July 4: Seattle to Tokyo

We set out for our adventure early Thursday morning. We packed up all our stuff and walked a mile to catch the bus to downtown Seattle, where we transferred to a bus to Seatac airport. As we were getting on the second bus, Jordan left the camera bag with our nice digital SLR on the bench, and someone told us just in the nick of time. That would have been a not-so-good start to our vacation!

The flight was uneventful, although the in-flight entertainment system is a really nice feature! Some trivia, games, and 3 movies later, our first introduction to Tokyo was all the green rice paddies and forests intermingled with buildings as we flew over. The rivers were highly managed with concrete banks, but beautiful in their meanderings nonetheless.

JapanSaipan 014
Originally uploaded by memevolve

After we arrived in the Narita airport, we exchanged some money and found the train we needed to get on to go to downtown Tokyo. The 90 minute ride started out with vistas of undeveloped countryside and farmland, and gradually got more and more dense and developed as we got closer to the heart of Tokyo.

Upon arrival at Tokyo station, we promptly became lost. The informaiton desks helped a bit, but the arrows directing us to trains was initally confusing (why do diagonal arrows indicate u-turns?)... so some helpful strangers pointed us to the appropriate subway trains. We then realized that while we had a JR rail pass, that didn't mean we could use the subways too, so we had to figure out the subway system and automatic pay machines.

This sign is one of many we saw in the subway systems that were somewhat humorous! But I guess they totally work, because everyone was basically polite! And super quiet, no cell phone use at all on the subways.

Once we got to Akasuka-mitsuke station, we walked out onto the street and right into one of the nicest hotels we have ever been in. Going up the escalator to the front desk, first we had to pass by several japanese businessmen lounging in the restaurant area, smoking, and looking rather shocked to see us there...

That was the first clue something was amiss. The 4 hostesses that greeted us and asked us very politely and formally if we wouldn't mind waiting in line for the front desk, and directed us to the proper place and stood with us... that was the 2nd clue.

And then we checked in and paid and saw that the first night was NOT 5000 yen each as Amy originally thought when she booked the room, but rather 30000 yen total. So rather than it being a $100/night room, it was more like $300/night. Oops.

JapanSaipan 014
Originally uploaded by memevolve

We decided to stay for the planned 2 nights anyway, and after a refreshing cold shower and change of clothes we ventured out to wander around the side streets near the hotel. Turns out Akasuka is right in the heart of the action and we got to see many people walking the side streets on their way home from work, or out on the town in fancy clothes... and so after checking out the scene a bit we decided to stop in at what looked to be a dive bar serving cheap chinese (sort of) food. The food was indeed cheap, and super delicious! We sampled some noodles and soup and dumplings, and a couple other small things that we didn't recognize. A bit more walking around the side streets, watching all the people and looking at the closed shops and super crazy pachinko places, and we were ready to hit the sack.

3 Weeks in Japan & Saipan

JapanSaipan 002
Originally uploaded by memevolve

We've been back from our 3-week vacation for about a week now, and the jet lag is finally starting to go. Our yard is horribly overgrown but we are choosing to ignore it for another week, while we adjust to non-vacation life again! And we just finished downloading all our photos, so now is the time to share them and some stories, before we forget too many details. :)

Neglect-o-blog

Well well, life can sure be hectic. I know I always say this, and I always hope it will calm down... and it never seems to.

BUT! It's still good to check in every so often. And my friends who just had a baby and are blogging all about it have inspired me. I think they're doing an awesome job of keeping in touch virtually this way! Who knows how long they'll be able to keep at it, but hey it's a nice idea! :) Eventually consolidating all my online profiles would be nice. Hmm.

So, filling in on a year of absence... finally finished grad school, thesis "Global Climate Change and Earth Beliefs: Implications for Outreach." Presenting to my thesis committee and a few others was one of the most incredible things I've done, and I was so proud that my work was so well received! My advisor wants me to try to publish the results in both a science journal and a more mainstream outlet... but I still need to meet with him to start this process, gah!

As a graduation gift, Jordan got me a tiny dog collar and leash, knowing it was on my mind! We soon found the perfect puppy, an American Hairless Terrier and we named him Darwin. :) I was lucky to get to hang out with him and teach him a few things while job hunting!

We (Jordan and Darwin and I) camped in the Olympic National Forest for several days for our first anniversary and it was great! So beautiful.

And during the summer I joined an Ultimate Frisbee team and since then have been trying to learn the skills needed to be the best midget ultimate player ever! :)

Environmental communication/outreach jobs, especially those focused on climate, are few and far between here. Since moving isn't an option at this time, I went back to work where I worked as a grad student, but this time as their web manager. It's been good working with such talented and smart colleagues, but there is so much work to do and so little time and money.

My first day on the job I discovered my boss had just left for emergency family leave. He was gone for nearly 3 months, so I quickly had to learn what my job was and also was essentially filling in for him partially and we actually were needing to hire yet another person, so I feel like I had 2-3 jobs for the first few months! Now that he's back, it's been much better and I feel like I actualy have time to breathe and think! It was a crazy whirlwind of stress for a while though.

So... now that I'm feeling more settling into somewhat of a "normal" life and routine, I've been thinking about the next projects I may undertake this year:

• writing a couple articles about my research


• starting a garden in the raised beds


• taking a 3 week trip to europe or asia


• remodeling our master bedroom closet and possibly the bathroom


• writing and illustrating a children's book about climate change


• starting a family!

On top of that, I'll be 30 soon. It's quite sobering and makes me feel like I've accomplished so little at this point!

Well I guess I'd better get on all that huh?

Ah, Life.

So busy! Wedding and honeymoon went well! More to report on Darwin's Black Box (but later, during break).

Halfway through Autumn quarter and just signed up for next quarter. Right now I'm taking Intro to Stats, Governmental Response to Climate Change, and a Climate Change seminar. All good stuff, filling my brain with info that puts other people to sleep when I try to share. :)

Recently joined Facebook and Fantasy Congress at Charlene's suggestion, in good meme form. You should check them out!

Gah, that reminds me, I think my Friendster/MySpace accounts must be horribly out of date. Maybe I should just delete them... hmmm.

More later. Sorry to all of my peeps out there whom I rarely get to interact with during school! I miss you all!

Darwin's Black Box: Background, Preface

First, a summary of Behe's experience.

Behe does not provide an author bio in my version. Wikipedia does, however. Gotta love those glasses. :) He has mainly a chemistry background. He does not support Young-Earth Creationism, rather he supports common descent of species and scientific consensus on the age of the earth. As far as I can tell, he has published only one peer-reviewed paper, which mathematically attempts to show evolution to be improbable.

The reviews listed on the back of the book are from a philosopher (David Berlinski), journalists (James Shreeve, Will St. John), a chemist (Robert Shapiro), and a biochemist (James Shapiro).

The 2-page preface sets the tone for the rest of the book, by first suggesting that there is scientific controversy over many fundamental concepts in biology and other fields, and then goes on to apologize for the complex details he will be presenting in the book, as his main audience is the public who has no background in biochemistry.

A couple grevious errors occur right away in the preface, which must be addressed.

Behe suggests that "the origin of the solar system (the question of how the sun, planets, and their moons formed in the first place) is still controversial." An endnote refers to a scientific paper in the "Notes" section in the back of the book.

First of all, it's important to note that all areas of science usually have some kind of controversy, and that is to be expected, because we don't know everything! Nor will we ever. There will always be unexplored details, new discoveries, and alternative hypotheses in some areas of every field. This is the not same, however, as implying that there is major disagreement over if something happened by natural means or supernatural miracles (which is what Behe seems to be implying here). It is certainly expected that there will be "controversy" or debate over what amount of angular momentum in the collapsing interstellar gas is necessary for formation of our primative solar nebula (one such topic reviewed in the paper Behe referred to).

Behe's second misstep is when he says that "evolution is a flexible word," with various meanings, and that Darwin and the scientific community use/used the word to mean "a process whereby life arose from nonliving matter and subsequently developed entirely by natural means."

That is not true. Interestingly, Behe does not give a reference for that particular definition, even though he claims Darwin used it in that sense.

In fact, Darwin did not define evolution, it was already an accepted concept in his day. He merely introduced the idea of HOW evolution occurs (through natural selection and small changes over geological time). In the Origin of Species, he does not address abiogenesis (how life itself arose) at all, only how species are related by common ancestors.

Some of my previous posts have explained how evolution is defined as "change over time," and how biologists separate microevolution from macroevolution. It certainly is not a concept that is used to explain how the first life arose on the planet...only how that life, once it existed, could speciate and be the common ancestor of all other life.

Additionally, Darwin's theory of evolution through natural selection is constantly subjected to vigorous testing. In fact, when new species are studied in an evolutionary sense, the first step is to try to disprove that it is subject to evolutionary forces. And so far, the theory has withstood such attempts, and is now generally considered to be so probable it is considered as fact in the same sense that the theory of gravity is considered to be fact.

That is not to say that it is a closed chapter... there are many many details of how evolution occurs that we don't know... just like we don't know all the details of just how gravity works. Science continues to explore and refine!

That's all for now... more later! :)

Review: Darwin's Black Box

Last year when I graduated with my Biology undergrad degree, my sister gave me this book by Michael Behe and I promised I would read it after I finished Origin of Species by Darwin. :)

Well that time has come and I've been slowly getting further along as time permits. I think providing an online critique would be useful! So I figure I will offer my opinion on this book a chapter at a time, as I progress through it.

If you recall, last year the Intelligent Design movement picked up speed and Behe was on center stage for some reason. If I remember correctly, he testified in the court case with the Kansas school board, and appeared in various media outlets...

The subtitle is "The Biochemical Challenge to Evolution." For background, I should note that my undergrad education involved several courses in biology, evolution, chemistry, and molecular biology. I took 2 courses (which is 20 weeks, or about 200 hours of study) that specifically focused on biochemical structures, an intro to molecular biology, and molecular evolution.

I provide this background so that you can understand where I'm getting my information... I'm not trying to make it seem like I am an authority, that I'm higher class, or that I have more intelligence than someone who may disagree, rather that I have spent a considerable amount of time studying these topics so I think I may have more information to add than someone who hasn't spent this kind of time on it... and I hope I can present information in a way that is accurate and sums up the complex relationships involved, and makes it easy to understand for those who haven't had the luxury of such study!

Ok, on to some review...

Summer!

Finally, summer has arrived, and I'm free from school!

Quick update:
Still working 20 hours a week...
Trying to get thesis survey project approved so I can send it out SOON...
Trying to get our yard in shape for September wedding...
Planning wedding...

Yeah, so after finals and a week to chill and think and plan my next few months, I realized that we only have like 2 months before our wedding!!! And we really haven't done much. I bought my shoes and dress off ebay. I have designed the invitations. We registered with Macy's online (well, it was mostly me because Jordan doesn't care about nesting).

So, my hopes of having a relaxing summer are quickly disappearing. But, we have been able to have a bit more of a social life, so I'm grateful for that! I miss all my good friends!

I'm home sick today and trying to take it easy, so I thought I'd *sigh* update the ol' blog. I've also been catching up on some pleasure reading and thought I'd post a little about that. Well...not sure if you can call it a "pleasure"... hmm. :) You'll see.

So here's a shout out to the world and my buds! Hope you're enjoying your summer!

GAAAH

Have I mentioned how painfully full my life is right now? Working 20 hours a week and going to grad school full time is INSANE. Right now I'm supposed to be writting a survey design proposal that's due Monday, and I'm no where near even having the background information needed to begin it. So I'm here, wasting time. Sigh. Ok back to work. Only 5 or so more weeks until SUMMER!!!! When I will have TONS more time to clean up this house, get the yard in shape, hang out with friends I miss terribly, and plan a wedding. :)

Spreading the memes...

From Charlene's blog. Seems neat, and possibly doomy. I like that.

Johari
Nohari

Stupid Biology!

I have a love hate relationship with biology. Most days I am in awe and highly appreciative of it's hard work over the millenia. But some days, like today, I'm just pissed.

Today I received some bad news about the health status of a good friend I have known for most of my life. It came as such a shock, and even though I had contemplated this possibility, I truely did not believe it would occur so soon.

I wish grad school wasn't so time consuming. :( I fear I have been a poor friend recently, and I hope I can do better in the future.

This has been a very difficult day. I can't imagine how these past few days have been for Dawn and her family. I know things will be okay though, because she is one of the strongest people I know!

Text Adventures!

This is so great, I had to blog about it. My friend Charlene sent it to me... only you old school computer RPG types who understand what <g> means will really appreciate it.

Pastafarianism

I know many of you are quite familiar with the Church of the Flying Spaghetti Monster. Well, good news! It might become official. Here's an entertaining interview with our beloved founder, St. Bobby Henderson. He totally cracks me up.

Pics

Some people have been asking for pics, so I thought I'd post them here to save email bandwidth. :)

OMG

Yes yes, I'm alive! Thanks for all the letters of concern (Keith)... hahahaha Wow, I really suck. I was dying pretty much all quarter.

Sooo.... last quarter was interesting to say the least. I was so ready to just quit a few times! But I got through it, learned a lot, realized I'm in the right field for my interests (whew!), and got good grades to boot: 3.5, 3.7, 4.0. Yay! :)

Winter break was awesome. Jordan had most of the time off with me so we had a lot of quality time together! Hanging out, cooking meals together, playing WOW (see previous post) and leveling our characters to 42... watched King Kong (great movie)... got reacquanited with family/friends we had been ignoring...

And to top it off, Jordan proposed on Christmas Eve when we were with his family. It was very unexpected and very special! He had to ask twice because I didn't realize what was happening. hehehe :) The answer was "Well, yeah!" (duh)

So this may very well be my last post until who knows when, next fall. This quarter I'm taking classes on Global Climate Modeling, Watershed Ecology, and a very special class where we work with State legislators (picked by the governor to be on an ocean policy committee) to draft policy memorandum on various topics, including climate change and watershed stuff (my areas of interest). Several field trips will be in order, to some rivers and possibly Olympia!

Then in the meantime, we are in negotiations/planning for the wedding, likely to take place in the summer. We both want to keep it small and have it at the farmhouse. Other than that, nothing has been decided yet.

An exciting few months to look forward to and try not to die from! hahaha :)

Hope all my homies are doing well! I hope you all know I wish I had more time to chill! Hopefully when grad school is over, I'll be able to have a life again. Then again, sometimes I just need some prodding to blow off homework. It's not in my nature but hey people can change, right? Especially when the amount of homework is impossible! :)

Wow

The title is a double meaning! Ooooh

Who knew grad school would require so much reading? Yeah I guess I've heard that was the case, but didn't really believe all the hype. But it's true. Or maybe it's just some crazy hazing initiation process, to break us in.

So, for the past couple weeks, it's been a crazy menage of classes, new job, and trying to get a group presentation ready for this coming Thursday. It's a lot to juggle, and I've dropped a few "reading" balls, but I'm hoping that after the presentation is done with, I'll have time to play catch up.

The classes have been really interesting. I'm not horribly bored with the microeconomics, and the marine science class is a great review of some stuff I was briefly introduced to before. The cream of the crop is the Marine Affairs class. Each day has been a different speaker. Usually some well known researcher from various fields related to marine stuff... resident at the UW. It's been really interesting, and inspirational. And from what I've read for that class so far, a lot of good material to digest! Maybe I'll get around to throwing a couple quotes up.

The job is insane, but good. Computer support/help desk + no organization + lots of past errors + 400 users, not all on XP SP2 + old blaster worm variant infecting tons of machines and creating a reimaging backlog for us = DOOOOOOOOM. But at least I have stuff to do, and at least not all my coworkers suck, although some are real losers. :) And at least I'm not a total n00b with the skills, like I was worried about.

And finally, in my moments of complete stress out on my schedule, I take a couple hours here and there to relax and play World of Warcraft with Jordan. It's great fun, you should join us. :)

Getting my Learn On

So yesterday was day 1 of orientation for new grad students at the UW School of Marine Affairs. I'm all signed up for my classes! I'm pretty excited. This quarter, I'll be getting some program requirements out of the way:

Marine Affairs
Surveys a wide range of academic disciplines and substantive problems pertinent to interaction of human beings and the world's oceans and coasts. Management of living/nonliving resources, shipping, scientific research, pollution, recreation, and others.

Applied Microeconomics for Marine Affairs
Surveys a wide range of academic disciplines and substantive problems pertinent to interaction of human beings and the world's oceans and coasts. Management of living/nonliving resources, shipping, scientific research, pollution, recreation, and others.

Marine Science in the Coastal Zone
Presentation and analysis of the marine science of estuarine, coastal, and open ocean systems, including evaluation and interpretation of scientific information necessary for management. Lectures, discussions, and readings emphasize the relevance of natural processes to marine environmental management and decision-making.

Whee! :)

Another cool blog

My mom just forwarded me this link. This guy is a scifi writer but has a lot to say about other interesting topics as well. Go check it out! :)

Woo hoo!

I got a new job. I'm so stoked.

I was having issues working for the small group of people that make scientific kits for children. There were a lot of problems in that office, and if I were a more laid back non chalant kind of person, who doesn't care about dealing with strange business owners and their family, or who doesn't care that the working space and file managment are so horribly disorganized that it makes it difficult to get things done--all on a daily basis--if I didn't care about those things, the job would have been a decent one. The pay was ok (although low for the services I was providing), and the science aspects of it were interesting. The past couple weeks, they had also started a weekly event where they send out the 20-somethings working there for a few drinks. Yeah, it's a nice way to get to know each other I guess, but I didn't like feeling like I had to go or risk political disfavor.

So..... my new job will be awesome, because it has some major perks, like tuition assistance, health insurance, higher pay, flexibility, and a boss who is all about organization and streamlining processes to make things easier. It's a computer support position at my school, so it will also be convenient in between classes. It won't be as much science, but that's okay. I'll take geeks for lack of scientists. :)

Cool Blog

I stumbled across this cool blog during some cactus research at work today. This guy is funny, artistic, and a good smart liberal too. ;)

Evolution

Ok, so for anyone who would like to begin a discussion about evolution and related topics, let's get it on! Hey, at least you'll help me feel like that $20K still left to pay off for my education is going to be worth it. :)

Those in agreement, those with a bone, and devil's advocates who can keep my logic pure are all welcome!

As with any communication attempt, agreement on a definition of terms is helpful. To begin, I figure I could provide some biological definitions of common words in this debate. I bet you'll notice right away that the scientific definitions used in the Modern Evolutionary Synthesis can be quite different than the common usage of the same words among the American public.

Evolution

Generally means "change over time," but specifically refers to a change in the proportion of a particular version of a gene in a given population between one generation and the next.

So if rat eye color depended on only 1 gene, and if I took a group of 50 red-eyed rats and 50 blue-eyed rats and bred them, then counted the reds/blues in the offspring... the percentage change from 50/50 to whatever the result would be called "evolution." If there was no change, you would say that eye color did not evolve in that generation.

Natural Selection

Charles Darwin was the one credited for the theory of evolution by natural selection. Before him, scientists agreed that life forms evolved, but they didn't know just how they did it, or what forces were acting on their changes.

Darwin outlined 4 prerequisites that have to be in play in order for natural selection to act on a population of creatures and result in evolution:

1. Individals within the population must vary (no clones allowed)
2. At least some of this variation has to be heritable and passed on to offspring
3. Not all the offspring can survive, due to resource limitation/predation/whatever
4. Individuals that are the most "fit" are more likely to survive and reproduce, passing on their more adaptive traits to their offspring

Natural selection is essentially proven many times over, because we can monitor traits from generation to generation and see that those with inadequate traits will die while those with more "fit" traits survive.

Like any scientific theory, natural selection is falsifiable, which means that it is possible to disprove it. One example that Darwin himself suggested: if you ever found an organ in a creature which benefited another species (instead of the species the organ existed in), evolution would be occuring without natural selection. Natural selection requires evolution to act in the interest of the species it is acting on.

Fitness

Fitness is an attempt to measure how well adapted an individual is to their environment. This is approximated by looking at how many offspring are produced by an individual over their lifetime. There are several different models, but the most common ones take into account differences in gender and genotype (a definition for another day) among a species. It's usually compared to an average, and sometimes looks at multiple generations of offspring (children, grandchildren, great-grandchildren, etc.).

Adaptation is a term used to describe evolution that increases an individual's fitness.

Mutation

Genetic material (i.e., DNA), can be changed in many ways. Copying errors during cell division, exposure to radiation or certain chemicals/viruses, etc. These changes to the genetic code are called mutations, but they can be good, bad, or neutral to the organism. Bad mutations are eliminated over time by natural selection because they lower an individual's fitness. Neutral mutations don't do anything, and so natural selection doesn't act on them. Good mutations are retained because an individual's fitness would be increased, they would have more children and pass on the good mutation to them, and so on.


Well that's enough for now. We can spin off topics from this or further clarify definitions if there is enough interest. Comments, anyone?