All the cool kids update their blogs

I'm not now, nor have I ever been a cool kid, but maybe I'll post a small update.

Just a wee tiny bit of news, you know.
Like how I live in Japan now and have been here for a month and will stay for another two months.

The last four weeks have felt simultaneously eons long and seconds short.  Maybe this is how the passing of time feels for everyone all the time but for me, I have to ponder, "wow, that happened two weeks ago? That felt like forever!" or "I can't believe I've already been here for 4 weeks, wow, where did the time go?"
But enough waxing on time relativity in the frame of human perception.  How about the good stuff?

I and two other students from USU arrived in Narita International Airport at 3 pm on August 31st (Friday, or Kinyoubi).  We found our bus to Tsukuba, enjoyed site seeing out the window on the nearly 2 hour ride to our new home, and were welcomed in Tsukuba center with smiling, familiar faces (at least to me).  The students who came to USU for a month this summer had volunteered to greet us and help us settle in for our first night in Japan (hereinafter referred to as 日本, which is pronounced Nihon, and literally means the origin of the sun).

 Our rooms are small, the weather was very very hot and humid compared to what we were used to, and the showers cost Y100 (~$1.30) for 10 minutes. Unfortunately, there is no pay per minute option, you can only pay in 10 minute increments.  I find it annoying because I rarely spend more than 2 minutes with the water on.  Otherwise, I'm having a really fabulous time.  There are a few convenience stores (conbinis) nearby, like 7-11 and Lawsons.  The Lawsons is a hyaku en shop (Y100), and most things are Y105 there (the extra 5 is for tax).  From fruits and veges to bread, eggs, and coffee..I actually do a fair amount of grocery shopping there and the prices aren't all that different per quantity than what I can get at the grocery store 15 minutes' bike trip away.

Our tutors are students who went to USU in the summer, and they've been helpful in showing us around and helping us with paperwork.  Additionally, they've become good friends!  Not only that, but I've managed to stay in touch with some students who came to USU two summers ago, and these friendships have grown as well!

We went to the mall and then made sushi together!


I love my classes.  I find Japanese language and kanji to be challenging but fun and very useful.  I'm starting to be able to piece together simple sentences, and read simple signs.  learning kanji also increases my vocabulary and understanding of how words go together.  Plus, it's a venue by which to make friends.  One of the girls who came from USU is in that class with me, and we've made a few friends with whom we've gone to Tokyo twice.  Both times were fabulous experiences!

Working in the lab has also been highly enjoyable so far.  Miyazaki-sensei has been very accommodating and hooked me up with Tsubasa-san, a student who intends to go to USU in the winter to take me under his supervision.  Tsubasa-san has been incredibly kind and understanding, even with our massive language barrier.  His English is pretty good, though, so we generally get by ok.  The other students in the lab speak English a bit less fluently, so it's always a fun round of charades when we communicate.  Miyazaki-sensei's lab is about determining the mechanisms by which certain food compounds protect against metabolic disease.  I have learned the Western Blot technique and have been helping with taking the blood glucose levels of the experiment mice.  Tsubasa-san's experiments are based on theaflavin compounds isolated from tea, and whether they have a protective action against diabetes and hypertension (and if so, how that action works).  It's really cool that I can work in a lab that is different to my toxicology training but sort of a flip side of the same coin.  It's also a very different experience because Miyazaki-sensei has 10 students compared to my advisor's 2.  And it means lab is fun every day because there are a lot of friends with whom to work!

I love it here.  I'm learning a lot, sweating a lot (ok, not loving that part)  and making a lot of new friends.  I miss C, my husband, of course..and my friends and family. No doubt about it.  But nevertheless I'm trying to make the most of this opportunity and fill every day with a little bit of joy and knowledge.

On Christmas, consumerism, and charity

I stumbled upon this video while pondering gifts to give to friends and family this Christmas.  It is December after all, and with the calendar page turning, so plans for end of year holidays commence.  My extended family started a tradition a few years ago where we don't buy each other material goods, rather we donate to causes that we think our "gift recipients" will appreciate.  I think it's a great tradition because 1) it helps people who actually need things we take for granted, and 2) it's a lot easier to mail my grandma a card than a package. What can I say? I'm super lazy.

In all honesty, though, I think it brings out the true spirit of Christmas - helping those less fortunate than yourself.  Regardless of what you think of Christianity and Christmas, in the Bible Jesus was always on about loving your neighbors and giving up worldly goods.  Seems like the right sort of idea, if you'll be celebrating Christmas, to celebrate it as the guy you're celebrating would.  So it's weird for me to think of Christmas as "that time of year when I finally get that gadget I've had my eye on" as Best Buy or Walmart would have me to believe.  And as tempting as that shiny new Nintendo game system is, that's maybe not the entire point of the holiday.  At least, not for me and my family.

Anyway, this particular project caught my eye because it's an inexpensive and energy efficient solution to a problem that plagues many people who live in dense, windowless housing:  indoor lighting (during the day in this case).  I'll let the video speak for itself; really, it's three minutes long.  I know you have three minutes to spare.

See?  How cool is that!  Using the simple but profound principle of light refraction to provide indoor lighting for crowded, windowless homes in the dense urban jungle of Manila, Phillipines?  I can't believe I didn't think of this for my own house, so much cheaper than installing a skylight...
This project (check out their website at aliteroflight.org) and many other projects out there are SO easy to support.  I'll definitely be sending out some virtual checks to this organization in honor of my family members for Christmas this year.  As far as other end of year holiday traditions go, such as Hanukkah or Kwanzaa, or even winter solstice rituals for the Pagan crowd,  I'm afraid I'm not well versed.  In fact, if you do celebrate Pagan rituals, Kwanzaa, Hanukkah, or other end of year festiveness..let me know about your traditions!  I love learning! In the meantime, however, for this post please pardon my Christian mindset, and consider home-made presents, sustainable gifts, or contributions to (reputable) charitable organizations in lieu of (or addition to!) gadgetry, big-box-store toys, etc. etc.  The greatest gifts are the ones that improve lives, in my opinion.

If this project doesn't float your boat, there are lots of other cool organizations working to better the planet. If you're at a loss for ideas on what to look for, altgifts.org is a great resource for connecting you to worthy charities for all sorts of causes all over the world.

The Role of Diet on Cancer

When I was about 18, one of my parents' best friends, Marge*, contracted breast cancer.  Marge and her family had moved away when I was 10, but they stayed in touch with us and we visited each other about once a year or so.  Because no one so close to me had ever had cancer, and cancer kills people, it was a Very Big Deal.  She underwent a mastectomy and when the biopsy of her lymph nodes turned out clean, she opted out of chemotherapy in favor of a lifestyle based treatment.  My father thought it was stupid, and that she was taking crazy risks with her health considering that she had a family who depended on her, but when he was down visiting Marge and her family he learned that she had chosen a vegan diet over chemotherapy after reading The China Study by Dr. T. Colin Campbell.  Keep in mind that Marge and her husband Boris are both PhD's in agricultural engineering - with a strong emphasis in science, particularly agricultural science.
For them to go vegan was also a Very. Big. Deal.

The China Study is a book compiling both global epidemiological studies linking diet with certain cancers (Breast, colorectal, and prostate especially) and mechanistic-type animal model studies comparing  the effect on cancer that diets based on the milk protein casein have to diets based on plant-derived foods and proteins.  Marge and Boris talked my father (who has a PhD in genetics) into reading it while he was there.  He did indeed read the book, and came back home a vegetarian - not quite a vegan, but avoiding milk products nonetheless.  My mother was devastated (and to this day refuses to forgo meat), but I was thrilled.  Now I had some solidarity in my carnivorous household, as I had been vegetarian for two years at the time.

The book describes a compelling link between animal protein, particularly dairy protein, and many diseases.  Cancer, diabetes, heart disease...they are all very strongly -and globally- correlated to meat-based diets.  Keep in mind that correlation never equals causation, but these correlations backed up with the animal studies and the sheer volume of epidemiological data truly paints a stark picture.  Countries that eat the largest amount of meat and drink the most milk have the highest rates of a slew of different cancers.

However, one can be a vegetarian and still eat a very unhealthy diet.  After all, mac-n-cheese is vegetarian.  So are potato chips and Oreo cookies.  The clincher for me to actually really think about the food I eat, and check for nutritive value beyond "well there are no animals in the ingredient list" has been the toxicology course I'm taking this semester.  My professor has put a large emphasis on carcinogenesis - all heavily drawn from the most recent research from top labs, including his own lab's research projects.  Lots of foods are full of carcinogens, including many vegetables and grains and herbs, but cooked meats are particularly "bad."  Cooked meats are hosts to a smorgasbord of carcinogenic compounds.  These compounds are often taken care of by the body's defense system, however the occasional DNA mutations that arise from the onslaught of carcinogenic chemicals accumulate over time...and they may be mutating DNA in key locations that control cellular laws.  These particular DNA mutations can lead to altered cellular activity, and ultimately cancer.


Honestly, I know that few people can give up meat cold-turkey (pardon the pun).  In fact, it would be silly to expect that, because to most people meat is tasty.  I just wonder if it truly would be so difficult for most people now to simply eat meat in moderation.  Eat meat a few times a week instead of a few times a day.  Or enjoy smaller portions of meat and larger portions of vegetables and fruits - not just grains and starches like corn and potatoes (fries are not vegetables, regardless of whether school cafeterias would like them to be).  I know the dairy, beef, pork, egg, poultry, etc. industries are not happy with these ideas and stand to lose a lot of money if Americans reduce their meat consumption even by a third.  But the quality of life to be gained is worth it, and I would urge everyone to at least give it a try.  Broccoli is not your enemy - it is full of fiber (preventing cancers of the gut) as well as chemicals that actively help your body fight carcinogenic compounds.  So not only would you ingest fewer major carcinogens, but you would consume a greater volume of anti-carcinogens.  It's a one-two punch K.O.!

Speaking of one-two punches, I found a video on Youtube that has little to do with cancer, but could lower your blood pressure and release feel-good chemicals into your brain...especially if you like kittens:

On Medical and Science Ethics: The MMR Vaccine Fiasco

There is a reason why I am a student of a science heavily focused on public health.  Human population health is important to me.  In my view, a healthy society is a productive one, and a healthy environment with accurate science is the most conducive to human health.  Therefore, in the quest for knowledge about health, the issue of scientific and medical ethics is near and dear to my heart.

There are a multitude of ethical quandaries that the average scientist wades through during their career.  If your data aren't as nice looking as you'd hoped, the standard deviations a bit further from how you expected them to be, you might be tempted to alter results a little bit to make it fit your expectations.  If you're doing a study on human or animal subjects, you might be tempted to take short cuts for the sake of reducing cost/energy/work.  If your study is paid for by an interest group, you might feel pressured to ensure your data fits the expectations of your financial backers.  It would seem as though these are all obvious, black-and-white, cut-and-dry issues.  Clearly, you think, I will just report the data as they are.  I will run the experiment in the best way with the best statistics I can afford.  If the interest groups don't like the results, well that is the risk of science.  Unfortunately, not everyone is able to overcome their personal interests or those of their financiers.   Even more unfortunately, these ethical mistakes can have huge implications on public health.

The MMR vaccine is a combination vaccine protecting the body against the mumps, measles, and rubella.  These three diseases used to be common afflictions, but they could be quite dangerous, and if left unchecked for too long, or if the body doesn't respond to medications, can lead to permanent injury or death. They are also quite infectious, and it used to be that almost every single child would get at least one of the three diseases in their lives.  The MMR vaccine was developed to protect children from these illnesses.  However, some anecdotal evidence suggested that the MMR vaccine was administered to some children who immediately started showing signs of autism, a developmental abnormality that leads to varying degrees of behavioral disorders.

Andrew Wakefield was a medical researcher who conducted a study based on these claims and suggested that within days after vaccination with MMR the 12 children in his study had developed symptoms of autism and gastrointestinal issues.  These results were recorded and published in a 1998 Lancet article entitled "Ileal-lymphoid-nodular hyperplasia, non-specific colitis, and pervasive developmental disorder in children."  The publishing of this article subsequently led to a drop in vaccination rates and a surge in childhood disease rates.
In 2003, a British journalist named Brian Deer launched an investigation into this research and discovered that Dr. Wakefield's findings were not what they seemed.   Dr. Wakefield had received money from a law firm wishing to pursue a lawsuit against the vaccine companies, but he had not listed this as a potential conflict of interest in the publishing process of his paper.  He also had not disclosed that the 12 anonymous children participating in his study were very carefully selected by anti-MMR campaign groups to provide specific evidence.  Anyone who has ever taken a statistics class knows that the key to statistical relevance and true scientific research is that your samples must be as random as possible.  Another key is that your sample size must be as large as possible.  12 subjects that were hand-picked for the cause is not a good scientific approach to the problem.  Small studies should make way for larger studies, and subsequent research inquiries with larger sample sizes were never able to replicate the results that Dr. Wakefield published.

The study was since retracted but the damage is far-reaching.  Many parents are still hesitant to vaccinate their children because of the fear of regressive autism.  Some of my cousins refuse to vaccinate their children, fabricating exclusions based on religion in order to allow their children into public schools where vaccinations are required.  I even have friends who have not vaccinated their children because they fear the "jury is out" when it comes to whether vaccines cause autism.  For me the biggest issue is that with all the blame placed on the MMR vaccine causing autism, the true roots of the disorders are not actively being sought and the issue will indefinitely persist.  It is an injustice to the very nature of science and public health.

This example of unethical scientific conduct is far reaching and extreme, but even smaller issues may have unintended consequences, and the risk to public health is not worth a paper being published when the methods and financial backers are not fully disclosed.

If Lady Gaga were a doctoral student

If there was a movie made of my life, where the mistakes weren't my fault and there was more dancing and costumes made out of serological pipette tips, then this music video parodying Lady Gaga's "Bad Romance" would be it.
Sadly, the issues with my project all stem from my own ineptitude.  Today, I literally had to throw a $500 kit into the trash after making a critical error, ruining the plate, at the 2nd-to-last step.  After 8 hours of working on it.  Pro-tip:  Always, ALWAYS, ALWAYS double check your pipette settings.  Even if you normally use the exact same pipette for the exact same thing and you were the last person to use your pipette for what you thought was the exact same thing.  It is a habit you will thank me for when you are trying to multitask and catch yourself about to pipette 100 ul of solution into a well where only 25 ul should go; then you will rectify the issue and you won't run out of your solution before the plate is actually filled.

Regarding reallocating lab supplies for clothing efforts, I feel guilty even considering making a pipette corset, those things are like $0.90 each!  Would they still be sterile after a night on the town?  Could I still do cell culture with them when I tire of the outfit?  And then there's the issue regarding the fact that I actually can't dance.  Maybe I can be the backup dancer in a disposable biohazard suit in someone else's lab life.

Forgive my frustrated post today.  All is eventually well; I still have enough sample for another plate so I'll order another kit.  An expensive mistake was made, but it is definitely a mistake that I won't ever make again.

The Sad Grad, or the post in which I introduce myself

I am a grad student at a small university in a small town encased within a small valley.

The views are beautiful,  the people are great and the buses are free...so perhaps woeful is the wrong term to describe my general demeanor as a resident of this gorgeous place.  We'll run with it anyway because of all of the sad phenomena that affect me:  horrible winter air quality, increasing tuition rates, and the difficulty in procuring fresh vegetables 9 months of the year, to name a few.

My Master's project research is on the impact of the air pollution on human health.  I collect and study human blood samples and compare it to results obtained from exposing petri dish cells to the same pollutants.  My hobby 'research' projects include local and global feminism, soil science, nutrition and politics.  All of these topics and more may come up in future blog posts.  They'll probably be brought up in conjunction with one another.

In my personal life, the aspect most important to me is my family; namely my husband and our pets.  I married my high school sweet heart, now a full-time grad student at the same university.  My husband studies inorganic chemistry and has a disdain for biochemistry (which is silly because biochemistry is clearly the more interesting topic).  His lab coat is much, much grosser than mine; likewise his lab bench.  We are both massive science nerds who wear thick glasses and have poor fashion sense.  I like him a lot!  As for our menagerie, our little zoo includes a precocious puppy, a callous cat, and two grumpy goldfish.  The trend has been to adopt a new pet or two every year:  the puppy was rescued from the local humane society two weeks ago, the cat was rehomed from a local foster pet service two years ago, and the goldfish were found in an empty classroom three years ago.  There was a mouse that I lifted from a live trap in a grain research lab last year (to continue a trend of a new pet every year) but died just after the dog entered our home (fright?  too much attention?  old age?  I'll never know the cause, only the heartbreak).

I'm not very good at taking pictures, so here's one my husband took to help prove what a beautiful view I enjoy every single day (except on bad air days, sigh):