Wednesday, March 31, 2010

Who owns you?

Or, more specifically, can anyone (a private business, another person, the government) own the knowledge about your own genetic code?

Thankfully there are some things working through the legal pipelines to finally answer this question:

No, no one can own the information about the DNA in your body.

The genome is the sequence of nucleotides (A, T, G and C) in every cell in our body that, in particular orders, give the instructions for what a gene will do, where it will be expressed and when.

Although we sequenced "the human" genome, each individual has small differences that make each of us unique. These differences can be a single nucleotide change (for example, a change from an "A" to a "C"), or an insertion or deletion of sequence.

There can be some confusion when discussing "alleles" related to certain genes, specifically with respect to diseases like cancer, that I'll try to clarify here.

For the most part, we all have the same set of genes. Every human has the BRCA1 gene. It is located on chromosome 17:

However, there are small differences in the sequence of this gene between individuals. Each unique change or set of changes to the BRCA1 gene can be described as a different "allele" of that gene. I like to think of a particular gene as ice cream, and alleles as flavors of ice cream. You can have many different flavors of ice cream, but the frozen deliciousness you are eating is still ice cream. Think of it this way (purely made up example):

Vanilla = Normal gene sequence = BRCA1_allele1
Cookie dough = Mutation from A to T at position three = BRCA1_allele2
Chocolate = Mutation from C to A at position seven = BRCA1_allele2

Just because there is a small difference does not mean that there is a new gene, it is just a variant (or allele) of the same gene.

So, why do people want to look at the BRCA1 gene, with respect to breast cancer? Well, most of us have the vanilla allele - our BRCA1 gene works fine and doesn't cause any trouble. But, researchers identified an allele, we'll call it the Mint Chocolate Chip allele, that misbehaves, and is linked to a higher incidence of breast cancer.

What private companies have been doing is trying to justify patenting the sequence of the BRCA1 gene, that they own the right to knowledge about whether you have Vanilla, or Cookie Dough, or Mint Chocolate Chip.

"Precedent indicates that laws of nature or natural substances can't be patented, although significant transformations to natural products can lead to a patentable process or product. The USPTO grants patents to isolated DNA based on the conclusion that they are "distinctly different in character" from the DNA that is present in human cells."

What private companies have been doing is trying to justify patenting the sequence of the BRCA1 gene, that they own the right to knowledge about whether you have Vanilla, or Cookie Dough, or Mint Chocolate Chip.

It looks like now, this will be changed.


Tuesday, March 30, 2010

The world is such a small place

Here's a list of the countries from which ISP addresses originate, who have looked at my blog (if even accidentally for a second or two). Neato! I hope to visit each of these countries someday!

Country Name
United States
United Kingdom
Trinidad And Tobago
South Africa
Czech Republic
Russian Federation

Monday, March 29, 2010

Congratulations are in order

Scott placed first at the Graduate Exhibition and I place second! Yay!

We celebrated last night by going to the dollar theatre with some friends to watch Sherlock Holmes!

In other news,
- the graduate exhibition music/theatre performances on Friday were pretty spectacular
- the "Out of Hand" variety show put on by Penn State students was unbelievable. They were all great, but Nathan Kepner was world-class. I would go see him again in a heartbeat!
- Aro is now on his countdown to knee surgery and being neutered - Friday's the day. Dum, dum, dum...

- - - - - - - - - - - - - - - - - - - - -
They just updated the website for the Grad Expo.

Saturday, March 27, 2010

Better than alarm clocks

I would not be surprised if these dogs had an internal timers.

4am seems to be a regular for Aro, but I can usually ignore him back to sleep until just about 7.

I used to be a morning person, so I'm not really minding the wake-up calls, and I do enjoy the walks (although they'll get much more enjoyable above freezing).

This morning, as a result of getting up early, I'm going to make biscuits for breakfast for us. Then Scott has to go into lab to meet with prospective Chemistry students. My plan is to catch up on house-work, take the dogs on a play-date with our neighbor's very friendly black lab (wish us luck!), practice my 5 min poster talk for tomorrow (meaning I should come up with a 5 min talk), and think about labwork a bit.

One of the biggest joys, and the biggest drawbacks, of grad school is that it never ends. There's never a point where I'm "done for the day". There's always more to think about, more to do, problems to work out, troubleshooting. It is wonderful and awful at the same time. Today, though, it is leaning towards awesome, because I've steadily been making progress (a great motivator), and am excited to work through some more ideas.

Better get to those biscuits!

Friday, March 26, 2010

Thursday, March 25, 2010

thought for the day...

I re-connected with a good friend today, and wanted to share this quotation:

Benjamin Disraeli:

Action may not always bring happiness, but there is no happiness without action.

Tuesday, March 23, 2010

Who knew I was such an exhibitionist?

Today Scott and I finished designing and submitted our posters for the 2010 Graduate Exhibition.

Friday is the Music/Theatre performances:

Music and Theatre

Friday, March 26, 2010
7:00 to 10:00 p.m.
The State Theatre, 130 West College Avenue

Sunday you are all invited to see our posters and ask us questions at the Research Presentations:

Intended for the Public

Sunday, March 28, 2010
Open to the Public, Noon to 2:30 p.m.
Alumni Hall, HUB-Robeson Center

Here's a sneak peek at my poster:

Monday, March 22, 2010

candy coating...

I especially like this quotation from Phil Plait at the blog, Bad Astronomy:

"once you buy into one flavor of candy-coated nonsense, they all start to taste pretty good. But we have to be adults here, and understand that you can’t live on candy. In fact, too much makes you sick."

Right now my brain is a little fried from working on my poster all day, but this was enough to pull me into focus, if only for long enough to share it with you. :)

food for thought

An image taken from this blog post.

Sunday, March 21, 2010

quiet time

I like getting up early and having the morning to enjoy the quiet, catch up on dishes, laundry, email, and maybe read with some hot tea (or hot water with grapefruit juice this morning).

This morning already I've taken the dogs out, done two loads of dishes, folded laundry from last night, and...nearly died from holding in my laughter while secretly watching the dogs.

After feeding the dogs, I sat down with my hot water and grapefruit juice (half hot water, half grapefruit juice, a twist on hot lemonade - also very tasty), and my book on the couch. The dogs (Both ~10lbs; Aro, a half-chihuahua, half-rat terrier, and Chip, a chihuahua) started playing. After a few minutes it quieted down and the dogs laid down in the sun. Aro jumped on top of his kennel to snuggle on the towel there, and Chip laid down in front of the kennel. A minute or so later, Aro left to get some water and Chip took his place on top of the kennel, on the sunny, warm towel. Aro came back, wanting his spot back, or at least to share, jumped on top of the kennel also. Chip, being nice, or so I thought, got off and let Aro snuggle back into his original, sunny spot.

As Aro got comfortable, Chip wandered around the kennel, appraising it, then decided to pull the towel (Aro and all) off the top of the kennel! It was entirely unexpected and so funny I had to hold my laughter in. It took a few seconds of tugging before Aro realized what was happening and jumped to his feet. But, he had no traction or way to keep the towel from it's impending slip off of the kennel. Stifling my laughter, Chip continued to tug and it reached the point where Aro rolled off onto the ground and the towel came off easily. I couldn't hold it in when, as a disoriented Aro looked around, Chip arranged the towel on the sunlight in front of the kennel and proceeded to make himself comfortable. Sigh, big brothers...

This entire scene occurred in complete silence, aside from my little slip, and so did not disturb my morning quiet.

As I write this, I hear that the dishwasher has finished with load #2, so I think I'll go unload that, then do some yoga before the sleeping giant upstairs starts to stir. :)

If I have time I might try a new recipe. I found some bran in the cupboard and was trying to find an alternative to the traditional use of making bran muffins. I came across this recipe for bran pizza crust and thought I might be able to co-opt it into a cinnamon roll dough. If
I try it, I'll let you know how it turns out.

Monday, March 15, 2010

Happy Pi Day!

In honor of Pi day, I'd like to make a heart-healthy pie.

Here are some recipes I'm considering, but I'm really leaning towards the crustless coconut pie shown above. I might just end up making biscotti, but there will be something delicious in the oven tonight!

In other news, the dogs did well this weekend, playing quite a bit - and no accidents! We'll see how today (first full day since the soil incident) goes.

Back to Pi day...
Being a mathbionerd, I try to realize when I'm being sensitive about math/science topics and when there is reason to be upset about something.

Well, I'm upset with Stephanie Meyer for picking on Calculus. Math gets such a bad rap, but she constantly harps on it, over all other subjects in the Twilight series. Great, she's getting young, impressionable teens (mostly girls) to read, and all she does is dog on math as being frustrating, hard, and something to just skim by. Way to go. Maybe Stephanie had a hard time in math, or maybe that's what the preppy, popular kids do - make fun of the nerds. Well, this mathbionerd is not taking this lying down (I'll be sitting while I type, thank-you)!

I'm not asking that she love Calculus, although I certainly did and still do, but did she have to pick on the little guy? It's almost passé to hate math, be a little creative.

To be fair, moving from a large and well-supported school district in Phoenix to a small town, I could see my 13-year-old self identifying with Bella, wanting to downplay any smarts because they just make you stick out; in a class of 48 knowing the right answer is showing off, being smug, and loses you friends faster than most other social faux pas.

Okay, I get that. Math, however, is a constant struggle for people. From a very young age children are conditioned to expect math to be difficult, and to expect that they'll hate it. Certainly not everyone wants to major in math, but the logic and critical thinking skills developed in this most basic of sciences are invaluable to any life activity. Brushing aside the fact that math is applied to nearly everything we use in daily life (optimizing soda can designs), and is a tool utilized in all STEM and social science research, learning how to do math, in general, prepares us for the world.

Math teaches us to be patient (trying to rush will result in silly, avoidable errors), that the right solution can be reached from a variety of paths, and even in cases where exact solutions are unknowable, we can identify sets of acceptable, and equally valid answers.

So why, oh why, does anyone, especially writers of young adult novels, feel the need to vilify Mathematics?

Thursday, March 11, 2010

bad dogs

We came home expecting maybe an accident because we left them alone for the whole day. Instead, it was far more extreme than what we could have imagined.

What we came home to today...

we're not going to discriminate...

but we really hope some private organization hosts the prom, so they can discriminate against gay students.

Way to go Mississippi. Your name may be full of homo-morphic letters, but you are setting a precedence of being a very homo-phobic environment.

I'm not happy that private organizations will discriminate against gay people, but it is their right, as a private organization to decide who attends about their own events. But I don't think a public school should be able to discriminate by simply farming out events and trying to wash their hands of any responsibility.

Wednesday, March 10, 2010

sex determination on a cell by cell basis in chickens

The link below is to a great summary of some brand-spanking new research into sex determination in chickens.

The sex determination system in birds is quite different in birds than mammals - so different that it is not unheard of to have a half-male, half-female bird. Using this unique phenomenon researchers have been able to study the fundamentals of sex determination in the chicken.

Tuesday, March 9, 2010

Luxating patella

Aro has two luxating patellas (one on each back leg) :(

They get graded on a 1-4 scale (1 minor, 4 nearly incapacitated), and Aro is currently at a 3 in one leg and 3.5 in the other. This means that in each back leg his patella (kneecap) is never in the proper place, but can be manipulated into place (sometimes with difficulty). Poor puppy, no wonder he limps and has such an odd stance. He will certainly need surgery to fix this because it will only get worse as time goes on.

I felt so bad taking him on his evening walk today, knowing now how much pain he must be in with these old-man knees. And he's still just a puppy!

The good news is that, with surgery, he can live a long, happy, productive doggy life, with the use of both of his scrawny doggie back legs.

It's a genetic disorder, and apparently very common here in PA with all the puppy mills. I forgot to mention earlier that Aro came from an Amish puppy mill. They don't care whether their puppies have genetic disorders, and probably don't even have any puppy long enough to realize it has this specific disorder. It makes me so angry to think about that they keep breeding a dog that will give its offspring such a high probability of inheriting this awful condition.

And a little bit of good news: No accidents in the house today! Nothing chewed up! Yay!! And Aro and Chip love each other:

free wi-fi in the hospital, who knew...

I have 20 minutes to kill, sitting here in the hospital after getting my second rabies vaccine. Got here at 10:30, and will head out around 11:30, not too bad. I was expecting it to be longer.

And the bonus: Free wi-fi! Lol, the hospital is better than Starbucks.

I know, I know, I could be using this time productively to, oh, proof-read a paper, or work on some other results, go through emails even, so why and I here writing to you all... because I can! There's something satisfying, like a personal triumph, when one finds free wi-fi, and I, having triumphed, need to show off. :)

In other dog news, the UK is considering advanced legislation against acts by "dangerous dogs". Previously they banned four "dangerous" breeds of dogs, and gave themselves rights to sanction dangerous dog acts (for any breed) in the public sphere, and now are potentially giving the government the ability to sanction dog owners for acts in private residences.

I disagree with the assumption that some breeds are inherently dangerous and should be banned, but do agree that any dog that attacks a person or another dog should come up for a review for the public's health and safety. No, I don't think it should immediately be put to sleep, but I do think that a record should be made, and an investigation should consider what actions are appropriate given the particular offense.

Yes, larger dogs can, in general, do more damage, but, just like people, there are both genetic and environmental components to behavior. If we start damning dogs because they were unlucky enough to have a particular genetic heritage, that seems to open the doorway to charging people for being born with particular gene variants associated with aggressiveness, or considering a person with an allele associated with alcoholism as having a "pre-existing" condition even if they've never swat a fly or drank a drop, respectively.

Monday, March 8, 2010

and now for something completely different

As you may or may not know, the "theme" of our wedding was "sustainability". We tried to stay as local and ec0-friendly as possible, including compostable plates and cups and locally made chocolate favors in recycled paper boxes.

Well, here's another take on ec0-friendly: sustainable lingerie!

I'm all for making fabrics of sustainable materials, but please don't go rush out and buy something just because it is made of a material that's more sustainable that what you're wearing now. That just boosts the overall amount of clothes in the world.

How about if, in addition to developing environment friendly fabrics and dyes, we also thought about limiting the amount of clothes/products we buy overall. Ask yourself, Do I really need 10 pairs of jeans? Do I have to have new clothes every season? Can I fix my clothes myself (re-sewing a button, patching a hole, mending a tear) instead of throwing this out and buying something new?

I made a decision last year to keep the quantity of clothes I own roughly the same. That is, if I want to buy something new, consider if it is going to replace another article of clothing that really does need replacing, or, if it is something new, will it add something substantial to my collection? For example, I realize that going into the "real" world, I need to have clothes that are appropriate for interviewing and visiting prospective employers. I did purchase some clothes for my trip to the NIH, but I was careful to choose things that I knew I could mix-match and re-wear. I've already worn everything several times with other outfits (a nice sweater that can dress up or down and a black skirt). I also wore the super-cute pair of black heels that I've owned since my junior year of high school (at least 10 year old now), that I simply took to the cobbler in town to have re-heeled for $12. So, rather than buying a new pair, spending more than I wanted and contributing to the local dump, I get to wear my favorite shoes, and spent only $12!

Yay for being eco-friendly! We just have to remember not to lose the forrest for the very pretty, trees.

no reason to duplicate

I figure that most people who read my blog are also my facebook friends, so I try not to duplicate anything here. For that reason, I encourage you to go look at my facebook photos to see some more pictures and videos of Chip and our houseguest, Aro.

An update on my dog bite: yesterday one of the puncture wounds was starting to look pretty angry (red and swollen for about a half-dollar radius around it). I washed it several more times throughout the day with warm running water and soap, and then kept it covered with a bandage with antibiotic, deciding that if it was worse, or no better, to day I'd go in. Well, looks like good ol'fashioned soap and water did the trick! I really wish there was more emphasis on how effective simply cleaning a wound can be. There is no need to default to antibiotics - useful as they are - because, as we know, over-use can lead to anti-biotic resistance.

Sunday, March 7, 2010

life is never boring in our house

Yesterday started with Taekwando for Scott and a trip to Lowe's for seeds, pots and soil for me. The afternoon consisted of Chip getting attacked by a monster dog at the dog park (the most terrifying event in my life to this point), me getting bit trying to save him and now having to go through a series of rabies shots. (Don't worry, we're both okay now.) We spent the night cuddling Chip, filling up on take-out chinese and de-stressing on the couch. Especially after not having eaten all day, that greasy, americanized Chinese food has never, ever, tasted so good.

This morning started with laundry, dishes, breakfast, grocery shopping and then driving to Lewistown to pick up the foster dog we saved from a neglecting home because PAWS has NO room, NO open foster homes and 20 dogs on the waiting list (see post below). Aro and Chip get along surprisingly well, especially considering how Chip is a cranky old man and usually can't stand puppies. After a couple hours home Chip started to bare his teeth at the incessant poking of Aro, so I put Aro in his kennel and Chip is sleeping in Aro's dog bed.

Now, finally, I'm sitting here enjoying the quiet before going to make dinner (homemade pizza) while Scott, Chip and Aro, all nap.

Here's a video of Aro and Chip's first meeting (Chip uses his kennel as a "home base").

Friday, March 5, 2010

My bleeding heart is getting me in trouble again

After adopting Chip through PAWS I'm really supportive of encouraging dog adoption through shelters rather than randomly picking up a dog through craigslist or some other website. Similarly, I think that people who need to give up their animals should do so through shelters. This ensures the animals have proper nutrition, medical treatment and will go to vetted, loving, responsible homes, rather than get chucked around from home to home.

Yesterday I saw an add on our local craigslist for a "free dog". The very cute chihuahua-rat terrier mix has recently found itself without a home because of its owner's financial hardship, and so she was trying to find the little guy a good home online. I sent her all of the information for our local PAWS shelter but she responded that she didn't have a car or means to get the dog to the shelter.

This morning I called my only contact at PAWS (a wonderful woman who could have been upset with me for messing up the order of things, but instead was absolutely lovely), and she put me in touch with the right people. We figured out that PAWS is severely understaffed (both paid staff and volunteers) and have they have no place to house the little dog. However if we could serve as a foster home, then they would gladly accept him and find him a forever home.

So, Sunday I (or we) will be driving to Lewistown to pick up a 10 month old mutt. Then, Monday I'll take him into the shelter to get up-to-date on shots, and hopefully plan a time for him to be neutered. The woman who is giving the dog up mentioned that her husband used to be abusive to her and the dog, so I'm hoping we can start to heal some of that damage. Hopefully Chip will play nice, and like his temporary friend.

In a somewhat-related train of thought, here's a really snazzy slow-motion video of a variety of dogs. I am amazed at what we can capture on film now.

Going to pay for this later...

I woke up about 3:00 this morning, heart pounding, wide awake. I tried for half an hour to go back to sleep but my mind was having none of it, so instead I've been pretty productive, reading through papers, catching up on new research, and planning my work for the day. I'm sure it'll catch up to me soon, but I figured why try to fight it. I can take a nap later.

It is one of the joys of graduate school (and a great advisor) to have a flexible schedule.

One of the articles I came across, however, an editorial in Nature asks, Do scientists need a PhD?

I suppose my answer would be the same as concluded in the paper:

"The answer is not clear-cut."

The process is highly individual, and the end goals can be very different, especially depending on the field. For me, personally, I would not have been able to learn about so many different research paths without coming to graduate school. In the community I grew up in, I didn't really consider being a professional scientist and graduate school has really opened the door to the multitude of paths available for a career scientist (in industry, government, public policy, and academia - both large universities and small colleges). Without going to graduate school, I do not think I would have been exposed to so many different ways of approaching and interpreting scientific research and would not have been pushed to develop my critical thinking skills.

So, for me, for the career path I want, yes, this scientist needs a PhD.

Wednesday, March 3, 2010


I have a book that I've only half-read, by Loren Eiseley , born in Lincoln Nebraska, went to UNL and then researched at University of Pennsylvania. He was an "American anthropologist, educator, philosopher, and natural science writer".

In the book he muses about how dolphin cognition evolved, compared to cognition in modern humans. Dolphins do not have digits, like we do, no thumbs to pick up and explore the world (or press the space key as I type). They live in an underwater environment with few natural predators, in social groups, and do not need to spend their time farming or toiling most of the day away like we humans do, just to survive. So how might a dolphin think? How do they perceive and inquire about the world around them?

And clearly, they do inquire and learn new things:

Tuesday, March 2, 2010

grounded guardians

With so many of my friends and family having children, it is nice to see that there are some rational resources for parents:


Science-based parenting (rational dads)

As a cool tech aside, even though I love my apple, this panasonic (slip Core i5) is pretty sweet.

Monday, March 1, 2010

Faster than a speeding camera shutter? I think not...

Here's some pretty cool video of hummingbirds flying.

I remember when I lived in Arizona and walking to the bus stop one day we found a hummingbird nest with a tiny little egg shell in it (barely larger than a tic tac). They're really wonderful birds to watch, with such unique adaptations, such as their long skinny tongues, and the absolutely fantastic way they've managed to flap their wings to stay in one spot in the air.