Monday, June 30, 2008

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.

Sunday, June 29, 2008

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.

Thursday, June 26, 2008

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

Wednesday, June 25, 2008

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
Clif bars

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
Environmental Education
Computer image editing

Passing this on to the next person...

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

Tuesday, June 24, 2008

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.

Sunday, June 22, 2008

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

Saturday, June 21, 2008

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.

Thursday, June 19, 2008

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?

Monday, June 16, 2008

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!).

Sunday, June 15, 2008

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!!

Saturday, June 14, 2008

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

Friday, June 13, 2008

New post below old post

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


Wednesday, June 11, 2008

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.

Tuesday, June 10, 2008

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.

Sunday, June 8, 2008

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.

Saturday, June 7, 2008

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.

Friday, June 6, 2008

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.

Thursday, June 5, 2008

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!"

Tuesday, June 3, 2008

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:

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.

Monday, June 2, 2008

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.