she blinded me with science

It begins...

2009-11-15T14:31:43Z

Ah, yes, the cats are already looking forward to sucking out the baby's breath.

22 weeks

2009-10-16T15:19:38Z

22 weeks
Originally uploaded by sclatter

I have endeavored not to bore everyone with gory pregnancy details, but there has been some call for tummy pictures. So here you go! Yeah, it kind of freaks me out that there's another person living in there right now. There are a few more.

An Only-In-Baltimore news story

2009-09-07T17:32:37Z

Attack of the Belt Bandit. Sorry the website is super annoying, but the story is irresistible. :-)

Hi from Heathrow

2009-08-23T10:13:06Z

So I'm in Heathrow, and I've just spent 5 pounds on an hour of wireless. I sort of felt required since Mom subsidized this fancy new iPhone for me. It's cool, I'm not going to lie. I'm getting used to typing on it, too. Slowly...

Some thoughts:

Flying internationally just highlights how miserable domestic flights are.
England is clearly not the US when seen from the air. No baseball diamonds.
The terminal here is full of very chi-chi shops. Who buys this stuff?
I disapprove of airports that rely heavily on buses to unload planes.
I hate not knowing my gate number.

I might should find some food...

Starting to think maybe I can ride after all...

2009-07-10T02:09:19Z

Today was my fifth lesson in my return to riding. One thing I like about this facility is that they seem to mix up their lessons. My last two lessons have been outside of the ring--one in the cross-country field and one on trails. The trail ride was complete with cantering (really, at least a hand-gallop), water crossing, and jumping small logs that blocked the trail. For a show-ring rider like me it was almost too much!

Today we were back in the ring, rather to my relief! My horse was Ace. I asked Javier, our instructor, how the horse is (I've yet to ride the same horse twice). He told me that Ace was about as good as it gets. Excellent. Off we went to warm up.

Javier told us to warm up on our own, and he would critique. I started Ace in a little trot and started to feel him out. I found him right away a little fussy, sensitive. Not a bad thing, necessarily. So I started to ask a bit more of him and he started to come on the bit a little for me. Great! Would he leg yield? Yes he would. So I sat the trot (not bad) and asked for a little shoulder-in, then pushed him out of it into a little more forward trot. He was getting quite nice, actually, though occasionally he would get a little testy. I imagined I was asking him to work harder than he preferred to.

So Javier called us in, and started answering some individual questions. After helping another girl with her canter, he sent me out to the rail by myself to trot. I didn't quite understand what he was asking me to do (sometimes his accent is hard to understand) so I just went out and tried to put together a nice trot. Come to find out, he was using me as an example to the other students for "what to do". I can't even remember all the nice things he said I was doing--I sort of thought to myself, "yeah, I guess I was doing that" but it was sort of subconscious. My riding brain is returning! Also he specifically complimented my sitting trot.

And then he let me canter jumps! I have always been terrible and trotting jumps. It was such a relief to canter them. I was allowed to jump more jumps than anyone else--even the water jump! And my eye still works! w00t!

OK, that was alright. I guess horses are still pretty ok. :-)

stupid shower

2009-07-01T00:51:28Z

In our eensy weensy bathroom we have this pod-style shower enclosure that's been kind of a pain from day one. It's not properly leveled so water pools in the corner, the floor has soft spots in it, and despite lots of extra caulking it leaks like crazy out the bottom of the door. All that got worse a couple of months ago when the floor actually developed a crack. I patched it up with marine sealant--ugly, but so far effective. And so we've been shopping around for a way to replace this nightmare.

Yesterday we happened to stumble across the same actual product on the Lowe's website. Curious, I checked out the reviews. They were the worst reviews of any product I've ever seen on the internet. Every single reviewer had the same problems we've had--leaking and cracking, soft spots in the floor. Many had cracking within just a few months of installing the shower. I started feeling pretty lucky that the thing lasted us for two whole years.

I think I want to redo it as a tile surround. I guess we'll see.

Back in the saddle

2009-06-06T19:23:21Z

In "why didn't I do this sooner" news, I went for a riding lesson today, nearly five years after my last one. It was harder and easier than I expected. The instructor was pretty complimentary, and I do feel that it's just going to be a matter of getting the muscles back. I'm hoping to be in fighting form by the end of the summer.

Seriously, why didn't I do this sooner? Having just gotten a wild hair this morning and done it, I really haven't any clue. I just took the first google hit and went. The barn is fine, standard school barn, the school horses are in good shape. The stalls seemed pretty clean. The place was awash with teenaged girls, as one would expect. They didn't seem to go in for any exotic tack like some school barns I could think of. I think it will be a fine place to get going again.

I guess the few times I've thought about riding again, I thought I'd have to call around, I'd have to find the right place, I'd have to work out a budget, blah blah blah. Today I decided not to let the perfect be the enemy of the good, and I just went. The cost isn't so bad. I will have to cut back in other areas, but it's not huge.

I just feel great now. I feel more myself than I have in ages. Energized and optimistic. I really hope a little equine therapy will improve my general attitude and help me power through work!

Synchrotron humour

2009-05-09T01:16:32Z

Yeah, I said humour.

Actually, only 9 beamlines is lousy if that's true. NSLS has dozens.

An excessively eventful trip to BNL.

2009-05-01T02:24:17Z

I get a sense of foreboding every time I turn down the insurance on a rental car. It was particularly keen when I picked up the car on Tuesday night. I had a little mental conversation with myself about it. I hadn't been in an accident for over ten years, there was no reason to suspect that I'd be in one in the next two days. Besides, my insurance covers rentals.

Pretty heavy-handed foreshadowing, right?

I debated about driving the maybe one mile from the dorm to the beam-line Wednesday morning, but I reasoned that having the car might be the difference in getting away to have lunch or not. Also, I had to check in at the admin building and get the parking permit, so it would be better to have the car there.

I signaled and slowed down to make the left turn into the admin building. A car comes up on my left side and slams into the left front fender.

What!?!?!

I have no idea what the woman was trying to do. I didn't really talk to her. I felt kind of bad for her actually. She called her husband, and he showed up and yelled at her a lot in Chinese. The police came. I called my insurance, and the rental car company. It was complicated. I called the beam-line staff to say I would be late.

Serendipitously, I happened to have rented from Enterprise. Enterprise has an office at BNL. Enterprise actually has an office in the admin building at BNL. That would be the admin building where I was going to check in, and where the wrecked car was now sitting. I didn't have to worry about the tow truck, or waiting for an Enterprise rep to come do a damage report. I just walked into the building, talked to the rep, showed him the car and handed over the keys.

The rest of the trip was ok. It was not the smoothest time at the beam-line. The samples were really sticking in the sample holder. My shoulders were aching from loading and unloading samples. By the time I was walking back to the dorm at 11 pm I really wished I had a car. BNL is very, very dark at night.

I finished early today so I headed over to the student and post-doc lounge to wait until it was time to leave. I knew I was supposed to have access to it, but I'd never been there before. It. Is. Awesome. Pool table, ping-pong, Foosball, big screen TV, comfy sofas. But, most importantly, Massage Chair. A good one. Oh My. My poor aching shoulders thanked heaven.

Are you jive turkeys, or just the regular kind?

2009-05-01T01:56:49Z

BNL is lousy with wild turkeys.

The solution to work/life balance: Bagel Bites

2009-04-10T13:29:58Z

Yesterday our department had its annual big named lectureship lecture. We alternate between the Christian Anfinsen Lectures and the Thomas Hunt Morgan Lectures. On Anfinsen years we get a biochemist type, and on Morgan years we get a geneticist type. This was an Anfinsen year. (Actually, I think we've had three Anfinsens in a row, but that's a long story.)

The speaker was Dr. Elizabeth Blackburn. She gained fame in the world at large a few years ago when she was dismissed from Pres. Bush's Bioethics Council. As she explained to us at the student luncheon, she just wouldn't sign off on a document she didn't support. She considered it self-evident, as you wouldn't sign off on a research paper you didn't agree with. We all nodded in agreement.

But beyond the political business, she's quite a famous scientist for her work on telomeres and her discovery of telomerase. She received a Lasker for example. I guess at one point Time named her one of the top 100 most influential people in the world.

I thought she was surprisingly personable. I had expected someone a little forbidding, but she was funny and charming. She is from Australia originally, but her accent seemed somewhat washed out, probably due to her many years in the Bay Area. (She works at UCSF.)

At almost every student luncheon with a woman scientist the issue of work/life balance comes up. All the female grad students are eager to hear someone say it can be done--science and family. Dr. Blackburn was no exception. And she was more optimistic than most. In retrospect I imagine this is because she is on the other side of it--her son is grown now. Most female scientists we meet with are younger, and are in the midst of it. Dr. Blackburn pointed out that we'll likely be in science for forty years. Raising kids just doesn't take that long in the great scheme of things. And, she said, there are "devices" that can be utilized. Devices such as, well, were we familiar with Bagel Bites?

Bagel Bites? Yes, we were aware of Bagel Bites.

Well! She went on in her charming, gentle Australian accent. Bagel Bites could be found in the freezer section at the grocery store. They come in a big box, forty of them. And how long do Bagel Bites take? Twelve Minutes! (This she said, triumphantly.) You take a sheet and cover it with foil so it's nice and shiny, an you put the Bagel Bites on it, and the go in the oven for Twelve Minutes! And they come out nice and bubbly on top. And you take them to the event, and the other parents have brought a nice salad or something, and the Bagel Bites are GONE. Big Hit. Seven/eighths of the salad is left, but the Bagel Bites are GONE.

She explained that she made it through preschool this way, and wondered if it would work the same in Kindergarten. It did! And on through school, so that even as her son was a Senior in High School, she was showing up to the events, good involved parent, Bagel Bites in hand. No time for baking fancy cupcakes, but it didn't matter anyway!

The take-away message seemed to be that you can manage if you use your wits, and make some relatively minor trade-offs. I walked out feeling like maybe it can be done.

Why is it ok to say, "I don't like kids"?

2009-04-09T13:31:12Z

OK, lately it seems like I've heard or read a lot of people saying that they don't like kids. It always makes me really uncomfortable. Why is that ok to say? If the person were to say, "I don't like elderly people," everyone would consider him a shallow jerk. It's not like kids are a monolithic group any more than any other group of humans selected on one intrinsic characteristic.

Truly amazing video. (with sheep)

2009-03-18T18:42:03Z

You must watch this.

Singing for the dead

2009-03-16T03:56:47Z

In other downer news, I cantored for a memorial mass this past Monday. The deceased was 32 years old, same as I am. I was told he was found floating in the harbor, but foul play was not suspected. No one knew more, so one was left to draw one's own conclusions.

The church was fairly full, but it did not seem that there were many church-goers in the congregation. I usually only sing for weekend masses and the occasional Holy Day. I am used to the congregation participating, even if in a rather desultory fashion. The folks at the memorial mass just sat and stared at me. Most did not even bother with the pretense of holding a hymnal. It was unnerving.

The mass overall gave the impression of a check box being checked. Father Burke gave a nice if somewhat generic homily, and there was one short eulogy. It all made me wonder what this guy's story was. In any case, I hope he is resting peacefully.

I was given $35 for cantoring the mass. It's the first time I have ever been paid to sing.

Black Bean Soup of Optimism

2009-03-16T03:45:12Z

I've been feeling down for a couple of weeks in a non-specific way. I suspect it started with work and hormones, then snowballed with failing to eat properly and not getting enough exercise. If I'm down, I don't feel like cooking, so I don't eat well, so I feel like crap. Vicious cycle, that.

Last Saturday my 97-year-old great-grandma had a major stroke, so I went to go see her in the hospital. Amazingly, she is still hanging in there, though she cannot swallow properly any longer. Pneumonia is a serious danger. I'm glad I got to see her, but the event seemed to just throw me totally out of balance. It was kind of a rough week. It got so bad it was clear I couldn't just muddle through anymore. So I tried to get in some long walks and make a point of more healthy meals.

And it helped. Yesterday I felt better than I have for a while. I started soaking some beans for soup for dinner. For lunch I made pasta with a tomato-spinach-mushroom sauce. (Hardly liquid enough to be called a sauce, really.) I started making the black bean soup I'd planned. I sauteed the onions, carrots and celery in the dutch oven, then added the beans and plenty of water. I cooked it all up for a while before I realized that we weren't going to be hungry for it last night after our big lunch. So I stuck it in the fridge to finish today.

When I tasted it today I realized it was tragically bland. I dumped in some salt, cumin and cayenne, then added a can of diced tomatoes and half a bunch of kale torn into bite-sized pieces. Cooked it down, adjusted the spices. It needed acid, so I threw in the juice of one lemon.

It was great. I was so pleased. It seems rare that something so economical to make turns out to be really satisfying. Now I have a couple of days of healthy lunches in the fridge, and I'm feeling like this week is looking up.

Excellent source of protein!

2009-01-14T21:08:49Z

The Chinese think silkworms would be excellent food for astronauts. What is baffling to me, having raised silkworms once, is how space travellers will come up with the prodigious number of fresh mulberry leaves the little suckers need to thrive. But I think the worst part is the idea of chemically processing the silk and using it in some sort of bastardized "jam" concoction. shudder

We should all become periodontists.

2009-01-12T23:35:13Z

I confess, I didn't go to the dentist for 15 years.

The last time I went before my drought, my parents took me. If I recall correctly it was over my summer vacation when I was at Notre Dame. They gave me a fluoride treatment, because I was still a kid. For many years I didn't even think about going. Then I started thinking I probably ought to go. When I got to JHU I bought the dental insurance, and proceeded not to use it. Finally, for no particular reason I made an appointment.

The guy I went to for my check-up was young and humorless. He poked around for about two minutes, took some x-rays, and referred me directly to a periodontist. A gum guy. I have dental calculus, and recession. He didn't even give me a cleaning.

While the earnest and sober young dentist has a tiny, shabby office, the periodontist has a large one in a chi-chi complex that also contains a Williams-Sonoma. He was older and cheerful, asking me if I knew why I was there, as if my teeth had been caught speeding. He poked around in my mouth for about two minutes, dictating numbers to a polite and well-groomed assistant. (This is the true measure of the well-to-do health-care office--a bevy of polite and well-groomed assistants.) He explained that I was in no real trouble, but I did have build-up to be removed from my 15 years of dental absentia. This build-up would be removed in two visits (tops and bottoms) each of about 1/2 hour duration. I spent maybe 10 minutes with the doctor.

On checking out I learned that the 10 minutes I had spent would be billed at $100. Each 1/2 hour scaling session would be $500. Would I like to put down a 20% deposit and book an appointment now, or wait for insurance pre-approval?

The pre-approval should come in 3-4 weeks.

Roof

2009-01-10T17:22:30Z

One morning this week I opened my eyes and the first thing I saw was that the bedroom ceiling was dripping water.

"Oh shit."

When we bought the house the inspector warned us that the roof, though newly tarred, was iffy. So we added to the contract a one year warranty on the roof, and happily signed. I guess we should be grateful it's lasted two years, but now, definitely, we have a problem.

I suspected it might also have something to do with the tree as well. Last time I walked the dog I took the route that cuts behind the house, and from a distance I could see that a decent chunk of the tree ended up on the roof. That sort of thing can poke holes in flat tar roofs like ours.

Apparently it did, and also our flashing isn't up to snuff, and also we have the whole initial crumminess going on. Rather to our relief, the low bidder has come in at a price of $1875 to remove the tree, flash everything, and install a new "torch down" roof. I'm not sure how this torch down roof thing works, but I've read enough to know that it does involve a flaming torch, so I'm in favor of that. Oh and we're also getting silver coating, which should help the upstairs not be a sweltering oven in the summer.

So, overall not the complete disaster one might expect from having to replace your roof. And it's always good not to have to worry about rain water dripping on your sleeping head.

BOOM

2008-12-31T15:56:35Z

A neighbor's tree snapped off in the middle and fell against our house and into the driveway. Hooray for the Sawzall!

Welcome to the 21st century.

2008-12-30T20:02:58Z

After much mulling, we decided to take half our Christmas dollars and buy a modest HDTV. (The other half gets socked away responsibly.) Wowzers! All those pixels are almost overwhelming!

Audiobooks

2008-12-12T02:08:14Z

I listen to audiobooks while I work in lab. It's the only thing that makes the monotony of endless pipetting more bearable. (Sadly, no boy bands come and sing to me when I am pipetting.) Interestingly, I find that I'm more accurate when I listen to books than when I do not. When I am not listening to anything my mind wanders, and I forget what I'm doing. Following the narrator seems to sop up my extra brain cycles but still leaves me with enough attention to pipet.

I subscribe to Audible and I recommend them. I am on the two-books-a-month program. It's a luxury, but a pretty reasonable one. I really hate their website, though it's better than it used to be.

I often download audiobooks that I would never read on paper. Frequently I get pop non-fiction. I find that Classics aren't always a good pick--I don't think they make a lot of money so the production values can be poor. The reader can make or break an audiobook. I will forgive a book much if it is well read, but cannot listen to a reader I don't like.

I prefer men as readers, but I hate when men try to do women's voices.

A few of the audiobooks I've enjoyed recently:

Einstein: His Life and Universe by Walter Isaacson
All the Pretty Horses by Cormac McCarthy
No Country for Old Men by Cormac McCarthy
Amsterdam by Ian McEwan
Buying In by Rob Walker
Interpreter of Maladies by Jhumpa Lahiri
The Red Tent by Anita Diamant

The Cormac McCarthy books have a great reader. I highly recommend listening to those. I don't think I would have enjoyed reading The Red Tent, but listening to it was pleasant. I am now listening to The Story of Edgar Sawtelle. It's a retelling of Hamlet, so you know it's going to be a downer, but the writing is lovely.

Cancer: cured?

2008-12-05T01:38:34Z

3-bromopyruvate

Get used to the sound of that, as you may be hearing a lot more about it.

Our weekly department seminar today was given by an older biochemist by the name of Peter Pedersen. He's interested in a long-known property of cancer cells called the Warburg effect.

To understand the Warburg effect you must understand that our cells can generate energy through two distinct pathways: aerobically through oxidative phosphorylation (a.k.a. "ox phos") or anaerobically via glycolysis. Ox phos is much more efficient than glycolysis, so cells generate the vast majority of their energy through that pathway. Sometimes cells must use glycolysis, for example when muscles are operating under anaerobic conditions. Cells generating energy through glycolysis accumulate the waste product lactic acid.

Otto Warburg noticed that cancer cells, unlike most normal cells, do a lot of glycolysis. They get a significant portion of their energy in this way. Highly glycolytic tumors can be identified using PET scans, and represent about 95% of all tumors.

Pederson thought that if he could find a way to inhibit both glycolysis and ox phos in cancer cells without affecting normal cells, that he could, you know, cure cancer. At this point in the talk I was thinking, oh brother. Fat chance of that.

Well, it kind of seems like he did it.

The drug is 3-bromopyruvate. In vitro it kills cancer cells in minutes. They chew through all their energy and drop dead. (If you're wondering if it's apoptosis or necrosis, the answer is a little from Column A, a little from Column B.) Ok, but cyanide will do the same thing, what about normal cells? Normal cells seem to tolerate it fine. Why? I don't think he's really proved this at all, but the hypothesis is that it's because the cancer cells have to make a bunch of gateways to dump out all the lactic acid they are producing from glycolysis. These gateways are promiscuously allowing the drug to enter the cancer cells, but it just doesn't get into the normal cells.

Ok, so what about in vivo? He showed slide after slide of rats, mice and rabbits with huge disfiguring tumors. They were given the drug and the tumors disappeared. Not shrunk (the usual metric in cancer talks), gone. The animals lived out their lives without relapse and died of old age.

Seems that he's trying to raise the money for clinical trials. He has enough drug synthesized to treat 100 patients. This could be the real deal.

The Pilgrims from Uncanny Valley

2008-11-25T19:59:37Z

The Biophysics office staff loves holidays. That's cool, because they throw parties with free food and I, as a grad student, approve of parties with free food. They also put up nice decorations all around the building. When the Halloween decorations came down, the Thanksgiving decorations went up.

That day I took the elevator down to the basement to get ice, and met the Creepy Elevator Pilgrims. Now, while our elevator is creepy, dimly lit and tends to trap people with no provocation, here the creepiness refers to the Pilgrims. These are large cardboard Pilgrims, a husband and wife. They are straight from the Uncanny Valley, taped to the back wall of the elevator, posed holding hands. They made me very uncomfortable.

Later that afternoon my husband asked me if I'd been in the elevator. To which I exclaimed, "The creepy Pilgrims!" Yes, exactly. We agreed that it was unpleasant to look at them, but also impossible to turn your back on them. The Pilgrims seemed malevolent.

So my husband (this is why I love him) printed out speech balloons for the Pilgrims. "Hello!" says the woman. "We're going to eat you!" says the man. He surreptitiously taped them above the Pilgrims' heads.

Since that time, someone has reposed the male Pilgrim with his hand to his mouth, clearly miming the eating gesture he would using when consuming elevator riders.

Five things

2008-11-24T20:47:54Z

'Cause I'm waiting on a spin.

Five Things I was Doing 10 Years Ago

1. Still working at Netscape, but not for long.
2. Realizing my relationship wasn't going anywhere, and I didn't want it to anyway.
3. Riding my horse regularly.
4. Riding my motorcycle regularly
5. Corresponding with some random Canadian kid who contacted me from my people.netscape.com page.

Five Things on My To Do List Today:

1. Re-make sucrose solutions and pour gradients.
2. Load my transcribed 16S rRNA onto said gradients for an overnight spin.
3. Go to seminar, maybe.
4. Experiment with darkening the replacement floorboards. I think I'm going to try making a wash with diluted ink.
5. Laundry.

Five Snacks I Enjoy:

1. Tortilla chips with good guacamole.
2. Hummus and pita.
3. Rice cracker mix.
4. Apple with peanut butter.
5. Popcorn.

Five Things I Would Do If I Were a Millionaire, in no particular order:

1. Buy a house with a bathtub.
2. Buy a horse.
3. Give more to charity
4. Get a housekeeper
5. Get my husband a big TV and an expensive cable package.

Five Places I Have Lived:

1. Elkton, VA.
2. Staunton, VA.
3. South Bend, IN.
4. Mountain View, CA.
5. Baltimore, MD.

Five Jobs I Have Had:

1. Lab glassware washer/grunt.
2. Camp counselor/TA.
3. Sys admin.
4. "Manager" of sys admins (FAIL)
5. Grad student.

Sucrose gradients

2008-11-08T22:56:26Z

Today I pumped out some sucrose gradients. It struck me that sucrose gradients are one of the more improbable techniques I use. It's a very classic technique; I was taught about them in undergrad. They're used for separation. You have a tube with a gradient of sucrose solution in it, denser at the bottom and lighter on top. You layer the stuff you want to separate on top, then you spin the tubes in a centrifuge so everything travels toward the bottom. More technically speaking, they are velocity gradients, not equilibrium gradients. That is, what matters is how fast the molecules you are separating are moving relative to one another; if you spin long enough they'll all get to the bottom.

Ok, if you have the picture in your head that I did, you are imagining tubes with some sort of thick suspension in them, thicker at the bottom than the top. If so, you would be as shocked as I was the first time I set up a gradient. My gradients are 10%-40% sucrose. Sucrose is plain old table sugar, of course (though we have to buy an optically pure grade since we use UV absorbance to detect our products). A 40% sucrose solution looks like, well, water. Maybe ever so slightly more viscous, like a Coke. And that's the heavy part.

How do you even set up the gradient? I'm very lucky--our lab has a Gradient Master! This machine is basically magic. You fill the tubes halfway with light solution, then you layer the heavy solution on the bottom until it reaches exactly halfway. It reminds me of a Black and Tan, only all clear and sugary. You put on the caps, and let the machine do the work. It rolls the tubes around for a while and beeps when it is done.

Then you have a set of tubes that all appear to be full of water, but really have your precious gradients. You carefully layer your sample on top and carefully balance the tubes and carefully load the centrifuge, all the while trying not to jostle the gradients and mix them up.

Then you spin. 25,000 rpm for 16 hours. I try to start my spins no earlier than 4 pm, for obvious reasons. The rotor is a swinging bucket rotor, which means that when it's spinning the buckets swing out sideways so the force is parallel to the axis of the tube.

The next day, you pump them out. We have nothing fancy for that. Just stick a tube to the bottom (careful not to mix!) and pump and fractionate into many little tubes. A trace from the UV spec shows where the product is. You choose the good fractions and move to the next step.

The one thing about sucrose gradients is that it's hard not to get the solution everywhere, and it is sticky, yech.