GEEKERY  
ADVENTURE  
CONTEMPLATION  

20170114

a journey toward parenthood

Nathaniel and I have wanted a child for a while, but we also wanted to wait until I was far enough along in my PhD program that I would not be sabotaging myself academically and professionally.  So after I passed my general exams (the Master's benchmark), I went off birth control and started tracking my cycles.  I was pretty confident it would only be a few months—most couples get pregnant within 3 or 4 months of trying.

A year of ovulation and pregnancy tests, temperature charting, and prenatal pills (just in case) later, we went in for the infertility diagnosis so we could move on to treatment.  That first year of trying was emotionally draining, but the following year of treatment was far, far worse.

We learned that my body produced too much FSH (follicle simulating hormone), which usually means that a woman has a low egg count.  Even if one could control the FSH somehow, the underlying issue of too few eggs would remain.  My day three FSH reading was usually around 24 or so.  Less than 9 is considered normal for childbearing age—to put things in perspective, my FSH reading was what should be more typical of a premenopausal woman in her mid forties, and I was only 28.  Over 19 means that many fertility centers won't even try to help you with your own eggs.  It also meant that our Aetna insurance was not guaranteed to cover anything, but we could appeal and make a case for coverage.

At first, I was still optimistic.  Of course I would get pregnant, right?  But then I didn't really respond to the pills they gave me to "ripen" more eggs.  So we moved onto the more powerful injectable medications.  In addition to going in to get my blood drawn every few days (which made me look like I was shooting heroin) and getting intrauterine ultrasounds regularly, I learned to give myself shots in my stomach to both encourage egg development and induce ovulation.  And despite all the needles and early morning poking and prodding, I still only produced one egg at a time.  Well, once I produced a lucky two.  Dealing with insurance was also beastly, though our center handled the brunt of it.

At some point during this process, Nathaniel and I realized that we might never be able to have our own biological children and we each went through our own depressions.  I was angry when television shows, movies, and books used pregnancy as a plot point, especially for a single sexual encounter.  I had a hard time being happy when friends and family announced their own pregnancies.  I had to avoid Facebook because everyone seemed to be talking about their kids.  Church was torture, especially when I listened to lessons or talks from the pulpit on parenting or families.  People unknowingly teased us about not wanting kids or asked us when we were going to have them or if we wanted them.  I had been that person previously, asking inappropriate personal questions, but now I know better.  As the receiver, I would respond with a smile, then go home and cry.

Then our story took a happy twist: after about two years of trying, I was pregnant.  We were actually taking a break from fertility treatment and were not at all expecting it.  N pulled the test out the trash and squinted at it to see the first signs, and I took a dozen more tests through the following days.  A huge burden had been lifted, and the grief had passed, replaced by joy.  I was looking up strollers and other baby equipment, and making plans on when to tell everyone.  I figured out how much weight I needed to gain.  I found a doctor and had my first appointment.  I got rid of my sharps container and used kitty litter to safely get rid of my remaining injectable medications.

I reminded myself that not everyone gets this lucky.  That year of grief taught me a tiny sliver about what it would be like to go through a lifetime of infertility.  It wasn't until I thought I had broken down every single emotional barrier that I got pregnant, or so I told myself.  I needed to gain that humility—I needed to be okay with every option, including adopting (which was easy—I was planning on adopting if I didn't get married), having a special-needs kid, or getting an egg donor (this last one was the hardest).  I needed to want to be a parent so badly that I would realize that being a parent isn't about defining my own identity, but about being willing to fill that role for a child who needs it.  I thought I had come so far.

And then I miscarried at just before 8 weeks.

I was in denial.  I kept reading online about how you can bleed and still be pregnant, even after passing pretty substantial blood clots.  I was in contact with my doctor, and holding out hope for the ultrasound in a few days.  I was tense as the technician looked.  After a while she apathetically told me that she didn't have anything to show me, then left me (without bothering to send in my equally anxious husband) to go talk to the doctor.  There I was, half naked and alone, with the devastating confirmation that I was no longer pregnant.  The icing on the cake was the terrible break-up music being pumped over the speakers.  After a while, she came back and, despite my having told her about the miscarriage concerns, she tried to tell me that maybe I just wasn't as far along as I thought.  I might have visibly rolled my eyes at her—I had been monitoring everything pretty carefully and knew when I had ovulated.  The baby was gone.

We took a while to mourn the loss, but eventually the grief passed.  We tried to look at the silver lining: now we knew I could get pregnant.  And so it was never as hard as it was before the pregnancy.  The darkest times had passed.

We decided that we were going to be parents one way or another, and that if I couldn't get pregnant again, then we would adopt.  We had the capacity to be loving parents, and we wanted to use that capacity.  Some infertile couples end up using that love through volunteering or their jobs, but given the nature of our careers, adoption seemed like the best fit for us.  (Though we understand that it's not the right choice for everyone.) That made things easier some days, but it was still a question of when: when should we make the transition from trying for biological children to trying for adoptive children?  Not yet, we felt, especially with so much uncertainty ahead with graduation looming and possibly new jobs on the horizon.  We didn't want to get all set up with the approval process only to relocate.

I started up acupuncture, since my insurance covered it.  I also consumed plenty of Chinese medicinal teas, many of which were incredibly bitter.  Eventually I stopped going because it was a lot of effort for no obvious benefits—I imagine it could work for some people, but it wasn't my thing.

My church asked me to speak on Mother's day.  I thought long and hard about it, and decided to do it. I basically just cried continuously, but told everyone that Mother's day can be hard for some people.  It can be hard for people who have lost their mothers, or don't get along with their moms, but also for women who have never married, who can't have children, or who have lost a child.  I told them that we were struggling to have kids and that biological children just might not be in the cards for us.  But I also gave thanks for my mother, grandmothers, and other women who have touched my life.  I learned to turn despair into gratitude.  Or at least to try to do so.

Eventually, we went back to western medicine.  We were going to do maximum dosage injectables on an IUI cycle to see how I responded.  If that went well, we could move to IVF.  But I didn't respond well.  At full dosage, I still only produced one egg, which meant that IVF wasn't worth the risk.  I took a home pregnancy test at the end of that cycle and saw a very slight line, but then I bled the following day.  Because the medications can mess up urine tests, it's not clear if it was actually a pregnancy, albeit short lived.

When we next met with the doctor, she told us that we should only try a few more IUIs on low dosage oral medication.  She said we had maybe a 5% chance.  Imagine taking twenty alternate universe versions of this situation: only one will be successful.  It's about the chances of rolling a total of 3 with two dice on a single throw.  It's low.

We wanted things to be more black and white.  We wanted "you can't have children" to make the transition to adoption easier.  But they kept stringing us along.  Adoption comes with its own set of emotional challenges, such as a mother choosing you to adopt her child, then deciding that she wants to keep her child.  Of course she has that right, but it's still difficult for the potential adoptive parents.  So we pushed it down the road...we decided that when we moved away from the area in a year or two we would begin the adoption process.  After about three years of trying, we were ready to be parents, but we could wait a little longer to make the logistics easier.

On another break from treatment, due to scheduling issues, I took another pregnancy test.  It was ever so lightly positive.  I tested again in the following days, and it was clearer: I was pregnant again.  But there was not a lightness or joy this time.  Instead, I felt mostly dread.  When would the miscarriage be?  Every twinge was a sign of loss.  Here comes the sorrow, here comes the despair.  I couldn't let myself enjoy it, at least not until I heard the heartbeat, or so I told myself.  But in the meanwhile, I was looking up really morbid statistics, like the chances of stillbirth or late-term miscarriage.  I even worried about having a child that would die young.

It wasn't until around the time I got a call from my nurse at the infertility center that I started to get excited.  She was calling to check in and make the plans for the next treatment cycle.  I was in a meeting at the time, so I listened to her long message with detailed instructions on how I was going to need to get medications from two different pharmacies (a standard one for the pills and an online order for an injectable to induce ovulation).  So I left her a message in return to say let's put a hold on that for now, and let's where this pregnancy goes.

The following day she asked me to check in with my insurance to see if they would cover early monitoring with them, and for the first time insurance was a breeze.  The insurance guy I talked to was incredibly helpful and cheerful, and it looked like everything was going to be covered.

I think there's something about telling other people that starts to make things real, even if those people are medical professionals and not friends or family.  We still were not really to tell loved ones yet, since in some ways, we would rather have waited to find out ourselves until things were more certain—the roller coaster of excitement and loss is exhausting.

The first ultrasound mid-week 5 went as expected—we saw the amniotic and yolk sacs.  But mid-week 6, I had some severe cramps in the early hours of the morning.  Here it comes.  N went for a walk with me, and we watched a Star Trek episode in the middle of the night to get our minds off things.  But the cramps turned out to be digestional, and N had similar ones soon after.  Still, it put us on edge, to be reminded of how suddenly miscarriage could come.

Two days later, we went in for the next ultrasound, and saw and heard a heartbeat of 116bpm.  That meant the miscarriage risk was around 18%.  It put us a little at ease, and even encouraged us to get a little excited, but the risk was still there.  Risk will always be there.

We told our immediate families and some close friends.  The weeks ticked by.  I defended my PhD and graduated.  Now I'm 28 weeks along, and everyone who sees me in person can tell I'm pregnant.  Frankly, we're lucky.  There are many people who deserve to be parents and don't get that chance.  And while I am very happy with out current situation, I would never give up the three years of heartache—it taught me some much needed empathy.  The pain of this journey may fade, but we won't forget it.  I think it makes me a better person, even if I still have a long way to go, because it's stripped away a lot of my desire to judge others and taught me about how to be more sensitive to others' hidden experiences.

For instance, I developed a much deeper respect for those that become parents either through an egg or sperm donor, or through foster care and adoption.  Being a parent is about the love you give your child, and while giving birth and breastfeeding are ways of showing that love, they are only some ways to do so.   And biological similarly does not necessarily help you be a better parent.  Again, it's all about the love and care you give the child.  This applies even if you aren't a guardian, but are an aunt or uncle, teacher or friend—if you have the love of a parent, you are a parent in your heart.

I also learned that there are so many kinds of infertility that it isn't really helpful or encouraging to share a success story for a type of infertility that doesn't match what the person is going through.  Like don't try to inspire someone with a story about surrogates when the person is having trouble making their own eggs.  There are a bunch of articles about dos/don'ts.  Even if you think you don't know anyone struggling with having kids, whether it's secondary or primary infertility, or recurrent miscarriages, I guarantee that you do.  About 6% of married women of reproductive age struggle with infertility.  That means that if you have 100 female acquaintances that get married at some point, about 6 of them have, are, or will struggle with this.

Miscarriage is a whole 'nother ballpark.  The stats on that are a little trickier, because most miscarriages are mistaken for periods.  Recurrent miscarriages (3 or more) happen in about 1% of women, but it feels like almost every woman has a miscarriage story, either her own, or one from a sister, mother, or close friend.  Miscarriage is incredibly common.  I say this not to diminish the emotional impact of a miscarriage, but to remind folks that 1) if you've gone through a miscarriage, please remember that you aren't alone and there are people out there that want to love and comfort you and 2) someone you know and love has gone through a miscarriage, even if you don't know about it—use that as a reminder to always be kind, sensitive, and loving.

There are also people who don't want kids, but get pregnant accidentally or feel constant social pressure to have kids.  There are infertile women who judge those who get abortions, and people on birth control who judge those who are pregnant.  It's so, so messy.

The more open I am with my own history, no matter the context, I find that many other women have their own stories to tell, be it about infertility, miscarriage, or being pressured to have kids.  And men aren't immune—just because they might not go through the same physical processes doesn't mean they don't feel the emotional pain.

So if you don't know, don't assume.  Just try to understand, but be very careful with your personal questions.  I learned not to ask questions about having kids directly—what you think might just be an ice breaker could actually hurt someone a lot.  I'm sure I am guilty of this in many domains, not just infertility, but my go-to ice breaker is now some variant of the vague, "So, what are your interests?"  (If you've made it this far, I'm probably preaching to the choir.)

And yes, you shouldn't need to tip-toe around worrying about everything that could possibly offend someone.  As long a you cultivate true love and respect for other people, that will shine through.  But that kind of love requires putting in the patient effort to understand our fellow men and women, just as one should to understand a child.

I'm putting my story out there because I believe it's important for these issues to be more public.  When you think you're alone, it hurts all the more.  But you aren't alone.

20160710

Black Lives Matter, Blue Lives Matter: Let's fix this mess

I have stayed silent on this issue because I haven't known what to say.  I didn't know how to begin: how could I contribute anything meaningful to the thousand of voices saying things more eloquently and passionately?  And then I read this today: a letter from a mixed race woman to quiet white friends.  This made me realize that not saying anything is a way of saying something.

So I want to say this: black lives matter and blue lives matter.  The recent (and not-so-recent) killings in both directions are completely unacceptable.  While I haven't been personally impacted by these events, I have loved ones on both sides, as do many people. But they aren't even "sides"; as Trevor Noah said, you can be pro-cop and pro-black.

Something is obviously broken, and I want to do my part to fix it.  For now, maybe all I can do is acknowledge that there is a problem and try to understand it better.  But if everyone did that, we would already have made a lot of progress.

The question isn't whose lives matter.  They all matter.  The real question is: what will you do to make the world better and safer?

Edit/addition: I just wanted to be clear that while "all lives matter," I wasn't trying to dismiss the BLM movement in any way.  BLM focuses on making the world better and safer for black citizens.  This is very necessary, and if successful, they will end up helping the world in more ways than they originally intended.  All I was trying to say is that it doesn't matter who you're trying to help, as long as you are doing something productive and not just dismissing the situation.

20160509

the first of the season

Today I harvested the first greens of the season—baby spinach and pea shoots.  The garden has started off lovely.

There are days when I can't believe it's not June yet, and then there are days I feel stuck in March.  But mostly, I just feel tired, and the date doesn't mean anything.

I started teaching seminary in January.  For those unfamiliar, it's a 6am religion class for high school students.  At first, it was very fun, but as time drew on, my excitement turned to exhaustion.  I love deep study of religious texts, but getting up early is not my strong suit.

Combine that with working in the youth program (a second church job), along with something about finishing my PhD in 2016, and you get a stressed, sleep-deprived woman. When I'm not worrying about implementation bugs in my statistical inference algorithm, I'm worried about teens cutting themselves.  It's fun.

I'm trying to find some balance now.  N is helping me so much; one thing he's doing is teaching seminary two days a week.  I need to start doing more things that aren't work and church. Gardening qualifies.

20160125

Suicides and "The Policy"

For those of you who aren't aware, the LDS church instituted a policy regarding LGBT families back in November. One of the major criticisms of this policy is it could potentially increase the suicide rate of LGBT Mormons. And recently, some numbers have been thrown around about the number of LGBT Mormon suicides since the policy was instituted.  I haven't fact-checked these, but as of January 23, the numbers I've seen were around 32.

I don't understand the policy, and I don't particularly want to defend it, but I do believe in statistics. The number of suicides alone is not enough to say that the policy has caused any change in suicidal behavior. We need to compare to the number of LGBT Mormons who would have done the same if there were no new policy announced.

We can't actually know what would have happened, but we can estimate it.  Ideally, we'd have data on LDS LGBT suicides rates, but I couldn't find anything quantitative.  So let's assume that most of these cases are Americans, and the average suicide rate in the US is 0.0211% per year, or 0.00451% of the population in the same 78 day period. The church reports around 6,466,267 members in the United States. This means that, if Mormons are typical in their suicide rate (which they seem not to be), there should be around 285 Mormon suicides in that same time period. Around 3.4% of the adult population identify as LGBT, so that takes the estimate down to about 10 suicides.

All these numbers come from Wikipedia, so I'm using questionable sources, but I didn't want to put too much time into this. But with this very loose estimate of suicide rate, it seems there would be a tragic increasea 220% increase.  That seems a little too large to be believable to me.

We could mirror stats on Jewish LGBT youth to help account for the fact that LGBT folks in religious communities are more likely to attempt suicide.  Along these lines, if we assume there are 219,853 LGBT Mormons and that they are four times more likely to commit suicide than national average, that would put our estimate closer to 40 suicides in the same time rangethis would mean that there was actually a decrease in the suicide rate since the policy was enacted.  This may not be as surprising as it sounds, since there was significant backlash against the policy, so LGBT Mormons may have actually received a surge of support from friends and family.

The point I'm trying to make is that it is very, very difficult to make any causal attributions in this case (or in general).  Suicide is incredibly sad regardless of cause, and I also mourn that any person could feel rejected by their religion.  We must take steps to help prevent suicide, and we must be loving and welcoming members of our respective communities.  But part of knowing what steps to take is to get real data on what's happening, not just jumping to the worst conclusions.  Big changes require strong evidence.  And probably lots of hugs in the meanwhile.

20160118

HDF5: where have you been all my life?

Nathaniel introduced me to HDF5 around the winter holidays (because, yes, that's the kind of thing we talk about while on vacation), but I just started using in in earnest this past week via h5py.  I may never go back to plain text data storage if I can help itwe'll see if I can convince you too.

This is a script that simulates a big matrix off random data, writes in both formats, and reads from both formats.  The syntax is similar for both.

To compare h5py against plain text, I ran the above (plus timing code added in) 100 times with different random data.  Here are the average results.

plain text
h5py
writing
9.44 sec
0.0634 sec
reading
7.94 sec
0.0051 sec
row access
3e-5 sec
6e-4 sec
col access
1e-6 sec
0.016 sec
file size
239 MB
77 MB

If your data is small enough or you need to access almost all of it repeatedly, plain text files might still be good for you.  I usually sample rows from large datasets that eat memory like chocolate cake. So for almost everything I do, h5py is the clear winner.

20160101

A letter to potential Trump supporters

Dear potential Trump supporter,

Let me introduce myself: I'm a politically moderate American citizen.  I know that I am moderate because I went to an incredibly liberal college and am a graduate student at a reasonably liberal university.  Meanwhile, the church that I attend is strongly conservative—this means I regularly witness both sides of the political spectrum.  I do not belong to a political party, and all I want (politically) is for the leadership of this country to make the United States of America the best country it can be.

The reason I am writing to you today because we are allies in this.  If you are considering supporting Trump in 2016, you see some appeal in his call to "Make American great again!"

In my opinion, none of the leading presidential candidates are great this year.  Clinton's lack of honesty is particularly upsetting, if unsurprising for a politician.  But I would vote for her over Trump, and I want to explain why.

It all comes down to fear.  I know that the recent terrorist attacks have been frightening, and that the idea of an influx of refugees can be unsettling to some, but we cannot be afraid of change.  The world has always been constantly changing, and the real challenge is not to resist change straight out, but to use it to shape our world for the better. All of our ancestors have felt fear and weathered change—from the men and women of the Revolutionary War to displaced Native Americans, from 1960s Civil Rights Movement activists to the refugees of far too many wars.  Change has shaped our history and shaped us as individuals.  Look back on your life and notice that your proudest moments most likely come from working hard and having the courage to overcome your fears—so too with our country.

My main objection to Trump as a political candidate is that he sensationalizes this fear and uses it to gain media attention and support.  Instead of encouraging us to have courage and find real, lasting solutions, he fans the flame of fear, then claims that he is the one to take it away with proposals that isolate large swaths of the population.  This is not the dynamic I want to have with my President.  I don't mind brutal honesty—in fact, that's one of the things I admire about Christie—but it is not acceptable to isolate citizens and make them feel uncomfortable in their own country.  How would you feel if your religion or ethnicity were singled out in a negative way?  We need a leader who is honest and can solve difficult problems without resorting to pointing fingers at demographic groups, especially not vulnerable ones like recent immigrants and refugees.

Some of my ancestors came over from England before the Revolutionary War and others were more recent immigrants from Poland—but all of my ancestors were immigrants to America.  Some sought religious freedom as they crossed the Atlantic Ocean as Protestants or as they walked across the Great Plains as Mormon pioneers—they were religious refugees in their day.  How can America be great if we treat the modern equivalents of our ancestors with disdain?

So here is my plea to registered Republicans and Democrats alike: don't make me choose between Trump and Clinton.  I would love to see a candidate I can support with confidence.  Better yet, I want to vote with regret, knowing that either candidate would "do our country proud," just in different ways.  But as it stands, it looks like I will vote with a different kind of regret, knowing that neither candidate can push our country toward the excellence it so rightfully deserves.

I don't want to see America revert to some old greatness.  I want it to continually improve, becoming greater and greater with time, just as individuals should strive to be better with each passing day.  That doesn't mean indulging in new ideas without thought, nor does it mean retrenching to some idealized past.  We need to find the path that balances old and new, conservative and liberal, and just and merciful to make America not just great, but exceptional.

Sincerely,
A registered voter

20151027

Black box variational inference for gammas

Whoa, this has been a long blogging hiatus for me.  I have no excuses other than I've been enjoying life and working hard.  So not excuses, reasons.

I return with a super light-and-fluffy post to share a guide to black box variational inference for gamma-distributed latent variables.  BBVI is very powerful, but I was having trouble applying it to gamma variables, so I asked Rajesh (its creator) for some tips.  I wrote the guide to try out his tricks on a very simple model and share them with other folks that might be having similar issues.  Have fun, ya'll.

20150716

the fastest way to embed fonts in a PDF (for me)

I needed to submit a PDF today with all fonts embedded.  I'm working on a Mac with TexShop, and after much angsty Googling, I found lots of answers that seemed to work for other people, but for one reason or another, weren't working for me.

This is what I ended up doing: I created the PDF like usual with TexShop (without all the fonts embedded...I'm looking at you, Helvetica).  Then, I used pdf2ps to convert it to a postscript file, and then Adobe Distiller to convert back to a PDF (with all fonts embedded).  There may be other ps to pdf options that do the font embedding (Dstiller isn't free), but I was sure Distiller did, and I was on a timeline.

This is the PDF equivalent of "just reboot it."  It's silly that embedding fonts is such a messy process.