Christmas is almost here!!!

It’s almost Christmas! I absolutely love this holiday! I have two Christmas music tapes (yes, tapes) that I put on in the morning sometimes. So much fun! I’ve been away from home so often that I usually wonder whether Christmas will actually feel like Christmas. For some reason, having a daughter makes all the difference. Especially having a daughter who can talk and laugh and make funny little toddler jokes and who loves Christmas trees as much as I do. Here in India we’re away from the commercialization of it, which is lovely, since I get to think about Jesus and what role he plays in my life (or should play) a little more easily.

Whenever I post something, I have to include a work update because I always have this invisible advisor professor looking over my shoulder who I have to … appease. Right now he’s telling me that writing a blog update is NOT cleaning data, but that maybe he’ll let it pass this time. But I’ll just mention – I’m going through some outcrossing data where the postdoc in our lab pretty much did the whole thing. I collected the families (seeds), but he grew them up (randomly) and collected leaves (randomly) and isolated DNA (in randomized 96-well plates) and ran the samples on ABI. It’s such a good idea to randomize your samples! I didn’t do that for my Oregon-wide stuff, and I wish I had. That way if one plate is contaminated or if there’s a problem with a run, it’s a little easier to find. I think.

One thing I didn’t emphasize when I was in the lab was the importance of every sample and every analysis run of that sample having a unique and descriptive name. (!!!) Learn from my mistakes, oh all ye people, and give all analyses of your samples unique and descriptive names. (!!!)

I think that I’ll have enough data to put together a migration paper about false brome that includes outcrossing, which could potentially capture rare pollen migration rates. Maybe. That’s probably going to far, but we can always hope. My most polymorphic locus had trouble in these datasets, which is a bummer, but I think I have enough data to put something together. But I have to make sure to go through all the data (some 12000 lines of data) and make sure the ‘rare alleles’ are really rare and not some run anomaly, as some have turned out to be. I sure hope my committee isn’t too antagonistic when I defend. It’d be sad to go through all this and not get my degree. I’ll stop by Oregon when I go home in Feb/Mar and go around to talk to them all. Hopefully they’ll not be antagonistic. Crossed fingers. I’m definitely a non-traditional student at this point.

Back to non-data things; I love Christmas! We erected our tiny Walmart tree in our living room, and it’s adorable. I’m getting quite used to having a small, fake tree – it has its advantages ☺. Our nativity scene is a beautiful sculpture made for me by my little sister, of Joseph with his arm around Mary who is cradling Jesus. We have a very small carved elephant looking on, and an amethyst tree providing some distant shade for the group.

It’s still hard for me to imagine having a childhood where religion didn’t mean that people thought their neighbors were going to hell, or that they thought you were going to hell, or else thought that you were a real lunatic. Okay, so I didn’t really know my neighbors, so I’m exaggerating. At any rate, religion in India generally means something a lot less…drastic. Probably because Hinduism fundamentally is a conglomerate of a bunch of naturalistic traditions, and is a lot more blatantly accepting of other religions than Christianity traditionally is.

Q (my husband) had trouble in Mormon Land, since for the first time in his life, he was labeled as unspiritual, simply because he wasn’t Mormon. That affected his view of things for a while, I’d say, but I think he’s reverting back to his pre-Utah state of really not worrying about what other people are doing. He’s so focused on his own spiritual studies that he really doesn’t have time to worry about the state of other people or what they think of him. He’s such a lovely fellow.

OH, How Could I Forget! I have a piano! A digital Korg sp-350, I think. It’s lovely! It’s not a keyboard at all, so the extras are minimal, but its piano sound is passable and its polyphony is alright and the action is wonderful. I did max out the polyphony playing some Debussy trills, but I’m okay with that. It’s SO nice to be able to play piano again! I didn’t realize how much I depended on it to sooth my ruffled feathers when I was angry, or to console me when I was sad. Piano is the one honest communicator, for me. It’s the one place where I can express an emotion as sincerely as I possibly can. Talking to people I’m always self-conscious or nervous. Playing piano I feel like I can completely bare my soul. It’s SO therapeutic!!!!!

Okay, the Professor is starting to send meaningful glances to the clock. I’d better get some work done.

MS, halloween, piano, and the rupee

I finally got some good comments back on my manuscript! It seems that I really haven’t a clue about writing. But with a good reviewer, hopefully I’ll learn enough not to need so much help next time. I keep hoping for that sort of thing, and so far it hasn’t panned out. Every time I start working through a new MS, it stinks. Writing is tough! Criminy! I should’ve taken more writing classes. For some reason I keep thinking writing should be simple, but for some reason it doesn’t seem to be.

While waiting for comments to come back, I started in on data analysis for my next paper. I think I have a good plan of attack, since the data are similar to my last paper. Go through the raw data quickly, then graph it out and look up all the outliers to make sure they’re real. So far, most of the outliers have turned out to be false. That doesn’t really engender confidence in the data, but I figure that outliers often skew the data more than simply another data point that’s like all the other data points, so it’s better to focus on them. If TM keeps healthy and can keep going to school regularly, maybe I can get the data screened in a month or so. That would be wonderful! Then plan about 6mo for writing the paper…

Bangalore weather is wonderful. I think the rains have stopped, again, so we have sunshine and pool time! Hooray! TM loves swimming. Being with her reminds me of how much fun swimming is. Actually, being with her reminds me of how much fun lots of things are. I think I was getting to be a regular stick-in-the-mud ‘till she came along. She loves fingerpainting, playing with blocks, imagining things… it takes me back to when life was interesting and you could have fun anywhere if you wanted to. Kids are sure great that way. Especially if you have about 3-4hrs/day when they’re at school, so they get a break from you and you can get some of your work done.

Q has been more relaxed lately, which is lovely. I think he’ll get a bonus this year from work, and we’ll shunt it right into our student loans. I would love to get those things paid off. I hate loans. He’s going to the gym now, and it seems to really help him deal with life better. In a stressful job like his, he absolutely needs the exercise.

Hey, did you know (you probably didn’t) that we had trick-or-treaters? Here in Bangalore? It was wonderful! All the kids in our complex, and many more it seems, turned out for trick-or-treating! Maya and I went around to our friends’ houses, which was lovely. I’d put together a quick-n-dirty cat outfit, with ears and a tail. She liked it… thank goodness she’s 2 and isn’t too picky yet. I’ve already ordered her outfit for next year from Grandma. I think she’ll like being a princess, and Grandma loves sewing things like that (at least, she did when I was that age). They really don’t sell Halloween costumes here… but the kids sure had some great costumes anyway! Probably ‘cause so many of them have lived in the States before, and have fond memories of trick-or-treating.

What else is going on… I’m giving piano lessons to the kids upstairs, ‘cause I think it’s really important for them to learn music, and it’s fun, and they enjoy it, and they’re so nearby, and they have people to help with Maya during the lessons. We’re learning some beginning guitar chords also. I’m only charging 500NRP/hr, which is peanuts in the US, but definitely par for the course here.

Speaking of US prices and the rupee, golly, the rupee has fallen to 50nrp/$. Quite painful. It’s good for any of you who want to visit India, though! Stop by! We even have the guest room somewhat cleaned up. ☺

Cheerio,
Rhamnites

Darwin

I’ve finally sat down to read Origin of Species by good ol’ Darwin. I was scared off of it by a professor who said it was dry as a bone, but since I’m trying for a PhD in Evolutionary Biology, I figured I should give it a shot. It turns out that I really really like it! It’s amazing what they knew back then, and how they had many of the same problems we have now with people who really really don’t like the idea of God working through natural laws to create things. It’s also very interesting to read what a very intelligent scientist has to say about inheritance when they didn’t even know what DNA was – Darwin didn’t know about Mendel’s work at all, so mostly people were just kinda shooting around in the dark when it came to inheritance. They knew things were inherited, but had no idea why some things were inherited and some things weren’t, and why some would show up in grandchildren but not in children – what an amazing puzzle! Completely weird. It’s wonderful what we’ve been figuring out now, what with DNA and epigenetics and all that. Pretty cool.

Darwin starts out talking mostly about agriculture. It turns out he has the same audience in mind as many of my Biology 100 students. People who are intelligent but who feel very deeply that the Creation must have been a single (or septimal?) miraculous event. Darwin’s a wonderful writer. He talks about how man has wrought pretty amazing changes in animals, so much so that different strains of an animal can appear completely completely different, and he gives many examples of them. Did you know that Darwin raised pigeons? I didn’t. And it turns out there are lots of different, some pretty weird-looking, pigeons, and most of the varieties, especially the wacko ones, were selected by man. You could go so far as to say they were created by man, because he would have seen some weird-looking pigeon, one with a rather large crop, for example, and started to breed for that trait. After many generations of selecting for a big crop, he ends up with a bird that has, whoa, such a big crop that it looks quite different than the other pigeons.

No need to be upset about this, we all know that agricultural crops look really different than wild ones. Cultivated strawberries? 20x bigger than the wild ones. Do you think the ancient Egyptians had tangelos? No, because we invented them. And wild watermelons are not red at all. And beefalos? Come on.

So once Darwin establishes that man can really change things, he sets up natural selection as being similar to man’s selection, in that things will change in order to be better adapted to where they are, simply because the ones that are best adapted to their environment will have more offspring than ones that are not adapted well.

He also spends quite a bit of time on how the whole species concept is fraught with difficulties. It is VERY difficult to determine what a species is.

I’m having a fun time reading it. Love this guy! Though I can see how a person who thinks anything other than a 7-day bazillion-species-at-once creation is blasphemous would put Darwin in the dust-bin pronto, probably burning it too. Ah well.

I’ll just say again that – just because we can explain parts of something doesn’t mean it wasn’t miraculous. If I’m having a miserable day and my husband comes home with flowers for me and we manage to fit in a 2-hr conversation, I’ll pray and thank Heavenly Father for such a wonderful miracle. As I did yesterday. I find no problems with learning a little bit about the wonderful methods Heavenly Father harnesses to accomplish His designs. Knowledge is… Beauty.

cross-reference http://miekesmusings.blogspot.com/2008/09/omni-say-what.html

Another draft, pets, and vacation time

Things are settling in. I sent off yet another draft of my paper, and now I’m starting to attack the data for the next paper. I hate it. This part is very tedious. I have about 70 folders with 20-100 files each, and all have to be compared and “cleaned.” Check for possible mis-labelings, discrepancies in data, possible errors in sample naming, stuff like that. It takes a long time. Hopefully this time won’t be as bad as for the last paper, since I’ve done it already. And I hope the analysis goes quicker, too. I don’t think it’ll be worth sending it to Molecular Ecology, though, since at the moment it looks to me to be simply a cut-and-dry description of genetic patterns in a recent invasion, comparing central to peripheral pops. Hmm. Well, we’ll see how it pans out. And I’ll just have to nail myself down to the computer during TM’s naptimes.

It’s vacation time in India, so TM’s at home, and the only worktime I have is during nap. Normal routine should kick in after another week, and then there’s another vacation sometime that I don’t remember when or how long it is… ahh well. I just hope I can pull off this PhD thing. It’s really irritating to have to keep plugging away at things that seem to show very very very slow progress. At least soon we’ll have a paper submitted. I just hope we don’t have to resubmit it… it’d be lovely if they accept it with only minor revisions. We’ll keep the ol’ fingers crossed.

My older sister even read my manuscript and made comments. I’ll take a look at it tomorrow. So nice to have people who can read things like this and critique! My other critics are too busy to really hack it apart, so I’m glad to have someone who’s willing to whack away at it.

Q is on his way to Delhi, again. His company’s having a big shindig up there, and off he goes. He comes back in a couple days, though, and then we’re going off to Coorg for a few days for a holiday! Only the 2nd holiday we’ve had since we were married 8 yrs ago! I’m so excited! We’ll see elephants, eat good food, play in the forest, whatever. Yay! And he needs the break – his body is really starting to wear down under the stress. His company is even cracking down on him, making him stop work for awhile, they’re so worried about him. I’m glad they’re willing to back down a little, ‘cause we’d all like to keep him in good condition for awhile longer…

We still have 2 fish alive, out of 8. I gave 4 away, of which 2 had babies. I’m so glad I gave those away! Yay! The tank’s not “cycling” yet, but I’m hoping it will in a month or two, sigh. Daily water changes ‘till then.

We narrowly escaped buying a puppy this week. I’ve been so lonely, since our neighbor’s been gone for a month, and Vivek was gone, and I’m left alone at home with a sick and/or on vacation 2-yr-old… very very trying. For some reason I thought a pet would help. But here it seems you can only get puppies or kittens, and Q helped me realize that it would really absolutely not help at all. So we’ll all try to be a little more cuddly when we can, and weather the weather. Ride out the storm. Yuppers.


I feel kinda boring today, but figured it was time for another post. So there you have it!

The Fish Saga and more

We want a pet. But cats and dogs need to be taken care of if one goes on vacation for more than a couple days. Cats you can leave alone for a weekend if you have to, dogs you can’t. I think. At any rate, I don’t think we can realistically take care of a pet right now. But how sad for TM! So we decided that a fish tank would be lovely!

The Fish Saga begins. We looked at tanks. We weren’t sure whether we liked what we saw. A neighbor offered hers, since they had recently failed to keep their fish alive. It’s a nice tank, so I decided to try to make a go of it. Before buying fish I filled up the tank to see if her equipment was working. After running it for a week the water finally started turning green, so I went out to get some more aquarium supplies.

I thought it would be good to get the environment up and running before buying fish. Thank goodness. I tried to find gravel, but after going to several hole-in-the-wall stores (most stores look kinda like that here), I couldn’t find what I wanted. So I bowed to pressure and bought sand. We put it in our tank and instantly the water turned brown brown brown. The plants I’d also bought were invisible. But surely it would settle?

After 3 days it did not settle, so I siphoned off a bunch of water and added more. Still cloudy. Hey, maybe I should’ve washed the sand first! It was probably dirty. (ha ha ha). So I took out all the water, then took out all the sand (it’s a 15gallon tank) and washed it. Yes, washed it. Dirty bathroom afterwards. Then put it back in, put new water in, and yes, it was still cloudy. It took about an hour of silent moaning before I finally took out all the water again and took out all the sand and cleaned the tank.

By the way, if your sand is deep, the lower layers go anoxic. Meaning sulfur-producing bacteria kick in. Meaning... it stinks. Just FYI. Did we have deep sand? Apparently...

Also FYI, Bangalore's power supply is ... irregular. That's the word. So you have to figure out how to keep your fish alive during a power outage. I haven't decided on that one yet. Cost of battery backups and inverters will figure heavily into my final decision...

I think that was a month ago. We have a dry empty aquarium. Today I handed our driver 500nrp and asked him to see if he could find some gravel. I think he knows what I’m looking for… we’ll see. If I can find some nice gravel and some plants (plastic this time, thank you), then I’ll add fish. But, oh, I forgot to mention – no testing kits here. That I can find, anyway. So how do I know what’s wrong when everything starts dying? So I asked my husband (does he have a blog nickname yet? I don’t remember) to bring some back from the states since he’s on a business trip. Aquarium test kits.

In the states I like to imagine that I would’ve had it up and running in about 1/3 the time, but then again, I’m sure I would’ve found other obstacles (like money, perhaps?).

Change Of Topic

My Paper. The one that was done? Remember? It’s not. Nope. Came back with more comments, and a “why don’t you delete all this and put in another couple figures and change all this” and my oh my I really am having a hard time nailing myself to the computer and finishing it. I could tell that my advisor was a little disappointed with the latest polishing job… not quite as sparkling clean as it should be, with me obviously apparently unmotivated. Sigh. I keep slogging. Never give up, never surrender!

Meanwhile, Q (my husband’s new blog nickname, that hopefully I’ll remember) just got his US citizenship! Hooray! Should make things easier. But I’m having trouble here in India.

Remember the visa trouble earlier? Did I write about that? Hmm. Anyway, I had trouble getting a visa. Now I’m having trouble registering. If you plan to stay in India longer than 180 days, you have to go register at the Foreign Registration Office. Bear in mind that governmental bodies here are arbitrary. Not standardized. Nope. And the man in charge of this particular office seems to have a really bad temper. He sent me away almost immediately to rearrange my application and bring more documents. Other people I talked to in line had been there 3 times already. He seems to have the idea that India’s consulates in other countries are messing everything up. Not helpful. Not. Would 1000nrp help things out a bit? I don’t know, ‘cause when push comes to shove, bribing just makes me mad. Sigh.

After telling Q what my problems were, he suggested I use the agency his work has hired. Absolutely, say I. So that’s my next plan. And if they have trouble, I’m bringing in my secret weapon – my mother-in-law. Q’s mom is amazing! Remind me to write about her sometime. She has a supernatural way of getting things to happen her way. You don’t want to be on the receiving end of it, but it’s wonderful to watch it work on other people. Hee hee hee. So for the sake of the FRO people, I hope Q’s work’s agency pulls through on this one.

MS #2.5 sent off for internal review

Another month has gone by. Things are slowly settling down. TM loves preschool (hers is called a nursery, actually), which is a big relief for me. They have pony rides on Tuesdays, lucky kid, and she takes a van to get there, which she also loves since they ride through villages and sing all kinds of songs as they go. I wish I could go too so I could learn how in the world they keep those kids under control in the car. I’d go crazy!

I just sent a manuscript draft to my committee! I’ve been working on this one for at least 2 years, and intensively for about the last year. Talk about taking the turtle and not the hare philosophy. But when you only have 3-5hrs/day and about 1wk/mo is taken up with TM being sick, and when you’ve moved twice, slow and steady is the only way. Here’s hoping! Only two manuscripts to go, by my count. Can I do that in a year? Sure depends, doesn’t it?

We’re loving our apartment. So far we have furniture, we have a phone, we have internet, we have a car (!!!!) and a driver and a cook who comes and cooks dinner for us, and a 3hr/day cleaning lady, AND a dryer (hooray!). I think all we’re missing is some curtains, dresser-drawers, and time to go through the boxes of old papers in the guest bedroom, and time to organize and update our filing system (heavy sigh).

I’ve offered my services as a collector to various people, since I know how hard it is to get samples of things from overseas. So I’ve been hunting liverworts, which is lots of fun. I considered shipping things under pseudonyms (i.e. “art supplies”), but my conscience is awfully persistent (it’s not loud, but it doesn’t shut up, either), so now I’m going to see how easy it is to ship seeds and liverworts back to the US. The US-side of plant shipments is pretty easy. The real trick will be the cane rat… Hmm… I emailed a fellow in Oregon who’s supposed to do that sort of thing, but I haven’t heard from him, so I’ll have to try to call APHIS sometime during US daytime. And what about the India side of things? No idea. But it’s worth a try, right? If I can’t get anything through going the legal route, then I’ll see what alterations I can make to my plans. Sigh.

What else… one of our neighbors has a 3-yr old daughter who gets along with TM pretty well, which is lovely. They play almost every afternoon, hooray! And the neighbor is really nice to talk to. She’s from Belgium and did a Master’s thesis in business something-or-other, so has a little idea of the headaches of writing. Most other people haven’t a clue, they simply assume I’m unsocial (I think they assume that but they didn’t really TELL me that… heh heh heh). They don’t understand that when Maya goes to school, I hit the books like mad. Do I feel a little guilty for not doing the social thing? Yuppers, especially when it’s such a big thing to do, like it is here. But hey.

It’s late at night, so my brain’s not up to par, but at least I got another post written.

Our Own Apartment, Bangalore

We finally got internet! It's mid-July and we still don't have enough furniture, though our apartment is comfortable enough. We just need more bookcases. And a bigger kitchen table, and chairs, and some chests of drawers. But since we had little furniture in the US, now we have to get it all here, and shopping is not easy. I always wondered why my mother-in-law seemed a big possessive of the gifts she gave me since many of them were so inexpensive. Now I know. Just going out to find something you want can be an all-day expedition, unless you know what it is and you are sure that the store you are going to has it. Things may be materially inexpensive, but the work that goes into finding them, well...

Our apartment complex is very nice, though the road leading to it is full of potholes. At least you don't have to drive through a slum to get here, like another complex we visited. And a slum here is probably different than a slum in the US -- here the really poor people live in corrugated tin huts with no running water or toilets, with open sewer, packs of wild dogs, etc. My guess is that the slightly less poor live in the homemade brick huts I see sometimes. In some of the fields we drive by there are tents of tarps or plastic covered with palm leaves, obviously used as housing for either farm hands or construction workers.

Despite the often horrendously filthy living conditions, most people make a supreme effort to maintain bodily cleanliness. Even homeless people wash every morning and I've seen very few beards anywhere.

With the help of a neighbor, we found a wonderful cook who comes for about 2hrs/day and cooks up the most wonderful meals. Food is super cheap, by the way. And we have a girl who comes and cleans for about 3hrs/day doing sweeping, mopping, cleaning cleaning cleaning especially in the kitchen where I think the old tenants didn't do a great job of cleaning so we're doing double duty.

People say it's really dusty here, but I think it's just that the floors are tile and if there's any dirt at all, it shows. I prefer that, since with TM's asthma it's better to know when things are dirty. :).
We don't have curtains yet, either. I have some quick-n-dirty ones I'd made in Oregon that I hung up, but I need to buy new ones. I don't know when I'll find the time for that, but hopefully in the next couple months. We found a daycare for TM and she's currently getting used to it -- more on that later, I hope.

Meanwhile, airline prices have risen so much that I can't go to the conference I wanted to present at in August, so I need to put together a bunch of slides for my prof so he can take care of my presentation for me. Oh my, I forgot I need to cancel. And I still have bills that need paying...I thought I paid them, but my aunt in California just sent me some more, so I'll have to find out how to follow up on them.

Mosquitos... everyone closes their doors around dusk because it's mosquito time. Yup. Ick. And of course they carry all kinds of diseases. The apartment people spray for mosquitos every day or every other day, which I'm not super happy with, but I guess it's easier than dealing with hordes of hungry bugs. Ick. Luckily the apartments here all have screens on windows and porch doors. But the screens aren't tight, so mosquitos still get through, which makes me laugh since it seems like it would be a simple thing to put a brush on the screen that would make it tight against the frame... oh well.

TM will probably be getting up soon and all I'll have done is talk to the cook, figure out our insurance, and look for bills. Oh well. Things are slowly getting better, as I knew they would, but it'll still take another 6 months or so I imagine for us to be settled. We still need a car... okay, I'm done for now :).

June in Bangalore

Paper is coming along fine, though slow. Sent out the first draft to coauthors, am now revising it.

We might get the keys to an apartment today, which means the slow process of moving should start soon, cutting into my writing time (2-3hrs/day at the moment). Today we went to the bank to set up a joint account, and we had to bring my husband’s mother, as she was “introducing” us, which is actually a technical term since the banks here are much more picky than in the US about who they give accounts to.

By the way, the new apartment is about 45min from here, and TM who is 2yrs old only lasts 30min with any ease. After that it’s a fight. And we’ll have to get our stuff shipped from storage to the apt, and unpack it. But we can’t live there yet ‘cause there’s no fridge, no clothes washer, no beds, and we can’t sleep on the floor ‘cause tile is dang hard. So we have to have beds, or at least mattresses, buy fridge etc, get it set up, all with a cranky (teething and often diarrhea-ish) toddler. ? And who knows how long it'll take to get phone and internet there.

Here’s how the trip to the bank went:

We left 11am (ick) but Vivek was up 'till 1am working so of course couldn't leave early...but that's too close to lunch for comfort, for Maya. Bank busy, and this is India I'll remind you... and I'd forgotten to bring proof of address. Angels slipped a phone bill into my mother-in-law's purse, though, so we were saved. You have no idea how mad my husband would have been if we would've had to go back home. Still took, what, 45min at bank, 30min to get there, 30 min back, 2hrs tot, 1:30pm when got back. At bank TM started getting diarrhea.

Public toilet -- no toilet paper, no soap, a hole in the ground and a bucket of water. Toddler with diarrhea. Okay? Was I happy? There are no words I can think of to describe how I felt. But happy is not one of them.

Changed her in the car on the way home. She fell asleep on the way home. Stayed asleep for another 30min after we got home, then puked herself awake and pooped at the same time poor kid so had to endure a full-body soap-up. In the bathroom without a tub. No tub. You just turn on a tap and do your best with the floor and a bucket and then try to swish the leftover water & goo into the drain as best as you can afterwards. 'Cause you'll have to climb over the wet floor to get to the toilet later. (modern toilets here thank goodness).

I didn't wash her hair 'cause there was no hot water 'cause you have to turn on the hot water heater (small, 1 per bathroom), and the poor kid was freezing, so her hair still stinks a little of puke. Fed her some fried-up rice chip sort of things (food is good here, thank goodness) and managed to convince her to sleep again after giving tylenol and threats and almost completely going crazy and chanting in my head in time to the fan "I wish I could die I wish I could die I wish I could die" while knowing that dying would only make things worse.

Isn't that a rotten thing? That there's absolutely no way out! And of course that's when you're supposed to realize the way out and I know that I really need to give up control but when you're surrounded so often by things that you really really don't like it's hard to remember that God can handle it and you don't have to…

In India with kid and no apt

We made it! We're here! 2 months since my last post. A few words of advice -- cancel your Sprint account before you leave. Also -- if you marry someone from India, get a PIO card (Person of Indian Origin). And if you have any children with aforementioned Indian citizen, get them an OCI card (Overseas Citizenship of India, I think). That will save you lots of trouble.

When you get to India, specifically Bangalore, do have a guide or someone who can take you around, unless you a) speak whatever language they speak wherever you're at, or b) have a close relative who has lots of time and is willing to take you under their wing. If you are travelling there with a very young child, well, I hope your relatives take good care of you, have lots of time to play with the kid, lots of toys, a playground nearby, etc. Did I mention toys and a playground? Have you tried to entertain a single 2-yr old child in a toyless flat lately, and no play area outside? I don't recommend it... If your very young child has allergies or special needs, I hope your relatives love the child enough to find ways of making things work for them. If you are planning on moving to a developing country with a very young child and don't know anyone there and are not naturally adventurous and garrulous and enterprising, uhhhh, well, how do I say it... don't?

We're extremely lucky to have my mother-in-law living here, since the temporary apartment set up by my husband's work is not really tenable for a 2-yr old. Especially since his boss realized that the office doesn't work well and they'll have to use the temporary apartment for an office for awhile. So yes, thank goodness my mother-in-law owns a flat. Though it's small, it has 3 rooms, and we've taken over two of them. What would we do if she weren't here? It would be fine if it were just us, but with a 2-yr old (and an active one at that, with allergies), it's tough. I should really play tourist sometime soon and take bunches of pictures and post them! Though we're in a giant city, we have cows, goats, and bulls pulling carts. Few cats, lots of dogs.

I'll try to write something more detailed sometime. Right now, TM's taking a nap, so I thought I'd jot down some thoughts. Basically, we're looking for a flat to rent, and once we're set up I'll be able to perhaps compile a summary of the emails I've been sending to family about the transitions. Setting things up here is nothing, I mean, nothing at all like setting things up in the US. Nope. But I'll learn...

Cheers
rhamnites

FSTAT analyses make a pretty picture

I should probably have a blog for different parts of my life – kids, healthcare etc, and PhD work. But I’ll just stick with this one.

My advisor sent me a paper (Waples & Gaggiotti 2006) that talked about the definitions of a population, and included some cool tests to see whether a group of samples were panmictic or not. How did I miss it? I’d read it before, but didn’t put the analysis together with what I wanted to do. It’s exactly what I’ve been looking for! Structure couldn’t do it, and Geneclass2 wasn’t quite it either.

The Structure analyses were a mess – Brachypodium sylvaticum has high inbreeding (really high, like FIS=0.7), and the source populations for the small area we’re working on right now are really admixed. Or so it seems. Whatever the problem, Structure identified the peripheral populations as belonging to distinct clusters, while the source populations were a big huge mess. GeneClass2 was fun, but the picture it painted wasn’t clear – I could easily tell which populations were sources for a lot of other pops, but it was hard to figure out a way to draw it out graphically.

Then I re-read Waples & Gaggiotti 2006 and found that they did a pairwise test (in FSTAT) for population differentiation, and when the tests were insignificant, they concluded that the populations were, well, effectively a single population. That’s just what I was looking for! We had sampled about every mile along three roads, and I wanted to see which populations (sample sites, really) were similar, thinking that would give a good idea of dispersal patterns in the area. I probably should have mapped out all the individuals, and it wouldn’t have been too hard, but I didn’t, so now estimating neighborhood size is out of the question. That would have been ideal. But this pairwise test for differentiation works pretty well! I’m happy with it, at any rate.

I drew up a picture on a map with sample sites connected that were not different, and sent it off to my advisor and other coauthor (the former undergraduate). I haven’t heard from them yet, but I’m hoping they’ll like it.

Meanwhile, the move to India is moving apace. My husband will come back to “collect” us on Apr 10th or so, then we’ll spend a few days in MD with TM so she can have a break from flying. Then we’ll fly to Frankfurt and from there to Bangalore. The last leg will be the worst, ‘cause she’ll be awake. Yoikes. Well, we’ll do our best.

In India, we’ll stay in a temporary apartment provided by my husband’s job until I can find an apartment we like, then we’ll move. Hooray! I really look forward to having a place of our own. Thank goodness his work is paying for the move, ‘cause it’s costing an arm and a leg. Anyway, then TM will have her toys and books again, and we’ll have more than one room to live in! What fun! I hope to find a school for her quickly, so she can get back to playing with friends and I can get back to work. I figure that after about a year of living there, we’ll be enjoying ourselves immensely.

My grandpa’s visiting this week, and I’m in charge of entertainment today and Friday, so there’s work down the drain, but it may be the last time I see him, so I’d better aprovechar, as they say in Spain.

Data analysis and moving preps

It’s been an interesting week. After coming back from Portland, at first I thought I could do away with Structure (Pritchard) analysis completely, which was quite exciting. Then my advisor said that’s not such a good idea, so it’s back on the books. Luckily, my former undergraduate had some really good ideas about what to do. The results have been multimodal, meaning that different runs give different results. Instead of putting ALL the data in, I took some of the peripheral populations out. It was still multimodal. Then I took all the peripherals out, and it wizened up! Though I haven’t been through all the results yet, it seems like the runs are more consistent. That’s very interesting. I’m planning on adding in the peripheral populations one at a time and seeing what happens. At my advisor’s suggestion, I also took out individuals that had an identical genotype to another individual in their population, and the runs were still multimodal. I get the feeling that there’s something here that should make sense but I’m not quite grasping. I may try taking out individuals that have genotypes that are repeated ANYWHERE, not just in their populations. Just for kicks.

Does it look like I’m running around in circles with this stuff? Yes, but I’m not really, I get the feeling that (since excluding peripheral pops got rid of multimodality) I’m closing in on something. Oh – there’s another program, InStruct (Gao), based on Structure, that actually takes into account inbreeding (a big factor with Brachypodium sylvaticum, since it selfs and outcrosses). Sometime inbreeding will make Structure tell you that inbred populations are admixed (intraspecific hybrids). That’s a major concern with our data, since some of our conclusions are based on the fact that putative source populations are admixed. Well, I ran InStruct and still got admixture! Hooray! That’s a relief. I was a bit worried about that. But now, of course, I’m going to have to echo whatever analyses I run with Structure in InStruct. That’s okay, though, now that I know they won’t completely contradict each other.

My former undergraduate just used another program, SpaGeDi, to look for isolation-by-distance (IBD), where populations near each other are more similar than populations that are distant. Well, I haven’t been able to look at her results yet, but I’m getting the idea that our data presentation will look something like this:

Genetic marker information (allele freqs, etc) (Arlequin, GenePop)
IBD (mantels, SpaGeDi)
ID of source populations (GeneClass2, Structure, InStruct)

I think that makes sense. We’ll see.

On the “moving-to-India” front, my husband came in on Thursday for TM’s 2nd birthday on Friday. TM was thrilled to death! The movers are coming next Monday and Tuesday, and then we’ll be living out of suitcases until after Apr 15, when we leave for India at last. Hooray! I still have to get my husband to fill out various moving forms – don’t let me forget. He did bring the Toyota sale bill with him, so the nice couple who bought our Toyota last month finally have a legal bill of sale. My husband leaves again on Mar 6th, then comes back Apr 15 to help us get to India.

I don’t have my visa yet – if I don’t get it by mid-March, I’m going to switch my application to a tourist visa. That would be a little unfortunate, since it means I’d have to leave the country every 6 mo, but at least I’d be able to get to India. I’m hoping I could change my visa once I get there. TM has her PIO card, though, hooray! That was a major relief. It looks like a mini-passport – pretty cool. And she’s so cute!

It’s Sunday, so I don’t really want to do shopping (even online), and I’m not sure what I’ll do ‘till TM wakes up. Maybe I’ll pick up Mark Twain’s Prince and the Pauper again, but it was a little stressful, what with having the nice prince kicked out into the streets and beaten, and having the pauper in a very stressful situation as well… I may just skim it and see what the details of the plot are. I don’t always like to see nice people treated horribly...

My husband said I don’t have any classics on my Amazon wishlist, so I updated it to include a lot of classics. There ya go. I keep thinking that I might not be able to get some of my favorite movies over there, and then I remind myself that I haven’t had them for years and years over here either, and got along just fine. J.

I do need a desktop computer, though, since I live in fear of my now ageing laptop giving up the ghost. It’s out of warranty. It has several thousand dollars worth of programs that I use for my work that I don’t have the discs for. Eeeek. I’ve been trying to decide between a Mac and a PC. I may stick with a PC just ‘cause I can fix things in it myself. A Mac is better, of course, but if I’m going to India I’d rather have something I can fix myself, and a Mac is not that… Also, everyone I work with currently has PC’s and of course it would be a little tricky to interface with a Mac. Ideally, I’d have both a Mac and a PC. Hee hee hee.

Well, I’m off to entertain myself on this lovely, drippy Sunday morning. TM’s sleeping great since I begged her to drink water only at night, hooray! It took almost 2 yrs to get a good night sleep. Wow.

Quick 1-night visit to Portland for committee meeting

I just got back from a whirlwind visit to Portland, Oregon. I loved flying in on the plane from Burbank, seeing the green trees. There were no leaves, no, the trees were green with moss, lichens and fungus. It was cloudy and drizzly. I love it! Nothing against Southern Cal, which I admit has quite a bit of charm with its snuggly warm sunny days, but I love the Northwest.

I flew in, then helped a visiting prospective graduate student find her way around, then had a meeting with my committee. Those meetings simply scare me for some reason. I don’t seem to be able to express myself well in front of them. They had a lot of helpful comments, though, and were not necessarily antagonistic, just, oh what’s the word, intense. It’s great to have a group of people intensely interested in what you’re doing, but for some reason I always feel like I’m about to do something wrong. Silly me. They agreed with my dissertation plan, which goes something like this:

Chapter 1: Introduction to dispersal and gene flow, from an article I have in press with Elsevier in their upcoming Encyclopedia of Ecology.

Chapter 2: Genetic marker development methods paper for my project, in press with Molecular Ecology Notes

Chapter 3: Oregon-wide dispersal/gene flow patterns for Brachypodium sylvaticum

Chapter 4: A small-scale analysis of a group of populations near Sweet Home (this is the one I’m currently getting ready to publish)

Chapter 5: Outcrossing data. I haven’t looked at this data much in-depth yet, but we have data from field-collected progeny that could be quite interesting. We’ll see.

I’m glad they liked my plan, and they’re not against me continuing to work long-distance, even if it’s from India. They’re very supportive, which is great! I’d like to meet with them again before we leave, maybe on a 1&1 basis. We’ll see if I can pull that off.

We had a fun lab party in the greenhouse and some of the other faculty showed up. I simply love our lab parties! Hot Lips pizza, which is simply scrumptious, some sushi made by a lab member, salad, chocolate, beer (Sprite for me), and wonderful company.

I spent Saturday morning with my former undergraduate, hacking away at some analyses for the paper we're working on. There's so much more to do! But we'll just keep working at it and hope for the best. Flew out in the afternoon after a lovely buffet lunch at House of India or something like that, and got home around 9pm to an ecstatic TM.

TM did great staying with my aunt and uncle. My mom even came to play with her on Saturday, which she really loved. But it was very very difficult for me to be away from her for so long, knowing that neither my husband nor I would be around. For some reason that just made it very difficult. I still have a tic in my right eyelid from the combined stress of everything. Hopefully it’ll go away soon.

Now all I have to do is manage to get our visas so we can ship our stuff to India (I didn’t know we had to have visas before shipping), get our current manuscript submitted to a journal for publication, and finish the 3 native plant garden projects that are jumbling around in my head.

moving, data progress, and evolution vs creations

My husband has found us an apartment! Actually, a townhome. We can get a townhome in Jakkur (N Bangalore) for the same price as our apt in Maryland. 2400 sq feet, even! Amazing. As soon as I give the final okay (I want to know if there’s a playground nearby), we’ll have a future address! I’m thrilled! Then I can ship our stuff over there. It’ll take about 2mo to get there, yikes. So we’ll be living out of a suitcase for 2mo? Sigh. Better to do that here, though, where we are living in someone else’s house, then to try to do it over there, with nothing.

On the data side of life, my former undergraduate’s data is finally cleaned up, I hope. I ran some STRUCTURE analyses on it and it looks really really cool! Populations that are near each other are often quite different, which is interesting. It looks like various source populations can give rise to a new population, whose resulting genetic structure is strongly influenced by the founders, probably until enough other seeds come along to influence the genetic makeup. Very exciting! Now we’ll just be running analyses, putting tables together, and stuff like that. I may actually make my deadline on this paper!

Speaking of deadlines, I’m meeting with my committee in 2wks. I think I’ll have a nice story to tell for the above stuff, but for the overall Oregon data, well, that’s another story. It’s a mess. I won’t even talk about it, ‘cause it’ll depress me.

I took about 2.5 hrs away from work time this morning to pack up various things that are cluttering our small room here in my aunt and uncle’s house. I took them to our storage unit an hour away, in San Bernardino. I hated to use work time for that, but I really can’t take TM with me. Sigh. And my Aunt was getting distressed at the clutter in our room. And I wanted to take pictures for the moving people. Excuses, excuses. At least we have a little more room here! And maybe less of a fire hazard.

On the way to the storage unit, my mom called me, frustrated about various political problems. Eventually we got on the topic of evolution. I’d like to vent a little if I can, though she and I already vented together…

Just because you might have an explanation for a miracle doesn’t mean it didn’t occur. I mean, if you’re praying for help because you have no food in the house, and your neighbor stops by with dinner, do you then figure that your prayer went unanswered, and that God doesn’t exist? I hope not (unless you really don’t want to believe in God in the first place, which is fine with me).

If you find out that the sun only appears to rise in the east and set in the west, but that the earth is actually rotating, does that make it less miraculous?

If you find out that a flint and steel make sparks because of a specific chemical reaction that is reproducible, is it less of a miracle?

With the people thing again – let’s say you’re really really depressed. You get down on your knees and say, Heavenly Father, I can’t take it anymore. My life stinks, and I absolutely hate myself. Please help me! Then you get a phone call from a loving friend who lifts you up. Just because you know what happened doesn’t mean it wasn’t an answer to prayer.

Now, I’m not saying that evolution as we understand it is perfect. That’s ridiculous. Science is inherently a field of discovery, invention, and learning. Just like our understanding of biology, of chemistry, of sociology, or art is always changing, our understanding of creation is also changing. That’s okay. Our personalities change, too. So do our understandings of faith and hope, as we grow or regress in various aspects of our lives. Life is about change and adapting to change and always striving to learn and be better people. But just because our understanding of things is not perfect, there’s no need to say that the premise of our understanding is completely false. Don’t throw the baby out with the bathwater, as it were.

And though even the word evolution seems to be associated with pure evil incarnate to many of my friends, I’d like to suggest that it’s merely an attempt to explain what we see in the world, and not threatening to God in any way, shape or form. God really doesn’t mind if we try to explain things that He does. I’m pretty sure he doesn’t, anyway. I hope he doesn’t abhor learning and growth. That wouldn’t make much sense to me.

And so far as I understand things, He works through natural laws Himself, doesn’t He? So maybe it wouldn’t be so bad to try to be more like Him by understanding everything we can about what He has given us.

And by the way, religion is NOT science. I love the various creation stories in the Bible. But they are not science. They corroborate and support science, or rather, science corroborates and supports them, but they are religious texts, not scientific arguments. Religious texts, so far as I understand, are made to try to communicate to people spiritual ideas. They take real events (though some would argue with me on that one) and attempt to portray the spiritual importance of those events.

If the creation story in the Bible is to be taught in schools, it should be taught in religion classes, as it is an attempt to explain the miracle of creation to anyone who reads the book. It’s kind of like a CD of the Messiah – what a beautiful piece of work! Anyone can listen to it and appreciate it. That is the final product. But if you want to scientifically analyze it, you’ll find wavelengths, chords, overtones, and all kinds of things… you could do all kinds of analyses with the numbers you could generate from that one work of music alone. But the analyses and the science behind them are NOT the music.

The creation story and evolution are two sides of the same coin. There is no inherent conflict. Who decided there was? Whoever it was, they did a good job. All they had to do was stand up on their soapbox and say “Evolutionists Say There Is No God They Are Evil” and voila, evolution is evil. Now, that’s power for you. It’s also a lie. I believe very strongly in God, and I don’t think that trying to figure out how things happen will diminish my faith. That would be sad, now, wouldn’t it?

Okay, I’m not really done, but what can I do. That’s how I feel. I wish we could all just get along. And by the way, if you happen to not believe in God at all, I’m fine with that, too.

Artist's Hour, with puke

India is getting closer and closer. I’ve sent off my application for a visa, and this week I also sent off TM’s application for a PIO card (Person of Indian Origin card, so she won’t need a visa for about 5 years). I still need to find an apartment.

Yesterday I took some time for an Artist’s Hour, as my Aunt calls it. She says that if I don’t get creativity time, I’ll struggle interminably through my PhD. So yesterday I went to visit one of My husband’s friends who has a huge house and a huge yard to go with it. He wants to change it over to natives, and is doing a wonderful job, but is intimidated by the size of his lot. I told him that the first thing we need to do it map out his property and get a paper design going. So I’m going to the library sometime this week to find out how to get a plot map. I also need to figure out how to map out the huge oaks he has on his property. Then we’ll draw the ideal plan to our hearts’ content. Wheee!

It was a lot of fun, and I feel rejuvenated, except that TM puked all over his nice wood floor and her own clothes to boot. I can’t wait to hear what the gastroenterologist says. She puked again last night, poor kid. I never thought I could be so immune to puke. It’s getting quite interesting, actually.

I got comments back from my coauthors on our methods paper. Hopefully we’ll get it sent out again this week to the publishers. And this week I also have to run STRUCTURE (genetic analysis program) on my former undergraduate’s data. Gotta get her stuff moving.

Oh, did I tell you? I sold the Toyota Matrix! I went from $8200 to $7500 just to get it sold, but it’s gone! Now we can pay off the Hyundai Elantra and start buying a car in India. My husband will be pleased.

Prepping for move to India

The holidays have gone, and my husband just left to go back to India. His job is so time-consuming that we didn’t get much of his time while he was here. Still, it was wonderful to be able to say, “Keep an ear out for TM in case she wakes up while I run to the post office.” Single parenting is hard. And now it’s back to single parenting again. But at least I get to sleep in a bed! I’ve been sleeping half on TM’s twin bed, half on three filing boxes sandwiched between her bed and the full bed my husband used while he was here. Now it’s mine, all mine! Sleep, here we come!

My methods paper has been provisionally accepted, hooray! We just have to make various changes, and we’re in. And the former undergraduate’s data is coming along well – I’ve almost finished going through it with a fine tooth comb. After I re-run all the analyses, I’ll be able to re-write the results and discussion sections of her honor’s thesis, and send it off for publication! I simply have to get that done before going to India.

The grant agency for the grant that funded my research asked us to present at the next ESA meeting… so we will. Of course, I plan on being in India, but I’m optimistic. Heh heh heh. That’s a long shot… I mean, who will watch TM while I’m gone? Her grandma? Maybe. I really don’t know. That’ll take some faith and prayers to pull off. And now I have to get as much data analysis done before Feb 7th that I can, since I’m planning on dashing up to Oregon for a couple days to have a committee meeting with my dissertation committee. Yoikes, as my sister would say.

Meanwhile, there’s the stress of moving to India. My brain is having real trouble wrapping itself around everything we have to do. I need to sell both our cars, but I’m not on the title for one of them, so I have to try to put myself on the title. I got my husband to sign a form before he left this time, so hopefully it’ll be enough to change the title, and hopefully it’ll happen fast enough for me to sell it without too much loss before we go. And taxes? What happens when you sell cars? Frustrating that we have to pay taxes when we already paid taxes on the money we spent to buy them in the first place. Oh well.

So. Sell cars. Get visas. I just sent off TM’s visa application, and it’ll take about a month if all goes well, ‘cause I applied for a PIO card that will let her come and go without a visa since her dad’s Indian. My own visa should, hopefully, be coming back any day now.

Need to find a house in India. Looking for something in North Bangalore, near the new airport, since my husband travels a lot. That puts me in the LDS church 2nd branch in Bangalore. Maybe they can help us find a house in the area, who knows. We also need to ship all our stuff to India. Where? When? It’ll take about 2 months to ship, and I’d like to be able to move into a house of our own as soon as possible.

Cars. Visas. House. Shipping. Oh, immunizations! TM and I have to get typhoid immunizations and whatever else they recommend. Sigh. And I don’t have a doctor in this area yet, and it’d probably take a month to get in to see a new doctor, and do I have a month? I don’t know. This is what happens when you move every single year. Besides the fact that I tend to put off going to the doctor.

Cars. Visas. House. Shipping. Immunizations. I think that’s it. Of course, then there’s getting set up in India once we get there – how long will it take to get high speed internet? To find a good daycare (play school)? Oh, those muscles in my right shoulder blade are scrunching together, tying knots in each other… I must find a way to relax.

My aunt has been going to AA meetings for maybe 20 years now, and has a lot of good advice about giving problems to God. I’m trying to do that, by letting Him take care of all the things that I really don’t have control over. But as you can tell, it’s kinda hard sometimes. I guess that’s the point, isn’t it…?

So I’ll just keep trucking along. I’ll get that paper out and go to India and try to find enough help that I can come back in August for the meetings, and be a productive PhD student. It’ll work out, with any luck. Si Dios Quiere, as I heard so often in Spain while on my mission.

Ttfn (Ta Ta For Now)
Rhamnites