Thursday, July 31, 2008

Where's George?

I've been thinking about money lately, currency to be exact. Not just because it always seems to be in short supply. I've switched over to a contracting position at work where we get paid every two (count 'em, two!) weeks instead of once per month, and I'm pleased. However, I'm also a little bummed out because I told Mr W that we'd take a trip to the Denver Mint before he went back to school. Lo and behold, there are no tours open before sometime in September, so we'll have to do it another time. Several people have mentioned that it's a worthwhile trip.

Have you ever gotten a dollar bill (or a five, ten, etc.) that has stamped on it? If you go to the site, you can enter the serial number of your bill and see where that bill has been. I've entered a couple of bills and it's a cool way to document how currency (and therefore people) move around, or as they say, how things move in "moneyspace". I had a stamped bill on my recent trip from CO-MN-AZ-CO, but I mistakenly spent it before I logged it in.

The site has a list of the "top 10 bills" that have been kept track of. Here's a sample, where one entry says, "Got it for change at a gas station when I bought a bag of beef jerky" and "Got it for change at Quizno's downtown St. Louis, MO"

They also have a page of interesting links about money. So, the next time you see a stamped bill, help generate some interesting data!

image from here

A great post on watching Blue Whales

CB wrote up a very nice bit on our whale watching trip that includes a map of our route, courtesy of his GPS and GoogleEarth. Go read it!

Wednesday, July 30, 2008

Watch it now, watch it later

CB and I had a great whale watching trip this past weekend. He makes his living showing people birds at extremely scenic places, and so has a nice camera for that kind of thing. I thought it would be cool to also have some video if possible, so we also took his video camera, which had about 25 minutes of battery life in it. I was in charge of getting video, and he took stills.

We've talked before about how carrying a camera changes one's focus (har har) while viewing nature. It's almost as though one has to choose between observing the animal and obtaining a sort of deferred gratification that comes from taking photos. For most of us, anyway. CB confirms that when you do it for long enough, you can indeed do both.

I was a shining example of not achieving either objective with the video camera on the boat. A Minke whale was spotted, and I rushed to get the video. I fumbled with the switch, and, to save battery life, looked through the viewfinder instead of opening up the fold-out screen that serves the same purpose. Turns out Minke whales are notoriously unpredictable in terms of where they come up after a dive, so we were looking all around to spot the whale. I tried to train the camera on the animal, but there wasn't much contrast in the viewfinder (grayish whale, grayish ocean) so I'm sure the image bounced around a lot.

Anyway, by the time the little light came on inside my head that said, "honey, put the camera down and just watch this creature," it was gone. Grrr. It didn't really sink in until the end of the trip, when the naturalist with us said something like, "I haven't gotten such a good look at a Minke whale for a long time, maybe ever."

We haven't looked at the video, and I imagine there might be a little bit of footage worth looking at, but I'm not hopeful. I've learned an important lesson, which is that the best way for me to experience this kind of thing is to use binoculars, not a camera. However, you can still see what this Minke whale looked like, thanks to CB's taking photos of it. That black and white thing is its flipper.

Sunday, July 27, 2008

Hello? Anyone home?

Well, no. I'm on vacation at the moment, in Santa Barbara. One of the most notable things is the weather, which is darn near perfect year-round. Today it's a little foggy and 71, while yesterday (Ooh, temperature extremes!) it was probably up near 80. While this is a very welcome change from Colorado (where it's been in the low 90's) and AZ where it's about like you'd imagine, this small range of temps makes people's comfort zones more narrow. We saw some old friends of CB's yesterday, and the woman was remarking how it was so hot.

It's all relative, for sure, but I wouldn't mind logging some time here at some point, for the climate, if nothing else. It seems to calm everyone down in a general sort of way. Although there are other stressors like lots of people, housing prices (OMG) and traffic. Speaking of housing prices, a little cottage around here at the height of the boom went for about 700K. With the housing slump now you can get that 2 bed 1 bath house for a much more reasonable 600K. Ouch. At the other extremes, my sister-in-law Mary says how we can all congregate in northern MN when society breaks down, but I'm not sure I can hack the -40 degree winter nights.

The whale watching trip was incredible and I'll write about it more in the very near future. If you ever get the chance to go on the Condor Express out of Santa Barbara, do it. We were 26 (nautical) miles out and it didn't take forever to get to where the whales were. We saw between 10-20 blue whales and I was able to get a sense of their immense size. We saw two whales that had radio-telemetry tags on them, that had just been tagged that week by folks at Oregon State. We also saw close to 1000 common dolphin and a couple of Minke whales. Pelagic birds too.

Good stuff.

Tuesday, July 22, 2008


I just submitted my manuscript and it feels great!

Hybridization or Contamination - Update

I mentioned in a post a week or so ago that I was looking for evidence of hybridization in two species that aren't supposed to hybridize. Well, the first round of cloning is over, and all the individuals so far that came up as hybrids in the single-gene assay are genotyping as one of the species, not hybrids, and not a mix of species.

I'm in the process of sequencing more clones from these individuals, but it highlights an issue in the search for evidence of hybridization. It will be difficult to show hybridization is occurring without additional markers. With this in mind, I have started a round of cloning and sequencing of the mitochondrial gene that codes for subunit 1 of an enzyme called cytochrome c oxidase (aka CO1) for the hybrids. That's right, the Bar Code gene.

Here's a computer representation of the enzyme, showing how its structure.

The barcode gene doesn't work for everything, and yes, it does sort of trivialize the process of phylogenetically distinguishing taxa, but I like the concept of the barcode because it simplifies it for the public to the extent that they can "get it" and learn more if they want. You'll notice I said "mitochondrial". Reach back to high school biology and remember that mitochondria are in the cytoplasm of the cell, not the nucleus, so they are present in the egg cell and passed along, intact, to the fertilized egg.

That means CO1 is a maternally inherited marker, and using it provides insight into another level or taxonomic organization. For example, I can't use it for the species complex of mosquitoes that I work with (of which one is involved in this hybridization), because this sequence is basically the same in all of them. However, if I'm trying to tell purported hybrids of two good species apart, this kind of marker will hopefully tell me at least who their mamas were.

Will that do it? No, I'll have to look at additional markers as well, probably something like my panel of microsatellites, which rely on differences in noncoding (therefore selectively neutral) nuclear variation. Only then will we be able to adequately characterize these critters and say whether they represent interspecific hybrids (ooh! another publication!) or sloppy benchwork.

Sunday, July 20, 2008

Plant Rarity (or, Plant of the Week part 1)

I was going to post about the plant I studied in school, and ended up with lots of things I could say about it (imagine that). So, I thought I would start with a bit about how I chose this rare-but-not-endangered endemic, and also how plants can be rare.

I found my study plant, Physaria bellii, or Bell's Twinpod, by visiting with the Colorado Natural Heritage Program's very competent botanists and giving them sort of a laundry list of what I wanted in a study system, and they were happy to oblige: I wanted the sites 2 hours or less from my home, I wanted to work with something that at the time of the conversation (September) still had vegetation showing so I could collect leaf samples for DNA, and if possible, something that was rare and hybridizing with a more common congener. But not too rare, as I didn't want to compromise the species by sampling it.

How about Physaria bellii? Okey dokey. Physaria bellii is named after the namer's colleague, which sometimes happens in science. The genus belongs in the Brassicaceae, or mustard family, and P. bellii is just one of several narrowly-distributed species of Physaria in Colorado. It is a habitat specialist, found mostly in soils from the Pierre and Niobrarra shale formations, which make up hogbacks running along the east side of the Front Range of Colorado from Denver north to WY. It will also sometimes be found in soils associated with red sandstone. The habitat is patchily distributed, and as a result, one might hypothesize there is limited gene flow.

In the process of studying this species, I came across a simple table by Deborah Rabinowitz, which is called the Seven Forms of Rarity. When you compare the various combinations of population size (large or small) and geographic range (broad or restricted), there are seven ways a plant species can be rare. You'll notice there's an eighth combination, but that's when the factors come together and the species isn't rare (large population size, broad geographic range).

Here's the table:

Physaria bellii comes in at the upper rightmost cell. It's locally abundant in its preferred habitat, but that habitat is rare, so it is as well. Notice how plants can be rare in a variety of ways, and of course this helps when trying to figure out how to conserve rare plants.

OK, a bit about the looks of this plant. As you can see from the picture, it's a low-growing plant, and has yellow flowers. Those flowers smell very nice, as I found out when I was growing them in the greenhouse to do crosses. I guess I had just never bent down close enough in the field to get the scent. They are pollinated by generalist pollinators, and can have 50-200 flowers open at one time. The flowers mature into the "twinpod", a two-part fruit that can have two seeds per side, but usually has one. The leaves are covered by tiny hairs, perhaps as a water-loss-prevention adaptation. The leaves are variable, but all spatulate with no sinuses, and this helps distinguish P. bellii from its relatives.

Next time - hybridization, population genetics and chromosome squashing.

Friday, July 18, 2008

I'm working on it...

I'm working on a new "Plant of the Week" post, but it always takes longer than I think to do it.

Happy Friday

Wednesday, July 16, 2008

Science Badges

The geeky girl in me loves this kind of stuff. The clever folks at the Science Creative Quarterly, out of the University of British Columbia have come up a bunch of science badges. Their official title is: ORDER OF THE SCIENCE SCOUTS OF EXEMPLARY REPUTE AND ABOVE AVERAGE PHYSIQUE.

If you are interested in science, how many are you qualified for? Here's a few that I qualify for, along with their explanation from the site:

The “talking science” badge. Required for all members. Assumes the recipient conducts himself/herself in such a manner as to talk science whenever he/she gets the chance. Not easily fazed by looks of disinterest from friends or the act of “zoning out” by well intentioned loved ones.
The “has frozen stuff just to see what happens” badge (LEVEL II) In which the recipient has frozen something in dry ice for the sake of scientific curiosity.

The “has frozen stuff just to see what happens” badge (LEVEL III) In which the recipient has frozen something in liquid nitrogen for the sake of scientific curiosity.

The “cloner” badge. In which the recipient has cloned something or other. Rules to a drinking game concerning this badge will be forthcoming.

The “sexing up science” badge. In which the recipient has had experience with things such as selective breeding, crossing, mate selection, prokaryotic conjugation, fertility studies, STD related microbiology, and/or any other acceptable interpretation of the badge.

The “destroyer of quackery” badge. In which the recipient never ever backs down from an argument that pits sound science over quackery.

And there are a couple that I wish I qualified for....

The “I work with way too much radioactivity, and yet still no discernible superpowers yet” badge.…Although not for lack of trying…

The “my degree inadvertently makes me competent in fixing household appliances” badge. Not necessarily a good thing.

I originally saw this on a great blog, "Not Exactly Rocket Science"

Tuesday, July 15, 2008

Ah, my own Vortexer

My new vortexer arrived, safe and sound, and I used it today while doing some DNA extractions. Handy little things. The lab is shaping up nicely.

Now, if my surge protectors/power strips would get here, I can stop playing "what's not being used and can be unplugged?" 7 pieces of equipment and 4 outlets.

Monday, July 14, 2008

I am so, like, going shopping!

My boss sent out an email today, saying that there was extra money in the budget that needed to be spent ASAP, and to get our orders in today. This situation, although rare, never ceases to amaze me, in that I wonder why the system doesn't allow for the realization of this much extra cash until so late in the budgetary game.

Hey, though, I can rise to the challenge. I spent a couple of hours looking over what I had squirreled away, as we have to stock up over the two month ordering freeze that occurs in August and September every year anyway, and came up with an order (actually 5 orders to 5 different companies) for about $4,800 worth of stuff.

Now I am in no danger of running out of PCR or sequencer supplies, and will be able to get back to the lab shortly and get back to work. I also have a hard time getting over how expensive some of the supplies are, with propriety mixes of stuff for the sequencer being the most outrageous.

Sunday, July 13, 2008

Learn something new today

Mr W is wary of bugs. Well, he's afraid of bees in particular, but interested in other types of arthropods. There are a couple of ant nests at the dog park we take Sally to, and we usually spend some time on our haunches, watching the ants and talking about how it is that they can lift things that are so big, where they might be going, how much it would hurt if you got a finger pinched by those mandibles, etc.

I have recently been turned on to TED, which is a collection of videos on a variety of topics, and if you have any extra time, check it out, I don't think you'll be disappointed. I have an interest (not quite sure what to do with it yet, but something will happen with it, I'm sure) in the communication of scientific information to non-scientific people. That's not supposed to sound disingenuous; I hope that by spending time with Mr W looking at ant colonies, he'll choose not to kick them as he goes by (which he did do, once) and instead gain some kind of appreciation for them.

If you follow this link, it's a 20 minute talk on ants by a researcher in SE Arizona, who studies what she calls "task allocation" in harvester ants.

Some fun facts:
A queen can live for 15-20 years.
All ants are colony dwellers
There is no central control - yet the ants work cooperatively
The four tasks in a colony (besides those of the queen) are: foraging, patrolling, maintenance and garbage detail
While ants have eyes, smell is the most important sense
Ants can switch tasks, based on the pattern of antennal contact in other ants they encounter

I still am having trouble figuring out how to embed video, but I'll work on it.

I like the tie-ins of her work to decision making in other areas.

Wednesday, July 9, 2008

Mentors, part 2 (belatedly)

I had a post a couple of months ago about one of my mentors from school. I met today with the other person I consider to be a mentor, and felt lucky all over again to have made these peoples' acquaintance. Most people move after they get their Ph.D., but I stayed in town and so have been able to cultivate professional relationships with these folks that I continue to learn from.

This mentor, let's call him Dr. R., started his job as a research geneticist on campus right about the time I started school. We went to hear him speak as part of a plant reproduction class, and I was hooked on the work they were doing and wanted to be a plant geneticist.

I can remember one of our first meetings, where I'm sure it was obvious that I knew hardly anything about population genetics. I nodded, took lots of notes and I think "got" about 50% of what he was saying. After 8 years, I get close to 100%, I'm happy to report, and I'm still taking notes at our meetings. So much so that he commented today, "you are the most prolific note-taker I know!" To which I replied, without a hint of sarcasm (I hope), "well, you say a lot when you talk."

I imagine he's repeated some of the same things several times, but he's walked me through the subtleties of doing the various analyses one does when doing population genetics studies. What are the assumptions of the test you're using, how does this software calculate this metric, how do you interpret this value. There's still a lot to learn, but I continue to be amazed and compelled by the information that can be gleaned from DNA-based data.

The best part? He was saying how he's co-author on a grant by yet another committee member of mine, and I chimed in, "well, my contract is up in a year, so if you need any help, you know where to find me". And, to my surprise (only because money always seems to be too tight to hire new people) he said, "we're trying to get funding to hire a couple more support scientists, so keep your CV current." Sweet!

Tuesday, July 8, 2008

Who has my Vortexer? The factory.

Well, I was finally able to talk to those in the know, and the vortexer was never ordered. Thankfully it's a several-hundred, as opposed to a several-thousand dollar piece of equipment, or I might not have been able to just order one yesterday. Money's getting tight here at the end of the fiscal year.

Probably like a lot of places, we can't order supplies or equipment from the end of July until the beginning of October, due to efforts to balance the books at that time. I'll need to inventory my stuff and make sure I have enough to do everything I'm supposed to do.

I did get the specimens' DNA extracted and PCR'd yesterday, and will check the PCR products on an agarose gel today. Then I'll run the PCR product through a kit that cleans out the unwanted reagents and use another kit to introduce the PCR fragments into bacterial vectors, as I begin the process of cloning and sequencing these fragments.

In other news, I'm finally meeting with someone to deal with my tree lawn, which looks horrible, as I have herbicided the grass and stopped watering. I just can't do the digging myself, so I'm taking bids from a couple of companies to install RR ties around the edge of the tree lawn, and I'll buy and haul mulch to cover it all up. It will be nice not to cringe a little every time I look at it.

Monday, July 7, 2008

Hybridization or Contamination?

I'm starting a new project at work today. It's the one that my coworker, out on medical leave, was to start and it got passed to me. The work isn't technically difficult, consisting of cloning and sequencing a region of ribosomal DNA, but I haven't done much of it yet, so will be well-versed in that by the time I'm done.

We're looking for evidence of hybridization between two species, P and R, that aren't supposed to hybridize.

Although we are starting with a region of ribosomal DNA, my feeling is that we'll need to look at other markers as well. Some specimens, morphologically, have looked "funny" to my boss, but he ID'd those as R. I can remember when he made his comment a couple of years ago, and of course my first question was, "do P and R ever hybridize?" At the time, he said, emphatically, "no". Then we found several instances, then several instances more once we started looking for them, of individuals who showed both diagnostic bands for both species on our species-level screening PCR.

So the plan is to sequence the ribosomal DNA of 5 individuals that showed both bands and that had their morphology examined by an expert (my boss). 3 were ID'd morphologically as P, and 2 as R. We'll run our panel of microsatellite markers on them as well. I did a small sample (1 per family, 48 families) of R, just to see what their microsatellite profiles would look like. I got about 20% with P profiles.

It's a cool conundrum. Stay tuned.

Sunday, July 6, 2008

How many places have you lived?

Mr W splits his time between his dad's house and mine. Both in the same town, so it is a relatively painless arrangement. Yesterday, Mr W asked me, "how many houses have you lived in?" I asked, "you mean everywhere I've ever lived?" Yes.

I had to think about it, but I finally came up with 17:

Cleveland: 2
Bowling Green, OH: 7
Norwalk, OH: 1
Fremont, OH: 1
Toledo, OH: 1
Fort Collins, CO: 5

I moved yearly when I was going to school for my undergrad, followed by the first round of grad school. Then there were several years of moving around when I was married, trying to find a place where we could live and both have jobs.

I've been in CO now for 11 years, this house for almost 3. Moving so often (well, it feel like it's been pretty often) has made me less of a pack rat than I think I would have been otherwise. Before every move I've gone through my things and made the "Goodwill pile" of items to give away.

My current house is by far my favorite, for lots of reasons. It's mine, for one, and I LOVE the area. I already know that it won't be the last place, though. At some point CB and I will get a place that will have to be larger than my little cottage. And when that time comes, I'll have my tape, boxes and Sharpie marker at the ready to get the job done.

Saturday, July 5, 2008

I should have said something

Mr W and I went to the city's fireworks display last night. I like doing this because it's a good show and we live close enough that we can get in and out on our bikes. There are a lot of people down there, and we plunked our blanket down right in the thick of things.

We ended up sitting next to some younger people, maybe in their early 20's. They were hip, tattooed, and two of them had young children (a year or so old). Nothing wrong with how the kids were treated, but it seemed like everyone but the one mom was smoking, right next to the kids.

I feel like such an old fart, but I feel like I should have said something to the mom that she shouldn't let people smoke so close to her kid. Period. They also cussed like sailors, but that's a different issue.

At least they weren't visibly under the influence; that job was ably performed by folks on another nearby blanket, who apparently figured we all had hearing impairments because they yelled through almost the entire display. Maybe the hipsters were too young to drink...

I know, I know, if I don't like the crowds perhaps I should stay home. Next year, I think I will try to put my blanket down in a less crowded location.

That said, the display was really nice, long enough, lots of variety and an over-the-top finale. Mr W was suitably impressed and, after all, it's mostly for him that we went anyway.

image from here

Thursday, July 3, 2008

Doin' it

The Blue Whale trip with CB is a go. I'm very excited, especially since I've been hearing about him seeing whales up in Nova Scotia the last few days. OK, some fun facts:

1. Blue Whales are the largest animal that's ever lived. I find that fascinating, given humans' propensity to obliterate life forms.

2. Another name for the Blue Whale is the Sulfur-Bottomed Whale, due to a coating of diatoms (small algae with elaborate silica shells) on their bellies sometimes.

3. A Blue Whale's lung capacity is 5,000 liters (1320 gallons) - phew!

4. A Blue Whale's top speed is about 30 miles per hour, but they'll go about 3 miles an hour when feeding and cruise at about 12 mph.

5. Ooh, here's that 1320 number again. A Blue Whale's heart weighs 1,320 lbs.

6. They eat mainly krill, small aquatic arthropods. Each one is small, but a Blue Whale can eat 40 million in a day.

7. A Blue Whale can hold its breath for 30 minutes.

8. Scientists estimate that Blue Whales can live up to 80 years, but it's really an unknown, they could live longer.
As the saying goes, it's for trips like going to see Blue Whales that we put in our time at work and endure some of the drudgery of day to day life, right?

Whale bones picture from here. Size comparison from here. Water shot from here.

Who has my Vortexer?

When my coworker, the one who is currently on medical leave for a kidney transplant (and who is characteristically chomping at the bit to come back to work) started her position a year ago, she and I were part of a group that was supposed to move into a refurbished lab across the hall. I have found that it's better if one tries not to wait for these kinds of things. Sure enough, instead of the lab being ready in June-ish of 07, it was ready in June of 08.

Since the coworker is gone, I've been unpacking boxes, and trying to figure out who gets what, as there are two other sub-groups of people with their own stuff in the lab. This has proved to be a bit of a challenge, as the person who actually ordered the stuff is on vacation, and other people seem to be busy with other things at the moment.

I've found most everything I need to work, and indeed there are duplicates of a couple of things (centrifuges, water baths) so I've chosen one to work with and figured we can sort it out later. This way of working, however, is frustrating and it took me about twice as long to set up a PCR today than it usually does. Finish setting up that piece of equipment, go to the stockroom and get supplies, go to old lab and borrow some buffer, go back to stockroom because I need something else, you get the picture. We're supposed to de-glove and de-labcoat whenever we leave the lab, so that adds time (although I snuck across the hall a couple of times like a gloved and coated fugitive).

But I can't find my vortexer. There's one in there, but it's been claimed by another sub-group and I don't know what kind got ordered, so who knows. Oh, what is a vortexer? It shakes sample tubes so that the contents get mixed. I use one several times a day if I'm in the lab; they're just really handy when you're working with small quantities of stuff that need to be well mixed when you take your even smaller bit out. I admit I'm a little annoyed that I can't just be done with the set up and get back to work. Oh well, I can do most of what I need to do.

Happy 4th to all.

Image from here.

Wednesday, July 2, 2008

Flash or Green Lantern?

I know, it's an age-old question, but if you could be any superhero, who would you be? It has been interesting to observe Mr W as he's transitioning out of little-kid literature and into stories that hold his interest going into second grade.

I think it's important that he continue to read out loud over the summer, so I've been trying to have him pick out some books at the library that he can read to me in the mornings. Lest you think that we sit peacefully, Sally at our feet, me fully dressed drinking coffee and nodding, it's usually him reading in the car on the way to camp. But it works out.

To that end, I've been looking for comic book type books for him to read. This has led us to traditional comic books with superheros and he really likes them. I think that format could be used for a lot of other topics besides fantasy stuff like superheroes, but I haven't found much other than the DC and Marvel players.

And if you haven't browsed that genre lately, you might be surprised to find that the characters have an edge to them, and considerably more angst than they had 20 years ago. Characters are more complex, perhaps more human, than they were before, maybe as a reflection of the mixed up world we live in.

So it pleased me greatly to come across a DVD at the library with episodes from "The Superfriends", which played as cartoons in the 1970's. The writers must have had a blast, because the villains are so clearly villainous that they say things like "for my evil purposes". And the heroes are all good, all the time. All cut from the same anatomical form, the male heroes are broad shouldered and have most everything covered. I was disappointed to see the only female hero was Wonder Woman, who gets considerably less material for a costume, but seems to be treated as an equal.

Anyway, Mr W loves the DVD, I think in part because it's so clear cut good and evil, and of course the good guys always win.

I think I'd be Green Lantern.

image from here