MBB: the Moronic Bumblers Building..

Laboratory update:
We have officially moved into our new labs at the Medical Biosciences Building at UMN. The idea was to have a location for all the immunologists to be localized in the same area to promote interaction. Unfortunately, the building is designed in a way that makes it more difficult to interact.

I admit, everything is new, and it's an edgier, artsier building than before. And best of all, I have gigantic windows with a great view... of the train tracks.

HOWEVER, overall lab space is diminished, storage is drastically reduced, and we've been plopped out by ourselves behind the football stadium. My giant windows are north-facing -- so it's frigid in here, there's not enough refrigeration capacity, and for a building that is meant to promote interaction, there are no large meeting rooms.

Good job, UMN. Your goal of making the University one of the top research institutions will surely work when you let administrative accounting control building design. This building had been touted as high-tech and state-of-the-art. So far the most futuristic bit I've seen is the motion sensor on the urinal.

Well done.

I say fever...

This music video is more than awesome.



Unfortunately, the rest of their stuff is pretty meh.

I don't want to grow up!

The new season of Top Gear is here!

RAD!




And I literally LOL'd at this while at work:

NOVA: science that is decades behind...

As I was setting up my TV to watch some Top Gear last night, I caught a snippet of a NOVA episode on PBS. It was about human origins, but in the 7 seconds it was on, I heard the narrator say, "millions of years ago, we were apes -- living ape lives in Africa."


AAAARRRRGGGGGHHH!

C'mon NOVA! You know better than that!
This is why people still think evolution is a lie.

Welcome to Mars...

Take a gander at these photos from the Mars Reconnaissance Orbiter.

Rocky Mountain High...

Colorado!

Just got back from a week in the mountains. We timed it perfectly -- the aspens were just starting to change color, and we got out just two days before the snow.

We spent most of our time in Rock Mountain National Park as well as a few days hiking in the Arapahoe National Forest.

There are hundreds of photos here.

And just to get you in the mood...


Yeah, I love Colorado.

An argument for living in NYC...

Oooh... how much would I love to go to this?

Author Salman Rushdie, Dredg Join Forces for SPIN Charity Event

On October 1, Satanic Verses author Salman Rushdie will join San Francisco rockers Dredg at NYC's Housing Works Bookstore Café for the third installment of SPIN's Liner Notes series, a special event that unites authors and musicians for an evening of collaboration -- and fundraising.

If you haven't been exposed to either dredg or Rushdie, I strongly encourage you to become so.

Things I love: 1.) Science 2.) Mini-golf...

It doesn't get much better than this, folks:

http://www.sciencefriday.com/videos/watch/10238


And the kid in the green shirt? Winner.

embracing mass media...

I doubt anyone actually listened to MPR this morning, as I recommended in yesterday's post. But if you did, then you got to hear a comment I sent in!

Now my opinions are on the internet AND the radio!
Woohoo!

If you missed the show, you can listen here.
(Kerri Miller reads my comment at ~44:40)

Mark Willette's Lonely Hearts Club Band...

Minnesota Public Radio will be discussing The Beatles Rock Band tomorrow (Weds, 9.2.09) at 10:00 am.

Midmorning's Kerri Miller said she'll be talking about how musical video games may change how we embrace music. Sounds promising.

Now I hope they do a show about Pearl Jam Rock Band.

Community-supported agriculture...

Ugh... two huge posts in a row. Sorry about that. Here's a shorter, less serious one.

Jenny, Chris, Minnie, and I joined together and bought a CSA farm share for the summer. For those ho don't know, CSA stands for "community-supported agriculture" and is a program that lets you buy a share of the crops produced by a local farm.

We picked the Women's Environmental Institute in North Branch, MN. Every week, they send a box full of fresh veggies to a drop of location and we pick it up. I had originally planned to take a picture of each box and post an update every week, but that just didn't happen. We're now on our 10th week and I've only photographed the first -- and smallest -- bundle of produce:



This lovely spread contains lettuce, kohlrabi, green onions, marjoram, a riot pepper plant, broccoli, and beets. All delicious. Since then, the boxes have become heavier and have included cabbage, leeks, basil, sweet corn, cauliflower, and more.

I even planted those peppers, and they're doing great. I think one of the many peppers that have sprouted is nearly ripe, and I might give it a try pretty soon.

The farm also has a salsa-making party this weekend. I think I should go.

Michelle Bachmann does a barking clown dance...

I just got done weeping for humanity listening to Michelle Bachmann talking about health care reform on MPR. Besides making a number of sweeping generalizations about how a public option will inevitably lead to gov't takeover, she also dropped a few other republican talking points poo logs golden gems:

Bachmann told Cathy Wurzer that "rationing is most definitely part of this bill... a lot of what this bill is about is having these various boards make decisions about reducing options and reducing care..." On her own website, she quotes Newt Gingrich:

"The inevitable result of this pressure to control costs will be rationing, whether it occurs during this administration or the next. At some point, the government will be forced to deny care to those who don’t meet the latest “quality-adjusted life years” cost-benefit analysis.

"So the decision on what treatment to pursue that once would have been made by you and your doctor is now made for you by a bureaucrat using a formula -- a formula to literally determine if your life is worth saving."

Apparently nobody explained to either of these two that rationing is exactly what private insurance companies already do.

Denial based on pre-existing conditions?
Excessive testing required before covering treatment?
Refusing to pay for life-saving techniques because they're "experimental"?

If health care is going to be rationed, do you want it done by a body under the control of democratic laws, or by a for-profit company that makes money by denying your care? Perhaps now is a good time to point out that insurance executives make far more money than any doctor you will ever see. And the first person to make over $1 billion in bonuses works for a health insurance company. Does anyone else see the problem with letting free market control your health care?

Here's another goodie from Bachmann's site:

There are too few shining examples of profitable and efficient government enterprise – take a gander at the failing postal service or struggling Amtrak, for example – for us to entrust the nation’s health care system to Washington’s management and oversight.

I have a couple things to point out here:
First, I'm willing to make a fairly rational guess that the USPS is failing because of the increase in electronic transfers of mail and files. If the gov't ran a newspaper that happened to be losing money, would you also say that it proves federal incompetence? Oh wait, the same thing is happening to every other paper in the country. Well, lo and behold, it's not just the USPS that's losing money. UPS is crashing, too. Private companies don't always beat out the gov't.

I'm getting away from myself. To be honest, I don't really want gov't health insurance if it looks like the post office because I don't like the post office. So let's instead look at a more appropriate comparison, such as the way gov't already manages health care.

Dr. Filice works at the Minneapolis VA Clinic, and says that it represents how all of America's citizens should be treated by the health care system.

"I think that the VA experience shows that it's possible for government to be a good player; an accountable player in that mix," Felice said.

Felice said the VA is a model that lawmakers should consider emulating as they try to overhaul the nation's health care system.

And I'm sure I don't need to point out that more than 94% of Medicare recipients are happy with their health care coverage.

Okay, so we all realize that providing a public option for the uninsured will cost money. This is true. And I hear a lot of people complain about not wanting to subsidize people's health care with taxes. Here's a newsflash for you: YOU ALREADY SUBSIDIZE CARE FOR THE UNINSURED. And you know what? It costs more than it would if they were insured.

Let me explain why this is...
Gov't health care centers, such as county hospitals, are required to provide emergency care for all patients, regardless of whether they can pay for it. If they can't pay, the hospital -- funded by your taxes -- has to cover the costs. Emergency care is exponentially more expensive than clinical care, which means the easiest way to reduce this tax burden is to provide uninsured patients access to preventive care. Allowing access to preventive care will also discourage patients from using the emergency room for non-emergency injuries.

So, do you want to reduce the cost of health care? Provide a public insurance option.

Biology 203...

I noticed my buddy Andrew has a link to this blog on his website, complete with a large title of "SCIENCE". I figure with such a kind endorsement, I really ought to post something about science. So let me tell you a bit about some recent experiments I've been doing.

Western Blot

Hopefully you remember the leukemia studies I'm working on. I've been busy trying to characterize these cancers, and today I'm going to describe a very powerful tool for doing that called Western blot. Before I discuss Western blotting, let me start with a related procedure called the Southern blot. I happen to be running both Western and Southern blot experiments, but the Southern is arguably more confusing, so I'll save the details for another day. But I mention it now because it was the first of the "blot" experiments to be invented.

Southern blot is unexcitingly named after its inventor, Dr. E. Southern. He developed a way to detect and quantify particular sequences of DNA in cells. Before long, the technique was altered to detect RNA, and was named "Northern blot" -- not because there's a Dr. Northern, but because of the play on Dr. Southern's name. Eventually, variations and combinations of the procedures led to Western, Eastern, and Southeastern blots as well.

The Western blot is the one I'll focus on today, and it too resembles the Southern and Northern blots, but it specifically detects protein instead of DNA or RNA. In my experiments, I'm interested in how leukemia differs from normal cells. If I can identify abnormal levels or actions of key proteins, they can potentially be used as treatment targets down the road. I won't get into extreme details, but let's say I think these cancer cells lack an important regulatory protein we'll call protein X (pX). pX restricts the action of other growth proteins, and thus without pX, the growth proteins go crazy. To test my hypothesis (that the cancer cells lack pX), I'll employ the Western blot to measure the levels of the protein.

Remember my post about antibodies, and how there can be an antibody specific for any possible protein? Western blotting takes advantage of this specificity by spreading out all the proteins in a tissue, and probing them with antibodies. Here's how it's done:

I start by making a soup of protein from my cells of interest. Specifically, I'm looking at protein in pre-B lymphocytes, but you can use any cell you want. I extract the proteins by breaking open the cells with a particular buffer solution. One problem with this is that the insides of cells also contain enzymes called proteinases that degrade proteins, and breaking the cells open exposes the two, and your proteins break down. To prevent this from happening, I add proteinase inhibitors to the solution.

After isolating the proteins, I treat them with reducing and denaturing techniques to uncouple and unfold the complex shapes proteins have. Incidentally, one of the reducing agents is beta-mercaptoethanol -- a chemical that smells so ridiculously awful, the bottle has a warning the says it is toxic because of the smell (think stinkbombs). Next, I separate the protein on an acrylamide gel by putting the samples at one end of the gel and running an electrical current through. The negative charge on proteins causes them to migrate toward the positive pole in the current, and as they move through the gel, they separate based on size (large proteins move more slowly through the gel than small proteins).

Now the proteins are spread all over the gel, but I can't really do much with them. If I want to analyze them, I need to get them out of the gel by transferring them to a special membrane. This is done in almost the same way as I made them migrate trough the gel, except this time, I use the electrical current to move them up and out of the gel. So if I put the membrane on the surface of the gel and apply the current, the proteins will lift out and stick to the membrane in the same pattern as they were before (sort of like lifting a drawing off of paper with Silly Putty). Now I have my proteins spread out by size, stuck to the membrane, and I can manipulate it however I like.

Now comes the "blot" of Western blot. I cover the membrane with a primary antibody for pX. In theory, it will bind only to pX, but proteins are notoriously sticky, and will bind to anything they can get their grubby little alpha-helices on. To prevent this, I give them a bunch of irrelevant dummy proteins to play with -- essentially "blocking" the nonspecific binding of sticky proteins. That leaves the antibody free to find pX. In the laboratory, we accomplish this by using a state-of-the-art protein compound called powdered milk.

Okay, I've covered the membrane with antibodies, and they have bound to my protein of interest, pX. Unfortunately I don't have a way to see where the antibodies have bound. Now I have to come in with a secondary antibody to find the primaries. This secondary antibody has a "marker" or "flag" stuck on the end that lets me see it. This flag can be a couple different things, such as a bioluminescent molecule, radioactive material, or -- in my case -- a fluorochrome. A fluorochrome is a molecule that emits light at a certain wavelength when stimulated by a different wavelength, thereby rendering the antibody detectable. Like this:



On the left of the picture is a "ladder" of known standard protein sizes, so I can confirm my protein is the right size. It just so happens that pX is ~62 kDa (kilodaltons), and as you can see, the more total protein I start with (10, 20, or 40 ug), the more pX I can detect.

And that, folks, is how a Western blot works.

Where the hell's that bass coming from?

Only a few people who read this blog will find this entertaining...



But everyone should think this is cool:

A heads up for nerds...

More immunology in the news today: Science Friday will be talking about B cells and antibodies at 2:00 on NPR. Tune in if you're curious. Immunology rules.

http://www.sciencefriday.com/program/archives/200907172

Of Genes and Antibodies (broadcast Friday, July 17th, 2009)

Researchers say they've identified the gene that tells the body to produce one type of immune antibody. Writing in the journal Science, a team of researchers describe the action of the BCL6 gene and its role in regulating the formation of certain CD4 T cells. We'll talk about the work, and its relevance to studies of the immune system and vaccine production.

Fifth year-itis...

I met with my thesis committee last week and discussed my research progress. They seemed genuinely interested in my project and supported my completion within the next year. So unless things really go to crap, I think I'm headed down the final leg to graduation. Hopefully at this time next year, I'll be done. Woo hoo!

Groceries: Gotten

I finally gave a sad farewell to my much-beloved Audi TT...




It will be sorely missed, but the parting was bittersweet, as it has been replaced by a new car. We picked up our brand-new 2009 Audi A4 Avant on 6/29:









It's nice to finally have a considerably more practical car than my old two-seater. I guess I'm just moving farther up the ladder of responsible adulthood. Maybe in the future I can get another fun little car... perhaps a Wiesmann?

You might even say I hate the post office...

I just tried to use my check card to purchase a $0.44 stamp at the UMN post office. To prevent ID theft, I write "See ID" in place of my signature on the back; that way, if someone steals it, they can't just practice signing my name.

Well, the young lady at the postal counter told me that they don't accept cards unless the signature is there. My signature is on my ID, so that's okay, right? Nope.

"We require you to sign the card, too. Even if it says 'See ID'."

That is one of the stupidest things I've ever heard. I even asked her if that didn't just defeat the purpose of writing "See ID." She was adamant that it had to be there. I told her I wasn't going to sign it, and she replied, "So do you still want to buy the stamp?"

Well obviously not, if you're going to make me compromise my security over 44 cents. Ridiculous.

Garden update (or, "Sunflowers: Take 3")

Back in May, I wrote about my newly planted garden. A month-and-a-half of photosynthesis has gone by, and I'm now ready for a horticultural update!

First of all, most of the plants are looking pretty good. The peas have gone all adolescent-growth-spurt and are dominating the garden plot, as evident in these pictures:

Before:



After:





The carrots, bell peppers, and tomatoes we put in around the peas and cabbage are all healthy-looking. I also put in some yellow wax beans since I last wrote about the garden, but only three out of a dozen or so have come up. Same deal with the six pickling cucumbers I planted: only one of those survived...

Here you can see some healthy red cabbage and rhubarb, and one poor, lonely cucumber. Sad.


I also planted some mini Indian corn (forgot to take a photo) and sunflowers. Unfortunately, squirrels apparently eat more sunflowers than John Peterson. So I constructed little quonset huts of chicken-wire to discourage them from trying again. No luck. So I tried another approach.
This one is sure to succeed:



Here's one of the adorable, persecuted seedlings I'm trying to save:



And in my smugness, I left a note for the scavenging flea-bags:







Currently listening to: dredg - Down to the Cellar

the pariah, the parrot, and Salman Rushdie....

Dah!

I've been looking forward to the new dredg release for quite awhile, but I've been so preoccupied lately that I completely missed the release of their new album.

I just remembered it today, and was powerless to avoid going to Target to pick it up.
I've already listened to it three times today. Awesome. Seriously. Check it out.



Currently listening to: dredg - Gathering Pebbles

ps... R.I.P. Michael Jackson. Weirdness and scandals aside, you were a genius. Shine on you crazy dancing queen. If I hadn't just bought my new album, I'd still be listening to "Billie Jean" just as I had been all morning long. In my secret heart of hearts, I always hoped you'd turn around and show us all we should still take you seriously. C'est la vie.

pps... And I don't even like pop/dance music.

The next seven weeks...

Woohoo!
Top Gear is back for season 13!



That preview probably won't be up for long, so check it out. If I'm honest, though, it looks like it needs more cocking about.

Betty White would call me a thief...

Wow. I listened to Minnesota Public Radio all through work yesterday, and they had a collection of really great pieces. You should give them a listen if you have a chance (click the links; embedding them apparently doesn't work on Blogger)

I was originally just going to write about Midmorning, which had a story on cancer research. For anyone who is interested in what I do, this had some useful info. They talked mostly about cancer vaccines, which isn't exactly what I study (although I did do research on them before joining my current lab), but there was some discussion about immunology, leukemia and lymphoma, and cancer research in general.

Midmorning then switched gears and talked with a pretty witty etymologist. Although impressively smart, I was a bit dismayed that he didn't know the origin of "moxie" (as any good New Englander does) and he got the explanation of "sympathy" versus "empathy" wrong. That's pretty weak...


On Midday, Gary Eichten spoke with Rep. Keith Ellison. I was fairly ambivilant towards the man before, but I'm a big fan now. I was impressed.

Ellison was followed by a speech given by Michael Pollan, author of "The Omnivore's Dillema" and ""In Defense of Food: An Eater's Manifesto." Really interesting topic.

And finally, to round it all off, the broadcast switched to Tim Pawlenty's press conference in which he announced he would not seek reelection as MN's governor. What a great day!

Memorial Day...

We went to Buffalo to visit the family over the weekend (well, not Memorial Day, since Jenny worked that day). Good times and great weather all around. We grilled burgers, brats, and kabobs (and bananas), and had dessert and wine out on the dock.

Chris and I took the canoe down the Crow River, opened some beers, and floated Huck Finn-style down the way. We saw some deer, muskrats, and a beaver (which caused me to spill my beer, as they tend to do). Fantastic.

The next day Jenny and I took the canoe to a spot farther upstream and did the same thing -- this time with Larry lounging in the middle with a fishing rod in hand. We're such bums.







Flickr set here.

Now I can hear "Celes' Theme" live...

Operation 88 Keys was a success!

For those who don't know, for our one-year anniversary I surprised Jenny with a piano. The whole clandestine enterprise was hampered by her current night float schedule, meaning that if I wanted to keep it a secret, all the pieces had to fall into place after 5:30 pm. At the last minute I managed to recruit some hale coworkers (mainly with the promise of beer) to assist with moving the corpulent klavier and, excepting a bit of rain while driving the piano home, it all went off without a hitch.

Well, technically there was a hitch, as that's what I had to attach the rented trailer to. That's a story of its own, really, because I borrowed Larry's Vandura for the job and the alternator crapped out just after I returned it...

Anyway, the tuneless, soulless piano was in the living room in time to surprise Jenny the next morning (along with a collection of Tchaikovsky sheet music), so -- all the subterfuge aside -- I'm a hero. I didn't have the foresight to have the video camera ready when she saw it, but I fished it out just in time to catch her playing one song. I'll post the video when I get around to uploading it.

e-i-e-i-o...

We just put in our garden for this year. And when I say "we" I mean "Jenny." I was doing other yard work at the time, but I did help construct that bicycle wheel contraption. Last year we were all about odd varieties, but this year we just went for staples: sugar snap and snow peas, yellow beans, yellow peppers, and red cabbage. We also got free seeds from the Living Green Expo for a few beets and one carrot, and Michelle got some lettuce (but Jenny spilled the pot... twice).



The tepee-looking thing at the back will eventually have gourds and mini-pumpkins when we get around to planting those, but you can see the little red cabbage plants interspersed in the plot. The big plant is the perennial rhubarb. Snow peas are buried in rows in the front and the sugar snaps and beans will (hopefully) climb that maypole.

We also put in some gladioli in front of the house, and have ambitious plans for sunflowers and Indian corn along the fence.

I've always enjoyed the idea of gardening, but I have no horticultural knowledge whatsoever, and the only real experience I had growing up was weeding -- not really the funnest part of the whole ordeal, if I'm honest. It's also difficult to hone one's skills when your garden is smaller than your car (and I have a small car).

I sat through a (not very good) workshop on building cold frames while at the expo, and I'm considering putting one together for next year to help extend the growing season (and expand plantable real estate).

That, of course, will never happen. Maybe I'll just ask Cindy Lueth if she has an old one I can have. I can't believe there are none listed on Craigslist. Lame.

Biology 202...

In an earlier post, I complained about trying to schedule a long experiment when sick. Now that I have a bit more time, I can explain what that experiment was all about.

This is a continuation of the leukemia studies I'm currently doing. I've been analyzing tumors to determine how certain genes promote leukemia, and I've gathered a fair amount of data about what the cancer cells look like and how they develop.

To understand the reason for my experiment, one must understand how cancers grow. Unfortunately, cancer is a widely variable disease, so there are a lot of characteristics that determine what sort of tumor you have and how it behaves. Fortunately, cancer has a set of identified "hallmark" characteristics that are absolutely critical for tumors to grow. Some of these include the ability to promote blood vessel growth within the tumor (angiogenesis) and the ability to prevent immune responses.

Two other characteristics are the ability of cells to divide forever (limitless replication) and ability to avoid death signals (evading apoptosis). The difference between these two is subtle but important. Normally, a cell has checkpoints that control when it divides and how long it can divided for. Similarily, if something goes wrong in a cell, there are checkpoints to prevent that cell from dividing and basically tell it to commit suicide. That means there are two ways for a cell to proliferate into a cancer: either divide at an alarming rate, or fail to die when they should.

To illustrate this idea, think of the number of people living in a town. You could get a population boom because people are zealously procreating with no second thought to contraception or family planning. In conrast, another town could reproduce at a normal rate, but due to longer lifespans, the old buggers don't die off. After a bit of time, both towns would be overpopulated. Essentially, the Baby Boomers represent both these scenarios...

That's right, I just called the Baby Boom generation a cancer...

So the question I have about my tumors is how they're growing: are they dividing too much, or just outliving their potential?

To answer that, you just have to look at how quickly cells are dividing. There are a number of ways to do this, but one common technique involves treating cells (in vitro or in vivo) with a green dye called CFSE. The dye gets taken up by cells, and each time a cell divides, the amount of green color inside that cell is reduced by half. Essentially, the green is diluted out. You can then tell how many times cells divide in a given amount of time based on how green (or not green) they are.

Another common technique is one I'm using called BrdU staining. Understanding this technique requires an understanding of what happens during cell division. For a dividing cell to ensure the right amount of genetic material ends up in the daughter cells, it makes a copy of all its DNA. When this DNA is replicated, it gets opened up and synthesized from molecules you may have heard of: A, T, C, and G. Bromodeoxyuridine (BrdU) is a an analog of thymadine (the "T" of A, T, C, and G), and can take its place during DNA synthesis. Thus, if you treat an organism with BrdU, dividing cells will incorporate it into its DNA in place of T, while non-dividing cells will not.

To detect the cells that have BrdU, you follow up with flow cytometry (which I described in my previous lesson). This lets you detect the BrdU with a fluorescent anti-BrdU antibody, so you can just look to see which cells are fluorescent to know which are in the process of dividing.

"But wait!" you say. "How can you detect DNA with an antibody? DNA is inside the cell! Antibodies can't get there!"
Yeah, well, that's an easy solution. Treating the cells with a permeabilizing reagent (often the detergent saponin) pokes holes in the cell membrane and lets antibodies in. Done.

So anyway, it looks like my cells are indeed rapidly dividing, because they have copious amounts of BrdU in them. Importantly, this doesn't rule out the possibility that the cells are also avoiding apoptosis. It's likely that both unchecked division and death avoidance is going on in these leukemias.

That's like having the baby boomers discover immortality. Scary.


Currently listening to: NPR - Science Friday

Green life...

The 2009 Living Green Expo is going on this weekend, May 2-3, at the MN State Fairgrounds.

Completely free admission, seminars, samples, and general good info. Ride a bike or take the bus to not be a poser.

If you don't go, you hate the environment. FACT.


Currently listening to: MPR - Midmorning (about trends in materialism, in fact)

NyQuil is the only true dream terrorist...

While perusing past Penny Arcade posts, I noticed a brief mention by Tycho of Le Chavalier d'Eon, which reminded me of a recent proverbial cold day.

I'm not an anime fan by any means. I never made it through Akira, and I can't deal with Full Metal Alchemist. So when Michelle returned from the library with the first episodes of d'Eon, I purposely stayed in the room with the intent of briefly looking up from my own business at regular intervals to ridicule absurdity as I am wont to do.

It turns out the thing was freaking awesome. It's historical fiction, based in 18th century France, and places a fantastical twist on characters and events during the pre-Revolution. I convinced Jenny to watch the first episode and it didn't take long till she was hooked too, and together we burned through the series in no time.

It's still anime, bogged down with excessive weirdness, and at the end I still didn't really know what happened. But it was intriguing...
And so, with true diplomacy, we decided to give a chance to other Japantastic shows. That's when Michelle returned again from the library with Paprika...

Well, we watched that -- and while it was artfully beautiful to look at, when the credits rolled, my sentiments were summed up with a well-placed quote from Mr. Greg Blacik's assessment of Vune's Jabberwocky-esque middle school extra credit composition:

"Makes perfect sense to me. 1000 extra credit points."

At least the theme song rules.

a diuretic a day...

I was steamrollered by a cold yesterday. Bah. It set on quickly in the afternoon and really got into swing in the middle of last night. I'm holding it at bay right now with ample doses of Dayquil and pseudophedrine, but that combination loops my brain right out of the galaxy with such efficiency that I'm not sure I'm any better off.

Yesterday I had planned to start a three-day experiment (which I'll describe later), but an afternoon meeting went late and I ran out of time to do it. That wouldn't be a problem, as I just pushed it all back a day, but now that I have a constant post-rollercoaster sensation of vertigo, I really only want to be at home.

My predicament has to do with the timing of this experiment. I'm supposed to start it at 3:00. I don't really want to stay here until then. I could start it now, but I'd have to pick it up again -- to misquote Dickens -- all the earlier the next morning. That means being at work at 5:30 am. The buses start running at 7:00 am, so I'd have to bike to work tomorrow.
With a cold.
High on stimulants.

Sounds like fun.

Where the awesomeness is...

This has great propensity to suck, I know, but the principle is just too awesome for me not to be excited.

There's no escape from Web 2.0...

I finally made the effort to set up a Flickr account. I'm not too fond of the way this blog handles photos, and I've heard not-so-great things about Picasa.

Anyway, now I can share a lot more at once, instead of just one or two. For now, I've only got Cozumel pictures up, but you can check out my photos here:

http://www.flickr.com/photos/mackis/

Remember it well...


Currently listening to: NPR - All Things Considered

Adios, ciudad del hedor...

My apologies for the lack of updates this past week. I happened to be occupied. It was an interesting experience, staying at an all-inclusive resort; it was fun, no doubt, but it almost felt like we didn't belong there. As if we were interlopers...

The time-share pushers were a bit flummoxed by us, not understanding why we'd prefer camping in MN to hanging out on a beach with a swarm of entitled Americans. I think I'll remember their looks of dismay forever...

It was a good time, and a nice change of pace to not worry too much about planning and being frugal. They still tried to rip us off a few times, but luck turned in our favor, and there were no worries. In the end, a bit of snorkeling, a lounge bed on the beach, sunshine, free drinks, and a good book were all that mattered.

I'll give some more details once I get my photos up.

Science Friday...

NPR's Science Friday had a great show today about particle physics and astrobiology. It was broadcast from the Origins Symposium and had a number of prominent scientists taking part. Their discussion was really good.

You can download both parts of the talk here:

Particle physics
Astrobiology

Sorry Mom, but you were wrong...

...video games actually improve your eyesight.
We gamers have known this for years, but good luck getting your mother to believe it. Now, you can just point her to good old peer-reviewed research to close the case. In Science, no less:

The Keen Eyes of a Gamer

By John Bohannon
ScienceNOW Daily News
30 March 2009

Video games, long maligned for promoting violence, may also have a good side: improving eyesight. Gory "first-person shooter" games, in which players must act quickly to kill their virtual opponents, seem to have lasting effects on a key aspect of vision, a new study shows.

In 2002, Daphne Bavelier, a cognitive neuroscientist at the University of Rochester in New York state, found that playing action video games improved visual attention skills (ScienceNOW, 18 April 2002). This time she compared avid gamers with nongamers on a type of visual perception called contrast sensitivity. It allows people to make out objects in dim lighting and to distinguish objects from a busy background.

Male gamers in their late teens and 20s, Bavelier found in a pilot study, performed significantly better than nongamers in the same demographic. To determine whether video games explained this difference, she and colleagues designed a video game boot camp in which 50 adult volunteers each played 50 hours of video games over a 9-week period. Half of the participants played two first-person-shooter action games, Unreal Tournament and Call of Duty 2, in which players must quickly detect and kill enemies to avoid being killed themselves. Meanwhile, the control group played The Sims 2, a "casual" simulation game that requires a great deal of observation and strategy but at a very leisurely pace. The subjects were tested for contrast sensitivity before and after the training.

Those who played the action video games showed a roughly 50% improvement in performance on the contrast-sensitivity test, whereas the control group showed no significant improvement, the team reports this week in Nature Neuroscience. Later testing of 18 of the subjects showed that the improvement had not disappeared after several months--even though these subjects said they had not changed their video game habits. Bavelier chalks up the change to "neural plasticity"--the ability of our brains to rewire themselves to more efficiently visually process the life-or-death scenes in action video games.

"The results are convincing," says Dennis Levi, dean of the School of Optometry at the University of California, Berkeley. "While we don't yet understand how playing action video games enhances visual processing, the very promising aspect of this is that it may provide a new method for treating patients." People with amblyopia--or "lazy eye"--suffer a severe loss of contrast sensitivity, and a regimen of action video games could complement other treatments, Levi says. The next step will be to test action video games that do not involve guns and mayhem.

Go ahead and secede, Texas. We all want you to, as well...

This is a few days old, but I haven't had a chance to post it yet. It seems a proposition to include creationism in science class put forth by the Texas Board of Education did not pass... BARELY.

This sort of thing really infuriates me. There is no debate about evolution in the science community. This shouldn't even be an issue. We don't teach numerology in math class, or astrology in astronomy class. So why should we teach creationism in biology?

I think if I was a teacher, and these types of standards were put in place, I would choose to teach all the "other" alternative theories besides Young Earth theory. The Yuga mythology, for example. I wonder how Ms. Cargill would like that...

I am ranting. Things could have turned out worse, of course -- they could have added subtle language questioning specific aspects of evolu-- OH WAIT, THEY DID.

I'd like to believe that the three people who read this a rational folks, and you're probably thinking, "So what? When did anyone with a useful opinion care about what Texans think?" Well, Texas is a big player in textbook production, so what ends up in Texas education standards will probably show up in your school, too.

AWESOME!

Full of win and christmas lights...

I'd hate to get in the habit of posting every interesting video that's on the web, but this is just too awesome:

My laboratory schtick...

While in Germany, I stopped at H&M and bought a nice shirt. I have discovered that when I wear it to work, I look like a mime:

What I made at school today...

Yeah, I was bored, so I took a photo of some DNA I isolated today.

I hate Macs, part 2...

Following up on my misbehavin' Macbook, I brought it in to the Genius Bar at the Rosedale Apple store. I don't know who thought it was a good idea to stuff one of these stores into a typical mall space, but it didn't work. Trying to sell and service computers, iPods, and iPhones in a space the size of Games by James just isn't a good idea. And nobody had any idea how things worked: you don't purchase items at the counter (that's the genius bar) -- instead the employees all carry little credit card machines. But no one knew this, so there was always a queue at the Genius Bar. Even if you DID know what to do, typically all the employees were talking to someone who doesn't know how to email, ala Best Buy, so you just had to stand around until someone could suck your money into the little machines attached to their hip like some emo cyborg.

In addition, the Genuis Bar was packed with people having problems with their Macs. And when you arrive, you're supposed to check in with the "Concierge", although there is no indication of this, nor who the concierge is supposed to be. My favorite was when the concierge told me they would come get me when it was my turn at the bar, and I didn't have to stand there but could go look around the store...

...

...Why would I want to do that, exactly?

To be fair, though, every time I've worked with Apple's service people, they've been very nice, helpful, and accommodating. Of course, when I opened my Macbook, the keyboard worked fine. But they went ahead and replaced the keyboard and faceplate anyway (mostly because they broke it trying to take it off, but whatever...). And they even replaced the two screws that were missing. Nice guys.

One amusing observation I made: the "Geniuses" behind the bar were discussing running Windows on their Macs. One even mentioned that she was happy because a friend was giving her a free copy. One of her coworkers replied that Apple has a program so workers can get free serial numbers. So not only do Apple's technical service folks prefer Windows, Apple actually provides it for them. Confidence-instilling, to be sure.

Currently listening to: Toadies - Sweetness

Own the gates of Neverland...

This is awesome:

Michael Jackson auctions off his stuff

There's some really cool stuff in there. I'd seriously consider buying some of it.
If I wasn't poor.

And I didn't have to attend a posh Michael Jackson auction.

More wins for science...

In an earlier post, I noted an example of Obama's attempts to restore the voice of science in laying out scientific policy in the government.

Here are two more wins for science and common sense:

Scientific consultation for endangered species

First steps for restoring the role of science advisors in gov't agencies

Hopefully you all remember some of the ruckus caused by the Bush administration's attitude toward science advisors.

I'll be quirky...

While driving to Taos, I couldn't help noticing as we passed through Albuquerque that the name of their stadium is "Isotopes Stadium".

Could Albequerqueans be so insanely awesome as to actually adopt "Isotopes" as the name of their minor league baseball team?

Apparently so:

The fictional Springfield Isotopes from the long running TV series The Simpsons were the influence for the new name of the team. In the episode "Hungry Hungry Homer", Homer Simpson attempts to thwart the team's plan to move to Albuquerque. Subsequently, when an Albuquerque Tribune online survey helped the team decide its new name, "Isotopes" received 67 percent of the 120,000 votes."

Lousy Smarch weather...

Rain, then sleet, then snow, then sub-zero temps.

Bah.

Science dictating scientific policy? Unpossible...

Obama reverses the ban on federal funding for stem cell research.

Well done, Mr. President.

I hate Macs...

My spacebar randomly stopped working on my work Macbook today. The only way I am able to write this is by using copy/paste on a text space from an old email. Oh yeah, and the Delete key doesn't work.

Nor does the apostrophe.
Caps Lock? Nope.
Arrowkeys? Nope.

Go ahead and try typing without any of those keys. I dare you. This is what is scienctifically known as "a pain in the ass". Macs are what are scientifically known as "pieces of crap".

I don't want to come across as a PC fanboy, but this is just another in a long list of issues that have plagued this overpriced white brick. For instance, after 2 months of use, the motherboard failed. Fine. It was still under warranty.

After that, it stopped ejecting CDs. It fails when trying to shut down, and it freezes when trying to wake back up. It refuses to register the first two or three keystrokes when I start typing. It is slower than my nine year old Dell. It is unable to multitask three or more programs. And about a month ago, it decided to stop printing in color (it thought the best thing for it to do was to randomly delete my printer drivers — that one I was actually able to resolve).

Computers will have problems; I accept that. But this is getting out of hand. If you pay double the cost of a normal laptop, only to find it sucks horribly you'd be justified in being upset. If you paid double for 10 Macs for your lab, only to have 8 of them break to the point of being unuseable, you'd be forgiven for going into conniptions. And let's be clear: I'm not making that number up. My advisor has a fear of PCs and will ridicule anyone who doesn't use a Mac, yet nearly all of his rigs have failed miserabley.

Okay, I couldn't take it anymore, so I had to finish this on my PC at home. Ahh... it's nice to have something that "just works" for once.

EDIT:I attempted to reset the SMC after shutting down the Macbook. When I tried to put the battery back in, I found it to be obstructed by A SCREW THAT RANDOMLY FELL OUT OF THE CASE FROM SOMEWHERE. I have no idea where it came from, nor whether it is important. That brings my grand total of spontaneously escaping screws up to 2. Three other screws in the battery housing are loose. What a marvel of build quality.

Resurrecting the dream journal...

I'm trying to get back to writing in my dream journal. It's something I did back in college, but I never put more than a few entries into it. It's not profound or pretentious or anything; it's just fun to look back and wonder what sort of crack I was smoking on any particular night.

I found it easy to update in college because I was at liberty to get up at 3 am, tumble from bed into my computer chair, and type some nonsensical ramblings while they were fresh in my mind before drifting back off again. That's not so easy to do when you have to get up for work, get cleaned and dressed, commute 45 minutes, and start work before sitting down to recollect your subconscious musings.

But I'm trying to do it again. My first foray back into my psyche probably won't go so well, though, because even immediately after waking I only remembered about the last 5 minutes of the dream. But it involved trying (and failing) to read aloud the (altered) introduction of "The Drawing of the Three" while driving somewhere with my family, a small lake of water just outside the back door of my parent's house, which housed a headcrab with an interest in attacking Chris (I unsuccessfully tried to shoot it with my transforming cellphone), and a large poo that someone had taken in the bathtub.

For the record, I did not smoke crack last night.

Currently listening to: Tom Waits - Never Let Go

This should please Chox and Vune...

Finally, after years of recommendations, I have read The Hitchhiker's Guide to the Galaxy. Vune was right all along: it's fantastically goofy and smart. I still think Douglas Adams doesn't write conversations well, and he bogged himself down a bit in parts, but overall it was a great read. Except perhaps for "So Long and Thanks for All the Fish" -- that one was a bit lame.

Now, to appease the long-suffering Eugene gods, I've picked up Stephen King's "The Dark Tower" series. I finished "The Gunslinger" and I have to say, I'm hooked. I'm a little worried that King bit off more than he can chew, but we'll see how it plays out... "The Drawing of the Three" is on its way as I type this...

So I guess I must acknowledge that all this time, Vune and Chox were right, and I should've taken their advice long ago. Once again, my friends are more well-read than I am.

Taos, NM

So many things have happened since I last kept this blog active, I'm not going to bother making a huge update. Instead, I'll probably just mention things as they come up.

Anyway, Jenny and I just returned from Taos, NM; I was there for the Keystone Symposium on B cells, and Jenny came along for a break from the emergency room. It was a good time -- as good as a week-long conference of science lectures can be. Taos was surprisingly warm, so it felt more like a winter escape than anything. We spent some time hiking around and looking at Pueblo ruins and petroglyphs, skiing, and exploring off-grid sustainable housing.

Once again I had to present a poster at the meeting, which went reasonably well despite the 10:00pm desire to go home and sleep instead of explaining the details of murine tumors.

Michelle, Jenny, and I took a trip to the MN Landscape Arboretum on return in order to see their orchid show. It was pretty meh, but the rest of the park looks fabulous. I'm looking forward to checking it out in the spring, and might even consider a membership there.

Anway, pictures from Taos:

Outside our B&B room:


Petroglyph at Tsankawi village in Bandelier Nat'l Monument:


Outside the Earthships sustainable housing community:


Tsankawi ruins again. There were pieces of pottery and obsidian everywhere:


Near the Rio Grande Gorge, looking at the Sangre de Cristo Mts:


Another petroglyph at Bandelier:


A reassuring sign at the top of Taos ski valley:


Ski bums at 10k feet:


At Bandelier:


At Earthships: reading up on the finer points of sustainable pooping:



Currently listening to: Pearl Jam - Tremor Christ