I am a fussy toddler…

Devotional Blog:

Topic: “Cultivating the quiet”, 01/08/12, Psalm 23: 1-6

Hey…I’m into January in this book…well actually I’m backlogged and still have some blogs from December’s month in the book to write but I kind of just dog-ear them and will get to them, eventually.

Interestingly this one came up. In a previous entry in the book the author had encouraged us to spend our time productively and not waste it and I wrote a blog about how taking moments to ‘space out’ and how valuable that can be for ones mental health. Now in this entry she encourages moments of quiet stating that a ‘quiet heart is a receptive heart’. 1 Peter 3:4 states, pulling from the previous verse–beauty…”should be that of your inner self, the unfading beauty of a gentle and quiet spirit, which is of great worth in God’s sight.” Pslam 23: 2 states: “He lets me rest in green meadows; he leads me beside peaceful streams…”

Flipping through the book this morning to find an entry dog-earred to write about I came across this and it hit a nerve for me. In the past few weeks my life has taken a tremendous turn. Continue reading “I am a fussy toddler…”

greener grass?

All your life you live so close to truth it becomes a permanent blur in the corner of your eye. And when something nudges it into outline, it’s like being ambushed by a grotesque.

~Tom Stoppard, Rosencrantz and Guildenstern are Dead

Devotional Blog: 10/22/2011, 10/26/2011, and 10/28/2011; “Being true to yourself” and “Fact and fiction”; Romans 12: 12-18, Acts 2: 32-39, and 2 Peter 1:15-21

I’m lumping these entries together because they speak of similar things regarding how we see ourselves compared to others, how others make us feel about ourselves and the alternate realities we concoct of a life ‘we want’ rather than the life we are supposed to be living. Continue reading “greener grass?”

the good, the bad…the beach

This past weekend Tyghe and I went to the beach thankful for the ability to escape flooding Bangkok, play some frisbee and enjoy the beach. We went to Phuket, a highly built up island in southern Thailand that is run for the most part by the Thai mafia from what we’ve been told and perhaps has links with Russian mafia as well–given the influx of so many Russian tourists, and all three languages (Russian, English and Thai) present on the island, it wouldn’t surprise me. In essence many who travel to Phuket accept the fact they will be overcharged for everything…absolutely everything. But I am not going to talk about our holiday…Tyghe will do a great job of that on his blog so see that for the vacay story and I believe he mentions what I will talk about. His blog will be a great sum up with pictures–the happy stuff which was indeed happy and I had a great time in that respect. Instead I will highlight one not so awesome experience as it resulted in an interesting topic related to faith. This is not a ‘devotional blog entry’…it’s a life entry…life based on faith. Continue reading “the good, the bad…the beach”

Marking memories

Devotional Blog:

Topic: “Mark It”, 10/21/2011, Joshua 4:15-24

First I have a confession…I’d forgotten that Joshua was a book in the Bible! Horrible of me! Raised in this faith and when I saw the verse for the day I did a double take and asked myself–“This is a book in the Bible?…DOH!”. Bible literacy fail. Yes, I know the story of the fall of Jericho is in this book but for some reason I had it in my head that this story was in Deuteronomy–don’t ask why, I don’t know. So, in all fairness when was the last time I heard of this book? Eighth grade Bible history class at Bellevue Christian School where I attended one semester, does that excuse it? Probably not, but its what I’m going with.

The book of Joshua is about the Israelites journey into the promised land. When the crossed the Jordan, the Lord dried up the Jordan momentarily so they could pass. God then asked Joshua (who was leading them, he was the right hand of Moses by the way), anyway he asked Joshua to pick 12 men to take 1 stone each from the riverbed of the Jordan = 12 stones. When they’d stopped at Gilgal the western border of Jericho God told him to set up the stones as a reminder for generations to come that the Lord had pushed the waters back for their forefathers to walk on dry land into the promised land.

Pam, the author talking about ‘marking’ things that matter in our lives to solidify a memory in a solid shape of sorts, like making a stepping stone and putting into a garden then adding stepping stones. Thinking back I can remember all my ‘mementos’, my ‘mark it moments’ and when I got them, how I got them and where they are today and why they mattered. Compared to other families we had a more mobile life growing up so some of these ‘moments’ are no longer with me so I carry them in my heart instead…in no particular order…just as they come to me. Continue reading “Marking memories”

Nepal: chaos, color and a lot of monkeys…

So kudos to my cousin Lauren and my friend Heather for reminding me I still haven’t posted about Nepal…but the Masala tea I sent them did make it to them…woohoo! Sometimes mail even from a US APO address may take a lifetime to reach its destination, it might as well have been put on the slow boat to China for all I know…except maybe that wouldn’t work–China is actually quite close to me. But you get the idea.

So back in August I traveled to Kathmandu, Nepal to attend a conference/workshop on Flu in SE Asia and it was quite interesting. Though the majority of the workshop didn’t really deal with my specific field I did learn a lot about epidemiology and analysis that goes with that kind of data which is supplemental and valuable to know. So that was neat.

The first day I arrived I was really tired and though I arrived in the afternoon I had little energy to venture beyond the hotel, Dwarika’s Hotel. I made it as far as the intersection. I don’t know what I expected, it was a lot more chaotic than I’d expected and there were tons of people. In my head I was thinking…damn if I can’t handle this how would I ever survive going anywhere in India?! Haha. I think it was just a lot to take in at first. The hotel was amazing, thank God for per diems and conference discounts that allowed me to stay there, it really was beautiful.

And just a note: In keeping with the chaos that Nepal was this blog is written in an organized chronological manner with absolute chaos with regard to the pictures and text. I’d like to think its my underlying ‘motif’ or ‘commentary’ on the crazy…but alas, I am not that smart to have thought that up prior. Instead its more a result of my lack in ability to use wordpress to post pictures in a non-chaotic format with respect to the text. I got better toward the end though. Continue reading “Nepal: chaos, color and a lot of monkeys…”

Digesting fictional fluff…

The Help by Kathryn Stockett

So if you read any number of reviews on this book, say in Goodreads for Amazon it seems readers have a ‘love/hate’ relationship with this book. The vast majority–of those at least writing reviews loved it. I myself grew hot and cold during the course of reading it. It deals with such an interesting subject and important awful time in history and it felt to me like it was written to go straight to movie–tragic and ‘feel good’ all at the same time, great movie fodder. But does that necessarily make good fiction? And low and behold where is this book now? In movies! I’ll be interested to see how they interpret the book in the movie. I have a rule of reading books before I see them in the movies as much as I can…and I’m not one of those people where the movie has to have every last exhaustive detail from the book for it to be ‘good’. I’m always interested in adaptations. And I think Kathryn Stockett makes a good point in her quote:

“Everyone knows how we white people feel, the glorified Mammy figure who dedicates her whole life to a white family. Margaret Mitchell covered that. But no one ever asked Mammy how she felt about it.”

To say the least, its a little discussed area of history…how ‘the maid’ feels. I found myself more excited about her blurb at the end about her physical experiences growing up in the 60’s in Mississippi and I found myself more compelled and wishing she’d written about that rather than this book. But to be fair I have always been more partial to non-fiction unless it’s a literary ‘classic’ ala Wuthering Heights or the Secret Garden. Is this book a ‘classic’? Um…no. It’s not bad…but it’s kind of a let down. I wish she’d developed some characters more and played down others. But I recognize the difficulty she must’ve faced writing characters she could not relate too.

I loved the relationship the author built between Aibileen and the little girl Mae Mobeley, my favorite part of the book and an important one as no child is ever born racist, it’s taught–many times harshly. And my favorite parts of the book had Mae in them. When she starts school her teacher Miss. Taylor shames her to no end because she drew a black child as something that makes her happy. Aibileen had been teaching her that there is ‘no color’, we are all the same and can love each other as such. While Mae is playing with her little brother she makes her little brother be the ‘black child’ and tells him no matter what she does he has to sit there and take it or he’ll go to ‘jail’ and then she proceeds to throw dolls at him, pour crayons on him then tells him lets play back of the bus like Rosa Parks etc…Mae’s father watches this and asks her who taught her this and she lies and says it was her teacher, when in fact it was Aibileen that’d been telling her stories…’secret’ stories.

Surprisingly the ending was not what I was expecting which is good, but I’m not sure I liked it either…I dunno, it was both sad and hopeful I suppose.

Continue reading “Digesting fictional fluff…”

Power outage kills 34 million state BEAST run, Investigator contemplates Linux homicide

As the title suggests I walked into the office this morning to two computers…both shut off. Now no one touches my desk especially when I have analysis running and we had a huge storm last night with lightening and wind and although Bangkok is a ‘1st’ world entity of itself some days the fact of the matter is, I live in a 3rd world country that is 98% agriculture. The result? 34,510,000 iterations of a BEAST run of 100 million completed and the analysis ends with the power cutting off. My poor linux, diligently plowing away at iteration after iteration, only to be thwarted when its attachment to life power is cut.


A check in tracer reveals that my posterior, prior, likelihood, tree likelihood and coalescent are all at ESS values in the red (under 100) and clock.rate is under 200 (in the yellow). So things have not finished ‘mixing’ and converging altogether.


Thankfully I started the same run on the Oslo Bioportal August 23, 2011 and currently the status is on resource/started. Unfortunately they do not give me an up to the moment snapshot of my analysis and I cannot check using Tracer with it along the way so it will march to 100 million generations until it is done. I was hoping to track my run as it went to see if it exhibited good mixing and convergence prior to 100 million iterations– but alas, I will never know. And if Oslo has a power outage–then the ‘gnomes’ or ‘gremlins’ are up to something … little bastards.

There’s something comforting about watching status lines flip by on an analysis, lets you know the computer is hammering away at the brick wall of analysis trying to find that one loose brick. That’s why I always like to run things on the terminal although I have to say the GUI for the program is quite pretty. Yes, I just called the GUI for a Bayesian analysis program ‘pretty’– sometimes I indulge in superficial scientific vanity.

So I’m torn on whether to restart the analysis from iteration 0 or wait for Oslo to cough up my results. Without status lines to watch much of my previous list of things to do while BEAST runs gets nullified… I guess the ‘analyst’ will have to actually go outside… see the sun… get some fresh ‘non-circulated’ air… engage in social behavior with others perhaps also affected, having lost analysis down the black hole of power outages and now venturing forth confused from their cave like offices into the bright heat of Bangkok… or I need to find a new program with status lines that takes a long time to run!


Witches Broom in Vietnam…

I decided to repost this from ProMed because I thought it was interesting…who comes up with these disease names!? When I saw it in my inbox of course I had visions of cult activities involving longan fruit in the jungles of Vietnam…yes I have an active imagination.

Witch’s broom gets its name from a deformity in a woody plant, typically a tree, where the natural structure of the plant is changed. A dense mass of shoots grows from a single point, with the resulting structure resembling a broom or a bird’s nest. [Source]

A quick shout out to ProMed which is a great resource for hearing about disease outbreaks of known or unknown etiology around the world…check it out!

But really, Longan fruit is quite prevalent in Thailand as well and it is quite delicious. So, fantastical imagination aside, see below, feel free to read the culti-c disease activities plaguing Longan in Vietnam!

Continue reading “Witches Broom in Vietnam…”

A Month in Thailand

A month in Thailand…amazing how quickly adaptable a person can become given continuously changing circumstances. I work in the Virology Dept of a U.S. military medical science institute (AFRIMS). My focus, dengue virus with perhaps occasional forays into malaria and avian influenza. Being raised in Hawaii and having traveled abroad to Central and South America I thought I was prepared for inevitable massacre of heat and humidity. Alas, nothing can prepare you for the literal melting of your body the moment you step onto the tarmac at Suvarnabhumi airport. I suppose it doesn’t help that I’ve decided to enter Thailand at the hottest time of year. No it’s actually perfectly in keeping in a life where I decided to go to graduate school in Montana, moving from Hawaii in mid-January and stepping off the plane to 10 below zero. Apparently I live for extremes.

Continue reading “A Month in Thailand”