Entries in Life

Review: Genome

mah@everybody.org — Tue, 16 Jun 2009 02:15:52 GMT

The crude distinction between genes as implacable programmers of a Calvinist predestination and the environment as the home of liberal free will is a fallacy.

This sentence is the sum of what Matt Ridley does so well in Genome. He takes conventional wisdom and turns it on its head.

He doesn't shirk from the most dangerous ideas that can accompany genetic determinism — eugenics, selecting for ability — but he also wraps up his book with a very good argument that free will and determinism are compatible. Yes, you may have a gene that makes it means that likely develop Alzheimers. But that doesn't have to run your life.

And then he flips it around: isn't it better for you — including your genes — to determine what you become than for someone else — the state, your peers, or even your parents — to proscribe a path for you?

I have my own Libertarian tendencies (strongly tempered by
communitarian Orthodox Christianity), so I find his reasoning pretty compelling.

Matt Ridley is a special kind of journalistic genius. He can wade through volumes of technical arcana and create something like Genome, a very readable, very enjoyable, book. If you want an overview of what we know about genetics (or what we knew 10 years ago, at least) this is a great place to start.

But, the book is over 10 years old. A lot has happened. He hints as much when he talks about developments in genetics that happened in the decade leading up to the publication of the book — sometimes dramatic developments.

The story wasn't finished when he wrote it and I am starting to look around for something more up-to-date than this. Like any good author, he has captured me and left me wanting more.

This week at the GRC

mah@everybody.org — Fri, 29 May 2009 16:25:15 GMT

This week I'm at the Global Health Council's conference in Washington D.C. IntraHealth (my employer) is working hard to promote our work in Capacity building and, especially, the work we've been doing in iHRIS and other projects with Open Source Software.

Listening to great speakers like Hans Rosling of Gapminder.org is always fun and entertaining. Hans promotes a fact-based world in a way that challenges a lot of our assumptions about the world and isn't
afraid to kill sacred cows. “You should forbid the discussion of ‘HIV in Africa'” he said at one point after presenting data that showed the differences of infection rates across the continent. (I had a chance to meet Hans and talk to him about the iHRIS software when he came to IntraHealth's event Wednesday night. He asked lots of great questions.)

But it is often said that conferences are most useful for what happens in the hallways, not the main sessions.

From the people I met during the conference, it made my time at the GHC36 much more valuble to me and, I hope, IntraHealth. Here are some of the more interesting people that I met at the conference:

Martin Namutso — Actually, I met Martin last year in Uganda when I helped him implement a new Knowledge Management portal for the Ministry of Health in Uganda. He works as an Open Source developer in Uganda, implementing Open Source solutions like iHRIS. It was good to catch up with him and talk about future prospects.

I especially like the story Martin tells about his decision to focus on Linux and Open Source right out of school in order to compete for different jobs than most of his Microsoft-focused classmates.

Paul Biondich — Paul is one of the creators of OpenMRS. He's a pediatrician and software developer bringing an Open Source EMR (Electronic Medical Records) system to low-income countries.

When I mentioned that I had worked on a pilot project in which I created a PHP interface into the OpenMRS's database schema, he asked for my help in maintaining the PHP interface to the OpenMRS API in any future work I do. I hadn't found this when I was looking before, so I readily agreed. Working with OpenMRS's API instead of the database directly would be a much more robust solution to building PHP applications that work with OpenMRS.

Jørn Klunsøyr — Jørn is a registered nurse and software developer at the University of Bergen where he works on mobile projects like EpiHandyMobile to make form submission
with cell phones much easier. Using a web-based application, it is possible to build forms and push them to a low-power J2ME cell phones. Later, after the data has been gathered, the data is sent from the phone via SMS, GPRS, or BlueTooth to the EpiHandy server and, from there, to applications like Clinica and
OpenMRS.

When he demonstrated the software, I immediately saw applications for iHRIS: making it easy to fill in the iHRIS information in the field when a laptop and Internet access might not be available.

Eric Woods — Eric Woods is the Executive Director and Founder of Africa Aid. His org is helping distribute cell phones to doctors across Africa. While the phones are useful in and of themselves, he is looking for applications and partners that would make the phones that much more valuble for the doctors.

One example he thought of was a cell phone directory. Making the contact information in iHRIS available to other doctors would make it possible for doctors to more easily consult with each other and develop relationships that they might not otherwise.

These are just a few of the people that stand out from those that I met. After talking to them, I can see ways that we could work together and I hope that before we meet at GHC next year, I will have worked with a few of them.

Hearing Voices

mah@everybody.org — Mon, 18 May 2009 13:42:11 GMT

My friend Jim has a couple of good posts on listening to people from the “ex-ex-gay” movement.

I think he is right: the Church does need to hear from people who have tried to convert from homosexual to heterosexual — especially those Christians who believed they could “convert” their sexuality from being gay to being straight. We need to listen especially closely to those men and women who have sincerely attempted to alter their own sexual orientation and failed.

Most importantly, those of us (and, yes, “us” includes me) in the Church who believe that homosexual relationships are sinful need to listen.

Before I tell you what I hear, let me explain a bit about where I'm coming from.

It is no surprise that there are a lot of confused people out there. And by confused, I don't mean the men and women who are homosexual. No, I mean the people who think that being a homosexual is, in and of itself, wrong. There is nothing wrong with being gay.

I would go further, though, and say that if you are not actively seeking a relationship with God, then you are not better off in a straight relationship than in a homosexual one. The primary concern is our relationship with God. Everything hinges on that.

In fact, morality doesn't matter. Morality plays no role in our relationship to God.

This should be clear enough from story of the Publican and Pharisee that the Orthodox begin each celebration of Great Lent with.

The tax-collector was the morally disreputable person in Jesus' day — the person everyone knew was doing wrong, cheating them out of their hard-earned money. In his place, I can imagine a gay man, someone all conservative Christians would “know” is a sinner.

The Pharisee stands there proclaiming his piety, ridiculing the tax collector. Likewise, I see many conservative Christians holding themselves up as moral examples, making a very public display of their moral superiority. They kick and scream when they feel they've been wronged — when someone has stripped their courthouse of the Ten Commandments or a crèche — and loudly condemn those whose sins are more public.

The answer is not to hide your sin, not to be discreet about it. “All have sinned” and no one persons sin is any less or any more than anyone else's. No one is perfect. No one can exalt themselves above another or look down on another. Jesus told us as much when he said it was the tax collector, not the pharisee, who went home justified.

Which means, of course, that I'm no better than the most flamboyant, promiscuous gay man. In fact, I have no right to comment on anyone else's sin.

I'm reminded of the story of Abba Sisoes from the fourth century:

Considered to be a very holy and venerable man, many drew near to Abba Sisoes while he was on his death bed. In his last moments, he saw choirs of angels and archangels, not to mention prophets, Apostles and saints. Wondering what was going on, those gathered around him asked, “With whom are you speaking, Abba?”

“With the angels,” he replied, and indicated that he was seeking to do penance before he left this life for the next.

Knowing his holiness, one friend said to him, “You have no need for penance, Father.”

Abba Sisoes replied, “I have not yet begun to repent.”

Here is someone no one thought could be condemned, yet, truly embodying the spirit of the publican, he felt he had not yet begun to repent.

At this point, I hope I've made myself clear: I am in no position to proclaim my own piety or tell others that they are condemned.

So what does this all have to do with listening to “ex-ex-gay” people?

One thing I hear is a gay man (Peterson Toscano, founder of Beyond Ex-Gay) who struggled for almost 20 years and spent over $30,000 to become “straighten” himself out. It didn't work.

At this point, it sounds like a bad Scientology tale.

The first thing that comes to mind (and Peterson says as much) is the obsession with sex. Since the focus is on sex continually, it heightens the awareness and temptation. In another video, Peterson even says that he had more sex when he was trying to “de-gay” himself than he has since he gave it up.

But that part of it, obsession with sex, seems to be a part of American Christian culture. Witness sites like Book22.com (a Christian sex-toys web store), or Christian sex toy parties, or even Exodus International's methods — at least, those Peterson describes.

The focus is on sex. Sure, we pay lip service to putting God before all else, but the idea of a married couple voluntarily abstaining from sex? That would be unheard of! Lifelong voluntary “marital fasting” that some saints of the Orthodox church undertook seems impossible and ridiculous to us. As one person described this fasting:

Rather than repudiating the legitimate pleasure taken in eating and in marital relations, fasting assists us in liberating ourselves from greed and lust, so that both these things become not a means of private pleasure but an expression of interpersonal communion.

The second thing I hear is the singling out of this particular sin. As Peterson says: “I thought I couldn't be gay and a Christian.”

While all Christians are called to live pious lives, many of us struggle with a particular sin or temptation. Sometimes, we sin and are not aware that what we do is sin. So, again, the focus on homosexuality, singling it out for special attention and treatment, and not on whether or not homosexuality is a sin, is where we're going wrong.

Consider the advice that St. Theophan the Recluse gave to a young girl: When confronted with a thought to pursue some sin, don't fight it. Don't grab onto it to beat it into submission. Instead, let it pass and immediately pray the Jesus Prayer: “Lord Jesus Christ, have mercy on me, a sinner!”

By turning our attention to God instead of the thought to sin, we redirect our energy. Note, also, the parallels between the Jesus Prayer and the prayer of the Publican.

Finally, and probably most controversially, it makes me wonder about things that we universally agree are wrong today, but that, at the time the New Testament was written, weren't seen as huge sins.

Slavery, for example. I see no evidence that new Christians freed their slaves or started treating them humanely. I also know of no restrictions on ordaining slave owners.

Yet, today, we see any kind of slavery, not just the brutal kind sometimes practiced in the early American South, as universally wrong.

So what's the point of all this? What have I found from listening to this ex-ex-gay man?

Well, to be honest, I haven't learned anything. I have taken the opportunity, though, to think through my prejudices and to clarify them a bit. Peterson deserves our compassion: he has been ill-served by a church that tried to take him down a road he simply couldn't travel — by a church that made his sexuality more important than his relationship to God.

The focus should, as always, be on God, not our sin.

Melancholy thoughts

mah@everybody.org — Sat, 07 Mar 2009 05:20:47 GMT

Have you not looked down ... at a city and seen how much it resembles an ant heap, full of blind creatures who think their mundane little world is real? You see the lighted windows and what you want to think is that there must be many interesting stories behind them. But what you know is that really there are just dull, dull souls, mere consumers of food, who think their instincts are emotions and their tiny lives of more account than a whisper of wind. (from Soul Music by Terry Pratchett.)

Sometimes, as I'm driving down the road, I wonder about the other people I see and where they are going, how it might be interesting to follow a random person and see what they were doing.

But the reality is that if I did pick a person to follow at random, they'd probably be going to work or home. They'd get out of their car, walk in a building, and wouldn't emerge again for several hours. And whatever fantasy I entertain about how exciting someone else's life might be would only be met by the reality of how depressing my own vicarious skulking was.

Life is never as interesting as we think it should be. Life is never as exciting as we wish it were. There are bright spots, glimpses of excitement, but these are not the norm.

I suspect that by the time they reach 35, most people have given up on whatever they thought life was supposed to be when they were 16, 17, or 18 and resigned themselves to the mundane and everyday. Perhaps this isn't true for everyone, but this is how I've experienced life.

What is there to show
for all of our hard work
here on this earth?

People come, and people go,
but still the world
never changes.

The sun comes up,
the sun goes down;
it hurries right back
to where it started from.

The wind blows south,
the wind blows north;
round and round it blows
over and over again.

All rivers empty into the sea,
but it never spills over;
one by one the rivers return
to their source.

All of life is far more boring
than words could ever say.
(Eccl 1:3-8 CEV)

We can, as I think I have done, manage to find a great deal of satisfaction, even joy, in our mundane little lives. Once we understand how little the world cares of us, the love we share with those closest to us becomes incredibly precious.

Amongst the black backdrop of life, we find that our accomplishments, our family, our friends are valuable precisely because of what they mean right now, not because we've managed to change the world forever.

Our friends and children will carry on without us. Even most people who couldn't imagine life without us now will manage to create a new, mundane routine without us after we move on.

We can realize all this and still, while we're here, savor the love of our wife, rejoice in our child's accomplishments, and enjoy the company of a good friend.

There is no such thing as a legacy except in our imagination. There is only now.

We cannot change the world, no matter how hard we try. As Moses wrote, and Jesus later affirmed: There will always be poor people. Someone will always be in need.

Still, this is not an excuse to do nothing. There is no utopia, and Sisyphean our task may be, but doing nothing will only lead to depression, despair and despondency.

Hope can only live in action. Hope and Love are all we have. We cannot save the world or accomplish world peace, but we enjoy this brief little spark that is our life before it fades.

Salt of the Earth

mah@everybody.org — Thu, 05 Mar 2009 03:18:47 GMT

Via Dan Lyke, this story seems to be making the rounds: Christian Salt.

"I said, 'What the heck's the matter with Christian salt?'" Godlewski said, sipping a beer in the living room of his home...

"This is about keeping Christianity in front of the public so that it doesn't die. I want to keep Christianity on the table, in the household, however I can do it."

We could just say he was confused. Or, more likely, cynical.

Last I checked, Christianity was in no danger of dying out. And tagging music or food with the "christian" label never seemed like a good way to actually be a Christian.

But I do think he'll make plenty of money from all the publicity he is getting. (That, and any anti-semitic foodies will buy the stuff in bulk.)

Do not resent, Do not react, Keep inner stillness

mah@everybody.org — Thu, 26 Feb 2009 14:35:43 GMT

Yesterday, I wrote about parenting in a way that caused offense to a number of my friends -- including my wife. For this, I ask your forgiveness.

Partly, I wrote to get a reaction -- with a title like "Radioactive Content", this should not be a surprise. I've revised it since to be less reactionary, but I spent a lot of time last night and this morning thinking about it.

A good part of that time, I spent obsessing about what I should go say to defend myself, trying to come up with something devastating that I could say to make it obvious I was right and everyone else had better toe the line.

This is something I struggle with constantly: trying to bend the world to my will, to convince others that I am right, that I deserve to be listened to.

Of course, you all know better. I'm a narcissistic blow-hard.

So I sat down this morning and read over Do not Resent, Do not React, Keep Inner Stillness by Metropolitan Jonah.

In it, His Beatitude reviews everything I've learned from a number of Orthodox writers, but it was a review I needed this morning -- a reminder not to provoke others, not to "enflame the passions". It was a reminder to keep from causing resentment as well as holding onto my own resentment.

It was a reminder that I am, as we pray before communion, first among sinners.

I ask your forgiveness.

HOWTO: Write without offending

mah@everybody.org — Thu, 26 Feb 2009 05:27:48 GMT

It is very difficult to write about a moral position without offending someone. dvfmama is probably right: I should just keep my mouth shut, or, in the case of this blog, not purposefully post incendiary statements. I'll try to do that more in the future.

For now, though, dvfmama and I have been having a very heated discussion about what I wrote. While she agrees with my practical reasons for two parents, she disagrees with the way I expressed it. She and others said I came across as "smug".

This leaves me confused. I don't think I'm better than others. I admit I've had a blessed, and, in many ways, privileged life. I don't think this makes me better than anyone else. I don't think this makes anyone else less "worthy" than me.

But still, that seems to be the sentiment I convey to many people.

It could well be that I've been so isolated in my experience that I can't convey to others the practical reasons for two parents, so I've challenged dvfmama to do it without offending people. Her background is completely different than mine. She may have a better chance of writing about this subject without offending others.

I still think it is nigh-on impossible to write that children need two parents without offending people, but if she manages to do it, I'll gladly admit it.

(Update: She did it.)

Radioactive content

mah@everybody.org — Wed, 25 Feb 2009 18:25:00 GMT

I'm going to take this from "hot-button" to radioactive.

Children deserve a resident father. Women do not deserve to have children simply because they want them.

...

There's a difference between what adults want and what children need, and children's needs trump adults' wants.

(from Are Fathers Optional?)

In case you hadn't caught the clue, I'm what most people would call a social conservative in almost the strictest sense of the word. When we make decisions that affect other people, we should consider their needs.

When we're thinking about bringing life into the world, we need to be especially sober.

Twelve years ago, Dolly was created and cloning became something that people began to think about as a possibility.

Articles were written about the possibility of men and women having themselves cloned so there would be mini-me's running around -- blatant testaments to their parent's vanity. Imagine! I could raise my genetic offspring without having to put up with a woman! seemed to be the gist of some of them.

But I do not recall the obvious narcissism being discussed. Suppose it is possible in a few years to have a child who shares all my genetic characteristics without the bother of first developing a lasting relationship with someone else -- or, for that matter, having much of any interaction with anyone else at all.

The narcissism seems so obvious. Perhaps it is because we celebrate narcissism in our culture that this doesn't bother us. Even many "christian" leaders seem to have discarded the idea that pride is the root of all sin and promoted their face and personality more than they've demonstrated humility.

I suppose it shouldn't be any surprise that, here in America, men and women feel the right to pursue their desire to have children, without intending to have any sort of relationship with the child's other parent. This is, after all, the land of individuality and self expression. Why not buy a child to raise as my own if I can?

I don't think it would be profitable to start legislating my morality -- how far would an anti-pride/anti-narcissism ordinance get, and would I be the first one charged?

When I read the statistics of how many people are being voluntarily raised by a single parent, whether that parent has 14 children or one, I feel like I am, as Father Stephen writes, standing on the edge of cultural disaster.

We've been here before and we'll move on. Life will continue despite a world that seems to be falling apart around us constantly, whether the immanent danger is climate change, abortion, or economic collapse.

(Update: The quote that started this post used to include a bit about "stigmatizing women" who choose to have children without fathers. People ended up responding to that, thinking I was directing my ire to women in particular, instead of anything else I said, so, even though I liked the responses, I took it out. I want to make it clear that anyone, man or women, who sets out to have children by themselves, intentionally depriving them from the start of their other parent, is wrong.)

Added: No one "deserves" to have children. No one has the right to have children. Parents have an obligation to provide the best household they can for their children. Going into parenting intending to short-change your children by eliminating one parent is not in their best interest and is an avoidable decision.

Ubuntu, for Humans

mah@everybody.org — Mon, 23 Feb 2009 16:21:33 GMT

Amber, a non-technical mother, tries Ubuntu. This sounds like dvfmama's use of Ubuntu. I'm a geek (like her husband) and my wife wants to learn how to use Linux. The amazing and amusing thing (to me) is that she when I installed Ubuntu on our kids laptops, dvfmama was the one who began talking to them about the philosophy of Free Software and the obligations of the GPL.

I wish Amber the best and hope that she can join the ranks of other "normal" people I know who use Ubuntu: my mother, my friend, Jim Bonewald, my cousin, Jeremy Stein (and the rest of his family), and of course, dvfmama and my kids.

Linux users may not yet be measurable, but we're growing. And a lot of credit goes to Canonical and Ubuntu.

Are we ready to spend?

mah@everybody.org — Thu, 19 Feb 2009 15:41:39 GMT

I don't know about you, but I don't want to spend money right now. In fact, for the past few of years, I've been relatively thrifty (compared with my previous, debt-building, ways). For a while, I imagined I was unique, that I was somehow getting ahead.

But a couple of years ago, at the beginning of 2007, I started reading articles that said that people were starting to save more. A significant amount of people had begun to feel uneasy, it seems, about all the debt they were accruing and starting to save more.

Of course, two years and a couple of stimulus bills later, people are feeling even more skeptical of debt. I don't know about you, but debt is one of the scariest bits of the possibility of losing my job. How am I gonna handle this mortgage!?! I can hear my inner-breadwinner screaming.

And with layoffs and unemployment growing at substantial rates, I'm sure many people are looking for ways to set aside something "just in case". Certainly they aren't likely to be building even more debt.

Further, I'm in line with Steve Ballmer, Microsoft's CEO, more than our politicians, when he says:

... over the last period of time, the balance has really shifted. Instead of innovation and productivity driving growth, it’s really been unsustainable levels, particularly of private debt, that have been a key driver of economic growth. (emphasis mine)

He continues: "In my view, what we now have will be a fundamental economic reset."

A fundamental reset.

Nudges to "free up cash" will mean I have more cash to put in the bank, to help stave off what seems like an inevitable doomsday scenario, not that I'm going to spend more just to get a newer, larger TV.

So politicians don't want to give us money, because we won't spend it. Instead, they give it to banks and dying car companies. Strangely enough, it seems to me that, of the two, the car company is the best way to get money into the economy -- especially if no one is buying cars -- since the car company will have to spend, spend, spend just to stay afloat. The banks, it seems, can't help but reward themselves with tax-payer-funded bonuses in obscene amounts.

But what do I know? I'm just a freetard. I don't have a degree in economics. And I certainly want to increase the liquid assets I hold right now and fill in the the debt hole I've managed to dig for myself.

I can't imagine others feel much differently. And giving bailouts of billions to banks will just aggravate that feeling, no matter how much they need or deserve it.

Update: I love this bit from winterspeak: The US household has gone from an unsustainable level of negative saving to a sustainable level of positive saving, as we all knew it eventually would, and this is only triggering the Apocalypse because academic economists have no idea how money works.

The mysterious delicate vietnamese flower

mah@everybody.org — Wed, 18 Feb 2009 03:47:27 GMT

After googling "Delicate Vietnamese Flower", I realized I hadn't talked enough about it.

It started as an a cute, ironic, and endearing term for my wife during the Clark Campaign -- anyone that meets her knows that she is anything but a shrinking violet.

Later, when we were looking for a domain for her blog, we tried variations on DVF and found dvfmama.com. And that, is how the Delicate Vietnamese Flower became known as dvfmama.

Ubuntu: Rite of Passage

mah@everybody.org — Tue, 17 Feb 2009 06:08:02 GMT

My son was annoyed that his school-provided laptop includes NetNanny configured in such a way to keep him out of game sites like PopTropica.

Now, I understand the desire to censor our children's forays onto the Internet. There is a ton of stuff out there that is a lot easier to get to than when I was a kid. And, often, as adults our first instinct is to protect them from where we know their curiosity will lead them.

But blocking game sites? Now you've gone too far!

Since I like to pretend I'm somewhat subversive, I was completely ready to let him install Ubuntu on the laptop. It plays into one of my goals for 2009: teaching my kids to program. I mean, sure, you can do it under Windows, but I'm just so much more comfortable with Linux.

There was one snafu: I neglected to backup and defragment the disk before starting, so we lost some files. But, once his sisters saw the wobbly windows they just had to have it installed on their laptops, too.

So now every laptop in the house runs Ubuntu. My daughter summed it up nicely: "I just feel so grown up now that I'm using Ubuntu like Mom and Dad!"

As if to make sure I wouldn't become too proud, she did add that she became acutely aware that I wasn't quite the Super Geek she imagined me to be when I managed to lose her weather charting homework.

Win some, lose some, I guess. But I count this as mostly a win.

Referrer Blacklist

mah@everybody.org — Sun, 15 Feb 2009 21:26:33 GMT

In addition to helping bring IntraHealth's web stats up-to-date, I've been working on my own. I've been playing around with Webalizer and awstats. While I prefer awstats, I really hate referrer spam.

Awstats allows you to specify a blacklist and suggests using MT-Backlist for a list of blacklisted, referrer-spamming domains. The problem? MT-Blacklist is abandoned and the author suggests using TypePad's Antispam service as a replacement. This is all well and good if you're just worried about comment spam, but it does me no good when I'm trying to keep referrer spam out of my parsed logs.

I looked around for someone maintaining a more up-to-date list, but couldn't find it.

Maybe that just means I'm the only person interested in such a list. Maybe the old list works for most people who want to use it. But I found several referrers that it doesn't block and added them.

If you're interested in a more up-to-date list, you can pull from my github repository. If you have domains to add, you can ask me to pull from your repository.

It may be that I am the only person interested in this, but if not, github will give us a way to collaborate on a list.

IntraHealth OPEN launched

mah@everybody.org — Fri, 13 Feb 2009 15:38:51 GMT

Almost two years ago, when I started working at IntraHealth, dcm told me about IntraHealth Open. Being a neck-bearded freetard, the idea really appealed to me: Use open source in the education of students in developing countries across Africa to build a workforce that could support the IT infrastructure of the continent without using Western consultants.

The use of Free and Open Source Software (FOSS) is essential to the goal. Using software that is freely licensed for perpetuity avoids the "First Hit is Free" model many software companies use to get developing countries hooked on their software. Building the use and understanding of FOSS into the curricula gives the students the skills they need to use software on the job. And deploying freely-licensed software like Ubuntu, OpenOffice, iHRIS Suite and OpenMRS into these developing countries will create a local demand for workers who can use, understand, and maintain the very software they've learned about in school.

I'm very excited about the new IntraHealth OPEN initiative. You can even take part. Senagalese musician Youssou N'Dour is working with other musicians to help raise funds for the OPEN initiative by making his music and remixes of it available for free download under a Creative Commons license. So go download some music and consider making a donation to IntraHealth OPEN.

UPDATE: Listen to dcm talk about Open in the Launchpad podcast.

Hotplugging disks on a headless Ubuntu Box

mah@everybody.org — Tue, 27 Jan 2009 05:40:02 GMT

Since I've been using Ubuntu, I've been blessed in comparison with Linux of even just a few years ago. Hotplugging cameras, disks, and almost any other USB device “just works”. As a general rule, I don't have to worry about configuring it, installing drivers, or compiling my kernel.

Still, there are some times I need to figure out how to do things at the lower level. Today, I wanted to figure out how to mount a usb drive automatically on a headless Linux box. Since Gnome isn't running and no one is logged in, the usual methods don't work.

After some poking around, plugging and unplugging a disk several times, I have a working solution.

The first thing to know is udev. udev is a user-space process that interacts with the Linux kernel to set up devices at boot time and, in the case of USB devices, as they are plugged in.

On Ubuntu, you can drop a file in /etc/udev/rules.d to tell udev to execute commands when it sees a particular device.

Setting up a USB drive is a two stage process. First, udev sees the disk and fires off a series of events you can hook into. Then, after you probe the disk, udev will fire off another list of events for the partitions.

To intercept these and call a script to probe the drive and mount the partitions, create a file named /etc/udev/rules.d/50-usbdisk.rules (there is a README file in that directory that explains the naming convention). Into 50-usbdisk.rules put the following text:

ACTION=="add", DEVTYPE=="disk", RUN="/usr/local/bin/usb-add-disk"
ACTION=="add", DEVTYPE=="partition", RUN="/usr/local/bin/usb-mount-partition"
ACTION=="remove", DEVTYPE=="partition", RUN="/usr/local/bin/usb-unmount-partition"

This will cause udev to run usb-add-disk when a disk is plugged in, usb-mount-partition when it sees the partitions, and usb-umount-partition when the drive is unplugged.

Next, create /usr/local/bin/usb-add-disk with the following contents:

#!/bin/sh -e

# Maximum times to probe a disk
MAX=30

logger "Probing ${DEVNAME} using parted"
COUNT=0
ERR=1

while [ $COUNT -lt $MAX -a $ERR -ne 0 ]; do
    sleep 1
    ERR=0
    parted ${DEVNAME} || ERR=$?
    COUNT=$(($COUNT + 1))
done

if [ $ERR -ne 0 ]; then
    logger "Couldn't probe $DEVNAME for media after $COUNT times"
fi

exit 0

This script will log a message that it is “Probing…” to syslog, probe a a disk up to MAX times (30 in this case), and, if it isn't successful after 30 probes, log a message to syslog about its failure.

A couple of notes. I'm not sure about the $((…)) syntax. It works in bash and dash, but I'm not sure it is a POSIX standard. Second, you may be wondering why I'm pausing and probing so many times. Usually this should work on the first try. Still the “disk” I was using in this case was my Blackberry's SD card. Since I'm a little paranoid, I have a password on my Blackberry. Every time I plug it into a computer, it prompts me for the password. Until I enter the password, Ubuntu can see the drive, but thinks the drive is empty. Once I enter the password, the disk's partitions appear. (Ubuntu doesn't appear to see the partitions until after parted probes the drive. If you know a better way to get the partions to show up besides probing the drive like this, please let me know.)

At this point (and, on most usb disks, this is almost immediately since you don't have to provide a password), udev will call usb-mount-partition. Let's give udev something to run. In /usr/local/bin/usb-mount-partition put the following:

#!/bin/sh -e

BASE=`basename $DEVNAME`
if [ -x /media/$BASE ]; then
    logger "Can't mount usbdisk, /media/$BASE already exists"
else
    mkdir -p /media/$BASE
    mount ${DEVNAME} /media/$BASE
    logger "Mounted usbdisk at /media/$BASE"
fi

exit 0

If everything works smoothly, the disk will now be mounted under /media. Whether the script is able to mount the disk or not, a message will be sent to syslog letting you know what happens.

When you want to unmount the disk, you should run umount first and then remove the USB drive. That's what you should do. But you might forget.

If you do forget, then you'll be left with a dead mount point. In that case, we have one more script to handle the clean up: usb-umount-partition. In /usr/local/bin/usb-umount-partition, put the following text:

#!/bin/sh -e

BASE=`basename $DEVNAME`
if [ -d /media/$BASE ]; then
    logger "Unmounting usbdisk from /media/$BASE"
    umount /media/$BASE || true
    rmdir /media/$BASE
else
    logger "Couldn't find mount point for $DEVNAME"
fi

exit 0

This script will umount any dead mount points and remove the mountpoint that usb-mount-partition created.

Make sure the scripts you just created in /usr/local/bin are executable (sudo chmod +x /usr/local/bin/usb-*)and that's it: your headless Ubuntu box should now be automatically mount disks.

If you want to signal some other program or run a script when the drive is mounted, you can add that to usb-mount-partition.

A couple of notes on these scripts.

First, it is a good idea to start your shell scripts with the -e flag. This will force you to handle any error conditions. For example, in usb-umount-partition, I run umount to unmount the drive. But suppose you already did this (as you should have). The umount command would return an error. Since I'm using the -e flag, I need to handle that, so I added || true. Handling errors like this really helps during testing to make sure errors don't hide in your scripts.

logger is extremely helpful for debugging. When I was testing my udev rule files, I found it helpful to pipe env to logger. I could just tail -f /var/log/messages and find out what environment my scripts were getting.

Most insane use of PHP to date

mah@everybody.org — Fri, 23 Jan 2009 13:57:22 GMT

One of the other developers for IntraHealth has been abusing PHP in every way possible. This time Carl may have gone too far.

We're putting together a “shelf-top” appliance for installations of iHRIS that don't have a server room to rack-mount equipment. As much as possible, we want to make it easy to plug the box into your network and go with as little fiddling as possible. To that end, I found the Mini-Box M200 with an LCD panel that we could set up with a simple menuing and configuration system.

In all the other projects we've been working on, we've used PHP because of, among other things, the low barrier to entry it offers compared to, say, Java. PHP has been irritating at times, but I think it may be worth it if it means that we can get more people involved in the client countries.

When I first saw the LCD panel, my thought was “You know, it'd be nice to have an ncurses front-end for that thing.” Then you could test in terminal window and deploy it without changing your code. Carl had the same thought.

So he began hacking out an ncurses-based menu system for the LCD display. And it's written in PHP. I don't think I'm going too far out on a limb here to say that this is the first PHP code designed to be used through an LCD panel.

This only confirms my suspicion that Carl is a genius, of the evil, insane variety.

Telling HAL about TUN/TAP interfaces

mah@everybody.org — Fri, 23 Jan 2009 03:39:58 GMT

Today, I started using Virtual Machine Manager (VMM) to help me with my development. Previously, I had been using VirtualBox. Both are GPLed, but VirtualBox is Dual Licensed with a more “feature-full” version that isn't GPL'd. The GPL'd version of VirtualBox doesn't seem like it is really intended for hard-core use.

So far I've really been liking VMM. It can bring up my instances at boot time and can run them headless. Nice. This will really help with the packaging work I'm doing right now for IntraHealth's iHRIS Suite.

Still, networking is a bear in both VirtualBox and VMM. I was able to use my TUN/TAP bridged network in VMM that I had set up before in VirtualBox. But only after I told HAL about the TAP interface.

Here's the deal: VMM uses HAL to discover the network interface. It then lets you use any of those interfaces that are bridged for your virtual machines. Alternatively, you can just use user-mode NAT, but that is less than ideal since ping doesn't work and it is harder to test network apps or ssh into your virtual box.

The problem: HAL only knows about physical network devices, not any TUN/TAP interfaces you have set up. Since my bridge was on a TUN/TAP interface, HAL didn't know about it and VMM couldn't use it.

After a little poking around, I found the command line utility hal-device that would let me add the interface dynamically. Now, when VMM queries HAL, the interface shows up. (By the way, since HAL communicates over D-Bus, I was able to use Emacs' D-Bus integration for debugging.)

Here's the script I wrote to add the TUN/TAP interface:

#!/bin/sh

hal-device --add '/org/freedesktop/Hal/devices/net_tap0' <<EOF
info.capabilities = {'net'} (string list)
info.category = 'net'  (string)
info.product = 'Networking Interface'  (string)
info.subsystem = 'net'  (string)
info.udi = '/org/freedesktop/Hal/devices/net_tap0'  (string)
net.address = 'ea:08:21:d4:c8:90' (string)
net.interface = 'tap0' (string)
linux.subsystem = 'net'  (string)
linux.sysfs_path = '/sys/devices/virtual/net/tap0'  (string)
net.interface = 'tap0'  (string)
EOF

I hope to have something more generic that will work with HAL and Ubuntu's networking soon so that any TUN/TAP interface is automatically recognised by HAL.

Switching away from Google Reader

mah@everybody.org — Fri, 23 Jan 2009 02:57:28 GMT

I have this “thing” about owning my own data. I probably won't be a real user of Tim O'Reilly's Internet OS. I like running my own mail server — not relying on Google for Domains, not giving Google more and more data to feed into their advertising.

But I've been using Google Reader. I'm not sure what Google is doing with that information, but, well, I can run my own feed reader on the desktop. So I switched to Liferea. Besides nice things like task-bar notifications, integration with del.icio.us — or, with a SMOP, my own GotNoBlog — it allows me to pull RSS feeds that require authentication so that I can read LiveJournal friends-only feeds now.

I've managed to reclaim a little bit of my data. Hurrah!

Whopper Sacrifice

mah@everybody.org — Wed, 21 Jan 2009 01:59:02 GMT

Evidently, I'm one of the few, proud recipients of a free Whopper from Burger King. It wasn't too hard to find 10 people on my "friends" list to dump, but now it seems like most of you won't have that opportunity to get free food the same way. I gave the burger to my son, anyway. It is rare that I eat anything more than fries from a fast food joint.

Cold as a...

mah@everybody.org — Sun, 18 Jan 2009 02:26:06 GMT

In order to avoid joining the club of wimps (some people can rationalize anything), I went out today and yesterday, the two coldest days of the week, and did 30 miles.

Part of it is the 6000 mile goal I set for myself. If I slack now, I'll have to ride doubly hard later on. Part of it was that I skipped todays this week already. I had to get the miles in to make my weekly goal of 120miles. And I did! I made 130 miles for the week. Yay, me!

The other part is just the fun of telling people "Oh yeah, I rode 30 miles in the freezing cold." Something about the surprise that it generates makes it more fun. I won't have the opportunity to provoke such reactions in the summer.

But I think 30 miles is my limit. It takes me around 2 hours to ride that far and by the time I get back home, my toes are numb -- even after I put on extra socks.

A God who Pushes Back

mah@everybody.org — Fri, 16 Jan 2009 11:47:17 GMT

In response to a NYT article about Mark Driscoll's Mars Hill church, my friend Jim writes "I personally find it a bit of a mystery that some people find comfort and hope in that sort of theological framework". By contrast, I can totally understand it.

I understand it, but disagree with it. My experience as a Christian, and a little healthy doubt, has lead me to reject my one-time fascination for hard-core, predestined-from-the-womb Calvinism. But, while I'm not comfortable with a Calvinistic god who is completely arbitrary -- one who has no real way of showing love -- I doubt an individualized god who looks like a friendly neighbor who practices a "live-and-let-live" philosophy.

It seems the Mars Hill congregation does not want a god who will smile on their imperfections, but what they've been offered, what they've found to fill their "God-shaped hole", is indeed not anthropomorphic. It is true that anthropomorphizing God, making him like our tolerant neighbor, is dangerously wrong-headed. But just because we have an incomprehensible god does not mean that we have a view of the right one.

A hint of what is so attractive about this "New Calvinism" can be found in Dostoevsky:

Taking freedom to mean the increase and prompt satisfaction of needs, they distort their own nature, for they generate many meaningless and foolish desires, habits, and the most absurd fancies in themselves. (source)

Mars Hill parishioners have pursued this false freedom and found it wanting. Naturally, they turn away from that. Of course, we are always in danger of following the wrong leader, but especially so when we feel weak and are offered something that looks unbending.

By way of contrast, I offer this quote from Father Stephen. His whole post is an excellent defense of un-individual, Trinitarian Christianity, but this is quote seemed most relevant:

An excellent example of this occurred once in an inquirer’s class I was teaching before I was Orthodox (I was an Anglican priest). I was teaching a class on Christian morality and offered as authoritative the traditional teachings of the Christian faith in matters of sex and marriage, etc. One of the couples in the class seemed upset by my presentation and asked, “What right does the Church have to tell me how to live my life?” I admit that I was stunned by the question, if only because of its honesty. I gave them a short answer, “Because you are raising my children.” The complete answer has more depth, but I thought they might find it helpful to consider that the world included someone other than themselves.

Open Source Talk

mah@everybody.org — Wed, 14 Jan 2009 12:31:51 GMT

(Took some more pics on my ride yesterday. Played with macro a bit, too.)

Last night, I gave a talk at the Central PA Linux Users Group (CPLUG) that I called "Bringing Open Source to Africa". While I could have made it more general and talked about the various Open Source projects that have grown out of or are centered around Africa -- and perhaps this is a topic for another time -- I focused on the projects that IntraHealth is doing and how we've created or used Open Source.

The talk was followed by some good discussion and I got to talk about KnowledgeTree some as one of my friends there had heard of it and thought it would be useful, but was a little scared of setting it up.

The biggest drawback was that, due to my poor planning, I didn't get a set of slides done till just before the talk. I was lucky here because other people at IntraHealth have done so many talks so I was able to use their material to create my own presentation.

(copy of my slides.)

mah@everybody.org — Sat, 10 Jan 2009 04:13:10 GMT

(Today, I took my camera with me on my ride. 30miles at 30degrees. Click the photo for a couple more.)

After flirting with Google's Picasa for Linux for managing my photos, I'm back to using f-spot.

I like the timeline and that it doesn't ask me to give a single "folder" for all the pictures I'm importing, but, instead, creates a directory structure so that my photos are sorted by date. Interestingly enough, it is actually better than Picasa for importing. Picasa won't automatically rotate images when importing them from the camera where f-spot will.

I still use Picasa for uploading pictures to be printed out (F-spot doesn't support uploading to Wal-Mart), and I love the online Picasa's ability to help recognise and tag people in photographs -- 7000 faces in 10,000 photos are no fun to do by themselves, but when Google picks out the faces and suggests names, it becomes a little game to see how good it gets and to see which person Google thinks looks like each of my kids.

(Yeah, I'm probably helping them improve their facial recognition software and they'll end up selling that to the TSA, but ... oh well.)

Wintery Mix

mah@everybody.org — Thu, 08 Jan 2009 13:26:00 GMT

Yesterday was a horrible day for riding. I thought of taking an hour at lunch on my beater bike, but I never managed to do more than think about it.

This morning, though, I was up and out of the house, biking down 272 towards Lancaster at 6:00 AM. I'm falling behind on my goal. Today I should be able to catch up some.

Small movies

mah@everybody.org — Wed, 07 Jan 2009 16:12:28 GMT

Last year, I was excited about two documentaries: The Singing Revolution and As We Forgive. Both of these movies offer alternative ways to see the world.

The Singing Revolution is a revolution unimaginable to most Americans. Most of us cannot imagine freedom without blood. Especially as we're in the midst of a war, surrounded by "Support Our Troops" bumper stickers, revolution without bloodshed seems, well, crazy. Crazy enough that a small documentary about one has done pretty well in theatres this past year and managed a place on the marquee amongst larger studios blockbusters. You may not have heard of it, but that isn't because it didn't come to a theatre near you.

Likewise, As We Forgive is an alternative path to justice. The movie tells the path some Rwandans chose after Genocide, after Gacaca courts, after the system had done everything it could. It tells the story of genocideers working to rebuild homes of their victims. The can't bring back the families they killed, but they can ask forgivess. Sometimes, the victims can even forgive. This stands in stark contrast to most American's sense of justice, where we can only imagine victim families giving victim impact statements in a court room, never living in a house built by, and next door to, their husband's murderer.

And as a new year starts, I discovered a new documentary project that I can get excited about. God's Garden is a documentary about the one man's discovery of genuine African Christianity. Not "white man's religion", but a Christianity that came to Africa before Europeans even knew it existed. An Ethiopian priest introduces him to St Moses and it changes his life.

I love documentaries like this. They challenge our view of the world and suggest that, yes, there is another way, a way of peace, forgiveness, change, and love. This is a good reminder when the way we so often choose is with violence, retribution, stasis, and resentment.