Done!

Really, totally, completely done! After having gone back and forth a number of times with the editorial office to finalize the dissertation, they finally sent me an e-mail that I've met their requirements. It's over!

Thanks to everyone for cheering me on, from the deepest of depths to highest of peaks, thanks for all your support, advice, good wishes, and all the other things I'm too emotional to think about right now.

Special thanks to Brazen Hussy for hosting InaDWriMo 2008. Having a counter and a blog to put it on to keep you painfully aware of your (lack of) progress helped me more than I can express. I would highly recommend putting up some sort of counter to help you with your goals. It didn't hurt matters that I had some pretty solid deadlines from the university to work with, but I had options if I failed to meet those. I could have postponed graduation with a semester without having to pay additional tuition fees by submitting in early January, I could have been stuck with having to pay for 3 credits of tuition next semester and graduated in May if I had decided to not finish by early January. It might have made things tougher, but they were real options that I seriously considered.

I think ultimately what pushed me through is the support from my family. They paid a really high price in terms of my absence of the past year. I hope it was worth it. I have some major repair work to do there. Hopefully I'll have some time now.

It seems like an incredibly long road, but I did finish up in 4 years. I started this program in January 2005. That's not too bad for having 3 kids (4, if you count the husband), one of which with special needs. I sincerely hope they will be rewarded for their efforts.

Thank you so much everybody!!!

Now back to regular blogging.

Dr. Makita

Yep! I managed to convince my 4 committee members that I am worthy. I successfully defended my dissertation. I got my committee members to sign the form, and I'm not giving it back.

So, that's Dr. Makita for everyone.

Tasks ahead

Thanks for all your encouraging comments. Twelve hours after I submitted, and I'm still running on no sleep and lots of caffeine. I killed even more trees today and printed out 3 copies of my dissertation to hand out to committee members. It's not over yet. I'm starting a new counter to keep track of the tasks at hand. I think I will keep this on top for a while, so I can amend as necessary.

1. Finish statistical analysis
2. Add to chapter 3 results section and discuss
3. Maintain cultures
4. Check reference list
5. Check buffering capacity of medium
6. Schedule exit seminar
7. Reserve room for seminar
8. Prepare mini version of exit seminar for defense day
9. Prepare exit seminar
10. Work more on chapter 4, topic 1
11. Work more on chapter 4, topic 2
12. Add in table for chapter 3
13. Get paperwork together for employment authorization
14. Organize defense date (coffee and stuff)
15. Ask hubby to help pick out clothes for defense and exit seminar
16. Buy shoes for F1-2 who is getting a brand new brace for his leg
17. Start job hunting
18. Incorporate committee members comments
19. Convert dissertation to pdf with Acrobat ("save as pdf" is unacceptable)
20. Submit final dissertation
21. Update CV
22. Defend dissertation

All this needs to be done by the end of the month. So I can guess I'm still in the running for InaDWriMo 2008, with adjusted goals.

Dissertation Submitted!

Submitted

If my writing is a bit disjointed (or as F1-1 would say, discombobulated), it's because I worked through the night, and turned in the dissertation at 6:30 am this morning. Yesterday a student colleague, our labmanager and I worked all day on trying to get a statistic calculated and tested that my adviser wanted me to add. I must have killed two trees in the process. All the intermediate steps needed t be analyzed carefully for model fitting, numbers to be used in subsequent steps, and such. I had only done this exercise in a class more than 3 years ago. And the others I worked with were a bit rusty themselves, but eventually we managed to figure it out for one of my experiments. I ran out of time to finish up the second, but now that I know how it's done, it ought to go quicker. It was too late to put it in the dissertation at this time. I'll add it in before final submission.

Now I've done 2 of the 3 submissions. I have to defend it in 2 weeks, if I pass, I'll have to incorporate comments from my committee members, before final submission.

No break for me though. I have to print the dissertation up for at least one of my committee members, take care of my plants in the greenhouse, start up fungal cultures for inoculation next week, finish up model fitting and statistics, incorporate last-minute comments from my adviser. Ideally I would also start working on my exit seminar, but that seems overly ambitious at this point.

I ought to feel elated. I always thought that if my adviser said my dissertation was good enough to be sent to the rest of the committee that it was just a formality from there on end, and pretty much a done deal. But now I feel numb, edgy, and unable to estimate whether it will be good enough. There are some pretty major gaps in my work that I am very painfully aware of. I simply ran out of time. If I would start on this project now, I would do a kick-ass job in a fraction of the time that I did a shitty job on this degree. It feels so inadequate. And deep down, I'm convinced that my committee members will see through the whole farce and realize that I'm just not up to the task.

I know it sounds pessimistic, and I probably shouldn't be writing this on virtually no sleep and lots of coffee, but there you go. That's how it feels. Not good at all. Just another hurdle in a string of them.

I'll be starting up a separate counter for all the steps that need to be done from now on.

A break from your regularly scheduled dissertation writing

Important breakthrough! Autism is linked to rainfall. Finally all speculation can stop. All kids can get immunized against dangerous, deadly diseases. Move to the desert, and you children should be safe.

In other news: I worked until 3 am last night. Check out that progress meter!

InaDWriMo 2008 Update

I underestimated the number of words of this dissertation. It'll be at least 30k, so the progress meter will be updated. On the bright side, I've done a good chunk already. On the not so bright side, chapters 1-3 are about to go into the 3rd round of revisions. The second round of Chapter 4 revisions still needs to be submitted. All 3rd round submissions need to be complete by November 14 at the very latest.

I have been working very hard, but very productively, so a pat on the back for me.

Welcome

Busy , busy. But I really ought to make some time to introduce my readers to yet another friend who started her own blog: Under A Creosote Bush. Inspired by InaDWriMo 2008, she hopes to let the world know of her world. And an interesting one it is!

Joyful!

I'm setting my progress meter to joyful right now! My adviser told me that chapter 2 is in good enough shape to send on to the rest of my committee. I'm tickled pink. This will give me enormous energy, hopefully enough to finish the last two chapters this weekend. Look at the progress meter, I must say it's good to see progress.

Update: Ok, enough joy. Back to work

Next!

I'm beat. I worked all day. It wasn't easy, but I managed to finish the second draft of my literature. The counter has been duly updated. The number of words hasn't changed appreciatively, so I kept the numbers the same. I'm going to bed now and catch some zzzzz's. I'll change my progress meter accordingly. Tomorrow: chapter 4.

Election night was good for me

Few could have imagined the impact it had on my productivity. Although I was a bit distracted by the tv, and wanting to check on election results, it did make me stay up late enough to finish the second draft of chapter 3. The counter will be updated appropriately. It turned out to be an additional 500 words, so I'll update the total number of words too, so as not to give myself an unfair advantage.

No celebration for me though, I have to move on immediately to the next one.

Also, of course, I have to eat my own words. More than a year ago, I claimed that if the US even had to ask whether they were ready for a black president, they weren't. Little did I realize that Barack Obama would fight the uphill battle, and aided by some bad choices by McCain, but most importantly (I think) by inspiring a new generation of voters, would win this battle. He fought a hard fight, and his win was well-deserved. I don't envy him his position to try and fix the damage of the last 8 years, and the enormous task to be everyone's president. He sure has poise, charisma, and the will the do just that. Time will tell.

Concentration issues

I stayed home today to write. And it's not going so well. I'm easily distracted today. I really, really need to submit this chapter today, and it looks like I might be up all night. If I could only get my act together now...

In the late afternoon, I'm going to the lab to quickly end an experiment that is a repeat of 2 previous ones. Last week I couldn't stand the idea of walking around the lab with nothing to do but water my plants every few days, so I figured I might as well start another experiment. Today is the last day for that, so I'll be going in to take the last batch of measurements, quickly run the statistics on the lab computer, then pick up the little girl and the big boy, then head back home to add the data to the chapter and send it off already.

Concentrate..... concentrate.....

Postponed

Dang! I don't think there is any way that I can turn in the next chapter today. I was really hoping that I could and working hard. But it'll have to be tomorrow, I'm afraid. That pushes everything up with a day at the very least.
So I'm hoping to do this:
Ch 2 2nd draft submitted
Ch 3 Tuesday Nov 4
Ch 1 Friday Nov 7
Ch 4 Sunday Nov 9
And then I'll have to get ready for the next round of revisions. And then another. All of these have to be finished by the end of November. It'll be really tough.

I'm working fairly productively today, it's just not enough. Back to work.

InaDWriMo 2008

Ok, I'll be participating in InaDWriMo 2008, hosted by Brazen Hussy.

Since I already submitted the first draft, I'll be counting revised chapters. I have turned in 1 first revised chapter, 4 more to go. If and when my adviser approves the chapters (with more revisions, of course), I can send them to the rest of my committee.

Because I'm doing revisions, I think I'm going to count the revised words per chapter, so if I revise chapter 1 (see below), I will count them as 3000 revised words, and count my way up to the approximately 20,000 it'll be in total. The word count is divided up as follows:
Ch 1. Literature review, currently 4000 words
Ch 2. Experiments with RGS, currently 6000 words
Ch 3. Characterize new pathogen and more RGS experiments, currently 5000 words
Ch 4. Side project, currently 3000 words
Ch 5. Overall discussion, currently 2000 words

Until this torture is over, the progress meter will be on top of the page. I submitted the revised version of chapter 2, which accounts for the 6000 words of progress made so far.

Thanks to Sciencewoman for encouraging me to do this.

It'll be a roller coaster ride. Hang on tight!

Next round

Hi everyone!!
I'm still alive. Barely.


It took several sleepless nights, and some cajoling to make the first submission deadline, but I made it. My adviser made it very, very clear though, that this is all contingent on my next experiment (which is in progress) giving the right results. So keep your fingers crossed. These plants are alive, and they do have a mind of their own. I'm coming up today for a quick gasp of air, before going back under for the next stretch of deadlines to meet.

I have to work on the experiment, analyze some more data of previously harvested experiments, revise the chapters so that they're in good enough shape to be submitted to the rest of my committee. I also have to start working on applying for a change in immigration status, and pay whopping fee. If I fail to graduate on time, I can withdraw that application, and re-apply at a later date. And re-pay the fee, of course.

Anyone want to get together for lunch, or coffee before all hell breaks loose again?

3rd down

I just sent off Chapter 4. While I was waiting for F1-3 this morning at her ballet class, I got quite a bit written for Chapter 5, so I'm hoping to wrap that up this evening. I haven't gotten any feedback yet on Chapter 3 from my adviser. I'm getting there. Not fast enough, but I can only do so much.

This afternoon we had lunch on the porch. I was feeling really drained. I'm running out of steam. After lunch I fell asleep on the porch chair. I must have slept for an hour or more. P1 didn't wake me up, he figured I needed the nap. I was furious with myself after waking up, but in retrospect it did give me the energy to finish off Chapter 4.

You know what's most frustrating about it all? That working to the pointing of killing myself now, is not by any stretch a guarantee that I'll make it on time, that my adviser will approve, that my committee will approve, that I will pass my defense, or that I will graduate. But I have no choice at this point but to go on. Ok, back to it.

It's getting harder

I may not be able to make it. Here is an overview of the dissertation:

chapter 1. Literature review
chapter 2. Really good stuff doesn't work in these cute plants
chapter 3. Really good stuff does work in this plant, and it does fantastic things
chapter 4. Data analysis of large scale experiment done by other people
chapter 5. Overall discussion

I sent off chapter 2 to my adviser two days ago, and yesterday I sent off chapter 3. He sent my chapter 2 back last night, telling me I have to add ALL my data in the dissertation, instead of writing, this experiment was performed X more times with similar results. That may be good enough for a publication in a journal, in the dissertation you need to provide everything.

It's not that I mind, really, it's not. But man, that is going to take me *Forever* with a capital F. I have to get all that data, perform statistics, prepare new table, figures, you know, the works. Can be done, but not on time!

I was hoping to submit chapter 4 today, but it's not looking promising.

After that I was hoping to write chapter 5. The BIG picture, how fabulous is all of this to the survival of the universe? Then I was going to go back and write the literature review of chapter 1. Then there are a bunch of other things that need to be written, a biographical sketch, a summary for the general public. Nothing earth shattering, just stuff that takes time. A lot of it. After proofreading and formatting, I'll consider myself lucky to turn this in anywhere near the deadline without rewriting an entire chapter.

I was hoping to get some more data gathered, finish up some stuff in the lab and the greenhouse. Pffft! No way! I'd rather get more data, than revamp old, negative data, but that's just me. You see, chapter 2 was the chapter where I summarized all my negative data, the stuff you don't want to be reminded off too much, the stuff that never went anywhere.

Anyway, enough ranting, back to chapter 4. I'm going to ignore chapter 2 for now, and get back to it when I'm further along. It just means that I will not be able to graduate this semester. And that is rather depressing.

Shortage

There may not be a enough coffee in the world to get me through the next week. Widespread shortages of coffee should be expected.

Oh no!

In my experiments I test whether an additive to the soil does good things to the plants. We'll call it RGS (Really Good Stuff) for now. When I add RGS, I also add (because it's part of the chemical) something we'll call ES (Extra Stuff). To verify that the observations are due to RGS and not ES, I have a control to which I add only ES. This is a negative control.

A while ago, I analyzed my plant material and noticed that the plants that had only gotten ES, tested positive for RGS. I had already seen that the observations weren't as expected. ES plants were behaving too much like RGS plants.

The next experiment had the same problem. As I was writing this up for the past few weeks, I had a real problem explaining my data, because the ES plants were doing weird things. I did some tests last night, and more detailed ones this morning. And the verdict is: someone must have mixed up the labels on the container and put a form of RGS in the container labeled ES. All the while I though I was putting in ES as a negative control, I was simply adding another RGS treatment.

When I started noticing these problems with my plants, I added another negative control to my experiments, to which I didn't add anything at all (no ES or RGS). Those experiments are still salvageable, because at least I have a negative control. The ones where ES was my only negative control are useless.

I now have to re-do the entire statistical analysis and go back over all my data, trying to figure out when exactly this problem occurred. On the bright side: my data makes much more sense now. ES plants were behaving like RGS plants, because that's exactly what they were. It's easier to explain, but I really didn't need to spend more time analyzing data, thank you.

I'll spend the rest of the day working on statistics, and making new graphs and tables for the chapter in question, and sadly, tossing out a bunch of experiments.

This is exactly what the negative control is supposed to do, though. Science did do it's job here, and let me know that something was up. At least I figured it out now, and not after the paper was published. I would have had a hard time explaining my data.

I also have to notify all the other people in the lab that might have used ES as a negative control. They're likely to run into problems too. If I ever get my hands on the person that mislabeled those containers....

Deadlines looming

I have been told that finishing your PhD is anti-climatic, because there is no single deadline. There are bunches of them. For example:

My first submission deadline is in 2 weeks. That means I have to submit the manuscript to the university for review of formatting issues and such. It will be incredibly difficult (if not impossible) for me to meet that deadline. There is no way I can put all my data in, and I don't have time to work on my data right now. All I can do is write. So I will hopefully submit the first draft to my adviser next week, so that he can sign off on that. This is necessary for me to do the first submission.

Once I've killed nearly myself meeting that deadline, I have to go back to the lab, gather more data, and revise the manuscript in about 2 weeks, so that I can submit the revised version to the rest of my committee too. More killing of myself to get it to them on time.

Time to sit back and relax? Hell, no! Of course, I will not manage to get all the data in on time, so there will be more crunching of data, statistics, quick repeats of experiments that need confirmation, and putting in the final data as I go along. Oh yeah, and prepare to defend. That would be the next deadline. In the third week of November I'm scheduled to defend my work. That means I have to convince a group of 5 or 6 faculty members that I am worthy of carrying the same degree they have. How am I going to fool these people into thinking that I am worthy?

Big sigh and a break after that? Hell, no! My committee members will give me a list of things to change in the final document, and I will work for a full week to implement those. There might even be some last minute data to be added. I would be surprised if there will not be any of that. The final submission deadline is in early December.

So you see, it's not one final burst of activity, culminating in this big sense of freedom. Right now, the road is blocked by 4 major hurdles, with hardly any time to breathe in between. Who ever thought this was a good idea?

Adding insult to injury, P1 is leaving for the weekend. As in: going out of town, and I'm stuck at home with a couple of little kids when I'm supposed to be working on this. Anybody want some kids for the weekend?

A Cyclone Living in Miami

Check out my friend's blog. She's from the Midwest, and lives (for now) in Miami. Will she need to rename the blog when she moves away?

Reasons to believe in god

I forgot exactly when this happened, but it was quite a while ago, so I'm guessing F1-1 was about 5, maybe 6 years old. He started a conversation about god. He wondered why people believe in god. So I returned the question:

"Yes, F1-1. Why *do* people believe in god?"

He looked at me with a blank expression for a few moments before he responded, very sure of himself:
"Because some houses have flat roofs on them."
Several moments of silence.
Then I said: "You know, that is as good a reason as any other."

It still is the best I've come across so far.

LHC--better late than never

As seen on Bits and Pieces:

go, Go, GO!!

That is the chant that's been going through my mind this week. It's the inner voice that is telling me that time is running out for real. This week, time has turned critical, and my inner voice is now so loud, I can no longer ignore it.
go, go, go!!

I walk through the hallways, to the greenhouse, up the driveway, in the parking lot. And every step my mind screams "go". The results of the experiments I'm setting up now will not come in time for the dissertation deadline. They are contingency experiments, in case the other ones don't turn out right. In case I can't make it on time for a December graduation. Time is really up. I can hardly believe it.

On the one hand, if I had worked at the rate I'm going now all along, I would have been finished a year ago. On the other hand, there is no way anyone can sustain this for any length of time. Every minute in the lab is spent near the greenhouse. Every one of my plant shelves will be filled to capacity after today. Every minute at home is spent either writing, or thinking about writing. It's this all-consuming drive that hopefully will provide the final push necessary. It will have to.

Anyway, enough time spent typing this blog post. It's been hard to take my raging mind away from work, but maybe it will refresh and reset me too. Another cup of coffee for the day, and the race continues. Hang on to your hats folks! The finish line is in sight.

Evidence for ID?

Of course not. But I wouldn't be the least bit surprised if the ID crowd used this study, interpreted the data to fit their dogma, and declared it irrefutable evidence for intelligent design.

Picture credit

Apparently, a study done by the French physicist Dominic Vella, concluded that the legs of water striders (the little animals with long legs that walk on water) are just the right length. If they would be any shorter, the animal would not be able to utilize the surface tension of the water well enough and would sink, if they were any longer, the legs would bend and cause excessive drag. Water striders legs are exactly right. Needless to say that some higher power designed them just so. [end of sarcasm]

Contrary to conclusions I expect to be drawn by the ID crowd, Vella concludes that evolution has tested the limits of the leg length and stumbled upon the perfect balance.

Zelkowitz, R. (2008) Water striders put best foot forward. ScienceNow Daily News. 8 August, 2008.

How religion poisons everything

(Nod to Christopher Hitchens)

Now that my 15 minutes of fame are over, back to your regularly scheduled blogposts.

In today's Science an editorial (1) by Ismail Serageldin (director of the Library of Alexandria, Egypt) highlights (I don't know if this link will work for everyone, you might have to have a subscription if it doesn't work, try the link to the summary in the reference below) the strengths and weaknesses of science in Muslim countries. And is it ever clear that religion really does poison everything.

More than a trillion dollars in cash, a population of more than a billion people, but:

an increasingly intolerant social milieu that is driven by self-appointed guardians of religious correctness, who inject their narrow interpretation of religion into all public debates

is limiting investment in science, and more importantly scientific results.

Serageldin also states that:

We must be able to question convention and arbitrate our disputes by the rules of evidence. It is the content of scientific work that matters, not the persons who produced it, regardless of the color of their skin, the god they choose to worship, the ethnic group they were born into, or their gender.

Now, in a substantial part of the Muslim world a statement like this might be construed as apostacy, and Serageldin would be well-advised to watch his back.

How sad that intolerance is preventing so much brain capacity to go to waste. The world cannot afford to exclude scientists.

Reference:
(1) Serageldin, I. Science in Muslim countries. Science 321:745.

Atheist state

In the comments section of the previous post, andrew stated that his grandparents remembered how horrible an atheist state was. There is nothing to prevent an atheist state from being horrible. That would depend on the individual leadership style (or lack thereof). I'd be the first to admit there are genuinely evil atheists. However, there is nothing inherent in being an atheist that guarantees evilness. There is, however, the inherent property of religious leadership that results in discrimination, forcing legislature on constituents based on imaginary friends, or so-called sacred books.

Nothing prevents atheist leadership from being bad, but religious leadership will always be biased to say the least.

I'm going to be famous!

This should attract some interesting comments, and maybe a few juicy christians for dessert too. I guess I'd better get some controversial posts up in a hurry.

Update: Hey, did anybody check to see what this did to my sitemeter? It's off the charts!!

Surprise!

I went to the Godless Brunch on Sunday!! And I have a picture of myself with THE big guy. Yeehaw!

Getting ready

Well, it's been pretty crazy since I last posted. I'm leaving tomorrow morning for the conference, and I only finished my posters around 3 am this morning. I took the files in to the local Fedex-Kinko to print them at around 3:30 am, and they should be ready by 4 pm this afternoon.

Other than that I have not prepared for the conference. I still need to put some software on my computer that I will need for a statistical workshop I'll be attending. I have to buy some supplies for the trip.

I did realize yesterday morning that I don't have any clothes to wear. I normally dress quite ehmmm... casually. And somehow what I did have that would be appropriate didn't fit. I guess I didn't get on the scale recently, and I have 10 extra pounds on me compared to the last time I wore dressy clothes. So I went out and spent (for our budget) an insane amount of money on a pair on pinstripe paints, a silk blouse and two dresses. $250 total. One of the dresses was especially expensive at $88. I don't think I've ever owned anything that expensive to wear other than my wedding dress. But I do think it's gorgeous. Very simple, but elegant. I should post a picture soon. I dropped all the clothes off at the dry cleaner this morning, it should be done by noon.

And that about sums up my preparation. I should still make a list of people that I need to look at up that the meeting. Stuff some recent pictures of my kids in my wallet, I always feel like such a bad parent if I have to admit I don't have any pictures of the kids on me.

There are a few things that I look forward to. One is that this might be the first time in a month that I can get some decent sleep. It looks like most activities are over by 10:30 pm, and start up again around 8 am. For someone who's been sleeping 2-4 hours a night that sounds fantastic. I might even get some shut-eye on the 3 1/2 hour flight, although I doubt that. Twelve people from my department are on the same flight, there will be quite some yakking away.

I also look forward to meeting up with colleagues I don't see very often, because they do their research on the research centers around the state and not on the main campus like I do. In fact, I'm sharing my room with one such friend.

And then there is one other exciting event scheduled, which I will report on later. It's a surprise. You'll have to come back to find out what it is. Ha!

Silence

Why is Makita so silent these days? Has she had enough of blogging?

Well, here it is guys and gals. I'm hoping that this is the home stretch, and is it ever torture!

1. My adviser is leaving at the end of this month, and although I have a co-adviser for the Fall semester it will not be the same.
2. I have to prepare and present two posters at a meeting at the end of July.
3. My first dissertation draft is due in early October. That is 3 months from now!
4. I'm still frantically doing experiments to get the necessary data. I just harvested one yesterday. While I'm processing those samples (plants, soil, and disease data), I have to set up the next experiment.

To prepare the posters for the meeting I've been up until 3-4 am in the morning almost every day for the past 2 weeks. There isn't enough coffee in the world to keep me awake anymore.

So you see, I hardly have time to read blogs (and I miss doing that dearly!), so writing blog posts myself right now is a bit tough, But I'll try to do better.

By the time October comes along it will be clear where I stand. Whether my work will be deemed good enough to graduate or not. December is the ultimate deadline for me. In terms of immigration status and funding. If I don't graduate by December, I will not graduate at all. And that would be a shame. So I suppose this means more sleepless nights, and less blogging for the foreseeable future. I will put up a post in the near future to introduce the newest addition to our family, so stay tuned!

Refinancing an adjustable rate mortgage

It's been an interesting few weeks. A bit scary, which among other things accounted for lack of posts.

Yes, we were amongst those that got a sub-prime adjustable rate mortgage two years ago. The rate was scheduled to go up on July 1, 2008. Two years ago that seemed really far away, and with the prices of housing going up so dramatically at the time, we would actually have some equity by the time July 1, 2008 came around.

The housing market went a little up after we bought the house and then came down with a thundering crash. May 2008 arrived, and we had to either pay the higher interest rate as of July 1, or try to re-finance. We received notice that our interest rate was about to go up to 8.5%, which would not have been an unsurmountable raise in monthly payments, but we'd rather not have to fall back on that option.

Over the past 2 years a lot about our situation has changed. We've worked very hard to keep our credit noses clean. Our income situation has improved some, becoming more stable and predictable. That helped. Our credit scores were more than 100 points higher than 2 years ago.

The main problems we were facing were:
The loan-to-value ratio was rather high, because our house did not go up in value as much as we had predicted. And of course, there's this pesky little thing of neither P1 nor I being US citizens or green card holders, and many loan programs required one of those.

On the bright side, since we went through the mortgage process 2 years ago, we had some experience, and we shopped around quite aggressively for low rates and lenders that would accept our immigration status. Also, we have invested a lot in the house over the past 2 years. Both actions paid off for us.

Our house appraised at a value high enough for us to qualify, the home improvements were assessed at $9,000, and without that we would not have qualified. We closed on our refinancing last Friday with a 6% interest rate, which was the best of 6 offers we received. There were other offers for the same rate, but with higher closing costs.

It's nerve wrecking though, even after the closing. The closing agent sits on the money for 3 business days (in our case, add the weekend to that), before they dispatch the funds (you know, just in case we change our minds). Then they dropped it off in the mail, and it took our previous lender a full 24 hours to process the payment once they received it. But I just checked, and it's been paid off!! Yeeehaw!!

I think in many ways, we are a success story. We bought the house a year and a half after we declared bankruptcy with a sub-prime adjustable rate mortgage. We worked on improving our financial situation and carefully managed what we had. We improved our home, and shopped around for a mortgage. We successfully refinanced a less than perfect mortgage that allowed us to buy a home when we otherwise would not have been able to. And now we have the home we wanted, a much better fixed rate, and a regular 30 year mortgage.

So here we are: homeowners with a regular old mortgage. The bank that owns our house right now cannot increase our rates. We are very pleased!

How many more will now be protected?

This morning I brought F1-1 (the oldest, male) and F1-3 (the youngest, female) to the doctor, for their annual well-child checkup. They are both doing fine. The oldest is 15 percentile for weight, 75 percentile for height (tall and thin), while the youngest is 15 percentile for both (short and thin). But perfectly healthy.

I discussed my wishes with the doctor, and she agreed it would be a good idea to immunize the oldest (he's 12) with Gardasil. The nurse came in, looked at the two kids in the room and asked in a very surprised voice who the Gardasil was for.

You see, Gardasil is a vaccine that is recommended and FDA approved for girls 9 years and older. It prevent infection with certain strains of human papilloma virus (HPV) that can cause genital warts and cervical cancer. Boys don't have a cervix, so, they don't need the vaccine, right? But who spreads HPV? Isn't it the boys who go from one girl to the next who spread it? In my opinion, both sexes need to be immunized. By the, I think that prevention of genital warts is reason enough, but prevention of spread to girls who then become at risk for cervical cancer, makes it a no-brainer to me. By the way, it appears that the virus causes not only genital and rectal warts in men, but also penile cancer.

I explained this to my son, and he agreed that it would be a good idea. Frankly, in my opinion, my 12-year old is not even close to being ready for sex, but that can change in a short time-span, and I don't really expect he will come tell me when he is. But I do want him and his future partners to be protected.

I explained it to the nurse too, and understanding came over her like a wave crashing on the beach. She told me she has three sons, and she will have them immunized too. I wonder, how many girls will be protected from getting the virus from these 4 boys?

Needless to say, my insurance will not cover the shot, because it is recommended for girls only (whoever thought that one up? Way to go!). At $251 per shot, and 3 shots needed in a 6-month period, it is also rather expensive. Still, it needs to be done. And the powers that be had better realize quickly that to protect the population, both sexes need to be immunized. In my opinion, not immunizing both boys and girls is rather sexist.

Shocker of the day

My boss has been really busy lately. I just figured there was another grant proposal deadline coming up. He's been hiding in his office, keeping the door closed and such. Finally he crawled out yesterday and called a lab meeting for today. To break the news: he's leaving! As in, he's quitting his job and moving to greener pastures. In 3 months! I'm shocked, shocked, I tell you.

I may have mentioned this before, but my adviser is just the nicest, most decent human being, and he certainly deserves good things happening to him. I suppose this is a good thing for him. And I've really tried very hard to show my support for him, and to wish him luck in his endeavors. I've tried not to be selfish, but the truth is: I'm worried sick.

He has done some of his homework already and he has lined up alternate advisers and placement for his students. He has another adviser in mind for me, and under the circumstances, I think I agree with his choice. I have to think it over, and talk some more to him about this. For now, I'm going back to being shocked!

Arrays again

Considering the fact that I'm supposed to present a poster later this summer on the microarray data that my adviser has collected in collaboration with another lab, I figured it was time to brush the old data off again. I must admit that I've been so busy that I haven't taken a look at the data in about a year.

My research has taken off in a different direction, then I got busy taking written and oral qualifying exams, and currently I'm furiously trying to finish up research by the end of the summer to hopefully graduate in the Fall. In addition I had gotten a bit frustrated by my inability to find software that would allow me to look at the data, maybe suggest some biological pathways involved, without taking one or more courses in how to work the software. That dilemma hasn't changed yet, but the date of my poster presentation is creeping ever closer. If you know of any good idea for affordable microarray analysis software, don't be shy, tell me about it.

I'm currently looking into an online package called Expression Profiler. Wish me luck.

Happy shopping!

At first I thought it was one of those e-mail scams: "You won 2 million dollars," or some equivalent. However, the amount was a lot less, and it seemed so... legit.

I did some research, remembering that indeed, I had done a survey like that, and eventually responded. And voila! I actually did win $200 to spend at Amazon.com.

Ooooh, now what? I'm going to buy stuff that I would otherwise never get, but that I really want! Suggestions are welcome.

Final results for the shuffle meme!

Here are the final results of the shuffle meme, with links. If you're not into heavy metal, you might want to skip the first link. The song carries very special meaning to me, and the lyrics hit home, especially in these times of war, but it's not for everyone. Also, not always could I find actual video on YouTube, but the songs were there.

CAE wins with 4 right, 1 half right
Anonymous got 2 (I actually know this is a single individual)
Sciencewoman had 1
Canada had 1

1. Gun down cold on a raw deal, home turf my battlefield. Expendable youth-Slayer

2. You can dance, you can jive, having the time of your life. Dancing queen-ABBA

3. Stuck on you, got this feeling down deep in my soul that I just can't lose. Stuck on you--Lionel Richie

4. Te regalo una rosa la encontre en el camino. Bachata Rosa-Juan Luis Guerra

5. There is a rose in Spanish Harlem, a red rose up in Spanish Harlem. Spanish Harlem-Various artists, Tom Jones was the one guessed, I listened to Rebecca Pidgeon's version, which I will post on this blog in June.

6. Bomba! Un movimiento sensual. Azul, azul (Bomba!)-King Africa

7. Del caribe aflora, bella, encantadora. En Baranquilla me quedo-Joe Arroyo. I've never been able to sit still when this song is playing. Gotta move the feet, gotta move!

8. Por alto esta el cielo del mundo. Obsesion--Various artists, I listen to the version by Los Trio, the one linked to is by Pedro Flores.

9. Is this the real life, is this just fantasy. Rhapsody-Queen

10. No hay dia que pase que yo no me acuerde de ti. Contra la corriente-Marc Anthony. This is my all-time favorite song from Marc Anthony. I don't like his English-language songs, but I'm absolutely crazy about his songs in Spanish.

11. Toen ik van de week je brief kreeg na een lange tijd. Hou me vast-Ruth Jacott. I could not find a video of the whole original song, I did find a latinized medley version of the songs "Vrij me mij" and "Hou me vast," the latter starts at 1:16.

12. Tu vida se parece a una novela. Mujer de novela-Grupo Niche. My all-time favorite latin band, they have numerous fabulous songs for listening and dancing. And I think this is my favorite song by this band.

13. Let me tell you now all that's on my mind. The only one-Lionel Richie

14. Kijan zot fe m'pa ka kompran zot ka viv kon si pa ni pwoblem. Zouk la se sel medikaman nou ni-Kassav'. Great song in the French-Carribean style called Zouk.

15. Man it's a hot one, like seven inches from the midday sun. Smooth-Santana

16. Old pirates, yes, they rob I; sold I to the merchant ships. Redemption song-Bob Marley.

17. Joseph's face was black as the night . Under African skies-Paul Simon and Linda Ronstadt. The version linked to is with Miriam Makeba.

18. Procura seducirme muy despacio. Procura-Chichi Peralta. Fantastic song to dance to, by Chichi Peralta who used to be part of Juan Luis Guerra's band 4:40.

19. In the sunlight of your smile, in the summer of our life. Beautiful Maria of my soul-Los Lobos. Soundtrack from the movie Mambo Kings. This is the English version, there is also an equally beautiful Spanish version.

20. Takmis koluna elin adamini. Simarik-Tarkan.

21. Acordate Moralito de aquel dia que estuviste en Urumita y no quisiste hacer parranda. La gota fria-Carlos Vivis

22. If blood will flow when flesh and steel are one. Fragile-Sting

23. Without dreams of hope and pride a man will die. Children of Sanchez-Chuck Mangione. No good video of this song, but a decent sound version.

24. When the lights go down in the city. Lights-Journey

25. Would you know my name if I saw you in heaven. Tears in heaven-Eric Clapton

Shuffle meme

Links added!! Like CAE I think I'm going to have to give more clues, it looks like my musical choice is too uncommon. But I still think that even the songs in Spanish should be recognizable by most people with some interest in latin music. Clues in RED.

I was tagged by CAE for the shuffle meme. She's tagged me a few times before, and no matter how much I promised I would do, I always postponed it, until I never did it. This time I'd better do it right away, with some necessary caveats. If nothing else, this post should demonstrate how eclectic my music collection is, and this is just the tip of the iceberg!

Step 1: Put your MP3 player or whatever on random.
Step 2: Post the first line from the first 25 songs that play, no matter how embarrassing the song.
Step 3: Post and let everyone you know guess what song and artist the lines come from.
Step 4: Strike through when someone gets them right. (I'll do bold)
Step 5: Looking them up on Google or any other search engine is CHEATING.

Caveats:
1. Since I don't have my iPod with me, I'm using iTunes in shuffle mode.
2. At first I was going to skip all non-English songs, but that made it almost impossible, since so much of what I listen to is not in English. I did have to draw the line somewhere, but I left some in. Good luck on those, it will be a fairly select crowd that can guess those. For #14 and 20, I had to actually look up the lyrics. I don't sing them, I dance them.

So here we go:
1. Gun down cold on a raw deal, home turf my battlefield.
This heavy metal band was one of my brother's favorite. It's a very intense song about the waste of young people being sent off to war.

2. You can dance, you can jive, having the time of your life
3. Stuck on you, got this feeling down deep in my soul that I just can't lose

4. Te regalo una rosa la encontre en el camino.
One of my favorite latin artists. This song was a HUGE hit in the eighties. He is originally from the Dominican Republic.

5. There is a rose in Spanish Harlem, a red rose up in Spanish Harlem.

6. Bomba! Un movimiento sensual.
Definitely a song to dance very provocatively to. I'm looking forward to link to the YouTube version of this song once it's been guessed. Multiple artists, anyone will be excepted.

7. Del caribe aflora, bella, encantadora.
Ok, I admit, there is no way I would have been able to guess this one myself. It's about a city in Colombia. Again, very popular and danceable.

8. Por alto esta el cielo del mundo.
Multiple artists have performed this, any one of which is acceptable. It's somewhat of a classic ballad.

9. Is this the real life, is this just fantasy

10. No hay dia que pase que yo no me acuerde de ti.
This artist is a popular singer/songwriter, originally from New York, but his parents were Puerto Rican. He used to be married to a former miss Universe, and is currently married to a popular female singer, and they recently enlarged the number in their household.

11. Toen ik van de week je brief kreeg na een lange tijd.
This is a song in Dutch, and it is unlikely that anyone visiting this blog would guess it, except those from a handful of countries.

12. Tu vida se parece a una novela.
This song is my favorite song from my all-time favorite Colombian band. They are very popular, but mainly because of some of their older songs. I dont know of any very recent songs that are so popular.

13. Let me tell you now all that's on my mind.
There is another song on this list by the same artist, and that song has been guessed correctly already. He was very popular in the 80s, you don't hear much of him these days, but a close relative of him is often in the tabloids.

14. Kijan zot fe m'pa ka kompran zot ka viv kon si pa ni pwoblem.
I had to look these lyrics up, because I didn't know how to pronounce or spell them. The group that performed this song is from the Caribbean and has defined the genre (I think). This song was wildly popular in the 80s, and describes how the genre is the medicine everyone needs (or something like that).

15. Man it's a hot one, like seven inches from the midday sun

16. Old pirates, yes, they rob I; sold I to the merchant ships.
Come on!! How could no one get this one? Very popular artist from the Caribbean, sadly diseased. He definitely represents the genre, and made it popular worldwide. A lot of songs had messages criticizing world politics, anti-war, anti-discrimination.

17. Joseph's face was black as the night Sorry, I couldn't find a good video of the original with Linda Ronstadt, this version is live with Miriam Makeba.

18. Procura seducirme muy despacio.
The artist that sings this song split of from the band that performed #4. He may not be quite as well known as the original band, but most people listening to latin music are likely to have heard this one. Great beat, my fingers itch to link to the YouTube video.

19. In the sunlight of your smile, in the summer of our life.
There are both a Spanish and English version of this song, it is part of a soundtrack. The movie is about two men from Cuba who move to New York (?), one of which is madly in love with a woman who stayed behind.

20. Takmis koluna elin adamini.
I had to look up these lyrics too. I don't know the words, or how to pronounce them. It is a Turkish song, nice beat. The artist makes kissing sounds in the song.

21. Acordate Moralito de aquel dia que estuviste en Urumita y no quisiste hacer parranda.
Folksy song from Colombia, nice beat. The artist is from Northern Colombia and his songs reflect the genres that originated there. This song is one of his more popular ones.

22. If blood will flow when flesh and steel are one.
The artist is from England (come on CAE, you can do it!), and the band he was part of was very popular too. This solo song was released in the mid-late 80s.

23. Without dreams of hope and pride a man will die.
The artist had a very popular album in the late 70s. His genre is jazz. According to Wikipedia he has released more than 30 albums since 1960.

24. When the lights go down in the city
25. Would you know my name if I saw you in heaven


Tags: If you read this, you have a blog, and you haven't done this meme before, consider yourself tagged. But don't feel pressured, I won't hold it against you if you don't do this. I can't be too judgmental, considering I don't do memes too often myself.

Say NO to violence against women

Please sign your name on the list of UNIFEM, the United Nations Development Fund for Women. Say NO to violence against women. It's enough! No more hitting, beating, punching, kicking, shooting, rape, burning, yelling, you name it. No more violence. I just signed my name. Now go ahead and add yours.

That t-shirt is the wrong color!

When PZ posted this link, and I clicked on it, the title of this post is the first thought that came to my mind.

The guy in the cartoon looks way too much like Steve Burns in Blue's Clues (ask me how I know). The green-striped shirt is a dead giveaway. The only thing is, although Steve is kinda goofy, and he doesn't usually find the clues first, he strikes me as a very logical guy, a good scientist.

Picture credit

Steve patiently collects his data (the clues), doing all sorts of smart things while collecting the data (like counting to 10, matching shapes, recognizing colors). He takes careful notes in his handy-dandy notebook, writing down each clue (a good notebook is the scientist's bible). And then he sits down in his thinking chair and carefully analyzes the data: he thinks, thinks, thihihinks!!. He uses his mind, takes it one step at a time, and collaborates with subject matter experts (pre-schoolers) to figure out what the clues mean, and what Blue wants to do. And when he doesn't feel well, he concludes that eating Mr. Salt and Mrs. Pepper's vegetable soup will make him feel better, which seems much more intellectually sound to me, if not tastier, than prayer.

Steve's got this scientific thinking thing worked out much better than the guy in the cartoon. I propose to change the shirt color on the guy in the cartoon. It doesn't reflect well on Steve. And Steve is my son's hero. We demand Steve's name be cleared!

Managing references 2: The search

This is part 2 on managing references. Here is part 1.

So I needed to find some software to manage my references and citations that would overcome some of the recent changes in my computing preferences. The change to MAC and my adviser's and university's preferences resulted in a switch to Office for MAC, and this made reference manager obsolete.

I searched the internet, and eventually came on a Wikipedia site that compared several reference managers. I found this very useful, because it provided a lot of information on a single webpage, allowing me to narrow it down pretty quickly.

I first made a list of managers that would work on my MAC:
1. 2Collab
2. Aigaion
3. BibDesk
4. BibSonomy
5. Bibus
6. CitULike
7. Connotea
8. Endnote
9. JabRef
10. Papers
11. RefBase
12. RefDB
13. Zotero

Moving on to the next table on the page, I realized that I wanted to be able to share my database with my adviser and colleagues. This might not be necessary but I don't like to be restricted. The boss uses EndNote, so the software needs to export to EndNote. This cut the following options from the list: 2Collab, Aigaion, BibDesk and CiteULike. The import format options did not remove any additional programs. Nine programs left.

Citation styles. In my field several different styles for in-document-citations and lists of references are used. I'm not entirely sure which one I'd like to use, but again, more options are better than less. And if my style is unavailable, being able to define my own might help. BibSonomy, Connotea, and JabRef were scrapped. Because Bibus still allows user-defined styles, it's hanging in there. Down to 6.

1. Bibus
2. Endnote
3. Papers
4. RefBase
5. RefDB
6. Zotero

Not all of the table provide useful information for the elimination process. The next one that will help me bring down the number of choices is wordprocessor integration. That is a BIG plus.

The restriction that EndNote does not work on the 64-bit versions of Windows, is of no consequence to me, there is no information on Papers, and I'm too lazy to go find that out right now. If Papers becomes a serious option, I'll have to go back and look at that. But at this point we say goodbye to RefBase and RefDB. We have the following left:

1. Bibus
2. Endnote
3. Papers (keeping this Word-integration thing in mind)
4. Zotero

The next set of tables don't change anything to this list, so we go back to the first table where the prices are listed. Price is important, but I'm willing to pay some for great functionality. And as a student, I do often get deep discounts. That is why price only now comes into play.

1. Bibus-free
2. Endnote-Academic version roughly $100
3. Papers-$24-42
4. Zotero- free

I was really interested in taking a closer look at Zotero at this point. Free sounds great, but m ore than anything, the integration in FireFox, the browser I already use anyway, sounded intriguing. Clicking on the Bibus link, I read that Bibus' functionality of MAC is limited. It should probably have been eliminated quite a while ago based on this. Bibus is out. Papers was 29 Euro, not unreasonable, if it's good I'd be happy to pay that. Endnote, being the most expensive of the options, even as a student, was eliminated. So this left me with Zotero. I'm trying it out right now, and I reserve the right to hate it, and go back to the list to choose something else. But with free you can't go too far wrong. If it doesn't work out, I can simply remove it, nothing lost but some time, right?

To be continued....

Managing references 1: Background

In the past couple of weeks, I've started writing. No, I don't mean blog posts (as some of you may have noticed), but really writing. As in: dissertation writing. I figured that now that I've recently reviewed the literature for my oral qualifying exam, this would be a good time to start writing chapter 1, the literature review.

In the past I've used Windows/XP, and for as long as I can remember using wordprocessors, I've used WordPerfect. The Reveal Codes option in Wordperfect is, as far as I know, unmatched so far. It was particularly cheap when I bought the academic version for students. To manage my references and citations, I used Reference Manager, and last year I purchased the latest version of that too.

Things have changed. My laptop was 7 years old last year, and consequently a bit slow (read: maddeningly slow!). I bit the bullet and converted to MAC/OsX. What a joy! One tiny little problem, WordPerfect has sold out to Microsoft, and is no longer available for MAC. I got Parallels Desktop, and ran Windows on my MAC, just so that I could run WordPerfect and SAS (for statistical analysis). I did send an angry e-mail to WordPerfect about this. I've been a loyal customer since the late 80s (version 4.2!), and this is what I get in return?

Then problems arose, because my adviser wanted to go back and forth with different edited versions of an abstract I was working on, and this didn't work well if I worked in WordPerfect, and he worked in MS-Word. Luckily, I could purchase a license for Microsoft Office for MAC through the university bookstore for about $12. This had the added advantage that the editorial office hands out dissertation templates for MS-Word, so that would greatly reduce the time I had to spend on formatting. Only now, Reference Manager doesn't work on my MAC. I need a new way to manage my references.

I will need to keep track of several hundred references (books, journal articles, abstracts, and such), be able to integrate the citations seamlessly into my dissertation. This started off my recent search to a reference manager that would:
1. work on Word
2. work on MAX OS X
3. allow me to format my references according to several different journal styles
4. not cost a fortune.

To be continued...

With apologies to Queen

Shamelessly copied from Stranger Fruit. It was simply too good. Originally from MartinC. All about the "movie" Expelled here.

Bensteinian Rhapsody

Is this stuff real science?
Or is it just fantasy,
That belongs in a place like
Bob Jones University?
Just close your eyes,
Don’t think, just accept ID
I’m a game show host,
I don’t know biology,
But this sleazy bunch, told me so,
It could be lies, how would I know?
So long as the check clears, it doesn’t really matter to me,
To me.


Anyone? I just filmed a sham,
Put some lies into your head,
Libelled Darwin, coz’ he’s dead,
Honor, you know I once had some,
But now I’ve gone and blown it all away-
Anyone? ooooohhhhh
Was it mean to tell those lies?
You’d learn more science by watching Rocky Horror-
Anyone? Anyone? My reputations now in tatters-

Too late, my crime is done,
Dembski told me I did fine-
Behe’s squirming, (he’ll be fine),
Goodbye science lessons-you’ve got to go
Gonna leave your kids behind and hide the truth
Adolf, oooooh (a shame he wasn’t atheist)
I’ll just have to lie,
I’ll just pretend that he wasn’t Christian at all-

- guitar solo -

I’ve got a little animation of a cell,
When in haste, copy paste, yes indeed that was the plan, though-
Copyright infringement lawsuit noose is tightening on me-
Sternberg’s ethics, (they’re a shocker)
How ‘bout Crocker, (off her rocker)
And what to say of Guillermo ? Guillermo-oh-oh-oh
I’m without tenure, and nobody loves me-
He’s just a headcase, embarrassing his faculty-
Spare us the whines of this mediocrity-
Please I pray – on my soul, Will you make it so-
Guillermo! No-, we will not make it so - make it so-
Guillermo! No-, we will not make it so - make it so-
Guillermo! we will not make it so – make it so
Will not make it so- make it so
Will not make it so – make it so
No,no,no,no,no,no,no-
That Eugenie, she’s a meanie, but there’s much worse godless foe!
Beelzebub sent Dick Dawkins and his friend, PeeeeZeeee- PeeeeZeeee, PeeeeZeeeeeeee!

So you think you’ll teach children, maybe open their minds,
Study nature, alter stem cells for cures of all kinds -
Or maybe, stop Gods plan that’s HIV,
Well if I had my way, I’d close you all down out of fear!

Science it doesn’t matter,
Lets teach theology,
Just pray when cancer strikes you,
Just pray there'll come a cure from ID

I should have stuck to game shows…….

Note to self

This post serves as a reminder to my self. May I return to it in 30-odd years and find that I've lived up to it. If not, may this post embarrass me and make me change my ways.

To love your children means to respect them. To respect them, means to accept their choices without comment. You may not always agree with the choices you make, but that is rather irrelevant. Although we may see children as little horcruxes, you have to let that piece of you live it's own life.

No matter what choice your children (or anyone else for that matter) make, it is theirs to make. And under no circumstances do you have the right to do things differently in their house. For example, if they use a dishwasher to wash and dry their dishes, and really prefer to do their dishes that way, you have no right to sneak into the kitchen early in the morning to quickly do the dishes by hand, and put them away before everyone gets up. It doesn't matter that you think using a dishwasher is wasteful, and for purposes of this discussion, it doesn't matter who is right. If you are asked to do thing their way or not at all, the right thing to do is to respect their wishes. No matter how much you think you're trying to help them, you're not helping by doing things differently than they are used to.

If their house is a mess, you can only clean it up if you are specifically asked to help out, or if you offer to help, AND the offer is accepted. If they say: "no thanks" they mean: "No, thank you for the offer, but we either prefer to live in the mess, or we prefer to clean it up ourselves. At any rate, if you clean it up I may never find my stuff again. No, thanks." This does not mean you're useless as a parent or grandparent. It just means that cleaning up is not what is expected of you at this point in time.

It might also not be appreciated if you tell them over and over again, how you do all your laundry by hand. It's not really fair to compare a single-and-retired-person household with one with three kids where both parents work full-time. But again, that's besides the point. If your children want to use a clothes washer for every piece of clothing they own, that's ok.

This is not to say we cannot have useful conversations about anything. There are ways of talking about things, and giving opinions, without being critical. And when you've giving your opinion, and your children find it a useful suggestion they will incorporate it into their lives. There is really no need to mention it ten more times to indicate that your way really is the best way. If your children do not change their ways, even after you have enlightened them about the best way, it doesn't mean they don't love you or like you.

The trick to getting along with your children is to treat them like you would any other adult. With respect, and this respect will likely be returned. Add a dose of true caring and love, and you can hardly go wrong. You can have intelligent discussions, and joyful reunions without strain. Isn't that the kind of environment you would want to see your grandchildren in, and the kind of example you want to set for them?

The week

Passing my orals was the beginning of a very productive week for me. Rarely have I been that motivated. Sadly, my productivity was ground to a halt by one of our cars breaking down on the weekend. It didn't help matters that some of the kids are home on Spring Break. Our car is still in the shop and it's going to cost a whopping $1200 to get it fixed. Another care is out of question right now, so we have no choice but to throw good money at a not so good car, in the hope it will last us for at least another year. We've had a rental car now since Monday, which we can no longer afford. It has to go back tomorrow, but our car might not even be finished yet by then.

This should highlight one of the problems of being a mother and a graduate student. Because P1 makes more than I do, and he has a (semi) permanent job, he cannot afford to simply take off some time to hang out with the kids. That is exclusively my job. If the kids get sick, or they are home for any other reason, I'm the one that has to stay home with them. It's not that I mind hanging out with the kids, but it is always my research that has to take a back seat. And that is incredibly frustrating.

Posting is light as a result of an overdose of kids and car trouble right now. If all goes well though, we'll return to our regular scheduled program soon.

Definitions

When you do research, the outcome often depends on the questions you ask, or the way you phrase them. For example. This study that is mentioned on ScienceDaily. Thanks to Coturnix for pointing this out.

According to the study results sex lasting 3-13 minutes is better than longer sex. What struck me, was how they measured sex, and I quote:

"...from penetration of the vagina by the penis until ejaculation."

It isn't just me here, right, who thinks that this definition is a wee bit sexist, and mildly male-oriented? No, wrong. It is big-time sexist, and grossly male-oriented. Nowhere was the female orgasm mentioned. If the male ejaculates before the female has an orgasm, is sex over? I think you might find a woman or two (billion) who disagree with that. And I suppose, vaginal-penetration is the only activity that counts as sex.

And what about gay sex? I guess when two women have sex, it's not really sex, since there might not be any penetration. And when two men have sex, I suppose one can have an orgasm, and then it's over. Had the question been put a little different, the results might have been dramatically different.

I'm hoping that this is just bad reporting, and that the researchers had a better, more representative way of assessing the time sex lasts. But it sure sounds that at the very minimum, gay sex wasn't considered at all, and heterosexual intercourse was defined by decidedly male actions without any consideration of what the woman (who presumably makes up 50% of the interaction) experiences.

And I quote some more:

"Past research has found that a large percentage of men and women, who responded, wanted sex to last 30 minutes or longer."

You think that maybe questions were phrased better? It is likely to change the 3-13 minute range.

1 year

It's amazing! It's been a year since I started this blog. Twelve months and 134 posts later, I must say that it's been even more rewarding than I could have imagined. Thanks to all who stop by, be it occasionally or regularly, thanks to those who comment, and those who don't. Happy blogiversary to me!!

April 1

Note: I really did pass my quals. It was not an April fools joke. Although when the date was schedule some naughty thoughts of what I could do to my committee did occur to me.

This morning I told F1-1 that his science teacher had e-mailed me to remind him of his comprehensive exam today. He looked at me blankly. I stared back "What? she didn't tell you? You have this oral exam today, and all the science teachers in the school are going to be asking you questions and it will be 80% of your grade for this school year! You're telling me you haven't studied for this?" [put on really grim face].

I could literally see the blood draining from his face. It was quite priceless. Hey, at least someone was feeling the same thing I did. He was downright panicked. I let him steam in his skin for quite a while, but eventually could no longer stand it, and asked him if his teacher hadn't told him it was April 1st either.

The relieve on that kid's face. He was seriously sweating it, and I think he's going to school to play the same joke on a bunch of his friends, although I suspect the exam will turn in an all-topic, worth 95% of your grade kind of thing.

Oral exam.... again

This morning, I passed my PhD oral qualifying exam. After I failed on the first try, this wasn't an easy process. I haven't been this nervous since my high school final exams in another life time.

Do I feel elated? Not quite the right word. I'm relieved to have it over with, but more than anything, I have this incredible urge to run around and do all the things that I wanted to do the past 6 weeks, but couldn't because I was either depressed from not having passed the first time, or too busy preparing for today.

I have stuff to do! I have to prepare two posters to present at a national meeting this Summer, I have to write a paper to submit to a journal, I have 3 experiments to set up, two to keep going, one to analyze. I need to blog more, and spend time with my family.

Aaahh, my family, what can I say? They have been indescribably wonderful through it all. The kids, have driven me crazy, demanding my undivided attention in both good and bad ways. In doing so, they have forced my mind away from my failure, forced me to think about things other than oral exams. They have forced me to see, again, that getting this degree is the best thing I can do for them in the long run. That I need to do this for them as much as for myself. My husband, tried his best to keep the kids away from me yesterday. I had gone into our office to study in a quiet atmosphere, and instead of P1 and the kids being far, far away, they all congregated in my room, making me laugh, and happy, even though I had this big dark cloud hanging over my head. I wouldn't have been able to this without P1. He's the best. Most of all, because he would have loved me no less, if I had not passed today. He wouldn't have been critical of me. He would have lashed out at my committee members, without ever considering that I did something wrong. He is my rock.

My adviser. He was supportive from the start. He probably was too overconfident for my first exam, but he was visibly proud of me today. He's always been very upbeat, with nothing but good things to say about me. He protected me from other committee members, while making sure they could ask their questions. He told me to refuse to guess, and I did, and when I was pushed harder, I refused even harder, and said that guessing wasn't going to make me a better scientist. I wasn't about to allow anyone to laugh at my foolish guesses.

I could go on and on, but this is probably enough. I passed, and I have to go. I have work to do. Have a glass of wine on me this evening! I know I will.

I'm not expressing my true feelings here!

As Coturnix and Mike O'Risal did, I checked my blog with the cuss-o-meter. How could I possible have come up with 0%?

Of course, the website that does this, is simply trying to get traffic for an online dating website. Which is why I'm not pasting the picture here. You'll just have to believe me when I say my score was 0%.

Anyway, if this is true, I'm not doing a good job. This blog is precisely so that I can cuss at the world as much as I want, and the world can read about it if they are so inclined.

Cuss-related anecdote:

When I first got to the US, I noticed within a few weeks that my level of cussing increased dramatically from what it was just a few weeks before back home. Nobody here understood what I was saying anyway, so if I just kept the tone even enough, I could say what I wanted, and I sure did so. Moreover, I'm familiar with a language that is perfect for expressing strong feelings (both good and bad), for which I find English quite inadequate. It was very satisfying to express myself, even though that would have been considered inappropriate at home.

Hooray for women being the change they want to see!

When Sciencewoman asked Alice Pawley to join her on Scienceblogs, she asked for help choosing a name. I thought it might be too obvious, but it seemed to me, "Sciencewomen" was THE choice. Even though Alice is not strictly a scientist, and quite proud of being an engineer, she most certainly uses scientific principles in her work, and the name was simple. I suggested it, and lo and behold, it was chosen as the new name for their joint blog. And to reward me for coming up with the obvious, I got this in the mail today:



I'm so proud!

Artificial photosynthesis

From Sciencedaily. Photosynthesis involves the use of light energy to oxidize water, and reduce carbon dioxide, thus forming sugars, and releasing oxygen. Scientists looking for new ways to produce hydrogen as a fuel source from renewable sources, report that an inorganic metal cluster can oxidize water to hydrogen and oxygen. This process of artificial photosynthesis uses a rare transition metal. Problem solved? Not quite:
Botar explains the next step: "Now the challenge is to integrate this ruthenium complex into photoactive systems, which efficiently convert solar energy into chemical energy". So far, energy is still obtained from a chemical oxidant.

The mysterious ways of Jesus

According to Mike O'Risal every few weeks somebody spots Jesus somewhere, and the image ends up on Ebay. What he doesn't realize, is that this is how Jesus helps his faithful followers. This is just his way of making sure that they get adequately rewarded for recognizing his holy image. And sometimes even those who don't believe in him! I wonder how that works. If you don't believe in Jesus, how can you be convinced he's the peeping tom?

Atheists all around

Shameless blogwhoring. Cuttlefish does it again!

Watch out! Those atheists are everywhere.

Ancestry

Alice at Sciencewomen opened up quite a can of worms. She invited others to blog about their ethnic stories. Where do I start? I'll try to do this systematically. Considering the terms, I prefer to use ancestry over ethnicity, but that is just my personal choice. I don't know the full story of my ancestry, but I know some, and can make educated guesses about other parts. People find it virtually impossible to place me. My first name is Indian, my middle name French, my last name German, I probably look a little Hispanic (I've been addressed in Spanish before), but my accent is none of the above.

Roughly, my recent ancestry (if you go back long enough, we're all out of Africa anyway), is likely about 1/3 African, 1/3 European, 1/3 Asian. It works out something like this.

From my mother's side: My mother's mother was half Indonesian (Asian) from her mother's side, her father was half Belgian, half Turkish. My mother's father was of mixed African descent and European descent, I don't know in what ratio. I might be wrong about his ancestry, but I'm probably not far off.

From my father's side: My father's mother was half Chinese from her father's side, while her mother was a mixture of African, European, and I seem to remember she once mentioned Jewish ancestry too. Like my mother's father, my father's father was a mixture of European and African ancestry, likely not 50/50, I think his parents were of recent mixed ancestry too.

I don't think I want my ancestry any more generations further back than that. It gets too complicated.

When I first came to the US, I never filled out the part of the forms that asked for my "race." Even if I had been so inclined, what the heck would I write? I was everything, yet nothing on the list. However, when I needed to fill out a W-2, I was required. I was told I could not get paid otherwise. I refused, the form came back, and I didn't get paid the first period. I studied the form. These were my options: White, Black, Hispanic, Pacific islander, Asian, and Other. But if I filled out "other" I had to mention what "other" was. Eventually, I checked "other" and filled out "human." The darn form never came back again, and I got paid the next period.

My Atheism

Inspired by a recent conversation with my mother, and kicked into high gear by VWXYNot, I figured this would be a good time to elaborate on my position as an atheist. It seems my mother never truly understood what I did (not) believe, which is probably an indication that we don't talk often enough. (Note to self: talk more often to mother).

I was not raised in a religious household. My mother had been raised catholic, my father protestant, but I don't remember my mother ever going to church or praying as I grew up, and my father was an atheist for as long as I can remember. I may be wrong about this, but I think my mother takes the position offered by Pascal's wager. (2nd note to self: talk more often to mother). She's not entirely convinced there is a god, but just in case there is one, she's unwilling to piss him off. Of course, I never did ask her what she thinks would happen to her if all this time she had believed in the wrong god, and one day she'd have to explain to her (the real god) why she wasted her entire life thinking the Jehovah guy (or someone like him) was real.

I did talk to my father about religion on numerous occasions, so I do know his position fairly well. His atheism was a result of what organized religion has done to people and the world over the centuries, and because it was incompatible with the scientist in him. This wasn't always an easy position. When my brother died very young, it hurt my father to the core to know that there was no afterlife, and that death was permanent, and that my brother's life was over except in our hearts where our memories keep him alive.

I don't think I ever truly believed in a god. I did on occasion attend church and a synagogue for some reason or another, and I'll admit to a few occasions where I shot a prayer up "just in case." But actually believe in the gobbledegook? No. Never.

My ex-husband always considered himself a christian, but didn't seem to mind initially that I was not. Eventually it became apparent that it was important for him that I went along with his christianity. So even though it didn't mean a damn thing to me, and he knew it, I got baptized, and we got married in a church. The funny thing is, he knew perfectly well that I didn't believe in the nonsense at the time, and that was fine, as long as I bowed my head and said the words. Ridiculous of course. My father (and I presume, my mother) at the time, didn't understand why I would do this, and just assumed that I had converted. Nothing could have been further from the truth, and in fact it was the beginning of the end of the marriage. Religion became a major source of contention, as my ex insisted on me attending church with him and performing in ceremonies that was all just a big joke to me. I wanted to keep the peace, and it really wasn't all that hard, and it didn't shake my lack of faith. I was never remotely tempted. In the beginning it wasn't a problem, but as time went on, it became clear he thought he could convert me. Fat chance! No amount of attending church or pretending to pray was going to change my mind. Quite the contrary!

Would I do it again if I had to do it all over? Probably, yes. For the same reasons as in the past. It didn't mean any thing to me, and therefore it didn't really bother me. Unlike maybe, someone who believes in Zeus, but has to pretend to believe in Buddha. That might be a problem, because one would have to betray the god one believed in. I didn't betray anybody, because I didn't believe in a god, and I didn't even betray myself, because I never fooled myself into thinking I did believe. It was all very easy. Bow head when told to do so, fold hands, say silly words, end with "amen." Very simple. The songs were kind of boring, but the choir sang nice. I can still appreciate the melodies and the poetry, even if I don't believe in it, can I? I like reading fiction too. And there was a sense of community that was very comforting. I could certainly understand why people were attracted to that kind of institution.

I don't think I could do that any more now. As I get older, I'm becoming more set in my ways and lack of believes. I don't "believe" in anything. I accept things based on the evidence I see for it. I haven't seen any evidence for the existence of god, gods, golden-egg laying ducks, elephants with 7 trunks, talking trees, flying tigers, immaculate conception, and the like, and therefore I don't believe in any of these. As any good scientist, I reserve the right to change my mind if I do see evidence to the contrary of the things mentioned above, or other unmentioned things I don't believe in. Pictures of one religious figure or another on pieces of toast are not evidence.

P1 doesn't believe in god either. But I'm a much more radical atheist than he is. He is for example in some ways superstitious, whereas I can joke about it, but no, I really don't mind taking cashier #13. In so far as there are degradations of atheism, I'm more atheist than he is. I must say though, that the fact he was atheist, was a big point in his favor when we first started dating. The older I get, the less able and willing I am to live with a believer in supernatural beings. It's a good thing P1 is very unlikely to change his mind in a hurry, because like before, it would probably be the beginning of the end. I would lose respect for him in a big hurry, and respect is another big pillar of our relationship.

I find it rather insulting if people ask me how I explain the existence of morality without believe. The bible is obviously not a source of people's morality (have you ever *read* that book? It's morals are horrible!), and if you think that you need to believe in god to remain moral, you don't need god, but the police right next to you all the time.

Although some people in my position might call themselves agnostic, and say that they withhold an opinion on the existence of an imaginary skydaddy, like VWXYNot, I'm perfectly happy stating that I don't believe god exists, until I'm proven wrong. And I mean *proven* wrong. I'm afraid that bible does not constitute proof, so you can spare me the quotations.

Oh, and if you wonder if people who don't believe in god can love (now who would come up with some ridiculous statement like that?), read the poem by Cuttlefish.

Back!

Well folks, I'm back. In more ways than one. I traveled last week to meet up with my mother in New York. I had either a really bad cold or a relatively mild flu, and was coughing, congested, you name it. Being in 20-degree weather didn't help matters. But it was fabulous! I bought the unlimited use for a day subway pass for $7 and had a blast going around town. I spent an entire day at the American Museum of Natural History. What a great experience.

But most importantly, I got to hang out with my mother. The older I get, the better I seem to get along with my mother. I really do admire her, especially for the way she's bounced back after my father passed away in June of last year. Like me, she misses him like crazy, but she sure is keeping very, very active. She's starting on her own PhD some time later this year.

I suppose that sort of settled it for me. I don't have a choice. I have put so much time, energy, blood, sweat, and tears into this PhD thing, I just have to give it one good, last shot. I have a year, I'm going to try and make it work.

I'm still undecided about the singing committee member. My adviser wants him to stay on. I don't know what I'm going to do.

On a lighter note, when I returned home, hubby came to pick me up with F1-2 and our youngest, F1-3 in the car. I got happy smiles from F1-2, but when I greeted F1-3, she turned her head and looked out the window. She was visibly pissed at me! Unbelievably, she ignored me for the better part of an hour, and whenever I tried to talk to her or offer her something, she would dramatically turn her head and look away. Eventually she did acknowledge my existence, and by now we're best friends again, but it took quite some time. While I was gone, I talked to her twice a day over the phone, and she sounded very happy. My husband says she was fine, and did not give any indication that she missed me, except for the first day when she asked for me a few times. Strange kid! If this is any indication for what's in store for us, we're in big trouble.

Knock...

Knock... knock.... Is anybody still there? You didn't all leave yet, did you? You didn't wait for me to come out from underneath my rock? Oh well. I guess I have to start building my readers base from scratch. If you did hang around waiting for me, thanks. I usually bounce back pretty quickly after disaster strikes, but it took me a while this time. And I may still not be entirely my old self, but that may have more to do with the horrible cold virus I've contracted than continued depression due to not passing the oral exam.

Over the past week and a half or so, I've been puttering around the lab, mainly doing stuff that I would have to do anyway, no matter what my decision is. Like cleaning up, organizing my samples, gathering my data, and such. My adviser is his usual friendly, happy self, full of encouragement. One of his best friends in the department, who is also on my committee, urged me to go on. He insisted that it's feasible to finish, and he agrees with my adviser on what I need to do to finish. Now, if we could just get the rest of the committee to agree....

A few minutes ago, I sent out an e-mail asking which dates int he end of March would be good to re-do my exam. That is a decision of sorts. At least it means I'll be taking the exam again. I reserve the right to bail out any time I feel like it, though, and call the whole thing off.

The thing is, what else would I do with myself? I'd be miserable at home, being in the lab is what I do best, it's what I love to do. So, gradually, I've re-entered the lab, even though I mainly do housekeeping right now. I have to write up a report on everything I've done so far, which is essentially the second chapter of my (intended) dissertation. If it wasn't for the nasty bug I caught, I might have made some progress on that.

On top of that, I'm leaving town for a few days and will not be back until Saturday afternoon. So, I'm putting any major things on hold until then. Meanwhile, I expect to be back to blogging as usual from now on. Glad you stuck around!