Friday, July 29, 2005

Mount Saint Helens

This past Sunday was planned to be a relatively dull day of driving between Portland (where we'd just visited a college friend) and Seattle (where we stayed for four nights). We left Portland a bit early, and so looked for things to do on the drive; we saw that Mt. Saint Helens was nearby, so we decided to spend the day there. The volcano erupted in May of 1980, and the surrounding area was turned into a National Volcanic Monument in 1982.

The mountain itself was shrouded in clouds for most of the day, but was very imposing nonetheless:

Mt. Saint Helens

Even miles away from the volcano there were no large trees; only small trees and stumps of larger ones:

New and old trees

In some areas the blown-down trees were still visible:

Trail through downed trees around Mt. Saint Helens
Note the hikers for scale.

There were also wildflowers covering much of the area, which made the scenery quite beautiful.

Wildflowers at Mt. Staint Helens

You can see all my pictures in my Mt. Saint Helens photo set on Flickr (I've posted 18 total), and can find more information on the monument at the USDA Forest Service Page and USGS Page, which includes an interactive map with points of interest.

I'll leave you with one final picture showing the power of the volcano:

Tree stumps

Friday, July 22, 2005

Off to Canada!

After I make this post, my SO and I will finally be off on our multi-week driving trip to Canada. This trip is built around my week-long field course, but will also include some time in Seattle, Victoria, and the Hoh Rainforest, as well as a few days with my folks. If you're curious what the scenery will be like, go take a peek at last year's hourly pictures.

More from the road!

Caterpillar time!

A caterpillar I spotted while doing some field work a week or so ago.

Tuesday, July 19, 2005

End discrimination against rats

While waiting (for three hours, grumble) in a doctor's office yesterday, my SO read "Honor Among Beasts" (paid subscription required), an article in Time magazine. The article talks about recent studies demonstrating that animals have more human-like emotions than many people previously thought, but it wasn't the studies that grabbed our attention; instead, it was the bias against rats.

When the article first lists social animals, it gives a long list of "nice" animals (dolphins, dogs, birds, etc.), and then includes rats at the end of the list as though they were a disgusting afterthought, saying, "and even rats".

Later in the article the bias becomes even more pronounced:
"Dolphins, dogs and primates are the usual suspects when scientists talk about higher mental functions, but fairness, at least, extends even deeper into the lower animal kingdom. If you watch rats wrestle ..."
Ever wondered how to push a biologist's buttons (or at least this one's)? Just say something like that.

The first error in this quote is the implication that there are "higher" and "lower" animals; this is evolutionarily inaccurate (for the same reasons that the evolutionary ladder idea contained in the TTLB ecosystem rankings is incorrect).

Making things even worse, the author includes rats in the list of "lower" animals. While it is possible to argue that some animals are more complex than others on a gross morphological level (e.g., humans are more complex than sponges), attempting to place rats in a category of "lower" animals (compared with humans) is ridiculous, especially given that the author has included dolphins and dogs as "higher" animals.

The problem with labeling rats, but not dogs and dolphins, as "lower" animals is that rats are evolutionarily closer to primates (and thus humans) than dogs and dolphins are. As you can see in this wikipedia entry summarizing molecular-genetic work on mammals, both rodents and primates can be grouped into superorder Euarchontoglires (wikipedia page), while Carnivora (including dogs) and Cetacea (including dolphins) can be grouped into superorder Laurasiatheria, an equivalent lineage to Euarchontoglires.

So, if you're going to assume that the evolutionary ladder idea is correct and argue that animals close to humans are "higher" and all other animals are "lower", since rats are more closely related to humans than dogs and dolphins, you can't simultaneously argue that dogs and dolphins are "higher" animals while stating that rats are "lower" animals.

What we're really seeing here is the common misperception that rats are just red-eyed, blood-hungry vermin whose only function in this world is to spread horrible diseases and make 1950's housewives shriek from the tops of tables. Domesticated rats and mice make exceptionally good pets, are probably less dangerous than your average dog or cat, have very human-like behaviors, and are cuter than cuteness itself (see my baby mouse photo archive for evidence). Wild rats and mice are just like any other animals trying to fend for themselves.

And yes, based on the molecular evidence I described above, rats and mice are more closely related evolutionarily to humans than either cats or dogs (or horses, dolphins, aardvarks, birds, lizards, sea anemones, or nematodes, either). Get used to it.

Conyers on Rove et al.

Rep. Conyers has been has been blogging up a storm on the current Rove scandal relating to the outing of covert CIA agent Valerie Plame. A post Conyers made yesterday has a nice summary:
We learned from Downing Street, that the White House was willing to "fix the facts around the policy," no matter the cost in lives or our nation's reputation. Rovegate involves the same modus operandi: When faced with a growing scandal before the election, Bush righteously promised to throw out any and all leakers. McClellan went so far as to tell us it would be "ludicrous" to accuse Rove or Libby of leaks. Now that there is no doubt that those statements are false and, presto, the standard has changed to "if someone committed a crime."

Friday, July 15, 2005

Time for a break ...

Those of you who've been following this blog regularly know that this past spring was hectic, as it was filled with grants, committees, and other such work. This summer was supposed to be a break from all that: a time to relax, catch up on reading, get some perspective, and get energized for the fall.

Well, as you may have noticed, that hasn't been happening much around here. My summer field course has been requiring huge chunks of time, both getting supplies (which I have posted about) and actually teaching the course (which I haven't written much about). Additionally, the wiki that I set up months ago has been more successful than I'd hoped (with thousands of page edits, more than ten thousand page views, and another instructor partially running a course on it), so I've been spending a lot of time working on that, including moving the entire site to a commercially hosted server. I've also been blogging up a storm (at least for me), and actively following political issues that I normally wouldn't have paid much attention to.

While everything I've been doing has been fun, I've been doing something, and more often than not something which requires a good amount of work and thought at a computer, virtually every day this summer.

In short, I'm working my summer away.

Well, starting with this post that's going to change for a bit here. My SO's birthday is approaching, and within a week we'll be off on another multi-week trip to Canada. These two events have motivated me to call a temporary halt to official blogging, primarily to help motivate me to relax away from a computer.

Never fear; this doesn't mean there won't be any posts. However, the posts that are here will likely be sporadic and personal in nature: cataloging our travels, sharing pictures, and/or other such fun. If you want good biology or political writing in the next month, go visit Pharyngula, Orac, ConyersBlog, or any of the other excellent blogs out there (see the sidebar for more ideas). If you want pictures of mice and reports from Canada, stay right here.

And also, since my SO's birthday is coming up, I'm going to be completely silent for a few days as I give my SO a present with no material basis, and which is quite literally priceless (or should I say "worthless"?): my undivided attention (of course, many other presents are coming as well). For the duration of my SO's birthday celebration I'll be shutting down my precious Debian box, ignoring my Windows box (which will be significantly easier than the first item on this list), and not doing a thing online (or otherwise) to distract myself. To my SO: happy birthday!

A collection of random links

I've collected a lot of links in the past couple of weeks; it's time I sorted through them and posted at least a few of the good/interesting ones.

Here's a collection of blog links:
And some recent news links:

Thursday, July 14, 2005

UCCountVotes is looking for help

USCountVotes, the organization started by Kathy Dopp (whose analysis of 2004 presidential election data in Florida spawned much discussion), is looking for volunteers, as well as sustaining members, to help support the organization (see their PDF brochure).

Here's what USCountVotes' mission statement says about their goals:
"USCountVotes is a scientific research project whose mission is to objectively investigate the accuracy of elections in America through the creation and analysis of a database containing detailed precinct-level election data for the entire United States."
The group has already published some very thorough statistical analyses of the past election, including Analysis of the 2004 Presidential Election Exit Poll Discrepancies (PDF, which I wrote about here) and Patterns of Exit Poll Discrepancies (PDF).

The Sketpics' Circle is coming

Orac is hosting next week's Skeptics' Circle, and he's already put up a call for submissions (that guy is way too organized; I don't even know where I'll be staying in a week). Send him your best skeptical writing by 9 PM EDST next Wednesday to be included.

Skeptically analyzing exercise equipment

The American Council on Exercise has commissioned a number of research studies to examine the effectiveness of various exercises and exercise eqiupment. The studies cover a wide range of topics, including analyses of ab workouts, sports bras, and super-oxygenated water. While I'd like to see more detail in the methods and results, the studies appear to be well done and are a good skeptical look at modern exercise hype.

In their ab workouts study, the researchers compared 30 men and women performing "traditional crunch, modified crunches, partial body weight exercises and exercises using both home [including the Torso Track, Ab Roller, and AB Rocker] and gym exercise equipment [including the captain’s chair]". They measured muscle activity to quantify how much the exercisers were working (and if they were working the proper muscles), and found that the bicycle maneuver (a floor exercise), captain's chair (a piece of gym equipment), and crunches on an exercise ball were the best exercises (see here for instructions on how to do the good exercises, including images).

The home ab exercise equipment didn't fare too well:
"[T]he Torso Track appeared to be marginally more effective than the traditional crunch. However, this training benefit is likely offset by the lower-back discomfort reported by a significant number of subjects while using the Torso Track.

The Ab Roller was proven to be virtually no more effective than the traditional crunch while the AB Rocker was shown to be up to 80 percent less effective.
Their other studies make for interesting reads as well, though they generally show results that any good skeptic would already have hypothesized.

[cross-posted at The Gym at Rhosgobel.]

Southern California blood shortage

Red cross image
The Southern California Red Cross is reporting that they have a severe blood shortage. In an e-mail I received a few days ago they said they had only a three-hour supply of 0- blood, and on their website they report the following inventory levels ("based on the desired seven-day supply"):
  • 0.4% of O-
  • 2.5% of O+
  • 3.7% of A-
  • 3.8% of A+
  • 8.1% of B-
  • 1.9% of B+
  • 8.1% of AB-
  • 15.2% of AB+
I donated blood a few weeks ago, so I can't donate now. Can you donate? If so, go to or call 1-800-givelife. Even if you're not in Southern California, I'm sure that other areas of the country need blood donations too.

If you think you can't donate blood because of medications or some other condition, you might want to check again. As I wrote about here, many medications and conditions that people believe exclude them from donating blood actually don't.

So please, go donate.

Wednesday, July 13, 2005

Tangled Bank #32

Tangled Bank Blutton
The 32nd Tangled Bank has been posted at Techno Gypsy.

Automatic restarts

My SO and I just finished baking a cake, and upon coming back to our computers we found that both of our Windows boxes, on which we'd left quite a bit of work open and in-progress, had rebooted themselves automatically.

The culprit was Windows XP's automatic security updates, which by default automatically downloads and installs updates at 3am every day. The default setting also automatically restarts the computer once the updates are installed; if you're not there at the precise time to stop the reboot, Windows just closes everything and reboots. Have anything open in your browser that you didn't want closed? Too bad.

To stop the automatic rebooting you can change the automatic updates settings via the "security center" in the control panel, but doing so results in a very large "CHECK SETTINGS" warning.

This has to be one of the most annoying "features" I've ever seen. Is Microsoft actually trying to encourage me to use Linux more?

Monday, July 11, 2005

Why have I started blogging on politics?

Long-term readers may remember that when I started this blog, I explicitly said that I would not blog on political topics. At the time, my idea was to focus on biology, education, and other topics that interested me; I decided that I'd rather stay out of the frenzied fray that political blogging often becomes, and I didn't think I had much to add to the political arena.

However, a quick look through my recent posts demonstrates that I've abandoned any notion of being apolitical, and, if anything, I'm now focusing more on politically-related topics than biology and education. I'm not altogether happy about this shift (I am a biologist and an educator, darnit), but I thought I'd outline the reasons for the change.

In the time since I started this blog, many things have happened. First, I've watched as California's governor has cheated education out of $2 billion dollars, and I, and more importantly my students, have suffered as a result. And the governor isn't satisfied with stealing just $2 billion dollars; he wants to permanently decrease the funding for education, legislate how teachers get tenure via a ballot initiative, and give himself sole discretion to enact large mid-year budget cuts to education in the future (posted about here).

I've also watched a presidential election occur, and was awestruck as the media and public blithely ignored the numerous reports that there may have been election fraud. There wasn't even a thorough public investigation. I also discovered, during the election, that a decent fraction of the people who supported Bush didn't even understand his basic policy positions, and thus didn't know who they were voting for. During the election I read a lot of posts describing how the current administration was against science, and against sanity (like, say, the realization that climate change is occurring), yet the current administration is still in place.

In just the past few months, I've seen even more evidence that climate change and environmental impact reports have been doctored so that the "scientific" conclusions justify the administration's policies, whitewashing the real science in the process. Even worse, agencies in the government are actively working to hinder consumer safety; for instance, they prevented food producers from testing their food (at their own expense) to ensure it's safe, and have failed to mandate safeguards to prevent the transmission of easily preventable diseases, such as mad cow disease.

And we can't forget the war in Iraq. Evidence has surfaced showing that the administration may have lied to the American public, and the world, in order to invent reasons to justify an invasion of Iraq. Documents state that the UN and "diplomacy" were used solely as smokescreens to "trip up" Saddam Hussein. These are lies that, if true, have led to the deaths of more than 1,700 Americans, tens of thousands of Iraqis, and the injuries of tens of thousands more people. More than half a million Americans signed a letter asking for clarification on whether the administration did in fact lie, and how did the administration respond? They said that they had no intention of responding. What did the media do? Largely ignore the issue.

And in the course of this war, has the administration ensured that people are treated humanely and fairly? No. The administration has decided that the Geneva Conventions don't apply to prisoners captured on battlefields, and is holding people indefinitely, in legal limbo, in offshore prisons. Some people have been held for years without trials or criminal charges, while others face the possibility of having their torture-extracted confessions used against them in secret trials. The United States is torturing prisoners. I thought I would never write that about my country. But there it is, backed up by (among other things) a 500-plus-citation work by a major international organization specializing in international relations.

In short, I've watched as my country has done things I never thought it capable of.

When I started this blog, I didn't want to be defined as just another liberal-freak blogger, and I didn't want to get caught up in flame wars that distracted me from my planned focus on biology, education, and personal topics. However, my sense of outrage has since grown enough to overcome those concerns, and I've also come to believe that engaging in a public dialog about our nation's policies can be an important use of a blog, if only because it motivates me to learn more about current political events.

I will try, as I have so far, to treat political issues as factually as possible. I don't particularly enjoy reading long rants about topics, and I don't plan on writing many. But I will keep writing about things that I find to be particularly outrageous, or of some special interest, and I hope that in doing so I can do some small bit of good.

Sunday, July 10, 2005

Tangled Bank coming soon

Tangled Bank Blutton
The next Tangled Bank will be hosted this Wednesday at Techno Gypsy; send your submission to

Cranberry upside-down cake

My SO and I made this cake shortly after reading the recipe (Rees 2005) in Fine Cooking magazine a few months ago, and we loved it. It's a rich sour cream cake covered in gooey, brown-sugary cranberries. My SO prefers this cake to the more typical pineapple upside-down cake, though I must sadly admit that I can't recall ever eating pineapple upside-down cake, so I can't compare the two. Since we made this last week, it seems like a good end-of-the-week recipe blogging post.

Aside from having to bring all the ingredients to room temperature before you start, this cake is easy to make. It doesn't need icing or frosting, and can be served only 20 minutes after it comes out of the oven.

For the cranberry topping:
6 tablespoons butter
1 1/3 cup packed brown sugar
1/4 teaspoon cinnamon
12 ounces (~3 cups) frozen or fresh whole cranberries, brought to room temperature and patted dry

For the cake batter:
12 tablespoons butter, at room temperature (very soft)
1 cup sugar
3 large eggs, at room temperature
2/3 cup sour cream, at room temperature
1 teaspoon vanilla extract
1/2 teaspoon table salt
1 3/4 cup flour
1 teaspoon baking powder
1/4 teaspoon baking soda

0) Bring the ingredients to room temperature; we usually leave them out on the counter for an hour or two. When the ingredients are at room temperature, preheat the oven to 350F.

To make the cranberry topping:
1) Put the 6 tablespoons butter in a 9" round cake pan, and put the pan in the oven until the butter melts.
2) Remove the pan from the oven; use a brush or tilt the pan to lightly butter the sides of the pan with the melted butter.
3) Thoroughly mix the brown sugar and cinnamon into the butter.
4) Distribute the cranberries evenly on top of the brown sugar mixture. Set the pan aside until the cake batter is ready.

To make the cake batter and bake the cake:
1) Cream the butter and sugar: mix until the sugar is completely incorporated into the butter, and the color and texture have lightened.
2) Add the eggs one at a time, mixing thoroughly after each addition.
3) Add the sour cream, vanilla, and salt, and stir to mix.
4) Add the flour, baking powder, and baking soda. In theory you should sift these together first, but we typically just add them all to the bowl and then mix the flour, baking powder, and baking soda together as we incorporate them into the batter. Mix until smooth.
5) Spoon the cake batter into the pan on top of the cranberries, and level the surface.
6) Bake at 350F for 50-65 minutes. To test whether the cake is done, poke a toothpick into the center of the cake and then remove it. If the toothpick pulls out only dry crumbs (or nothing), the cake is done; if the toothpick pulls out moist batter, bake the cake a few minutes more and test again.
7) Cool the cake on a rack for 5-10 minutes, and then invert the cake onto a plate. Remove the pan and let the cake cool at least another 15 minutes before serving. Serve warm or at room temperature.

We bake this cake in a silicone nonstick cake pan, which probably helps the cake release from the pan.

Whole cranberries are easily available (and cheap) in US supermarkets around Thanksgiving. They freeze very well, so we typically buy lots of them at Thanksgiving and then freeze them; we've found that they keep at least 6 months in the freezer in their original packaging (plastic bags with holes in them).

This recipe was modified from Rees 2005; the primary changes we made were to increase the amount of topping and simplify the cake batter slightly.

Rees, Nicole. 2005. Moist, Tender Snack Cakes: A bowl and a whisk are all you need. Fine cooking 68: 42-46.

A summer dinner

On Friday night my SO and I had broiled wild salmon (with wasabi-ginger mayonnaise), fresh corn on the cob, and, for dessert, homemade peach pie. It was nothing special, but it made me feel like summer had finally begun. Maybe this is our equivalent of dandelion wine.

Friday, July 08, 2005

Privacy on the web

[Part one of a three-part series detailing the uses of Privoxy and Tor.]

Most websites these days are filled with ads (note, dear reader, that this site is ad-free), and the majority of websites track their users' behavior through the use of cookies, webbugs (1x1 pixel gifs), scripts, server logs, and other tools. Even my humble site tracks your activity; the counter service I use (sitemeter; which is frequently used by bloggers) places a little script on each page, and based on that script I can typically determine when you visited this site, your IP address, which page you entered the site on, how many pages you loaded, how long you kept loading pages, and what link you followed to get to this page.

Don't worry, I'm not out to track your individual behavior. My counter service only lets me see data on the last 100 visitors (because I'm cheap and don't pay them), and I use the data solely to see how many hits I'm getting, if I'm getting any referrals from sites I don't already know about, and what pages people are viewing. The service only tracks your IP; I don't know your name.

The point is, though, that it's terribly easy to track people's activities on the web. If a person is running their own server, and thus has access to the server logs, their website doesn't even have to have a script running on the page to get all the information I described above; it occurs automatically when you request a page from the server.

While your IP address can't give a website administrator your name, the cookies on your computer can. I recently went to a Pepsi website (based on their recent Star Wars movie promotion), and clicked on a form to enter a sweepstakes prize number. Even though this was the first time I'd ever visited a Pepsi website, all of my personal information (name, address, e-mail) was automatically filled in on the form.

How had they gotten the information? They'd used cookies placed on my computer to identify that I was a Yahoo! user, and had apparently gotten the information from Yahoo!. Pepsi was doing this in good faith (to make registering easier), but the point is clear: it's easy to pull private information from the content contained in cookies. I was recently browsing through the text of all the cookies on my computer, and found my full (real) name, multiple personal e-mail addresses, passwords, and other private information, all stored in plain text in the cookies. There were a lot more cookies that contained encrypted (or at least unreadable) information; I have no idea what information they contained. It wouldn't be hard for a website to access that information, link it to my IP address, and then keep a database of what I, personally, do on the web. Sites like Amazon do it all the time, and there's even some evidence that they alter their prices based on the presence (or absence) of cookies on your computer..

If you don't like all this, there are things you can do to help prevent sites from tracking you. One option is to restrict how sites can set cookies. Unfortunately, many websites now rely on cookies to function (ever wonder how Flickr and Gmail remember that you're logged in?), so preventing all websites from setting cookies isn't a workable solution. However, you can set Firefox (and other browsers) to force all cookies to be "session only", which means that they'll be deleted once you close your browser. Additionally, most browsers allow you to add sites to a "blocked" list, which prevents those sites from ever leaving cookies. Firefox extensions like cookie culler (which I wrote about here) can make cookie editing somewhat easier, but it's not a complete solution to the problem.

However, manually configuring your browser can only do so much. It's a pain to try to figure out which sites need cookies, and which don't, and it's frustrating to have to filter through your cookies day in and day out, slowly building up a block list.

And cookies are only part of the problem; even if you were to block all cookies, websites can still log a great deal of information about you just based on your page accesses. That's where programs like Privoxy and Tor come in. Privoxy focuses on filtering web content to enhance your privacy and reduce the number of ads rendered on pages, whereas Tor focuses on preventing websites from tracking you by anonymizing your IP address.

In the next post in this series I'll discuss installing, using, and configuring Privoxy; in the third post in this series I'll do the same with Tor.

Thursday, July 07, 2005

London Bombings

I have little to say that hasn't already been said (e.g., Orac's sentiments mirror my own), and if you want more information on the bombings via the blogosphere, BoingBoing has assembled a large collection of links.

Wednesday, July 06, 2005

Downing Street Minutes basis for FOIA request

Rep. Conyers and several other members of Congress have filed a Freedom of Information Act request for documents relating to the Downing Street Minutes. Conyers blogged about the request here, and copies of the letter are at Raw Story. Rep. Conyers has also formally asked for hearings on the matter in the House Committees on Judiciary, Armed Services, International Relations, and the Permanent Select Committee on Intelligence.

Tuesday, July 05, 2005

Is nothing simple?

I've spent all day today and much of last Thursday and Friday placing orders for field equipment for my course this summer. Of course nothing has been easy; a disturbingly large number of items are out of stock, most websites appear designed solely to frustrate potential customers, nobody can give me solid shipping cost estimates, and everything is further complicated because these are international orders (e.g., I still haven't found a reasonably priced supplier for ethyl acetate [insect killing fluid] that will ship to Canada).

The most enjoyable part of the day? When one company's website lost my shopping cart after I'd placed 45 items in it.

And I thought spending money was supposed to be fun ...

[update 7/15/05: Everything is ordered, has shipped, and at least half of the items are already in Canada. Yay!]

Monday, July 04, 2005

Anime Expo 2005

Anime Expo sign, without people

This was the first fan convention, of any genre, that my SO and I have attended. I'd heard that it was big, but even so I was amazed at the size; Anime Expo's press release says that they expected 35,000 attendees this year. The convention was held at the Anaheim Convention Center (home of the AACR meeting Orac recently attended), which is absolutely huge.

The exhibit hall (aka dealers' room) was where we spent the majority of our time, and it was packed full of people:

Anime Expo exhibit / dealers hall
Exhibit hall of AX 2005; we weren't even at one end of the hall for this picture.

Yes, it was that crowded (compare it to Orac's picture, possibly even of the same hall, during the AACR meeting). There were a lot of sellers present, and some good deals could be found, though much of the merchandise was depressingly similar. Currently popular shows (e.g., Full Metal Alchemist, Fruits Basket, Naruto) had tons and tons of merchandise available, but older (and less popular) shows had extremely little available. While we didn't look at everything, I don't think we saw a single piece of merchandise (other than manga) for Tokyo Babylon, Mirage of Blaze, or some of our other favorite shows.

One of the coolest features of the convention was the manga library. This was a whole room dedicated to manga; after turning in your badge and bag(s), you could browse through the manga (they had hundreds of volumes), pick any two books, and sit down to read them. The library was open 24 hours a day, and you could enter and leave as often as you wanted.

This library room is a feature scientific meetings should adopt; imagine your favorite meeting having a room packed with the latest journals and books, all available for your browsing, any time of day. It'd be great for those bits of time that aren't filled with other events, or if you wanted a break from the meeting. We spent a few hours in the library between events, and had a blast.

Of course the convention was swarming with cosplayers. I didn't take too many pictures of them (partially because they were already being swarmed with photographers, and partially because there are many other places to get cosplay pictures, e.g.,, but it was quite enjoyable to admire the costumes and try to figure out who everyone was. It was especially fun when multiple cosplayers from the same show got together:

Full Metal Alchemist cosplayers
A horde of Full Metal Alchemist cosplayers

In the picture above we have at least five Eds (all played by females), four homunculi (Lust, Pride, Greed, and Envy), two soldiers (Colonel Mustang and Brigadier General Hughes), one Winry, and (we think) one fake Elric brother. Not in the picture, but in the area, were at least one other Envy and an Izumi.

Cosplayers made the convention very enjoyable to wander around (much more visually interesting than a scientific meeting), and also created some scenes that I suspect Orac didn't get to see during his meeting:

Lonely samuari
A samurai practicing on the roof of the convention center

I'll close with a picture of my favorite cosplayer of the entire convention:

Japanese Stormtrooper
A Japanese Stormtrooper!

Saturday, July 02, 2005

Friday, July 01, 2005

Mad cow disease in US cattle

The USDA confirmed last week that a cow, identified in November of 2004 as possibly having mad cow disease (bovine spongiform encephalopathy, BSE), did indeed have the disease (AP story, USDA press release). Mad cow disease, which is linked to variant Creutzfeldt-Jakob disease (vCJD) in humans, is caused by infectious proteins called prions. Prions remain infectious even after cooking, washing, and boiling (NINDS 2005), and even autoclaving can fail to destroy all prions in a sample (McDonnell and Burke 2003).

The prions that cause BSE are spread almost exclusively by consumption of infected animal tissue. Thus, even though prions are difficult to destroy, BSE is one of the most preventable animal diseases around: stop feeding dead infected animals to cattle, and you should completely prevent the spread of the disease (and stop feeding infected cattle to humans and you stop vCJD). Britain enacted a ban on feeding meat and bone meal (MBM, rendered tissues of dead livestock) to cattle in 1988, whereas the US waited until 1997 to enact a "ruminant-to-ruminant" feed ban (Pruisner 1997, USDA press release; see below for more information on this feed ban).

The recently confirmed case of BSE comes from a cow which was apparently born before the feed ban in the United States. Thus, it is highly likely that this cow got BSE by consuming feed which contained BSE prions, which leads us to two conclusions: 1) BSE was present in the animal(s) used to produce the feed fed to this cow, and, 2) it is possible that other cattle raised at the same time on the same feed are also infected with BSE.

Just this week the USDA reported that the cow apparently came from a herd in Texas, and they are attempting to track down related animals. When the case was first confirmed the USDA only reported that "there is no evidence the animal was imported" (AP story). The USDA press release from last week says an investigation is ongoing.

The USDA has responded to this newly found case of BSE primarily by mandating that anytime an initial BSE test for an animal returns a positive, the agency must run two more tests on the animal's tissue, instead of one, to confirm the presence of BSE (USDA press release). That's it.

The agency is mostly testing "high risk" animals, which are:
Nonambulatory cattle;
Cattle exhibiting signs of a central nervous system disorder;
Cattle exhibiting other signs that may be associated with BSE, such as emaciation or injury; and
Dead cattle. (information from USDA BSE Testing Program FAQ)
The agency details its testing strategy in this PDF (USDA 2004). This document makes it clear that the goal of the USDA's testing is solely to determine if BSE "is prevalent at a specified level in the sampled population" (USDA 2004). While the testing can be used to infer the prevalence of BSE in the cattle population at large, this testing regimen is not explicitly designed to do so.

In other words, the USDA is not testing whether the cattle currently being processed for food are free from BSE. In fact, the USDA has actually prevented some beef producers from voluntarily testing all of their cattle for BSE (I wrote about this here), and the majority of animals the USDA tests would never have been fed to humans anyway (since they are high-risk). While limiting testing to at-risk animals makes some sense statistically (if you're looking for a disease it makes sense to look in the high-risk population), it is hardly reassuring from a public health perspective.

We now have a known case of BSE, and thus we can no longer state that the prevalence of BSE in US-born cattle is 0; thus, there is a possibility of a public-health risk. Since this is the first US-born cow the USDA has found BSE in after a large number of tests (USDA reports 388,000 tests have been run), the USDA is saying that we can infer that the prevalence of BSE in the cattle population is relatively low (USDA press release). However, while running 388,000 tests sound reassuring, testing for BSE is quite difficult and inefficient, as the USDA (2004) report indicates:
"The earliest point at which current testing methods can detect a positive case of BSE is approximately 3 months before the animal begins to demonstrate clinical signs. Also, the incubation period for this disease - the time between initial infection and the manifestation of clinical signs - is generally very long, on average about 5 years."
In other words, cattle can appear perfectly healthy for more than five years while infected with BSE, without showing any symptoms. These non-symptomatic BSE-infected cattle would not appear to be high-risk animals, and thus would have a very low likelihood of being tested under the current USDA testing plan.

So, it is possible that other cattle from the infected cow's herd, which may also have been infected with BSE, were sent to slaughter before they exhibited symptoms, and thus they would probably not have been tested for BSE before becoming food for humans.

Additionally, the government has not closed off all possible mechanisms through which infected animal tissues could be fed to cattle. An AP article has more details:
The Food and Drug Administration (FDA) promised to tighten feed rules shortly after the first case of mad cow disease was confirmed in the US, in a Washington state cow in December 2003.

"Today we are bolstering our BSE firewalls to protect the public," Mark McClellan, then-FDA commissioner, said on Jan. 26 last year.

The FDA said it would ban blood, poultry litter and restaurant plate waste from cattle feed and require feed mills to use separate equipment to make cattle feed. Chicken litter is ground cover for the birds that absorbs manure, spilled feed and feathers.

However, last July, the FDA scrapped the restrictions. McClellan's replacement, Lester Crawford, said an international team of experts assembled by the Agriculture Department was recommending even stronger rules, and the FDA would produce new restrictions in line with those recommendations.

Today, the FDA still has not done what it promised to do. The agency declined interviews, saying in a statement only that no timeline exists for new restrictions.


Ground-up cattle remains left over from slaughtering operations were used as protein in cattle feed until 1997, when an outbreak of mad cow cases in Britain prompted the US to order the feed industry to quit doing it.

Unlike Britain, however, the US ban has exceptions. For example, it's legal to put ground-up cattle remains in chicken feed. Feed that spills from cages mixes with chicken waste on the ground, then is swept up for use in cattle feed.

Scientists believe the BSE protein will survive the feed-making process and may even survive the trip through a chicken's gut.
The presence of these loopholes is worrisome, especially now that we have confirmation that BSE exists in the US population of cattle. These loopholes clearly demonstrate that the government is failing to do everything it can to prevent BSE from spreading through the US cattle population. Instead of saying that they'll immediately work to prevent all possible methods of feeding infected animal tissue to cattle and humans, and working to ensure that animals fed to humans are safe, all the USDA did was mandate that one more test be carried out on already suspected animals.


AP. June 19, 2005. Activists demand US enforce ban on slaughterhouse waste as livestock feed. Taipei Times. (link)

AP. June 24, 2005. Tests Confirm Second Mad Cow Case in U.S. Yahoo! news. (link)

National Institute of Neurological Disorders and Stroke (NINDS). May 2005. Creutzfeldt-Jakob Disease Fact Sheet. (link)

Prusiner SB. 1997. Prion diseases and the BSE crisis. Science. 10;278(5336):245-51. (full-text)

McDonnell G and P Burke. 2003. The Challenge of Prion Decontamination. Clinical Infectious Diseases. 36:1152-1154. (link)

Radagast. October 14, 2004. Science and Politics. (link) July 1 2005. Home-Grown 'Mad Cow' Traced to Texas Herd. (link)

USDA. 2005. USDA Announces BSE Test Results and New BSE Confirmatory Testing Protocol. Release No. 0232.05. (link)

USDA September 2004. USDA BSE Surveillance Plan: Background On Assumptions and Statistical Inferences. (PDF link)

USDA FAQ. USDA's BSE Testing Program FAQ. Last access date: July 1, 2005. (link)