Friday, December 31, 2004

Satellite Photos of Tsunami Effects

DigitalGlobe | QuickBird Images of Tsunami Sites
Caught this on Slashdot this morning, it's a link to some before and after photos of Sri Lanka and Banda Aceh. At first I didn't realize how much they showed, as you could see many of the homes were still standing. The most striking before and after difference I noticed was in one before photo there is a soccer field, in the after photo it looks like a black patch full of debris.

Thursday, December 30, 2004

Why is Linux Cool?

how-to record on your ipod (for free) - hack a day -
I've got an iPod, along with millions of other folks out there. As much as I like my iPod I wish there was an easy way to record sound with it, one that doesn't cost $50.

It looks like someone figured out a way to do it without people needing to buy extra add-ons from third parties (ahem, Belkin). Install Linux on your iPod, use Linux to record through the line in, listen without prejudice to whatever you've just recorded. In my case, it would have been great to have those Biochemistry lectures recorded. Too late now (though I did manage to pass the class with a 3.0).

NPR: All Songs Considered: The Best of 2004

NPR: All Songs Considered: The Best of 2004

I love this little quote from NPR's list of the top albums of 2004 (the music snob in my likes this list so much better than the iTunes Top 100... egad... most of the music on there is crap, but then again most people buy crap when it comes to music). I believe these are the comments of Jeff Tweedy talking to an interviewer about the latest Wilco album A Ghost is Born.
"I had lots of arguments with people about this record. Most of them went like this: Them: It's so noisy. Me: Yes, but there's some poise within that, like on 'Hummingbird' and 'Handshake Drugs.' Them: The guitars sound deranged. Me: When was the last time you heard such dramatic derangement? Them: The songs seem sorta blasted apart. Me: At a time when so many songs seem prefabbed by some software program, is that such a bad thing?"

-- NPR reviewer and music writer for the Philadelphia Inquirer, Tom Moon

Wednesday, December 29, 2004

From the "I Heard it on NPR" Desk: The Merchant of Venice

this is an audio post - click to play

There's the URL for story on NPR. Anytime I try to edit a post from the computer in the office it eases the entire post if I try to use the link utility. I think it has something to do with either the fact that the computer is running MacOS 9, or the most current version of Mozilla I can find that will run on MacOS 9 is from 2003 (a customized version of 1.3.1, when the current Mozilla version is something like 1.7.5):

Monday, December 27, 2004

How To Speed Up Firefox (Helpful Vanity)

How To Speed Up Firefox (Helpful Vanity)
This may prove useful to a few of us out there. I've been using Firefox/Firebird/Phoenix for some time now. It finally seems to be gaining critical mass. All I can say is download it and give it a try. You won't know what you've been missing until you use it for a week or two, start to find some extensions and themes that you like, and realize that IE is sooooo 2002.

Anyway, this little link above may vastly improve even the Fox's performance, which ain't shabby to begin with.

Saturday, December 25, 2004

PlaneShift - A 3D Fantasy MMORPG

PlaneShift - A 3D Fantasy MMORPG
This looks interesting to me. I played Star Wars Galaxies when it first came out, but as my time became more occupied with real world necessities and the cost didn't get any lower I gave the game to my brother Rob so he could try it.

This MMORPG is free to use, and open-source, which I dig on both fronts.

Inside Milkshake Joke

Blogger seems to have choked today so I couldn't directly edit the audioblog post I made. It requires a little backstory.

A few weeks back Ellie came to me to tell a story about one of her coworkers going to Best Buy with their mother. The mom wanted to get a gift for her 10 year old daugher, so she went over to the Best Buy employee in the music section to ask for a CD, but she didn't know who the artist was. So she tried to sing it:
"My milkshake brings all the boys to the yard, and they're like it's better than yours, damn right, it's better than yours. I could teach you, but I'd have to charge."

The guy from Ellie's work was quite mortified that his mother was singing this in the middle of Best Buy, and I must admit the image of a 40-50ish white woman singing it in there is quite funny to me. Apparently the Best Buy employee had a look on his face like he was fighting an internal battle not to explode in laughter, while Ellie's coworker was try to get his mom to stop, and explaining what the milkshake was all about. That is another humorous image for me: a white guy trying to explain to his middle-age mom about why Kellis' album probably isn't what she wants to get for her daughter, in the middle of Best Buy.

For the last several weeks it's been a running joke for me to start singing that song at inappropriate times for fun. This morning I rendered a choral edition for the family, while wearing some of my new Christmas gear (my father-in-law got it all on tape, I have a feeling it will be humorous for years to come). Ellie wanted me to call her cousins and sing it in the phone, but I'm not convinced it would be funny without the backstory. Instead I decided to audioblog it for posterity. Unfortunately I screwed the words up, but sometimes that's the funniest part so I'll just leave it like it is.

this is an audio post - click to play

Thursday, December 23, 2004

Today Has Been a Mixed Bag

It’s been tremendously quiet around the lab today. I got to work around 7:30am and turned on the lights. As I walked toward the Food Safety & Toxicology Center all the lights in the offices are off, with the exception of the one next to mine on the 3rd floor. I wonder if it is foreshadowing how quiet the building will be today.

I started with some cell culture work, changing the media to keep the B cells (the cells that make antibodies for the immune system) happy. Cell lines don’t know about holidays, they just keep growing. Nothing too exciting happening around the lab, a few people roll in to take care of what they need to and not much more.

I got a call from my mom last night. She and my youngest brother were coming to East Lansing today to do some errands and they wanted to meet Ellie and I for lunch. Ellie couldn’t get out of work, but we all met at the Marriott and exchanged gifts with one exception; this morning we left David’s gift under the tree. Whoops.

My Mom, brother, and I made the quick trip across the street to visit the only Indian restaurant in downtown East Lansing (I do love Indian food, but Ellie’s not one for spicy food so it’s relatively rare we go). I was in a hurry to get back to work because I set a meeting with one of my old professors, Dr. Roth, at 1pm. We talked for a good half-hour over a nice mix of Indian dishes. It was really nice to see them both. I was especially happy to talk to David, as I do a really bad job of keeping in touch with him. I try to call my middle brother, Rob, every week or two to hear about what he’s been up to down in Texas, especially after he and his girlfriend broke up. Dave is in the same town with me and I hadn’t talked to him since we helped my Dad move out of the old house. Ellie tells me when she talks to him at work, but it’s not the same as sitting down with him and just talking. It was a good meal with good conversation and company. I wish I hadn’t been in a hurry to get back to work.

I needed to meet with Dr. Roth because I’m coming closer to the end of my current lab rotation and will need to make a decision soon about what lab I want to do my dissertation work in. Making a decision about which lab I liked better would be really difficult because the experimental work done in both is excellent, the people are fun to work with, and the labs are both reputable in their fields.

It seems the decision will be a bit easier than I anticipated.

Tuesday I was driving in the car with some other graduate students and one asked what I wanted to do. Not having a specific answer I chose the one that was probably the most accurate: "I want to work where I can pose the questions that interest me and find the answers." One could probably work in academia, government, or private industry and do that, but to varying degrees. Academia would have the most freedom, but the least resources. Industry would have the most resources, but the least freedom. Government is somewhere in between, but the politics does play a factor here from what I’ve been told. Why am I writing about all this? The point is in academia one needs to stretch monetary resources to accomplish the goal, so professors cannot always afford to take as many students as they might like.

I knew another student, Pat, who had worked in Dr. Roth’s lab at the same time I did had already committed to returning to do his dissertation work. I like Pat, and we’ve known that we both had some similar interests in terms of where to research, so we knew it might be a possibility that we might both want to work in the same lab, but there would only be resources for one student. So I met with Dr. Roth to ask if he would be interested in taking a second student. If he were then my decision about where to do my dissertation research would be difficult, if he weren’t it would be simple. While he told me that he thought the work I’d done was good, they didn’t know that there would be the resources to take another student. It would be worse to take two students and not have the money for both of them to do their research than it would be to have to chose between two. I understand and appreciate that decision, but it does leave me a bit sad.

Some of my favorite memories of school and work are from the time that I spent working in Dr. Roth’s group. At this point it looks like that’s what they will stay. Next I need to talk to Dr. Kaminiski (who I’m currently rotating with) check whether he has the resources to take another student.

So today has been a mixed bag so far. Happiness tempered with a touch of disappointment. Such is life sometimes, and that’s part of what makes it great.

SwitchProxy Tool for Mozilla

SwitchProxy Tool for Mozilla

This little Firefox goody caught my attention after a viewing of checking out It appears to be an extension that allows one to quickly switch between proxy servers (what is a proxy server you ask?) through a toolbar. There are two reasons I like this idea.

The first is that if I'm off-campus and want to use the MSU Library to download an article I have to go through a bunch of menus in whatever browser I'm using to set up a connection through the MSU proxy server. Once I've done that I can usually get the research articles I want, though there have been occasions were it still didn't work and I had to wait until I got to campus to read a research article.

The second reason this interests me is the idea of anonymity. I've had a passing interest in encryption, anonymity, and privacy on the net. This Firebird extension would seem to be an easy to use tool that improves access to anonymity.

I really don't have a need for any of those things as it comes to the 'net, as most of the things I find interesting or view on the web would be boring to the majority of people. Yet my Libertarian side gets all riled up when I think about the protection of privacy. I make a concious decision about my privacy as it comes to the 'net, but I worry that most people don't have a clue about the ability of others to monitor what they do online. Medical records, financial records, and personal writings can be of a very personal nature; why would one who worries about their records treat their online persona differently? I think the answer if they simply aren't aware of the risk to their privacy. This is why I think a simple browser extension is worth attention.

Monday, December 20, 2004

The Reasons I Love the Public Library

Books, books galore. Films for $1. CDs for your listening pleasure. The ability to request things they don't have through interlibrary loan.

I wanted to start a list of things I intend to borrow from the library, starting with the films I've wanted to see but maybe forgot about at some point.

1. 400 Blows
2. ABC's of Newborn Baby Care
3. About Schmidt
4. Alias Season 1
I never bothered to watch it on TV, but maybe Ellie and I will enjoy it on DVD?

This was just starting in the A's for DVDs in the library collection. I started going through and just marking the entries I knew I'd go for. I made it through the first 972 possible records before I decided to come back to it later.

this is an audio post - click to play - The Podcast Directory - The Podcast Directory -- The Place to Find Podcasts

I just recently got turned onto Podcasting, and have been using it to enjoy WGBH's Morning Stories. Now I'm working on finding some feeds that will bring me music I've not heard but will likely dig on.

Saturday, December 18, 2004

WinDirStat Home Page

WinDirStat Home Page
This was exactly what I needed for my C:\ on the home PC. It had become rather full, so much so that I couldn't properly defragment it. I was looking for a tool to graphically represent what each directory took up in terms of space, and I knew of a Linux tool to do it (called Filelight). After a little digging I found a somewhat similar Windows utility to accomplish the same idea.

What I found was in my very old IE temporary internet files directory I had a 500Mb disk image for Gentoo Linux. That puppy got the Strong Bad style "DELETED!" Now I can peacefully defragment that disk volume.

COX-2 Inhibitors and Cardiovascular Toxicity

A great deal of media attention was paid to Merck's pulling of Vioxx (rofecoxib) from the market, and now on the heels of that Pfizer announced some danger in high doses of Celebrex (celecoxib) the COX-2 inhibitors are getting a lot of media attention. While I think COX-2 inhibitors deserve some more examination, I also think the media is getting a tad hysterical about the whole thing.

My experiences in toxicology at this point are solely with liver and immune system toxicology, but we've discussed the COX-2 inhibitors this semester so I thought I might put out the ideas I've learned about them.

First, it is important to understand what COX enzymes are and why they're important in our biology. Cyclooxygenase (COX) comes in two forms, COX-1 which is expressed in nearly all cells continuously, and COX-2 which is inducible in response to injury or invading germs (it is also mostly found only in inflammatory cells of the immune system). COX is an enzyme that converts a fatty acid (arachidonic acid) from the cell membrane into compounds called prostaglandins. Prostaglandins come in a many forms, and depending on the mix of enzymes in a cell different ones will be produced, mediating differing effects. Prostagladins can be proinflammatory, antiinflammatory, and probably other effects that I didn't take the time to look up. The slowest step in the making of prostaglandins is the step that COX enzymes catalyze. Once made prostaglandins can also be made into thromboxanes, hormones important to blood clotting.

Pfizer and Merck were both involved in clinical studies where they were trying to find their COX-2 drugs may prevent or slow the growth of colorectal cancer (which causes 10% of all cancer deaths). It was a reasonable hypothesis to pursue, as some antiinflammatory drugs are useful in the treatment colorectal cancer. Researchers have established that a drug called sulindac, a Non-Steroidal Antiinflammatory Drug (NSAID) that inhibits both COX-1 and COX-2, is helpful in treating colorectal cancer. Often the undesirable effects of NSAIDs like aspirin are blamed on their inhibition of COX-1, as normal prostaglandin production in the stomach is necessary for making the mucous that protects the lining of the stomach from self-digesting. Researchers thought that it might be possible to get the beneficial effects of COX inhibition in the treatment of colorectal cancer without the undesirable side effects like stomach ulcers.

What researchers at the National Cancer Institute observed was that those people who took the highest doses, 400mg to 800mg, of celecoxib (Celebrex) had 2.5 times the risk of having a fatal or non-fatal cardiovascular event (things like heart attacks or strokes) when compared to those taking a placebo. This was in 1 of 2 studies Pfizer had going. The other study only had doses up to 400mg and revealed no increased risk.

It looks to me like this is a case of "Dosis facit venenum," or "the dose makes the poison." All this hand wringing and fear-mongering in the media, and we're talking about a small fraction of people. The recommended dose for celecoxib is 100mg-200mg for osteoarthritis and 200mg-400mg for rheumatoid arthritis. Osteoarthritis accounts for something like 80% of all arthritis, so most of the people taking celecoxib would not be likely to be at risk for "fatal or non-fatal cardiovascular event." What really bothers me is these drugs are being painted as risky, when they pose little risk for most people and offer excellent therapeutic help to people suffering with arthritis pain!

Being in pharmacology (not pharmacy) I'm of course interested in how this observed effect works mechanistically. In my pharmacology class we did get a plausible hypothesis, but it has yet to be proven.

Our bodies have many different kinds of cells, and they often respond differently to a given stimulus like a drug. I alluded to the idea that COX can be important to many processes in the body. It's not accurate to look at prostaglandins as all good or all bad, they must function in a balancing act. One of the things that they help to balance is the formation of clots in the body. COX-2 helps to produce a prostaglandin called prostacyclin, which normally dilates the blood vessel and inhibits clotting.

If we selectively inhibit COX-2 we'll reduce the amount of prostacyclin produced, and thus decrease blood vessel diameter and increase clotting. At the same time COX-1 is still functioning and producing prostaglandins and thromboxanes that can increase clotting. By inhibiting solely COX-2 and not all COX forms we may create a situation where the clotting stimulus is on, but the anticlotting signal is switched off, leading to clots that could float around until they reach a constricted point in the blood vessels, and then stick, reducing blood flow. Boom, stroke or heart attack.

The research that generated this hypothesis was done in mice, so it can't be said for certain that it holds true in humans. It does give a very serious hint at it though.

Internet Explorer 6.0 Chokes

It seems that IE 6.0 chokes on the Sidebar just like IE 5.1 on the Macintosh computers at work. I apoligize to all those who still use it, apparently 90% of internet browsers. Mozilla performs just fine, as far back as version 1.3 (the last version of Mozilla that I can find that will work on MacOS 9).

For my PC browsing needs I using Firefox, and have been since version 0.5. Firefox finally hit 1.0 recently, and is far ahead of Internet Explorer in my opinion. Like anything there is an adjustment period, but once I got used to tabbed browsing I can't stand going back to this single window browsing that I must use with Internet Explorer.

I may try some searching on the internet to try to determine why IE doesn't play nicely, but I'm not too inclined. Even the AOL browser is now based on Mozilla, so I'm optimistic that the next version of IE comes out, whenever it may be, it will perform better.

Friday, December 17, 2004

this is an audio post - click to play

Fixing Things Until They Break

Ellie called me on the phone and told me there was a bunch of typos in my blog post, and that it was long, so now I've edited it to try to find the typos.

Finally I've got the comments function working on ol' Blogger. Originally when I had them enabled Blogger didn't offer a comments function, so I was using a third party script to do it. When Blogger added the comments feature I figured I might as well switch to that one. Eventually I took them off because there really wasn't much being written in the comments, not that most of my posts inspire commentary. When I decided to turn them back on they didn't work for me, likely due to my mucking around with the template (I've been trying to get the Sidebar to look like I want in all browsers for months now, and I kept having problems with it).

Finally I tired of trying to manually get things to work and thought I might try starting fresh. Since I've grown weary of the old template for the site and Blogger added some new ones I thought I'd try a new template. This would hopefully solve the problem of the comments and the Sidebar at the same time, but I'd lose my customizations. Oh well. I made a backup of the old template and pulled the trigger on the new template. I do like it's appearance quite a bit better. It looks like the Sidebar is working much better for Mozilla. In IE 5.1 on the Mac the Sidebar ends up at the very bottom of the page, and I haven't checked with IE 6.0 on a PC, I'll be looking forward to seeing how it looks. I still haven't put my blogroll back up either.

The comments do look like their working again, so I'm pleased about that. The overarching idea is I tried fixing the blog until it broke, and now I'm fixing it until it breaks again. I'm really trying to resist the urge to tweak it too much. Eventually that always leads to some kind of nusiance cropping up.

I made the previous post about using SELinux on my home Gentoo box. I'm thinking maybe not at this point. I read through the documentation before I tried it and found that I'd need to recompile a custom kernel for Linux. I'm not afraid to do it, as I've done it before to get the network cards working in it, but it takes hours to recompile the operating system and I'm not quite certain I recall how I configured the network card to work. I think I'll put that project on hold, especially since if I don't get it to work it will mean I have to unplug it, hook up a monitor, and take several hours to fix it. I don't feel like doing that right now. I'm still very new to Linux administration, so to add a customized security system is a tad overwhelming to me at this point.

Next I thought about using a more secure form of PHP (a scripting language for web pages) to replace what I've got running on the Gentoo box. Again I got to thinking "I just got it working like I want, and now I might end up unraveling all that work just for some more security I don't even need at this point." That will go on hold. Perhaps I'll try that after something like SELinux.

Finally I thought "Well, it might be interesting to get SSL running on the Apache server, that way the pages are all encrypted as they travel through cyberspace." Again, not something to tackle lightheartedly. These things can be so complicated that if they don't go off just like the documentation says then it means hours of seaching various internet forums for information that might help one to fix the problem, or might be totally useless.

All in all, I'm going to resist the temptation to make my little home server into a tight, secure Linux box and instead opt for something that simply works (that last part sounds like an Apple "Switch" commercial).

Gentoo Linux Documentation -- Initial preparations

Gentoo Linux Documentation -- Initial preparations

This is the handbook for installing SELinux on a server. I'm planning on giving this a shot sometime soon for my home server, since I finally got it to run LAMP properly.

Tuesday, December 14, 2004

Found the Time to Post

Last night I finished the semester around 10:00pm, having just turned in my Biochemistry final to the professor. Both of them down in the same day, at the very start of finals week. Now the baby can come without me worrying about making up exams and studying for them with a crying infant. That will be for next semester.

I keep grinding away on my project at work, but have been somewhat discouraged today. I've been using a technique we call Western Blotting (the name of the assay is a bit of a science joke, a story perhaps for another post) to check protein expression levels of a specfic protein. In a Western Blot one sticks proteins to a membrane and can then detect the protein of interest by using an antibody to identify it. If things are done correctly it is possible to probe with an antibody, strip off the antibody, probe with a different one, strip, probe again... you get the idea. The problem is the stripping agent can also remove the proteins from the membrane, so if done repeatedly the signal from the proteins is diminished.

I got a protocol to strip the Western Blot I had and I actually used more mild conditions than were recommended in the instructions, but all the proteins were stripped off in the process. Ugh. Frustrating, because it takes about 3 days to run a Western Blot. I started it over today.

Friday, December 03, 2004

Reds, Blues, and ...... Purples?

Being Friday, having completed today's experiment, and procrastinating on the Biochemistry final studying I found myself over at the blog of Lawrence Lessig after first checing out the 2004 Weblog awards.

There I found a link to some depictions from the 2004 Presidential election. We've all seen the Red and Blue maps that basically show most of the US as Republican voting territory with isolated states that vote Democratic. This web article from someone at University of Michigan shows an interesting way of looking at the maps.

I was particularly struck when the nation was broken down as Red and Blue counties. It starts to look very much like a Republican nation. Only when they factor in population and represent it as size of counties does the picture become more like the popular vote would reflect.

Finally, when they use a gradient coloring with Red and Blue representing 100% Republican or 100% Democratic respectively does the character of the nation really start to become apparent. Purple would be a 50/50 split. It was fascinating to me to see how the US looked when presented this way. Give it a gander if you get a chance.

Thursday, December 02, 2004

Am I Really an Anarchist?

I caught a post of Justin Roggow's over at Neural Fusion this morning, so before I got to real work I thought I'd play along and try out one of ol' Internet personality quizzes. Seems I score as an anarchist. Funny thing is I think anarchists a missing the point. Justin came out of the quiz as Jewish, although he's claims atheism.

You scored as Anarchist. Coochy choochy coo, what a cute little ANARCHIST we have here.
You see everything as a means to an end, and that end is You. You don't understand why some saps do community service cause you wouldn't be caught dead picking up trash unless you were in an orange jumpsuit. You're also pretty angry at the world but are too self-concerned to do anything about it because you are an anarchist. Understanding this statement would practically kill you,













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