonstrating how the greed of publishing companies in a dying industry are attempting to use their financial power and influence over government to squelch dissenters that oppose their bottom line. Let’s face it. With electronic distribution of written material available, the publishing industry as we know it is dying. There’s no way to stop it aside from them increasing their hold of copyrights and copyright law. There is no reason that publishing companies should be taking any sort of “ownership” of research that they publish. With the minuscule cost of publishing something online today, the publishers truly have almost no overhead to publish a scientific article. This was not the case 20 years ago when they had to print and ship their journals across the globe, but today they simply have to put it online. Their work is practically done for them by PubMed, the Google of biomedical science research. Sure, they need to find peer reviewers (one of the cornerstones of research), but do you think that publishing companies actually pay these reviewers? (No.) If that’s the case, why are they still charging thousands of dollars to researchers in order to publish an article? I think it’s because they used to have a reason to, and now that they don’t, it just means bigger profit margins. People don’t like it? They’ll pay the government to make them like it.

This article and the /. post made me start to wonder if an open access journal had already been started. A quick Google search showed me that it had: the Public Library of Science (PLoS). The PLoS is an open access journal published in the United States that guarantees that all of it’s material is available free of charge online. Not only that, but everything is released under a liberal Creative Commons Attribution license, the researchers retain their own copyright, and most importantly, the article is fully available on the day of publication. People don’t have to wait until tomorrow to learn about the discoveries of today. They can just dive right in. This is in stark contrast to the practices of current publishing conglomerates, who take over copyright and make non-subscribers wait a year or more (if at all) to access the material. Now, surely this is good for the publisher’s bottom-line, but you have to stop an ask yourself: Is this good for science?

Since most government-funded scientific research is done at large institutions with many faculty researchers, the scientists might not fully understand the problem. Their institutional affiliation gives them the ability to join together and pay the large fees for a subscription to the most popular journals. But some smaller institutions do not enjoy the luxury of being able to subscribe to anything. And even the largest institutions can’t subscribe to everything. There are simply too many journals. There are also many individuals, like students, and private researchers who wish to learn about what innovations our tax dollars are leading to and where these innovations might lead. Open access would likely generate a renewed interest in basic science and discovery, helping to fuel growth of the field. So should this even be an issue in today’s society? I mean scientists are generally trying to help us better understand the world we live in, the diseases we fight, and the things that affect us. The fact that a project has received a sliver of the ever dwindling government funding demonstrates that it’s a worthwhile project that will very likely yield extraordinary results for the world. Shouldn’t those results be available to anyone?

The PLoS has grown stronger since its inception, but it’s still generally small potatoes compared to the likes of Nature Publishing Group and even JACS. The PLoS now has separate journals in many of the biomedical sciences like biology, genetics, and medicine, and they even have a fast-track publication called PLoS ONE for those high priority articles.

So how is it that this journal, with its inherent ability to accelerate scientific discovery, has managed to stay beneath so many radars? The answer to that is two-fold. The scientific community does not currently seem to recognize both the underlying problem with current publishing companies and the innate ability of a publisher like PLoS to solve this problem once and for all. At the heart of this issue is the notoriety of publication. In order to be successful as a researcher, scientists want to be published in big name journals. Every one of them would love to have a publication in Nature or the NEJM. It’s extraordinarily competitive, and thus only the best of the best research makes it there. But scientists have lost sight of the fact that this notoriety is man-made. Nature is only as famous as it is because everyone wants to publish there. They get the best articles because of it. So if they want to break free of the hold that publishers have over their research, they need to set their own standards. If they want PLoS or any open access journal to be able to defeat the giants, or even get them to start listening, they have to remind the publishers that without their research, the publishers have no industry. Scientists do the work, and they should get to say what happens to it. In all likelihood, any attempt to dictate terms to a publisher is going to fail (at least at this point). But the scientific community needs to remember that they hold the power. They are the ones doing the research, and they are the ones volunteering to peer review. If the publishers won’t meet their demands, they need to meet their own demands. So listen up scientists: In this age of the Internet, you do not need them anymore. Take your research and your peer reviewers and make your own, new notoriety. Once they see you doing that, they’ll either follow suit or not. At that point, it won’t really matter.

But the reason that this has not happened and probably will not happen in near future is that scientists don’t see the dire need for open access because most of them are given most of the access they need. The sooner they realize that they need to demand open access to their work so that other scientists and the public can benefit from it, the better. Once they get past the encumbrance of permissions and red tape laid out by the publishers, they can get on with their life’s work in a much more open, collaborative environment. Otherwise, the publishing industry is going to keep tying researchers’ hands behind their backs, making it harder for them to exchange ideas, just so that they can continue to squeeze every possible dollar out of this industry. This is not good for the scientists, and it’s especially not good for science.

Summer Research

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science-xkcdI’ve started a new research project this summer in Marcello Del Carlo‘s lab. Dr. Del Carlo is a new faculty member at Rush in the Department of Biochemistry. Our lab is affiliated with a clinical urologist faculty and we’re researching a urological disease called Peyronie’s Disease (PD) [Warning: male nudity]. From a biochemical perspective, we’re studying the process of growth and formation of a fibrous plaque underneath the skin of the male penis in a layer of connective tissue called the tunica albuginea. Currently, we’re analyzing both diseased and non-diseased tissue samples that have been surgically removed from patients with PD. In the future, we’ll also be working with a cultured fibroblast cell line doing similar work. So far we’re using Western Blots to identify and characterize proteins that are up- or down-regulated in diseased tissue compared to that of non-diseased. Our hope is that the studies will lead to a better understanding of PD and how the plaques form to aid in treatment.

In addition to research, Dr. Del Carlo is very interested in using FOSS as it relates to scientific research. By the time I met with him, he had already set up a database using PASSIM in order to keep track of tissue samples from patients. He also had the idea of using a WordPress blog as a sort of “online laboratory notebook”. I thought this seemed very in line with the Science Commons project, a derivative of Creative Commons. Science Commons is attempting to lower the barriers of scientific research, which is currently not nearly as “open” as it should be, considering almost all of it is funded by the U.S. Government. Most people believe that the fruits of governmentally funded projects should be available to the general public. In many cases, however, scientific research is locked down (for varying periods of time) due to copyright after being published in scientific journals. Since a scientist’s credibility is often judged by previous publications in journals, Science Commons is working to reduce the hold of copyright on this process, so that labs can publish data immediately to the web, allowing it to be indexed, freely searchable, and available immediately to anyone wanting to read it. This will continue to be an uphill battle since journals make a large amount of their money by licensing access to large academic institutions for their faculty. The idea that labs can make their data freely available on their own personal websites is being met with resistance. Still, I feel as a society we must push forward, despite the corporate interests, in order to do what’s best for the public. Plus, my thought is that journals will not suffer any major economic hardship. Their “seal of approval” by publishing the content will continue to be the scale by which research is judged. They would also continue to act as a collecting ground so that researchers looking for the latest data don’t need to worry about sorting through Google search results to find the latest findings in a field. Instead, some publishing groups have the gall to say that in order to publish in their journal you must leave the rights to your work on their doorstep, no matter who did the experiments. This will continue to be a very important issue in the scientific community in the future, and I’m hoping to gain a keener understanding of it over the next few weeks and months.

At least for now, I am the only one updating the Peyronie’s Disease Information Repository and it contains all of our experiments and results to date. Feel free to check it out, but unless it’s scientifically relevant, keep personal comments to my site.

Ben Stein Is Expelled

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I just saw a commercial on TV for a movie featuring Ben Stein called Expelled: No Intelligence Allowed. It appeared to be a documentary about religion and science. I had always assumed that Ben Stein was a fairly intelligent individual, but it appears that even if that is the case he made a mess of a film.

I will point out 2 things off the bat. I have not seen this movie. In fact, it just came out today in the US. There is a short video clip available to watch online, and I’ve gotten some information from Wikipedia. Secondly, while I disagree with his position in this debate, I am more disappointed in the way he appears to have addressed the facts. I would also like to take this opportunity to point out that Stein attempts to martyr himself (and drag you along) by asserting that if you want a career in anything scientific, you’d better not even watch this movie, or you’re risking your future. The implicit assertion here is that to question him is to prove him right. By saying he’s wrong, you’re proving that people who disagree with him will attempt to tarnish his movie. By disagreeing with his theory, you’ve been duped by the scheming scientists to keep any questions of Darwin’s evolutionary theory swept under the rug.

The basic premise of the movie is to demonstrate how a number of well-known scientific researchers have had their careers torn apart by proposing “Intelligent Design” as a means of explaining creation and evolution. I don’t doubt that they have. He then continues by asserting that this occurred simply because they attacked Darwinism and evolutionary theory. This is the assertion I have a problem with. No one is saying that questioning Darwin’s theories will ostracize you from the scientific community. The truth is, people should question Darwinism every day. The trouble is that it’s a pretty solid theory, and it continues to be proved right all the time. Indeed, the issue here is not that these scientists propose a competing theory to Darwin’s, but rather the theory they’re proposing does not assimilate well with scientific theory.

Let’s imagine you and a few friends are walking down the street and you see a man in a large coat and a black top hat. After chatting with him a few minutes, he briefly shows you his sleeves and hat and proceeds to pull a rabbit out of his hat. Everyone is amazed. You and your friends begin to discuss how he might have done the trick. One person says that maybe there was a false bottom to the hat, and the rabbit was hidden in it. That seems pretty reasonable, and you all agree that was correct. A little while later, another friend says that he believes that the rabbit was too big to be hidden in a false-bottomed hat. Perhaps there was some sleight-of-hand and the magician pulled the rabbit from under his coat and slipped it into the hat. That was also plausible. Another friend chimes in that he also agrees that the rabbit was too big for the false-bottomed hat, but perhaps it was really magic that made the rabbit appear in the hat. To attack this friend’s theory and call it silly is not the same as to defend the original one. In fact, there are plenty of plausible explanations that could account for the trick that don’t include “magic”.

I don’t mean to step on any religious people’s toes. If you believe in “Intelligent Design”, that’s great, but don’t assume that someone attacking that idea is defending another. The other has plenty of merit on its own. If you think that “Intelligent Design” explains things well enough, then why not think of the scientists as trying to figure out how God’s mind works? Really, that’s all Intelligent Design is doing anyways: accepting the explanation as “magic”. That’s fine and all, but it doesn’t help much when you want to try the trick yourself.

What really irks me about this movie is the tactics he used to produce it. In traditional Michael Moore style, Stein proceeded to interview a few prominent figures in the scientific community who deal with this debate and quote them to make it seem as if scientists have no idea what’s going on in our world. Most notable, for me, in that list was Richard Dawkins. Dawkins has made a career not out of simply telling people Intelligent Design is wrong and Darwin is right, but by explaining where and how the theory of Intelligent Design is flawed. Intelligent Design claims that the intricacies of the world are too numerous and perfectly fit together, so there must be designer (a watchmaker). Dawkins points out in his book The Blind Watchmaker that not only does intricacy not prove there is a designer, but also that if there were a designer, it did a pretty poor job in some cases.

The point of all this is not to attack religion or even the theory of Intelligent Design. The point is that it just doesn’t jive with scientific principles. Science bases its theories and assumptions on measurable facts, but Intelligent Design attempts to fill in all the little gaps in our knowledge with an idea that “if it can’t be explained, it must be because of God’s design.” Despite the flaw in that logic, the real reason that these scientists Stein presents in his movie were ostracized by their colleagues is because they were scientists proposing ideas that are not supported by any evidence. Evidence is a foundation of science. Would anyone have even heard of these scientists if they collectively decided that it was invisible pixies that threw together the first cells? I doubt it. They’d just be labeled delusional. But if the explanation has a religious backing, society doesn’t consider them delusional, and you’d better be prepared to withstand the full force of their wrath.