How does my garden grow

The mulch project drags on. If you've not been privy to this saga, I have a tree lawn that is hard to water and cut, so I wanted to cover it with something to make it look nicer. I stopped watering it some time last summer , and it has looked like hell for weeks (but the weeds were doing well).

Tom (or Saint Tom, as I will refer to the gardening services guy because he worked a miracle with his rototiller) turned up the soil on the tree lawn first thing Monday morning. Then on Tuesday the nice people from the landscape supply company unloaded the three cubic yards of mulch in the street in front of my house.

Come Tuesday afternoon, I'm ready to start raking dirt into its final formation, and moving mulch. Then the rain came. I know it's just a coincidence, but for the two days we've had torrential downpours in the afternoon. Wow, lots of rain.

So my mulch pile waits. I'm happy it didn't wash away with the rain, but now it will be a few days before I can work on this. It's just so funny how this project has taken a lot of mental energy, and then, once everything's in place, I have to wait on rain.

It's OK, though, it will look nice. In other news, get a load of my Black Eyed Susans! If you garden, get yerself some of these babies, because they look like this for weeks. It's the most amazing thing; they don't seem to be dying off. That's them in the picture above. You can also see the mulch pile, drying out from the first rain.

I'll post more pictures soon, when the light is better. I'm happy with my garden this year. One of the things I really like about gardening is how it changes over time. Sure, the garden seems to peak in terms of how much stuff is flowering, but stuff comes and goes and I love investigating to see how things are doing. I put in a bunch of perennials, but am leaving space for annuals that catch my interest.

And the pumpkin. I think it's cool how bees will sleep (that's what it looks like, anyway) in the flowers, which are probably 6"x6" (plenty of room). We've got one fruit that's really taking off, and Mr W and I look at it in the morning before we get in the car. The thing is growing 1/2" in diameter a day, it seems. For all the photosynthesis going on in that monster of a plant, I guess it's not too much of a surprise.

Plant Rarity - Plant of the Week (month? summer?) #2 Hybridization

I wanted to write about a few aspects of my research from school, specifically hybridization/polyploidy and population genetics . Here's a start on the hybridization stuff.

A couple of papers came out in the early 1990's by Norman Ellstrand, telling a cautionary tale that it was possible that rare plants could be hybridized out of existence by a process called "genetic swamping". Swamping occurs when the rare plant is outnumbered by a nearby closely related plant, and the volume of heterospecific pollen results in fewer and fewer pure offspring of the rare species. One of the best known cases of swamping is in the Catalina Island Mahogany (that CB and I got at least sort of close to when we went whale watching), Cercocarpus traskiae. It occurs on a specific soil type (on an island, no less), and the current population estimate is that there are 7 mature individuals and 20-50 immatures. Another species of Cercocarpus, C. betuloides var. blancheae, is also present on the island and studies have shown the two species hybridize. So much so that the original work by Rieseberg et al. (1989) suggested that there were only two pure C. traskiae individuals and what they thought were five more were actually hybrids.

This is a recent status report that has more details, but the short version is that C. traskiae is in a holding pattern after workers removed the more common species and fenced off the area against herbivores.

I looked at two species of Physaria, both endemic to Colorado. The rarer of the two is P. bellii, which occurs in three counties, and the more common is P. vitulifera, which occurs in six. That's a P. bellii photo up at the top, notice the rounded leaves. The ranges of the two overlap a little, and reports of purported hybrids in that area got me interested in the project in the first place.

But wait, there's more. This is a wierd thing about Physaria, but one species can have populations that are different ploidy levels. The genus is sort of wacky to begin with because of their generally low numbers of chromosomes. For example, in some populations of P. vitulifera, all members are diploid, with 8 chromosomes. Other populations are tetraploid, and have 16 chromosomes. They are all P. vitulifera, but the tetraploid ones have an extra set of chromosomes. It isn't known how the offspring do when a diploid individual crosses with a tetraploid, thereby making a triploid individual with 12 chromosomes. Generally, though, triploidy isn't a good thing, because it leaves some chromosomes without partners when it's time for meiosis. Below is a shot of P. bellii root tip cells, with 8 chromosomes.

So one of the things I investigated was the ploidy levels of a sample of P. vitulifera populations that were near P. bellii populations. The hypothesis was that if nearby populations of P. vitulifera were tetraploid, they wouldn't be a threat to P. bellii, which is always diploid and has 8 chromosomes. I was extremely lucky that there were so few chromosomes to work with, because I still did hundreds of squashes to get enough data to make some generalizations. The populations of P. vitulifera near P. bellii were generally tetraploid, except those that occurred close to the hybrid population, suggesting that hybridization between the species would likely be confined to known sites, and therefore P. bellii wasn't threatened by genetic swamping.

Above is P. vitulifera in the rocky soil that it's found in. Notice the leaves that are kind of violin shaped.

OK, enough for one post. I'll cover the population genetics stuff next time.

C. traskiae pic from here.

Ellstrand, NC. (1992) Gene flow by pollen: Implications for plant conservation genetics. Oikos 63: 77-86.

Ellstrand NC, Elam DR (1993) Population genetic consequences of small population size: implications for plant conservation. Annu Rev Ecol Syst 24: 217-242.

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 http://www.wheresgeorge.com/ 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!

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.

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.

Whoo-hoo!

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.

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.

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

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"

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.

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.

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.

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!

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.

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.

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.

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

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.

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

Another Rosy Bit

Rose Rustlers. Yup, pardner, there are some dedicated rose enthusiasts in the Lone Star State whose passion is to search out old varieties of roses and propagate them. They drive back roads, look around old cemeteries and generally keep their eyes peeled for a chance to get a cutting of an old rose. It is thought that settlers carried cuttings of their beloved garden plants with them from Europe, and as they moved westward they brought along these old varieties. So, there might be a 200 year old rose (or a clone or seed from it) growing in a forgotten cemetery in TX, just waiting for the rustlers. How cool is that? I like their emphasis on etiquette. They encourage education and information-gathering, and frown on people who cut and run. I don't see any reason why the practice of bringing cuttings over from Europe should be confined to TX, so maybe there's other old cemeteries (especially in the east) that house old rose varieties as well.

Plant of the Week - Roses

Roses aren't quite the dogs of the botany world, but they still have displayed an enormous variety of scent, color and form. Roses are part of the Rosaceae, with over 100 genera and more than 3,000 species. The family is divided into four subfamilies, but whether these groups are well-supported by DNA sequence information is still under some debate. The family ranks up there with the grass (grains) and pea (soybeans) families as the some of the most economically important crops.

The family contains many well-known fruits such as apples, pears, cherries, strawberries, and peaches. They all share a common floral formula, with some of the floral parts (sepals, petals and stamens) fused into a structure called a hypanthium. This shows different arrangements of parts, if you are interested.

Cultivated roses are often bred to be double-flowered, that is they have more petals than their wild ancestors. This phenomenon is thought to arise from mutations that tell the stamens (of which there are many) to develop as petals, which is apparently a "default" structure when other information is lacking.

In terms of cultivated roses, there are Old Garden roses and Modern Garden roses. The Old Garden roses bloom once in a profusion of double-flowered, highly scented blooms, on shrubby, disease resistant plants that are white, red or pink. Modern Garden roses are the result of selection for specific traits, and as you would imagine, the variety is pretty impressive. Within the Modern Garden roses, there are other classifications, such as miniature, and climbing, as well as the more familiar shrub roses. By introducing genes from a wild relative, (Rosa foetida), Hybrid Tea rose breeders were able to develop varieties with shades of copper, deep yellow, even lavender. In an interesting turn of fate, these same beautiful colors also brought along decreased disease resistance and scentless blooms, so they are bred more for color and are considered higher maintenance than other varieties.

Floribunda and Grandiflora roses are popular these days, and combine the best traits of Hybrid Teas with heightened disease resistance and more of that yummy rose scent.

The cut flower industry depends on perfect-looking specimens that often come from far away. As a result, the industry has been perhaps too reliant on the application of pesticides, and you can read about it here and here. I'm not sure if it's marketing or the real deal, but it seems that roses from Ecuador are really popular. Perhaps due to climate and soil, the flowers can be huge! In a great example of the consumer wanting to do the right thing if given the opportunity, Whole Foods and Sam's Club now offer Fair Trade roses from Ecuador. This certification protects workers (mostly women) from excess pesticide exposure while paying them a fair wage; everyone seems to win in this one.

I have two roses bushes in my garden. One's a 10 foot monster that was a housewarming present when my x and I moved into our last house. I wasn't all that concerned about the implications, it was a free rose bush! It has yellow-orange blooms that smell divine and it is about as unfussy as garden plants can get. The other one is a climbing rose I bought last year to grow up the corner of my house and it's got single flowers that are white on the inside and deep purple at the outside. I'd plant more, but I don't have any more room!

Hypanthium image from here. Rose farm image from here. Peach rose image from here.

Now We're Talkin'

This from Science Daily: USDA, Mars and IBM are sequencing the cocoa (Theobroma cacao) genome. It will take 5 years and is expected to lead to a better breeding lines. Why not? It's been done, without going the route of genetically modified foods, for many other domesticated crops. Better yields, increased pest resistance and more efficient use of water and nutrients are possible as a result of the effort.

I feel a little weird about Mars's role in this, though. I know that it's the norm in terms of funding for developing lines of corn, wheat, etc., but if Mars owns certain lines that are shown to be good for certain parts of the world, in certain soils, will small-scale farmers be able to get them? For a price...

And don't get me started on the risks of GM crops. I'm less concerned with the health risks than the environmental ones, such as the transfer of advantageous genes from crops to wild relatives.

From a chocolate-lover's perspective, the project will hopefully lead to better chocolate.

image from here

Ooh! My first meme

Saw this on friend LaGuera's site, and will play.

1. What were you doing 10 years ago?
Working for a company that made artsy rubber stamps, coordinating the process of turning artwork into the stamp and its label. Married, and trying to get pregnant, too.

2. 5 things on my to-do list today:
Return a call to someone at work
Go to a movie
Eat something cool on this hot day
Post to my blog
Snuggle with my guy

3. Snacks I enjoy:
Almost anything chocolate
Berries
Clif bars
Sunchips
Melon

4. Things I would do if I was a billionaire:
Buy land in ecologically-sensitive areas
Pay off my siblings' mortgages
Buy a winter and a summer house
Get my own plane to travel in
Figure out a way to contribute to scientific literacy
hey, I'd make a great philanthropist...

5. 5 Places I've lived:
Cleveland, OH
Bowling Green, OH
Norwalk, OH
Toledo, OH
Fort Collins, CO

6. Jobs I've had:
Day camp kitchen prep
Retail
Environmental Education
Computer image editing
Technician/Postdoc

Passing this on to the next person...
CB

And more people, if I can think of more friends that have blogs!!

Arty Science or Science-y Art

Just a quickie. I've finished the conference, attended some great presentations, got some good ideas to bring back to work, and presented my poster. I'm in AZ for a CB visit and it's HOT!

Here's a cool picture I saw the other day. It's made of pipette tips. I like his fancy tie.

Evol Conference 2

I went to an interesting talk yesterday afternoon and I'm going to have to track down the speaker to get more info. She talked about a technique they used to looking through sequence information for differences between closely related populations of sea urchin. This is one of the great things about genomics. When a whole organism's genome has been sequenced, many conserved genes are found for example, and the functions of those genes are known or hypothesized based on their structure and sequence.

So if one knows some target genes' sequences, if I understood this technique, one can amplify all or part of the genes, and then look for specific short sequences that are targets for something called restriction enzymes. When the DNA incubates with the restriction enzyme, it gets cut at those short sequences, and if the organisms have different sequences or numbers of base pairs around that region, it shows up as differently sized pieces when you visualize your results. I think she had something like 700 meaningful (as in they weren't noise) differences for her stuff, which is a large number, especially between two populations that are similar genetically (and physically, I assume).

It's for stuff like that that I get excited about conferences for. I'm having my coffee at my brother's now before I head down to the conference. I'll devote a glowing post to their hospitality soon, but suffice it to say that I am blessed indeed to have such wonderful relatives and only hope that I can return the favor sometime. Since my younger brother isn't here, we're scheming to see if we can all get together toward the end of the summer, maybe in SC.

And, I get to fly to AZ in a couple of days to see CB. Life, it be good.

image from here

Evolution Conference - 1

I've attended the first set of morning sessions at the conference, and am grabbing a quick bite before getting a good seat for the session I'm really interested in: Ecological Genomics. This is a direction I'd like to pursue with my mosquito research, and with the wealth of genomic information out there, it's a doable goal.

The average conference presentation goes like this: the speaker is introduced, and they talk for about 12-13 minutes while showing PowerPoint slides, then leave a couple of minutes for questions and the installation of the next speaker.

It never ceases to amaze me how many speakers run over time. Today, it was about 1 in 4. I think that's a lot, especially given the fact that it's not a huge deal to rehearse a 13 minute talk several times to get it down.

Some interesting talks though. My least favorite part is having to choose between the 10 concurrent sessions because there's usually a couple of talks that I want to see that are at the same time and I have to choose.

OK, back to it.

Scenic Minnesota and the Energizer Family

We had a good day of mosquito collecting this morning. Got lots of egg rafts and a few adults. I'm not sure why the traps yielded small numbers of adults, but we left the traps out to collect again tonight and hopefully will get some more. There were plenty of mosquitoes waiting for us (slap, slap, slap), but mostly of the wrong species. Wrong as in they are nuisance species that bite but aren't good vectors for West Nile virus.

As I write this in the kitchen of my brother and his wife's house, he's frying up trimmings from these huge rib eye steaks in order to make a pan sauce to serve with the grilled steaks. I'm energized by visits with my family, nourished, even. Wow, he just flambe'd the stuff in the pan - blogging and a light show - cool. Anyway, while I am quite satisfied with my life in CO, I get a lot out of visits with my siblings. I'm nourished intellectually and emotionally in ways that help me remember who I am and where I'm going in this life.

Oh, and my favorite quote from the flight out here: "Minneapolis? I'm going to St. Louis!" This from a man already seated on the plane. Here's my favorite part, (emphasis mine) "How could THEY let ME on the plane?" Um, how could you confuse the two cities?

Conference Part 3

I'm off to Minnesota tomorrow, to do a bit of mosquito collection, but mostly to present my transect study microsatellite research at Evolution 2008. I'll try to blog a bit about it, as I'm sure there will be lots of good presentations. My poster looks great, save one small spelling error, and I'm quite happy with it.

The bonus is that I get to stay with my brother and his wife, and my nephews (sister's kids) are visiting, so we'll have a good time on that front as well. I also get to squeeze in a short visit with CB before he goes off to Nova Scotia with a tour (yea Puffins!).

My Own Personal Hybrid Zone

I studied plant hybridization in school, and from an evolutionary biology perspective, it's a fascinating phenomenon because of the tie-ins to speciation and adaptation. Novel combinations of genes are produced via hybridization, and those new combos may be just what's needed to adapt to a new habitat. Add the elements of time and some isolation and it can lead to new species.

Unlike zoologists, botanists aren't quite as hung up on whether "good" species (i.e. "real" species) need to be completely reproductively isolated from each other. In other words, two groups of organisms can be valid species based on genetics, or ecological factors, and yet (oops, I had this wrong in the previous draft) hybridize to produce fertile offspring. Often the hybridization comes as a secondary thing, and more often these days, from human disturbance that makes some sort of bridge that brings formerly isolated species together.

When I bought my house in 2005, the sellers had put in a nice little front garden, and landscaped it with xeriscaping species. The plants have largely performed as advertised, I don't water it much, and it looks nice. They planted three kinds of Penstemon, and those have really done well. So much so that I have my own hybrid zone, where parental species, as well as intermediates can be seen.

My camera, sadly, is at my brother's house in MN, so I can't take a picture, but these pictures, from the fabulous Wayne's Word website give you the idea. Notice how F1s (that's "first filial generation, or the first hybrid offspring of pure parents) are a nice 50:50 split. It's not always that clean, but gives bumbling scientists a clue that hybridization is occurring. Then, as hybrids cross with hybrids, and hybrids backcross to parents ("BCs"), you can get a wide variety of forms, and presumably different abilities to adapt to environmental conditions.

How do these biological mix ups occur? Well, you can blame it on the pollinators, who work a patch of flowers and end up transferring pollen between species. That's exactly how it looks in my garden, where there are plants with blue flowers, and pink flowers (who, of course aren't going to change, as they are perennials), and then the intermediate flowers have combinations of blue and pink. Maybe I'll get a cool new Penstemon variety I can propagate.

Happy Father's Day to all the dads out there!!

Hey! That's recyclable!

When I started my current job, one of things that impressed me (and not in the good way) was the amount of plastic "lab consumables" we throw out for lack of a recycling program. And it wasn't really that we didn't want to do it, it was more that there wasn't a market for it, so no one would take it.

There is some stuff that we use, like pipette tips, that have to be autoclaved and thrown away because they might have biological nasties on them. But there are other things, like the plastic bottles that non-toxic reagents come in, that could be recycled. And the boxes that hold those pipette tips have a nice #5 stamped on the bottom of each and every one. If I'm setting up a run on the sequencer to do fragment analysis with my microsatellites, I can easily go through 10 boxes in a day. I use the tips, I toss the box, repeat.

Just today, I read that our county recycling program at the landfill is now accepting most plastics stamped 1-7. Wow. It will hopefully cut way down on the stuff going into the landfill, and people can feel good about recycling. I'm going to send an email on Monday to the proper people at work to see if we can set out recycling bins and keep that waste out of the landfill. I'm actually kind of excited to do it; it assuages my guilt over throwing out all that plastic up until now.

Oh, and the reason that this great service is now being offered? The rising price of oil has made the price of recycling the more difficult to recycle plastics (#3-#7) more economically viable. See? And you thought there wasn't an upside to $4.00 a gallon gas...

image from here, recycling symbol from here

New post below old post

I finished a post on milkweed, but it's below my latest post, so scroll

d
o
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Busy, good

Things have been busy but good lately. I've been occupied at work with a number of things, and keeping busy at home. I posted a little while ago about how good it was to be in the middle of a good book, which I found (it's a mystery - genre, that is) and I think has been occupying me to the exclusion of writing posts. But I'm working on a plant post which I hope to finish tonight.

I've been getting ready to travel next week to a conference. The Evolution Meetings is a conference of several scientific societies and the stuff that's presented there always seems to jibe most with my interests. I'm presenting a poster called, "Genetics of Culex pipiens complex subspecies and their hybrids along a transect". That's the shortened version, if you can believe it. The poster looks great (imo) and after showing it to the boss, I'll get it printed.

We've also stumbled upon another incidence of hybridization that is interesting because it's assumed in entomological circles that the two species in question don't hybridize. Initially we thought the evidence was a result of contamination, but it now that we've looked for more of it, there's something going on. My coworker who is on leave was supposed to be the one investigating this one, but it looks like I'll be doing it instead. It's an exciting research question, and I'll get more experience cloning and sequencing bits of DNA, so that's good.

I'm also (finally!) moving across the hall into some new lab space today. Whoo-hoo!! No more sharing the placemat-sized space among three people. I'm sure there will be stuff that comes up in terms of what goes where and who gets what, but I'm really looking forward to working in the new space.

I'll be staying with my brother while at the conference, and it is always nice to be the happy beneficiary of their hospitality.

Plant of the week - Milkweeds (Asclepias)

I thought I'd start a feature where I could post some cool stuff about plants. Let's start with the milkweeds, in the genus Asclepias, and the namesake of the family Asclepiadaceae. There are 75 species of milkweed in the US, and the genus is distributed throughout. The common name comes from the milky sap, which contains several chemicals that are toxic to many herbivorous insects and can cause contact dermatitis if it gets on your skin.

Members of this genus are famous in that they are the sole food of the Monarch caterpillar (Danaus plexippus), which probably merits a post by itself, given its hefty migration. The caterpillars feed exclusively on the leaves of milkweed, and this confers toxicity to the individual through subsequent stages of its life cycle. I can remember learning about this in school and seeing a video clip of naive blue jays being offered monarchs, eating, vomiting, and then being offered a Viceroy butterfly, which is a mimic. Those savvy jays declined anything that looked like a monarch, thus showing us how mimicry works in nature.

The flowers are attractive to many pollinators, but this genus has an unusual pollination mechanism that favor certain sized pollinators. The flowers are unusual in appearance because they have an extra whorl of parts in addition to the usual four (sepals, petals, stamen, pistil) called the corona. Here's a page that I got these flower pictures from. Tucked inside each flower is a small black structure that is attached to something called a pollinarium (plural pollinaria). The pollinarium is the jackpot of pollen. It is a large amount of pollen in one neat package.

This is so cool. The pollinating insect, while moving around the flower looking for nectar, hooks a foot around the pollinarium and, if conditions are right, pulls the entire structure out of the flower. Upon removal, the pollinarium starts to dry, and the arms holding the packets of pollen, called translator arms, reorient themselves such that, you guessed it, when the insect lands on another (hopefully) milkweed flower, the pollinarium is inserted into the proper place on the new flower.

The fluff on attached to the seeds is an effective dispersal mechanism that helps spread offspring away from their parent plants, presumably to reduce competition. It is as good or better than down as an insulator.

A nice gallery of eastern US species can be found here.

Blue jay pic from here. Pollinarium from here. Pink flower pic from here. Orange ones from here.

Post Secret

Have you seen Post Secret? It's a site for a project by Frank Warren, who started it by handing out blank postcards that people could put their secrets on and then send to him. It has grown into a community art project with thousands of postcards.

He has the website, has put out a few books of the postcards, and tours with some of the cards. Some are funny, some are sad and some are thought provoking. They update the website Sunday mornings.

Horse Racing?

The Belmont Stakes are today, in a few hours. Horse racing wasn't even on my radar before I met CB, who is a fan. I have since learned a bit (a very little bit) about it, and it strikes me as a unique sport/past time/spectacle.

First, there's the wagering. It's such an integral part of it, that the odds are given for who is likely to win the race, and people of course can bet on it. While people bet on all sorts of things, not the least of which are sporting events, you don't see the odds posted at a Rockies game (hint: don't bet on them to win. Not lately anyway...).

Then there's the money that is poured into these animals. Some really high end horses are owned by groups of people. Last I heard, Big Brown, who is favored heavily to win today, was worth $60 million. And that's not going to come from his work on the track. No, he will be much more valuable in a futures game with his gametes, that is he'll work as a stud. His owners may chose not to let him fulfill his potential as a racing horse, as he could hurt himself and not fulfill his mandate as a passer-on of lightening-fast genes.

Finally, there's the element of luck. For something that so much money is riding on, luck, to my eyes, plays a disproportionate role. There are a lot of horses who "should" win a particular race, but don't for some reason. Bad start, slight lameness, stumble at the wrong time, whatever.

So while I am putting in a few hours at work today to try to knock out the conference poster and square up some preliminary data to show the boss when he comes back on Monday, I'll be excusing myself around 5 pm EST and finding a TV that's showing the race.

image: Coglianese Photos

UPDATE: Big Brown, for some reason, came in dead last today. This is what I mean by that luck thing. No good reason given yet for why he ran out of gas, but there won't be a Triple Crown winner this year.

Conference, part 2

Well, I've just come back from the final dinner of the conference. I wanted to go because they scheduled David Quammen to speak. He's a scientific journalist who recently had a piece in Harper's on Tasmanian Devils and the cancer that threatens to wipe them out. Here's a link to the Science Daily story about it. It's a transmissible form of cancer that is spread by normal scuffles and physical contact. It's highly aggressive and animals live for about 90 days after they are infected. Up to 50% of populations are infected.

Unfortunately, plans changed and he instead spoke about the importance of the work people were doing who attended the conference and the need for that information to be disseminated to the public. Very true. As an example of the public's scientific illiteracy, he told a story about how he was talking about Ebola virus and at the end of it, someone commented "yeah, and that's found in spinach!" Um, that would be E. coli... There's a lot of work to do.

His point was that one of the ways information gets from scientists to the public is through journalists and the media. He urged the audience to not reject requests for information from the media, saying that it's common for people to fear being misquoted (or just plain getting it wrong), but that they normally have a chance to fact check before the piece goes to press. I think his point is well taken. There is a phenomenal amount of research being conducted on more things than we can imagine, and the basic ideas can be explained in plain english.

I'm all for scientific literacy, and I also believe that Americans in general want to be informed, they just get fed so much stuff, it's hard to discriminate. I don't have an answer for that, but if reputable publications make an effort to at least talk about findings of interest to the public, it would be a big help. I also think science writers might be able to put the information into context (so important) and that could make it more relevant.

For example, I was talking to a dog park friend this afternoon and she was describing work her sister does, looking at depletion of minerals in soil in poor countries. Blah, blah, yawn - until it's put into the context that these minerals are micronutrients that aren't getting to the people who need them, and it becomes a public health issue.

So, I think Quammen has an excellent point. A vast amount of science happens without the world ever knowing about it. I was amazed at all the facets of infectious disease ecology that came up just at this little two day conference. The media can do better at, as Quammen said, "connecting the dots" for the public, who should know more about topics that affect their lives.

Amazing Iceberg Shots

Antarctic icebergs - several flavors now available! Hope CB gets to see these when he takes a tour group down under in November.

All pics from the Daily Mail's website.

Conference #1

I'm attending a conference this week at the request of my boss, who is out of town doing fieldwork. It's on the ecology and evolution of infectious disease and so far it's been moderately interesting, but what it's really done is to get me excited about the next conference I'm going to in a couple of weeks, the Evolution meetings in MN.

What I mean is that I realized today how I missed that energy of being at a conference. How discussion (when it isn't an attack, as occasionally happens) occurs at the end of talks and people have ideas and share new ways of looking at data, it's one of the best parts about doing science, in my opinion.

I'm in the throes of making a poster to present at the conference. I chose a poster partly because I hadn't done one for a while, and also because it gave me more control over when I would present. I'm presenting my research on the genetic characterization of two subspecies of mosquito and their hybrids along a transect.

I like the Evolution meetings because I find their content most in line with my own research interests. Does that make me an evolutionary biologist? I suppose maybe. I'm interested in hybridization, adaptation and population dynamics, so it fits.

And I had the realization lately that these processes are what interest me, so I'm not going to get hung up on not being able to work with plants right now. The mosquitoes are a good model organism for a lot of reasons, not the least of which is that no one cares if you put the extras in the -80 freezer when you're done.

So, I'll post my poster when I'm done with it. I like it so far, but, like my brother said, it always takes longer to make one than you think.

Restroom Wisdom

Saw this on the inside of a bathroom stall today:

"100 things went right today!"

Cool Illusions at Scientific American

Scientific American magazine has an issue called "The Neuroscience of Illusion". It's about how those wacky optical illusions tell scientists about how our brains work.

Here's the link:
http://www.sciam.com/article.cfm?id=the-neuroscience-of-illusion

Indeed, the illusion they show at the beginning of the piece sure looks like it's moving, when it's not. CB bought the issue to show the birders he works with how brightness and color perception are relative. For example, do this one (credit to Edward H. Adelson of MIT):

Look at the squares labeled A and B. Are they different? They sure look different, but, no, they are the same shade of grey. You can print it out and cut out the squares if you like.

I've been thinking about the brain and all the cool gadgets that make up our sensory machinery. Mr W's had a thing lately for the "Magic School Bus" books and videos. We checked out a book on the senses and we read it every night for bedtime stories for almost three weeks. When you think about how sensory input is translated into nerve impulses, it is pretty darn amazing. Especially sight and hearing. Things most of us take for granted are incredibly complicated.

Apparently our visual system is pretty easily fooled, to which the abundance of optical illusions can attest. This is likely because shared networks in the brain. The article says:

But the same neural machinery that interprets actual sensory inputs is also responsible for our dreams, delusions and failings of memory. In other words, the real and the imagined share a physical source in the brain.

No wonder why we sometimes can't believe our eyes. Poking around, I found a contest whose site has lots of good illusions. There are some good blogs too here and here.

Another miss

There was a pivotal day that happened when I was getting divorced. When the first year "anniversary" of this date rolled around, I thought to myself, 'grrr, one year ago today...' (insert anger and sadness here). Then the two year anniversary of that date came up and I thought, 'wow, it's been two years...' (insert annoyance here).

This year, I missed the date entirely. Forgot about it. I realized over the weekend that this day passed about a month ago and I didn't even think about what it "meant".

Misstep or something else?

Well, I finally found out about the postdoc/lab manager job I'd been so excited about. For some reason the professor didn't return my email, but I saw on her website that she had hired someone. I sort of felt like my inquiring about the salary before even scoring an interview was a misstep on my part that may have cost me the position, but I'll never know.

Live and learn.

Do these things "happen for a reason"? I don't really believe that, but I've learned a valuable lesson with regard to the timing of when to talk about money. I also think that opportunities come up for people who are more or less looking for them.

As far as being able to learn the techniques I want to learn, and do the kinds of studies I want to do, my present job offers a lot. Besides being extremely flexible in terms of projects and work hours, it pays well and is reasonably well funded in terms of equipment and supplies. The only downside is that I miss the collaborative aspect of being in academia, but maybe I can find it if I work at it a bit.

This all has me thinking too about what I see myself doing 5 or 10 years down the road. I would like to have more responsibility (with a corresponding hike in pay), and I'd like to get back to working with plants again some day. But the mosquito gig has been good to me and, most importantly, it's what I make it.