Tuesday, September 30, 2014

Scientific Thinking

I was having coffee on campus with my friend Rachel this morning, and as it does every week, our conversation spiraled wildly out from our own research woes and successes (she's a biochemist) to the general state of the world.

One thing we share in common is an appreciation for science--we take pleasure in viewing the world through that lens. Perhaps it goes even deeper than that: we find it difficult to view the world any other way. But what glory there is to be found in knowing why, or if not knowing why, trying to find out (see: spiders can learn).

Today, we wandered into the topic of anti-vaxxers and anti-GMO-ers. She railed a bit on bubble-headed celebrities misleading the herd but I thought that there was more to it than that. It doesn't take much time on the internet to discern wide and relatively deep anti-science sentiments in the US and Europe. These views usually cross class, race, education, and even political boundaries. 

Vaccinations have been tested over and over using the most rigorous standards for clinical trials (randomized, double blind, etc.). They save lives. To argue any other position with respect to vaccinations is to engage in anti-scientific thinking. 

Same with GMOs. As Rachel aptly pointed out, there is no difference, none whatsoever, in the DNA of a tomato, an E. coli bacteria, or you, except in the particular sequence of the molecules in the DNA. The building-block molecules are all the same. We have been selecting horses, dogs, corn, thousands of organisms, for centuries, in some cases hundreds of thousands of years, to change those organisms to suit our fancies or our needs. Techniques to create a RoundUp-resistant wheat strain are based on the exact same theories that humans in the middle of the Eurasian continent used to select wild grasses that had heavier seed heads lo these many centuries ago. We've managed to speed the process up quite a bit, of course, and we use fancy machines and such. But the theory underlying the work is the same. And I would not for a moment defend some of the practices of the large agriconglomerates. But GMOs are not evil in and of themselves. 

No, the fundamental problem is that the average person does not understand science. She doesn't understand physics or chemistry. And she definitely has no solid grasp on genetics, the water cycle, or immunology. 

So we decided the solution was to stop teaching physics and inorganic chemistry. Oh, you want to learn about that? Then go to grad school. Instead, we think that kids in elementary school should be reproducing Mendel's pea experiments, that kids in middle school should be learning about global climate, that kids in high school should be learning about disease, epidemics, and epidemiological experimental design (Ebola, anyone?). You still think chemistry is important? Teach that through food science. Fermentation should cover most of what you need.

We need citizens who are prepared for the reality of our world. Who cares that a ball rolls faster down a steeper incline? Why in the world do you need to know about metal catalysts? Wouldn't it benefit our society now and in the future to have not just scientific specialists but all citizens thinking about how to address the problems we have now, not the problems science was dealing with 300 years ago?

We need citizens who can think rationally and critically. You read the headline "Breastfed kids perform better in school." You shouldn't view that as a refutation or acknowledgement of your particular social perspective. You should ask yourself, how were the participants in that study selected? Are they representative of a larger, general population? Were other factors taken into account? Could such a study be randomized and blinded, the gold standards for these kinds of experiments?

Too bad Rachel and I aren't in charge.

Thursday, September 25, 2014

Murphy Strikes!

My master's project is setting some land speed records. Feeding trials, lab analyses, statistical analyses of the lab data, collecting and reading papers, writing the thesis, writing papers for publication, preparing a talk or two, and taking classes--all of it getting squeezed into slightly more than one year. 

Since early July, I've been toiling daily in my advisor's lab. I'm sick of the place, that's for sure. About the only positive thing I can say is there are windows. The lab is in the basement of a 60-plus-year-old building. Lining the ceiling of the basement hallways are the steam pipes used to heat the building. They contain steam year-round even if they aren't sending heat to the rooms in the upper floors. As a result, walking to the lab is like taking a trip into the underworld: dark, musty, and stinking hot.

The only AC source in the lab is a puny window unit at one end. At the height of summer, even with the window unit going full bore, it was usually no cooler than 85 F in there for hours on end. The ceiling of the lab, like the rest of the basement, is festooned with pipes.  The cabinetry was new when the building was built. It has a quaint charm, to be sure. I'd take air-conditioned over quaint any day, however.

I had previously agreed with my advisor that I would try to finish all the lab work before classes started, which they will do on Monday. It was an ambitious plan but she has learned that she can push and I will deliver. So I was counting down the days of this last week.

I planned everything out so that I only had some fairly simple tasks to do this week. I wanted to take a short break before the term began since I have been working non-stop all summer. I was planning to run the last GC samples on Wednesday night, get the printouts on Thursday morning, interpret them, and email the data to my advisor that day. Then take a couple of days off. But I'm sure you can see where this is going. Murphy, who deserves his own special room in hell, struck with a vengeance on Tuesday. 

The GC, or gas chromatograph, is a box-like machine that heats up liquid samples at one end of a glass tube, heats them enough to turn them into a gas, and detects the molecules that float out the other end. The tube contains materials that cause the molecules to come out in molecular weight order: little ones first, then bigger ones. And the detector also measures how much of each molecule it senses so you can determine both which molecules are in your sample and the relative percentage of each molecule type. We are using it to determine which fatty acids are in the chicken tissues--did we successfully enrich the breast and thigh tissue with long-chain omega-3 fatty acids. It takes about 11 hours to run 16 samples. I have 32 samples per tissue so I set up 16 samples to run at 8am, return to the lab in the evening, and set up and run the second half. I'm sure you are thinking, why not run them all at once? That would make sense, wouldn't it?

It would make sense except that it's so hot in the lab that the hexane that we use as a solvent volatilizes in the sample vials as they sit in the tray waiting their turn. The increased vapor pressure in the tiny vials (they hold about 1.5 mL) pops their tops off and entire samples evaporate into the room before the GC gets around to them. Yes, in case you were wondering, I learned this the hard way. (If I were to write a "pro tip" addition to my advisor's procedure protocols, it would run into the dozens of pages.) I pointed a box fan at the GC and turned the AC vents in its direction but that didn't help.

I was already resigned to this every-12-hour arrangement. Although it's a pain and increases the overall time that I spend running the samples, that in fact isn't the problem. The problem is that the GC oven is cooled with various gases (helium, compressed air, etc.) and, sometime Tuesday night during my run, the compressed air tank ran dry. The GC is smart enough to shut itself down when it can't cool the oven. But I still have almost 50 samples to run! Here's where Murphy really got me: the gas tank supply company only delivers to campus twice a week.

Fortunately, one of those delivery days is Friday. I plan to camp out in the lab in the morning and wait for the gas tank guy to show up. I'll be running samples most of the weekend but I think, just maybe, if Murphy has already done his worst, that I will just finish before classes start.

Monday, September 15, 2014

Harry and the Coyotes

I lived in Salt Lake City for some years and, before I ruined my right knee, I used to go running in the foothills of the Wasatch Mountains in the early mornings. I had three smooth fox terriers then, Harry, Iz, and Dyna, and I would take them with me. Only deep snow or temperatures below 20F would stop us from going.

The dogs were young but relatively well trained and because the trails were in BLM-managed land, I let them run off lead. Despite the easy access of the trailhead at the top of a fairly tony neighborhood, the trails were not heavily used, at least in the mornings. There were vistas from some of the hilltops where you could see the city spread out at your feet.

One crisp fall morning, I managed to convince a friend of mine to accompany us. The trail began with a gentle curve around a hill, climbing slowly until it suddenly shot off in a straight line, mostly up, towards the hill tops. Once you rounded the first hill, you could no longer see the parking area at the trailhead.

We were around a mile and a half from the car when a pack of coyotes appeared on the trail, coming up from below us. They were somewhat spread out but were clearly operating as a unit. As usual, the dogs were ranging ahead. I managed to call Iz and Dyna to me and snapped their leads on, but the coyotes separated Harry from us and charged him.

He turned and ran, heading farther up the trail.

I threw the car keys and the leashes to my friend, told her to take the two dogs back to the car, and I took off after Harry and the coyotes. Her eyes were as wide as saucers but she turned around immediately.

The coyotes had a lead on me and it was a steep climb. By the time I crested the hill, I could see nothing, hear nothing. I began to call Harry’s name, but I was out of breath, freaking out, and what came out of me was panicked howling.

Suddenly, a man appeared, a bow hunter. He floated up from below me just like the coyotes had done. He told me he had been in the ravine below and had seen the coyote pack tracking us. He said he saw them separate Harry. He said, is that how you normally call your dog to you? I was sobbing and yelling, but I took a breath and said, no. He said, try to call to him in a normal voice.

Suddenly, in the thick scrub oak below us, we heard dogs fighting, one crying out in pain. The bow hunter shot off like he was one of the deer he was hunting, leaping down the hill before I could react. I followed as best as I could but I was dressed for trail running, not bushwhacking. I could hear the dog fight continue, but it was moving, changing location, heading down the gully. Then, suddenly, silence.

I caught up to the bow hunter. He said, we need to climb back up to get a better view. As we crested the top of the hill again, I looked back down the trail and saw my friend running up the trail towards us. She was yelling and waving her arms but she was too far away to make out what she was saying. I continued to call Harry.

The bow hunter and I waited on the hilltop while I periodically called Harry, pausing to listen in between. All we heard was the wind. I was mentally frozen, sure that the coyotes had killed my dog. The bow hunter kept telling me to trust my dog, trust my dog, be calm when you call him. Finally, my friend got close to us and I heard her yell, he’s at the car! He’s at the car!

When she reached us, and managed to gasp out, Harry was hiding under the car when she got there with the other dogs, I collapsed on the ground, sobbing. If you read historical fiction, you may have read something like “she fell onto the sofa insensible.” Well, I was insensible, literally without senses, for several minutes. My friend had tossed all the dogs in the car, not even stopping to check Harry for injuries, and turned around again. The bow hunter kept talking to us, made us drink some of his water, and jogged back with us to the car. I can’t remember what he said now. I only remember thinking, he’s in the car, Harry made it that far.

Once the coyotes separated him from us, Harry did run up the trail further, then down into the ravine. There was indeed a fight. He had a nasty bite on his right rear thigh, a puncture on the outside and more of a tear on the inside. Amazingly, that was his only injury. I think we can infer that Harry was more interested in getting away than making a point.

Somehow, he managed to keep running and make it to the car along a route he had never been before, and there he waited. Quite amazing, really. The event was physically and emotionally traumatic for him. The vet warned me that when dogs get into fights like that, it can take a couple of days for them to recover even though their obvious injuries are relatively minor (he didn’t even require stitches). Indeed, it took Harry four days before he moved off his warm fleece blanket nest at home for anything other than meals and potty breaks. The fleece blanket he was curled up in was a get-well present for Harry from my friend G and my running partner of that morning; they brought it over that day. I still have that blanket, or what’s left of it. It’s well loved, just like my tough little dog Harry.

Monday, September 08, 2014

Spiders in the Garden

Back in the spring, I planted four small spruce trees along the western fence line of my back yard. They aren't as tall as the fence and so do not provide me any shade yet. But they are growing. 

It turns out that spruce trees are excellent habitat for spiders. I've identified at least two kinds that took up residence in them over the summer. One kind builds funnel webs tucked in between branches. You can see them lurking at the center of the funnel if you sneak up quietly and make sure your shadow doesn't fall on the trees first. The other kind, a common garden spider, builds vertical webs between the trees and between the fence and the trees. The distances are around 3 to 4 feet, nothing particularly difficult for these spiders. The spiders started out quite small, maybe the diameter of a pencil eraser, but they appear to have had a successful summer of hunting and several of them have leg spans that are easily over an inch in diameter now.

I check on the spiders every morning when I let the dogs out for a last potty before I head off to the lab. Over the course of the summer, I've collected some interesting observations about these spiders and their webs.

First of all, when they were small, the spiders often centered their webs in the middle of the two objects. It is rare now to find a centered web. Nearly all the webs are offset closer to the trees. My cursory online research suggests that the spiders are simply adapting to the more likely position of prey, mainly flies, midges, mosquitoes, and the like.

But here's a really interesting thing. When the spiders started building their vertical webs back in the early summer, they would build them at a variety of heights. However, the dogs walk between the trees--the trees get watered and the grass grows green and lush there so it's a favorite pooping area, and the lane between the trees and the fence was part of Harry's daily perimeter check. And I mow the lawn of course. So the lower webs would get broken on a daily basis. 

It only took about 2 to 3 weeks but the spiders stopped building webs below Azza's head height.

That's right. I think the spiders learned that low webs were not productive so they all shifted their webs to about 3 feet up and higher. The dogs walk between the trees with impunity. I can easily push the mower between the trees and not touch a web.

In case you think that I am insane (I might be but this is not the best illustration of it), here's another example. I walk the dogs very early in the morning. Places along the sidewalk where bushes lean in close to mailbox clusters would seem to be reasonable locations for spider webs. But I never encounter webs in those locations, and I think it is because those spots are too highly trafficked--the spiders in those areas also learned that, although it might look like a nice easy distance, those are actually crummy locations for webs. I do find spider webs when I veer from the sidewalk however.

There is spotty research on this but it does appear that spiders will change the location, shape, and size of their webs in response to prey availability and type as well as competition with other spiders. One group of researchers did a cost-benefit analysis on spiders that move their webs. I turned up some amusing older references which state that spiders do nothing more than execute a fixed program, like a computer runs a program, when building their webs. Manifest destiny! But newer perspectives suggest that spiders exercise a degree of free will, that they can evaluate past experience and change their web parameters, when web building. That latter view is more consistent with what I observed, and that is a far cry from a computer running a fixed program!

I'd also like to briefly mention some super freaky little spiders that live in my front flower bed. I've only seen them there because in the front flower bed are two plants, mint and some other flowering thing, that produce white flowers. These spiders are tiny and pure white. They don't build webs; instead, they stalk their prey. And they mostly capture bees that visit the flowers. Truly diabolical.

Friday, September 05, 2014

In Search of BBQ

I've always enjoyed good barbeque. Because I've traveled a lot, I've had a chance to sample all styles of the craft, including barbeque on offer in places like Texas, New Mexico, South Carolina, Brazil, and China. I've tasted quite a variety of beef, pork, sheep, goat, chicken, and sausages made from their respective parts. I've had barbeque with dry rub spices, with tomato-sugar sauce, and with yellow mustard sauce. I've eaten meats cooked over wood, over gas, on a spit, on a grill, in a hole in the ground. Part of the pleasure of good barbeque is learning about the craft that the chef brings to the process. Part of the pleasure also comes from good sides. In the US, these tend to be white bread or corn bread, vegetables (usually boiled), beans, fried things, and cole slaw. Most good US barbeque places make desserts, usually cobblers or sweet quick breads that can be cooked quickly in large quantities; pecan pie is a common barbeque house dessert in Texas. A good chef will pay attention to the details of all these things.

I am not a strict follower of just one school--there are many paths to getting good smoked meat. I prefer pork ribs to beef but I'll never turn down an offer of the latter. While I'm not a paid food critic or a chef in my own right, I do think that I know when barbeque is done right.

I've not eaten good barbeque in some years now. I was on the hunt for a local source, and everyone raves about this family-run place in the next town over. I decided to give it a try.

It was horrible. Utterly horrible.

The cornbread was so sweet that I almost thought I had been served flan made with a dusting of corn flour. I like flan a lot. But I was expecting corn bread. I could taste nothing but sugar. I took two bites and left it.

The salad dressing was gelatinous, neon pink. Supposedly it was a raspberry vinaigrette. It is not difficult to whip up a simple vinaigrette on demand or even by the gallon each day of service. And local berry sources abound. No excuse for this nasty, processed crap from a bottle.

The sweet potato tots were fried in old oil. Under the slightly rancid flavor of the oil, I could barely taste the potato. They had not been made from pieces of sweet potato but pureed sweet potato and they were undercooked so they were mushy instead of crispy.

The sausage was identical in texture and color to the cheap "summer sausage" one buys at the grocery store, with one difference. This sausage had twice the normal amount of salt in it. There was so much salt that it made my tongue swell. I like salt. I usually add it to most of my meals. But this was extreme. I left most of the sausage on the plate. Artisanal sausage hit mainstream grocery stores years ago. There wasn't any excuse for this either. If they didn't have time to make it themselves, they could have easily obtained good quality sausage from other local sources.

The ribs were smothered in so much sticky sauce that I could hardly tell meat from bone. And the sauce had no flavor of any kind except sugar. I presume it once had other ingredients waved in its direction but it seemed to be a glaze made from sugar and nothing else. It overwhelmed the meat. It was so thick that it left me with no option of adding other sauces.

On top of this pile of disappointments, the meal cost USD 20. The portions were generous but charging this much for poor quality food was insult added to injury. 

I scraped the glaze off the ribs and brought them home for the dogs. Mimi ate one and threw it up around midnight. My feelings exactly.