No More Facebook

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Facebook was a wonderful way for me to keep in touch with a lot of different people, but I deleted my account a few weeks ago.

By the time I deleted my account, Facebook had given me A LOT of reasons to leave:  their increasingly complex and deliberately obtuse privacy policy and options, the frequent changes that defaulted to making information I was only interested in sharing with friends public (like status updates), making private information public without my knowledge, making it impossible for me to keep some information private without deleting it, making it difficult or impossible to remove some information, and using their terms of service to stifle innovation and (terrifyingly) bring criminal charges.

I know that my leaving Facebook has absolutely no effect on the site and isn’t going to influence their policies.  That’s not why I left: I left Facebook because it offended my ethics and endangered me professionally.

If you’re worried about privacy on facebook, but don’t want to delete your account, try this tool to help you fix some of the privacy issues.  Otherwise, delete your account and check out the Diaspora project.

What I’ve Noticed

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Mining companies like to claim that they’re bringing economic benefits, but cleanup and health costs far outweigh positive contributions to the economy.

After thousands of years, we’ve finally discovered what the argonaut octopus uses its shell for – it’s essentially a ballast tank.

HUGE step: we’ve synthesized life.

Autism doesn’t have anything to do with vaccines, but children of migrant parents in Europe are at higher risk.

Susan B. Anthony wasn’t anti-choice, no matter what this obnoxious group claims.

The economy is fossil fuels.

Public pressure actually changed the rainforest destroying policies of Nestlé.

Because of decades of unsustainable fishing practices, we are now faced with a very unpleasant choice: the loss of 20 million jobs now or the permanent loss of the fish.

Cypripedium fasciculatum

Cypripedium fasciculatum

The BP oil spill is an American Chernobyl.

Try this fun logic puzzle with the not so fun title non-normalizable probability measures.

Ultrasound could be a good method for male contraception.

We still don’t fully understand why the bees are dying, but at least they aren’t dying everywhere, as was previously believed.

The end of Usenet.

Acupuncture might not be completely useless.

Ugandan women have high rates of maternal mortality that their health minister blames on poor training for health professionals.  Considering how much of that mortality is due to obstetric fistula, focusing on preventing child rape might go further than additional training for nurses.

Oh look, MORE sexism in academia.

The water crisis in Yemen continues to cause conflict and cost lives. We should expect much more of this kind of thing as the climate continues to change.

Many of the people I went to college with probably shouldn’t have gone to college.  And that may have been a better strategy.

Texas is rewriting history for its public schools:

Several changes include sidelining Thomas Jefferson, who favoured separation of church and state, while introducing a new focus on the “significant contributions” of pro-slavery Confederate leaders during the civil war.

The new curriculum asserts that “the right to keep and bear arms” is an important element of a democratic society. Study of Sir Isaac Newton is dropped in favour of examining scientific advances through military technology.

Sculpture by Mia Liu

Sculpture by Mia Liu

“The other side” of Arizona’s immigration debate

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I’m not happy about the new immigration law in Arizona, but one of my aunts thinks it may be a good thing.  This morning she suggested I more carefully consider “the other side” because of the discarded items in the Sonoran:

It’s definitely true that Oregon Pipe is littered with the backpacks, water bottles, and other garbage of illegal immigrants entering the country, but problems of illegal immigration don’t justify a discriminatory law that probably won’t actually solve problems such as trash in the Sonoran.  Besides, the Republican Arizona legislature and their supporters don’t seem very interested in environmental issues.

Perhaps we should consider how our country’s policies are intimately linked to the horrific torture and murder of hundreds (and maybe thousands) of Mexican women and other violence, or that we helped put in power and supported dictatorial regimes that murdered their citizens indiscriminately, later leading to civil unrest and poverty.  We created or contributed to many of the problems that force people to flee their homes and families.  Addressing those problems is the real way to deal with illegal immigration in the long term.

In the shorter term, INS needs serious reform – not just for our current immigration issues, but for coming, far more serious immigration issues that we expect due to climate refugees (150 million in the next 40 years alone).  The impact of immigrants (legal & not) on our economy isn’t nearly as bad as most people make it out to be and it is actually positive in some sectors – I don’t think a guest worker program with steps to citizenship is bad idea at all.

I think that we can find practical solutions that don’t force us to sacrifice our rights or act inhumanely, but the AZ legislature isn’t heading in the right direction at all.

YUX

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Tree rings are fascinating and informative data, but the gazillions of formats used by different measurement and analysis programs can be a real pain in the ass.  Additionally, there are a plethora of reformatting programs that all do slightly different things.  Of course, many times none of them do exactly what you want.  I’ve often had to feed data through 2 or 3 programs and/or write my own formatting program to get it in a usable format.  Sometimes I feel like I spend more time dealing with formatting issues than actually analyzing our data.

If you aren’t having a problem with tree ring data formats, you should probably move on.  If you are, hopefully this will help.

This post is going to be about some common issues I’ve had with the formatting program YUX.  If you’re having trouble with COFECHA, try this.

Size problems

The first issue has to do with the size of the imported file.  If it’s larger than about 52kb, YUX will crash.

Also, you can’t include more than 200 series or 4096 years without causing YUX to crash.

Mixed up data problems

If you don’t insert a character for missing data, YUX won’t give you an error, but it will seriously fuck up your data.  Consider the YUX year by series output data for a set of six trees below.  What we expected was the output on the left; what we got was the output on the right.

Click to embiggen

I’ve color coded each tree and its rings so you can see what’s going on more easily.  Basically, YUX is sliding the tops of the series as far to the left as possible.  If the last year of growth for all of your trees isn’t the same, it’ll do the same at the end of the series.  We get around this in one of two ways: either we tell YUX to enter something (like NA) for the missing data (under option 3 in YUX), or we make sure the file we feed YUX is in order from longest to shortest series.  The latter solution only works when the last year of growth is the same for all trees and there are no gaps within a series.

If you need more help, I recommend searching or emailing the ITRDB Dendrochronology Forum.  They are remarkably helpful and very friendly in their answers to even the most basic of questions.

Coral

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Gorgonian Coral

Gorgonian Coral by Timothy G. Laman

If you want to see a coral reef, I recommend booking your tickets soon since they’re dying quickly from natural causes (made worse by people) and human causes.

Overfishing removes too many of the fish that eat seaweed, which then starts growing like crazy and poisons the corals.  Since coral reefs are important nurseries for many of the fish we like to eat, overfishing creates a nasty situation: not only are stocks suffering from too much fishing, it’s even harder to replace stocks because by removing the fish, we destroy their nurseries.

Does anyone know what fish are ok to eat from a sustainability perspective?  I would really rather not give up sushi.

To cheer you up, I recommend reading about how baby corals find a reef.

The Placebo Effect & the Power of Ritual

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Most (all?) cultures combine medication with ritual – something simple like ginger or pepto for your stomach combined with a prayer of some kind, for instance, or something less familiar, like this Paraguayan man who chants and sings before searching for the healing plant.  After growing up with chronic pain in a church that believed strongly in faith healing, I have conflicted feelings about ritual.  On the one hand, it really didn’t help me and made me feel quite guilty. On the other hand, many people seemed to gain real comfort from it.

I’ve been thinking about why rituals are associated with medicine in so many cultures, and I think it has something to do with the placebo effect.  This fantastic article summarizes how the placebo effect could be used to help with symptoms of some illnesses, how to get benefits of placebos ethically, and how the placebo effect may work.  I was especially intrigued by the idea that the medical care (the “ritual” of medicine) may help medication work better :

Some researchers argue that the real source of a placebo’s effect is the medical care that goes along with it–that the practice of medicine exerts tangible healing influences. This notion has received support from experiments known as “open-hidden” studies. Fabrizio Benedetti, a professor at the University of Turin Medical School, has conducted a number of these, in which patients receive painkiller either unknowingly (they are connected to a machine that delivers it covertly) or in an open fashion (the doctor is present, and announces that relief is imminent). Patients in the “open” group need significantly less of the drug to attain the same outcome. In other words, a big part of the effect comes from the interactions and expectation surrounding the drug.

I don’t think naturopathic medicine or homeopathy are going to cure my migraines, but I also think that there’s more to feeling better than taking a pill.  When I was a child with a bad chest cold, for instance, my mother would rub Vicks into my chest and back, wrap me up in blankets, and sing to me. It made me feel much better, and I’m sure that the care my mother gave me was just as important as the Vicks and Robitussin.