Oog Robot

22/7

2011-07-22T09:23:00.001+02:00

Screwdrivers

2011-03-30T11:25:00.007+02:00

So I performed an experiment on Monday which required a laser. This wouldn't normally be news for me, except that I needed a really strong magnetic field, around 10 Tesla, and had to fly via airplane to access this field. Now, if you've ever cleared security at the airport, you know that security can be a little bit silly. In fact, it can be really silly. I had one of these experiences a few days ago.

Let me start the story by listing what I had in my carry-on bag:

A class 3b laser driver and head (capable of blinding a person), which requires a power outlet

6 ml of insulin, a handful of needles, a blood glucose meter, and lancets for finger pricking (I'm type 1 diabetic)

A lot of electronics, including a motherboard (PCB) with an FPGA, several custom PCBs with my own ASICs, and a multimeter

About 20 or 30 meters of cabling (4m of which was 40 way parallel cabling)

A laptop with an extended life battery

A flat-head screwdriver and a torx screwdriver (I think the torx was a T6)

My keys, which contained an LED light, two hex keys, and a keychain screwdriver similar to this one

My dumb phone

A change of clothes (and an extra pair of underwear)

All the relevant papers for traveling, including e-mail exchanges with the lab where I was going to be working

I got to the airport early, figuring that clearing security was going to be a pain. I separated my diabetic stuff, and told the security officer that I was type 1 diabetic and that these were my supplies. I pulled out my laptop (as instructed) and put it in a separate container. I passed through the x-ray check.

The guy working at the luggage screener pulled another guy over when my luggage was passing through, and they had me come over to the machine. They needed to re-run my stuff in separate containers --- they said they needed a better view of the electronics. So I unpacked all the stuff, and they ran it in about five separate containers. On the last container, which contained the contents of my pockets, they pulled out my keys, pointed to the keychain screwdriver, and were like, "Um, what is this?" I explained to them that it was a keychain screwdriver, and they said, "We're sorry, tools aren't allowed on the plane. You cannot take this through, but everything else is okay."

Now, at this point, I'd like to give a little history. I received this keychain screwdriver as a present from my sister in December of 2009. It has been through security at airports at least 10 times (6 flights within Europe, and 4 flights to and from the US). I wasn't sure if they maybe misused the word "tool" --- they weren't native English speakers --- but I decided not to push my luck, and told them just to throw it away.

The flight back was the same, with security requiring me to re-run all the electronics, except nothing was confiscated. At neither location did security ask me why I was bringing a laser on a plane.

So, in case you are wondering, it is okay to bring a laser that can blind a person onto a plane, with a power source for at least a few minutes of operation (a laptop battery). You can bring enough insulin to harm a few fully grown people quite seriously, probably killing them. You can bring custom electronics and custom cabling onto a plane. You can even bring fully sized screwdrivers that are for security screws like torx screws (I find it unlikely that planes are going to use Philips or flat head screws). And you can bring all of this in your carry-on. But a keychain screwdriver? Well, my experience suggests there is a 10% chance that this will be confiscated.

I don't want to sound upset at the people at the checkpoint. They were nice to me, and I wasn't acting funny. I'm also a white male, which probably helped by not attracting suspicion. I complied with their requests immediately, and answered any questions they put to me. They had a line of people after me that were probably not happy about the jerk with the electronics having his equipment re-run. In fact, I'm happy with the people at the checkpoint. I needed to run a research experiment whose results are important to cancer detection. It was good for me that a laser, diabetic supplies, and custom electronics cleared the checkpoint.

It bugged me a little that my keychain screwdriver was confiscated but my torx and flathead screwdrivers were not. Did the security guys want to feel like they were doing something? I don't know. But a different question keeps nagging at me --- if I can bring a dangerous laser, deadly amounts of insulin, and custom electronics onto a plane, what purpose does "security" actually serve at airports?

Dogs in Elementary Schools

2011-03-03T08:36:00.006+01:00

If you have time, check out the article on therapy dogs being used in Iowa schools. The article claims that having a dog increases the amount of reading in the schools, and helps calm children down.

(The phrase "Corridor schools" refers to the "Technology Corridor," which is the locals' way of advertising the region between and including Cedar Rapids and Iowa City.)

A Complex Relationship with Food

2011-02-01T18:00:00.001+01:00

The relationship between people and food is complex enough to begin with, and it can be a little overwhelming if you're diabetic. In this post, after giving an overview of type one diabetes mellitus, I'm going to talk a little bit about the additional complexities that diabetics have with food.

A non-diabetic person has a working endocrine system that responds to natural increases in blood sugar levels by having portions of the pancreas produce insulin, which causes muscles and especially the liver to store the sugar. The liver acts as a buffer or gas tank; when you eat, it is like putting fuel in your body. The hormone glucagon has the opposite effect of insulin. Glucagon causes the liver to release sugar into the blood. A normal person always has trace amounts of glucagon or insulin in his/her blood. There is a good graph at Wikipedia that illustrates how insulin levels in a normal person's body react to sugar levels caused by eating and activity.

Keeping the blood sugar level below a particular value is important for many reasons that I do not fully understand. When the blood sugar goes too high, above about twice the normal value, the kidneys are overworked from removing all the sugar, and kidney damage can result. There are additional problems with blood vessels being weakened by high blood sugar. Keeping the blood sugar above a certain value is important because otherwise your cells would starve (leading to death). The combination of insulin, glucagon, intaking food, and the energy stored in your liver are all critical to keeping the blood sugar levels at a normal value.

A person with insulin-dependent diabetes mellitus (IDDM or type one diabetes) lacks the ability to produce sufficient insulin. A T1 (I will use this as short-hand for a type one diabetic, and it also makes me sound like a terminator) has the problem that his/her blood sugar would naturally go too high after meals, which can (over a period of years) cause kidney and blood vessel damage. T1s have the short-term problem that their energy reserves are too low. If a T1 performs vigorous physical activity and doesn't eat, the blood sugar will plummet, causing problems.

The way T1s normally solve these problems is by injecting insulin. There are two types of insulin: long-acting (basal) and short-acting (bolus). Long-acting insulin works over a period of roughly 18 to 24 hours, counteracting the "background" stream of sugar from the liver. Long-acting insulin is normally taken once or twice a day; in the Netherlands, doctors only prescribe it before sleep, though in America the dose is usually split between the morning and the night.

Short-acting insulin is taken at the same time as food. The short-acting insulin works over a period of roughly 4 hours. The amount of short-acting insulin I take is related to the amount of carbohydrates (sugars) in the food I eat. Right now I use about 4 units of insulin when I have less than 100 grams of carbs at a meal, 5 units when I have 100 - 110 g, and 6 units when I have above 110 g of carbs (I don't eat more than 110 g of carbs at a meal). This amount of insulin will increase over time, as my pancreas shuts down. Right now my body appears to produce enough insulin to cover about 60 grams of carbs; I need to inject insulin to make up the difference.

Unfortunately there are two big drawbacks to using the short-acting insulin. The first drawback is that the "response curve" of the insulin is set. The sugars in different foods take different amounts of time to absorb, but how and when the insulin acts is not variable. For example, when a T1 drinks 100 grams of caramelized dextrose, which the human body digests very efficiently, the blood sugar increases quickly and rapidly. In comparison, if I drink about 130 grams high-fructose corn syrup (which contains about 100 grams of sugar), my blood sugar would take about twice as long to rise. This is because the human body is less efficient at processing fructose than dextrose. How quickly a food is absorbed is known as the glycemic index, though this varies from person to person. The long and short of this is that foods with easily absorbed sugars (high glycemic index foods) will cause spikes in my blood sugar, which are bad. This is actually true for people in general; the South Beach Diet is a diet that partially focuses on eating low glycemic index foods, causing a lower variation in blood sugar. This type of diet is supposed to be better for you (you can also use it to lose weight, but that isn't the primary purpose of that diet).

Anyways, the important point is that if I'm not exercising (a different post entirely), then my doctor recommends eating food with a lower glycemic index, and eating it slowly. Foods that seem similar actually act very differently. Cherries have a lower index than raisins. Prunes are better for me than dates. Grapefruit is better than pineapple (but this is definitely only true from a glycemic index standpoint; in every other way, fresh pineapple is vastly superior to grapefruit). Anything made with processed, white flour is absorbed very quickly, so things like pancakes will cause spiky blood sugar.

The other drawback to the short-acting insulin is that there can be absorption problems long-term. Scar tissue builds up if a particular site is stressed repeatedly, and if a pocket of insulin isn't absorbed because of scar tissue, and the insulin is released quickly, a sudden drop in blood sugar can occur. Scar tissue is prevented by rotating injection sites; I use half of my body for a month, and then switch. During the month I also rotate within the site itself. I prefer to use the tops of my thighs in the mornings and the evenings, since the large surface area makes site rotation easy. However, it is a bit inconvenient at work, so I normally use my belly at work. Massaging the area before the injection (increases blood flow) helps a little bit, but massaging afterwards seems to cause bruising. Insulin can and does leak if the needle isn't held in the site; I normally count to 10 after injection.

Long-term, lowering the intake of insulin also prevents scar tissue problems. I am trying to eat a low-carb diet by using the Idaho Plate Method. In this method, you split your main plate into a half and two quarters; low-starch veggies occupy half, starch-heavy grains and veggies occupy a quarter, and protein sources occupy the other quarter. One piece of fruit can accompany a meal. The food has been a bigger adjustment than the shots or finger pokes. I ate a lot of pasta before learning I was T1, and right now if I tried to eat a meal with 250 grams of pasta and 500 ml of orange juice (both huge sources of carbs)...well, let's just say a meal like this is a bad idea at this moment. I could eat such a meal if I wanted to, but I'd need about two or three times as much insulin as a much healthier meal.

You'll notice there is no "dessert." Fruit is dessert right now. Sometimes I'll have a square of very dark chocolate with a meal or before I exercise, but right now I'm adjusting to eating less sugar. It isn't easy, but it reduces the amount of insulin I require and is going to be better for me long term.

Well, this post turned out a bit longer than I expected, but I hope it clears up how diabetics view food. We care more about the amount of sugar and how it is absorbed, in addition to the standard concerns about vitamin content and caloric content. All in all, the forced examination of my diet has turned out to be a pretty good thing. It wasn't a great idea to be eating a meal that was 300 g of spaghetti with 500 ml of orange juice as my primary source of energy.

In the next few posts I'll probably cover differences in vitamin sources from America to Europe (you'll be surprised, trust me), along with how diabetics approach exercise.

Selection Biases in Real World Data

2011-01-25T11:00:00.001+01:00

So a web-page depicting the average SAT score by state has been making the rounds a little bit in Iowa. Apparently Iowans are so smart! But something seemed fishy about the data...oh, right the participation rate is 3% in Iowa, and in general states with a lower participation rate have better scores.

Now, if you take the ACT data for 2010, Iowa is around 15th, but with a much higher participation rate.

Look at Maine! Maine is ranked dead last, 51st, on the SAT list, but 5th on the ACT list, up there with a lot of East Coast states whose students didn't do so well on the SAT list. New York is 46th on one list and 4th on the other.

Why the difference in Iowa's rank? And why the huge difference in Maine's rank?

Biases in the test-takers is likely to be at work. ACT has its mothership in Iowa City, meaning that Iowa is likely to be pushing the ACT for political-economic ties. In my experience, only seasoned test-takers in Iowa take the SAT. The ACT is "good enough" for most people, but because of the additional practice and the inherent variance of the tests, you can get a higher personal best simply by more tests (personal note from an MIT grad: I took each test 6 times, once per year from 7th grade to 12th grade). Thus it is likely that Iowans hoping to get into a selective school are more likely to take the SAT. A similar effect is probably at work with the ACT in states like Massachusetts --- lower participations rates in these states are being caused by forces which select for the best test-takers and smartest students.

Making the SAT difficult to take in Iowa might help the state look the best in the SAT rankings, even though the ACT is HQ'ed in Iowa City. But most of all, reading too much into improperly gathered rankings is dangerous.

The Design of Everyday Diabetic Things

2011-01-15T13:00:00.000+01:00

I figured I'd talk a little bit of the design of things used to treat insulin-dependent diabetes mellitus (IDDM). The equipment features interesting trade-offs between ease-of-use, safety, cost, effectiveness and comfort. There are two main sets of tools: one for checking glucose and one for injecting insulin.

The Glucose Meter

There are many different glucose meters, but I use a Bayer Contour, because that's what the doctors suggested. The meter requires a disposable strip every time I want to check my blood sugar. I insert the strip into the meter, and then hold a drop of blood to the test strip intake.

The gadget is the meter, the plastic container (above the gadget) holds the test strips, the lancer is used to prick fingers (I guess they didn't want to call it a finger pricker for whatever reaon), the mesh compartment holds microlets (finger prickers), and I have some alcohol swabs in the little compartment.

The meter with a test strip inserted. In order to get a reading I have to hold a drop of blood to the little chamber at the bottom of the strip.

What the meter looks like after a reading. I'm using mmol/L, not mg/dl, which is why the reading is so low. A person with blood glucose levels of 5 mg/dl would be in a coma.

The lancing device (finger pricker) with the cap off, along with an uncapped microlet and a capped microlet. You have to twist the cap off the microlet in order to use it; if a child swallows a capped microlet, the plastic is strong enough that the cap shouldn't come off. I think. I'm not really sure, and I'm not planning on running tests, but if you know a child who would be interested in swallowing one, please feel free to contact me.

The amount the microlet penetrates into your skin is adjustable via screwing the cap on the lancing device. Diabetics who prick their fingers a lot develop callouses, so depending on the thickness of the skin, the needle may need to penetrate farther.

I had initially thought the meter was really nice. They're really inexpensive, have some fancy features like alerts, and it is very easy to use. However, much like printers being cheap and ink being expensive, the meter is cheap but the microlets and test strips are very expensive. The microlets and strips cost about a dollar a piece, and IDDM people are supposed to check their blood sugar at least four times a day. You're also supposed to change the microlet (the needle used to prick your finger), as the microlet gets worn after use. In practice most type 1s I know only change the microlet once per day. Anyways, the $20 meter consumes over $1,000 of test strips per year (my insurance covers the use of about 1,600 test strips per year). Right now I'm checking my blood glucose levels about 7 or 8 times a day, since I'm still getting used to everything, but eventually it should go down to four or five times a day. If my insurance didn't cover the strips, I'd almost certainly use a meter with a strip disk, since they'd be cheaper long term.

Overall I'm pretty happy with the meter. It is a little bulky, so I'll probably pick up a smaller one that I could carry with me, but the fact that it was free and the strips are mostly covered by my insurance makes me happy.

Insulin pens

Once per morning and before every meal I have to give myself insulin. There are two types of insulin I use. Lantus, which acts very slowly over the course of about 20 to 24 hours, is called a basal insulin. I use Lantus once per day in the morning, though eventually I'll probably have to split it into a day and night dose. Apidra, which acts very quickly, is called a bolus insulin. I take Apidra before meals; the exact dose depends on the carbs in my meal, my current blood sugar, and the amount of sugar I expect to burn. The location of injection has an important role in how fast my body absorbs the insulin. Injecting in the thighs makes absorption quite slow, while the belly area absorbs quickly. I normally use my thighs for the slow-acting, and my belly for the fast acting. I have to rotate the exact site location, or else scar tissue builds up which can make absorption difficult.

The biggest danger with the pens is that I accidentally confuse the two types of insulin. While the pens are visually distinct, with different colors, I actually wish they were physically distinct --- in other words, the Lantus pen was larger than the Apidra pen. I'm not too worried about confusing the two, since I keep them in different spots, but it would be nice if they were more difficult to confuse.

I have my two pens with two sealed needles on the kitchen table. The pens are disposable; after the pen runs out of insulin, I throw them away. Before use, the pens have to be stored in a fridge. After use, the pens are good for 28 days. I write the date the pens expire after the first use, so I can easily track when I'm supposed to throw them away. The pens are small enough to fit in my pocket.

This is the dial on one of my pens. I choose the number of units to inject by rotating the dial.

This is where the needle screws onto the pen top, with the number of units of insulin units left in the pen displayed.

This is the needle after the seal is taken off. There are screw threads on the inside that screw onto the top of the pen. The needle is inside the plastic container, so it is quite difficult to prick your finger with this. If the needle falls, it won't jab anything.

The needle has two caps, an outer and an inner. The inner cap is color-coded to the size of the needle. Different injection sites require different needle sizes.

A 8mm and a 4mm needle attached to the pens. Before injection, two units are supposed to be "burned," or injected into garbage. Burning the units insures that no air is in the needle. My Apidra pen always has a small amount of pressure, which is why there is a drop of insulin on the end.

I think the pens have a phenomenal design. First of all, the screw cap allows the use of different needles. This is important because, as I previously mentioned, different sites require different needle sizes, and because the needle wears after use, a new needle is required every time. The screw cap doubles as a safety measure; you have to push and screw the needle at the same time to get the cap on, which kid-proofs the pen to a large extent. With a child, the real danger isn't that a kid plays with the needle; the real danger would be a kid injecting themselves with insulin. The screw dial also kid-proofs the pen to a certain extent. An additional feature is that as you inject, the screw dial resets to zero. This means that the default state of the pen is going to be to inject no insulin.

The injections are almost pain free. Insulin injections are subcutaneous, compared to vaccinations which can require injecting into a muscle. I barely notice them afterwards, which has contributed to how quickly I've gotten used to them. The needles and pens, while expensive, are also (almost completely) covered by my insurance.

As I stated earlier, the devices feature some interesting trade-offs. Overall, I've been very impressed by how little pain I've experienced. While I still wouldn't wish IDDM on anyone, it isn't as difficult to deal with as I had initially envisioned. However, my pancreas is still working at some fraction of capacity, so I'll have to wait and see if I think the devices are effective enough when my pancreas produces no insulin.

Diabetes FAQ

2011-01-11T11:13:00.004+01:00

I'm getting a lot of questions about type 1 diabetes; I figured a blog post would be in order.

What is diabetes? What is the difference between the types?
The two types of diabetes mellitus are actually quite different, though both diseases relate to sugar and sugar metabolism. Type 1 diabetes mellitus, which I have, occurs when the immune system attacks the portion of the pancreas that produces insulin. Insulin is necessary for the body to metabolize sugar correctly. Type 2 diabetes mellitus occurs when the body doesn't respond correctly to insulin. Type 2 usually occurs in older, overweight individuals that have eaten a lot of sugar.

What's up with the mellitus at the end of diabetes mellitus?
There is another form of diabetes called diabetes insipidus, or DI. Mellitus means sweet, whereas insipidus means tasteless. The terms relate to the fact that urine from a person with diabetes mellitus, or DM, is sweet (due to the sugar flushed out of the body), whereas urine from a person with diabetes insipidus is tasteless, or tastes like whatever urine tastes like. My high school biology teacher once told me that to diagnosis whether problems were DM or DI, people drank the urine. Is it true? I have no idea.

The symptoms of DM and DI are similar, but the causes and treatments are very different. Diabetes, in general, usually refers to diabetes mellitus.

What does having type 1 diabetes entail?
Essentially I have to give myself insulin instead of relying on my pancreas to produce it for me. This means that before eating anything with carbohydrates I have to give myself insulin. Anything with sugar or starch is high in carbohydrates, so foods like potatoes, candy, and fruity drinks require giving myself more insulin than meat or low-sugar foods.

Do type 1s ever develop type 2 symptoms?
"Very rarely." is the response I've received from doctors.

Isn't type 1 called juvenile-onset diabetes?
Onset of type 1 can occur later than age 40, and thus the terms juvenile or juvenile-onset are no longer preferred. Type 1 is often called insulin-dependent diabetes mellitus or IDDM. I was 26 at onset, and I know another type 1 who was diagnosed when he was 29. Type 1 is actually "better" when it occurs later in life; when kids are growing it is difficult to find the correct amount of insulin to use.

You have to give yourself a shot before you eat almost anything? Does it hurt? How much insulin do you use?
I do have to give myself a shot before every meal. I also give myself a shot in the morning of long-acting insulin that stays in my system for about 24 hours. The shots hardly hurt at all, and I have very quickly gotten used to them. I have also gotten used to pricking my finger to check my blood sugar. Pricking my fingers was worse at first, but is no longer a problem.

Right now my pancreas is still producing some fraction of the insulin that would be expected. However, my body will continue to attack portions of my pancreas, and eventually it will produce only trace insulin. I'll have to inject more insulin at this point.

The amount of insulin I use depends on the amount of sugar in the food I eat. I have to match my insulin dose to the amount of sugar in the food I consume using a carbohydrate-to-insulin ratio. The ratio will change as my pancreas shuts down, but it should stay the same afterwards.

What are the symptoms of being type 1 diabetic?
The insulin shots are to keep my blood sugar at roughly the level of a normal person's blood sugar. There are no symptoms if my blood sugar stays in the normal range. Problems arise if my blood sugar is too high or too low.

If my blood sugar goes too low, I notice it immediately, and I have something that has a little bit of sugar in it. I'm trying to find something with sugar that I don't like --- giving myself a reward when I don't properly manage my blood sugar seems like a bad idea. When my blood sugar is too low, my head feels a bit weird and my muscles jerk instead of operating smoothly. If my blood sugar goes way too low, very bad things can happen, such as fainting. Having low blood sugar is dangerous short term.

If my blood sugar goes too high, then I usually have trouble focusing. If it stays too high, then I usually itch. The itching is a personal symptom, which many people do not have. If it stays too high for too long, I can develop more symptoms, from the mundane like increased acne and increased thirst to the severe symptoms of weight loss, muscle aches and very blurry vision. My body has acclimated to high blood sugar, so it is difficult for me right now to notice when my blood sugar is high.

If my blood sugar is too high long-term, there are many complications for my eyes, kidneys, heart and lungs.

How did you find out?
Over the past three months at work, I've had tremendous difficulty focusing. I've also noticed that I've had increased amounts of acne.

During winter vacation, I spent a week in Boston. My hands started to itch, and while I didn't think too much of it at the time I did see a doctor when I was home in Iowa a week later. I starting having the more severe symptoms, including increased thirst and blurry vision. I thought my vision was blurrier than normal, but I've also needed glasses for a while, so I didn't really notice it. Then my muscles starting being sore when I walked up the stairs. I searched for the symptoms using my search engine of choice and there it was: diabetes. I saw the doctor the next day. My blood pressure was normal, my heart rate was normal, and my blood sugar was 4x the value it was supposed to be. Based on my age, weight and blood sugar, it was an automatic type 1 diabetes diagnosis. I had also dropped 2.5 kilos (about 5 pounds) in the week between the two doctor appointments. The doctors said that the decreased exercise (I ride my bike / walk a lot in NL) combined with my root beer, birthday cake and chocolate diet caused a huge spike in my blood sugar.

How does exercise work?
Blood glucose levels drop automatically during exercise, so I am supposed to only give myself a half dose of insulin at meals before I work out. After I get my levels stabilized I think I am going to join a gym.

Can you still drink alcohol?
Yes, but alcohol is tricky. Most alcoholic drinks are just fermented sugar, and consuming small amounts of sugar over a long period of time does not match giving a single injection of insulin, which works well for a meal. Additionally, being intoxicated is much more dangerous now than before. I didn't consume alcohol in large quantities before, just a beer every now and then, but I think I am going to consume even less now.

This all kinda sucks.
That is not a question, but yes, it is unfortunate. However, it turns out that people can adapt very quickly to adverse circumstances. I can tell that I am going to be able to live a normal life sans some special things required for eating food and exercise.

How common is type 1 diabetes?
In northern European populations, the rate is almost 1%, or 1 in 100 people (see the study in the next question). In America the rate is probably closer to 1 in 200 or 250 people (see the Wikipedia article). I haven't found great information on the rest of the world.

Is the disease genetic?
There are some very interesting studies on this question, particularly a study on Finnish twins. When a twin of an identical pair had type 1 diabetes, there was roughly a 50% chance that the other twin would also have the disease. There are multiple genes involved, which make occurrence complicated to predict. The 23andMe page on type 1 diabetes is actually a really good resource on the genes and appropriate studies.

Type 2 is also somewhat genetic, but is much more influenced by the environment, especially diet and exercise.

If your pancreas isn't working does that mean you don't need it? Can I stab it?
Only a portion of my pancreas isn't working; I still need some of the other portions. No, you may not stab my pancreas.

Do you expect that anyone is going to develop a cure in your lifetime?
No. It wouldn't surprise me if someone came up with a vaccine, but I doubt there will be a cure. Drug companies aren't very interesting in curing things, they care more about treating symptoms, which is a better income stream.

What was treatment like before insulin?
Controlled starvation was the "treatment" before insulin. I use quotes because nothing was actually treated, symptoms existed, but people would live longer. The life expectancy after diagnosis without starvation was about six months; it could increase to a few years with controlled starvation.

After insulin was successfully extracted in 1921 (the extraction technique's inventors won the Nobel prize in 1923), treatment was an insulin injection before any meal. I would recommend reading the book Breakthrough, though make sure you read the book's afterword to understand that some of the non-scientific portions of the book are fictionalized.

What can I do?
The most important thing you can do is take care of yourself so that you are less likely to develop type 2 diabetes. Eating foods with less added sugar, eating lots of fruits/veggies, having a balanced diet, and getting enough exercise are very important.

If you like you can donate money to a foundation like the JDRF or ADA, but I think being supportive of scientific research and politicians who support research is more important.

Finally, just treat anyone who is diabetic just like a normal person with specific dietary restrictions. Try not to confuse type 1 with type 2; while both types share the label of diabetes mellitus, the two types can be very different. If a diabetic suggests eating at a different time or a different place please accept.

Oh, and be very careful about brunch. We the type 1 diabetics hate brunch. Well, mostly hate brunch. It is too much food of the wrong type at the wrong time.

This is all really interesting, where can I find more information?
I would suggest browsing the JDRF website first, then maybe the ADA website. There is always the Wikipedia.

Worst Birthday Present Ever

2011-01-02T20:40:00.005+01:00

I found out I have Type 1 Diabetes Mellitus just after my 26th birthday. I am fine, please don't worry, it is just going to be a huge lifestyle adjustment in the coming months.

researchresearchresearch

2010-11-19T01:21:00.002+01:00

In case you're wondering what is happening in my life, please see the title. No new events, no crazy nights, no fun vacations. Until December. When hopefully things will pick up.

I should get a hobby. That involves people. Hmmmmm.

LISP at work!?!?!

2010-09-30T14:03:00.004+02:00

I get to use LISP at work! A standard CAD program, Cadence's icfb, uses a SKILL-based API. SKILL has a LISP-like syntax. I need to automate creation of a large number of cells, and the SKILL API is the easiest way to do that. This is going to be awesome!

Kwality

2010-09-21T03:11:00.001+02:00

Stay classy, Adobe.

Science disappoints

2010-09-16T16:56:00.005+02:00

Nothing makes me distrust a journal as much as ignorance of the state-of-art.

From a 2008 article in Nature Photonics!:

To date it has been thought that APDs are unable to measure the number of photons in a pulse of radiation or a short time interval.

And yet, from an article published four years earlier about APDs, we see:

A technique has been developed and tested that permits estimation of the photon number involved in a detection process.

Wow. Just wow. I would have thought the reviewing process for Nature Photonics would be rigorous. I guess you can't believe everything you read.

Open source!

2010-09-16T15:36:00.004+02:00

I'm going to be creating an open source library with all of my models - woohoo! Now if only I could decide on which license to use - current contenders are BSD, MIT, GPL and apache. Hmmmm.

Makefile for \LaTeX

2010-07-07T00:51:00.003+02:00

Due to some recent discussion on my previous LaTeX post, I thought I'd share the biggest advantage I think LaTeX has over WYSIWYG editors like MSWord: interaction with text tools.

First, let me paint you a few scenarios. You have images that you want to use in multiple places, like presentations, papers, and maybe even that PhD thesis you are planning on writing in a few years. However, the image format is going to vary from document to document; some documents, like presentations, call for much larger fonts, whereas your PhD thesis is going to have a clipped image size compared to any papers you'll publish. You want to be able to quickly reconfigure a set of images to have the same look and feel. You also want to view, easily, what processing you used on the image several years from now after you've forgotten everything you did.

Another scenario: a person is writing a book chapter and comes to you about using a variation of one of your images that she has seen in a paper of yours. She asks you to produce a variation of it.

Third scenario: one of your colleagues discovers a bug in an analysis script. You need to quickly track down all data that uses this script, and see if it affects any of your published data.

Fourth scenario: you're trying to remember exactly how you analyzed a set of data, but you performed the experiment several months back and can't remember the exact method you used to produce a figure in one of your presentations.

Fifth scenario: you're modifying a script that creates a figure, and you're concerned about comparing the different possibilities and still getting the final version correct. How do you track all the changes?

These scenarios illustrate three important ideas when publishing data: reproducibility, traceability, and configurability. I am going to share my method of (mostly) solving these problems using LaTeX and the make utility.

Make is a text-based utility that is normally used for dependency tracking in large programs. Back in the day, when compiling took a lot more time than it does now, it was important that code was only compiled when it was necessary. When a program called a library, it wasn't necessary to re-compile the library every time the program was changed. The make program is used to track these dependencies, but it is actually general enough to track a lot of dependencies, such as images in a LaTeX file.

Let me give you an example. Say you have a LaTeX file that includes two images: A.jpeg and B.jpeg. Both are created by eponymous scripts A.exe and B.exe. A.exe, though, relies on a lot of really complicated processing performing by complexProcess.exe. You also want to have the same look and feel for both images.

This is quite simple to accomplish if you are familiar with the make utility. You can create a Makefile that looks like the following, which tracks the dependencies of your data and processing:

A.jpeg: A.exe tempFileFromProcessing
    ./A.exe

tempFileFromProcessing: complexProcess.exe experimentalData
    ./complexProcess.exe

B.jpeg: B.exe
    ./B.exe

viewPdf: pdf
    acrobat paper.pdf

pdf:  paper.tex paper.bib
    latex paper
    bibtex paper.bib
    latex paper
    latex paper
    dvipdf paper.dvi

This looks complicated, but it is quite simple. The Makefile has the structure

makeItem: dependencyOne dependencyTwo
    commandOne
    commandTwo

To create makeItem, make checks that the dependencies are met. If makeItem and the dependencies are files, then make checks if the dependency files were last modified after the makeItem file, and will only run the commands if this is the case. In the Makefile example, A.jpeg depends on A.exe and tempFileFromProcessing. If either A.exe or tempFileFromProcessing has been modified after A.jpeg, then make will run ./A.exe (which should create A.jpeg). Similarly, tempFileFromProcessing depends on the processing script, complexProcess.exe, and experimentalData. If either complexProcess.exe or experimentalData has changed after the temp file, the processing will be re-run. This allows you to cache or save complicated processing, but still gives traceability into what processing occurs.

Making the file B.jpeg is simpler to understand, as it just depends on B.exe. If B.exe has changed after B.jpeg, make will run ./B.exe, which should create B.jpeg.

The same thing can be done with tables or experimentally derived values by having LaTeX include another .tex file that is generated by a script.

Getting LaTeX and BibTeX to generate a file can be a bit complicated. Using make erases this problem, as it does the same thing every time. To make the pdf, you'd type "make pdf" which would cause make to run latex, then bibtex, then latex, then latex again. You could type "make viewPdf" which would also tell adobe acrobat to show you the PDF file.

If you need to see which images depend on a specific script, you can have the script print out caller information (or use a logging utility) to check what data is passing through any buggy scripts. Just change the script and re-make the pdf, and you'll have all the contaminated data calls.

Okay, so this fixes two problems, namely reproducibility and traceability. It also makes it easy to change the file and see the results. You can change which experimental run you use for experimentalData, for example, to see how your A.jpeg varies based on which run you're presenting. But what about configurability? How do you make the plots look the same for each document, but use the same plotting scripts across documents?

You can accomplish that by using a convention for look-and-feel in the figure generation files. For example, you can pass a file to all of your scripts that contains information like the font, font size, and figure size to create. This allows easy configurability.

So there you have it - the biggest strengths of LaTeX compared to programs like MSWord. You can create documents that use the same plotting scripts, but with different look-and-feels, for publications, presentations, posters and theses. It is easy to trace the source of plots when you need to come back to that publication in four years but you forgot the exact processing. You get caching of complex processing. Finally, it is easy to track down what published data has images run through contaminated scripts. The fact that LaTeX is compiled gives you superior traceability, configurability, and reproducibility of your data compared to WYSIWYG editors like MSWord.

Compacting Conference Papers in LaTeX

2010-06-17T13:58:00.008+02:00

I have a conference submission due next week with one page of text and two pages of figures. I had to compact this submission like crazy, so I thought I'd post my notes in case anyone else finds them helpful. "Anyone else" includes a future me.

Margins

I used the geometry package to get my margins correct.

\usepackage[left=0.5in,right=0.5in,vmargin=0.8in,nohead,nofoot]{geometry}

Title

Unfortunately LaTeX doesn't seem to handle compacting titles, authors and affiliations very well. My start looks like this:

\centerline{\Large \bf Title Goes Here}
\medskip
\centerline{Author~Name~One, Author~Two$^{\rm \dagger}$, and
  Author~Three$^{\rm \dagger*}$}
\centerline{Primary Author Institution, Address, Country}
\centerline{ phone: +1-123-456-7890, fax: +1-234-567-8901, email:
  user.name@institution.edu }
\centerline{$\dagger$Affiliation $*$Affiliation}
\bigskip

%% Text starts here

Figures

I used the vspace command quite liberally to shrink the space between the pictures and the captions. An example follows. The "[h!]" command after the "\begin{figure}" tells LaTeX to try really hard to keep the same ordering as in the .tex file.

\begin{figure}[h!]
\vspace{-25pt} %% moves figure closer to previous caption
\centering
\includegraphics[width=3.5in]{figure_file.pdf}
\vspace{-5pt}  %% moves the caption closer to the figure
\caption{\textbf{Figure title} - a detailed description of the figure.}
\label{fig:block}
\end{figure}

Equations

I embedded my equations in a figure to save space. I also used the vspace command to help with space between equations.

\begin{figure}[h!]
\centering
\vspace{-20pt}
\begin{equation}
\label{eq:one}
\frac{\partial c}{\partial t} = D\frac{\partial^2 c}{\partial x^2}
\end{equation}
\begin{equation}
\label{eq:two}
{\rm SNR} = 20\log_{10}\left(\mu\right) 
\end{equation}
\begin{equation}
\label{eq:three}
\Delta{\rm SNR} = 10\log_{10}\left( f )
\end{equation}
\includegraphics[width=0.01in]{blank}
\vspace{-10pt}
\caption{\textbf{Equations}.  Eq.~\ref{eq:one}
  is foo, while Eqs.~\ref{eq:two}
  and \ref{eq:three} are bar.}
\label{fig:eq}
\end{figure}

Bibliography

I spent the most time messing around with my bibliography. I wanted no line breaks between the items, the bibliography in a smaller font, only the first author listed and no titles in the items.

Achieving no line breaks requires two things. First, you have to find the *.bst file that LaTeX uses and copy it to your local directory under a different name. For example, I was using the "ieeetr" style file, so I copied ieeetr.bst from the location LaTeX uses to my local directory as myieeetr.bst. You then must modify this file, and comment out the "newline$" strings in the output item. So in my case, the item

FUNCTION {output.bibitem}
{ newline$
  "\bibitem{" write$
  cite$ write$
  "}" write$
  newline$
  ""
  before.all 'output.state :=
}

became (notice the %'s before the two newline$'s)

FUNCTION {output.bibitem}
{ %newline$
  "\bibitem{" write$
  cite$ write$
  "}" write$
  %newline$
  ""
  before.all 'output.state :=
}

Next, you have to add the following to the top of your .tex file before \begin{document} but after the usepackages

\usepackage{paralist}

\renewenvironment{thebibliography}[1]{\begin{inparaenum}[[1{]}]}{\end
{inparaenum}}

I have no idea what that command does, but my bibliography didn't have any line breaks. The bibliography stanza that comes after my main text ends is (and you should use whatever you named the local file in place of "myieeetr")

\medskip
\bibliographystyle{myieeetr}
\footnotesize{
\bibliography{myBibtexFileName}
}

To shorten the bibliography even further, I removed all "TITLE={...}," lines from my bibtex file, and replaced the non-first authors with the "others" string. This causes a bibliography item to look like

 [1] M. Smith, et al., Journal Name, vol. 99, pp. 123–123, Jan. 2000.

which is exactly what I wanted. If I was a manly user I'd modify the bst file to do this, but I'm only a ~~lazy~~pragmatic user. If you modify the ieeetr bst file to do this please send it to me!

Columns

I used one column for the text and "\twocolumn" before the figures to help with reducing dead-space.

Page Numbers

I used a "\pagestyle{empty}" at the start to remove page numbers.

Fonts

Adding a "\usepackage{times}" will help with using slighter smaller fonts.

Conclusions

I hope some of these notes will be helpful if you want to use LaTeX for conference papers. It was a bit challenging at first, but I'm very happy with the final results. Please let me know if you have any trouble getting things to work above; I'd be more than happy to send you my .tex files so you can see how things worked for me.

Superb Supercomputer Treemap

2010-05-31T15:00:00.003+02:00

The BBC has a spectacular Supercomputer Treemap. It is definitely the classiest visualization I've seen all day. I suggest checking it out, along with the historical article on treemaps.

ACM Survery of Graphs

2010-05-19T09:46:00.005+02:00

ACM has an interesting survey of graph types. I don't like most of them, *especially* graph types like the stacked graphs in 1B that introduce correlations into the visual representation of the data that aren't in the data. The splom in Figure 2C, however, is a very nice representation that I'd never seen before.

Greater than One?

2010-05-18T14:01:00.002+02:00

Nothing increases my faith in science like seeing a highly cited article that experimentally measures a probability larger than one. Hmmmmmmmmm.

Game Review: Dwarf Fortress

2010-05-14T19:30:00.009+02:00

I've been pretty hosed at work lately, so I apologize for the lack of recent posts. It is hard to write a blog when you've spent the past few weeks writing a paper (or three) at work. However, I just wanted to practice my non-technical writing and talk a bit about a Dwarf Fortress, a game that I thought I'd review.

The game has three modes: fortress, adventure and legend. All three modes center on different aspects of a single world - for the sake of brevity I'll be focusing solely on fortress mode, which is a mode similar to Sim City but with a fortress instead of a city. Adventure is a hack-and-slash mode similar to NetHack, and legend is an encyclopedic mode that is still in the works.

Two shots from legends mode show information a dragon that was slew in the year 118. If you like reading encyclopedias, you'll love legends mode!

The basic premise behind the game is all there in the title. You have dwarves, and you want to build a fortress in the side of a mountain (mountain optional). If you enjoyed playing Sim City, you'll probably enjoy Dwarf Fortress, though it has a *much* steeper learning curve. There isn't an end goal to the game, though as your fortress gains wealth and population your fortress will receive noble dwarves, such as a baron(ess) or a count(ess). The easiest way to create wealth is through workshops, though other resource-gathering is available. The population either grows from natural procreation or immigration.

The entrance to a fortress is shown at the left-hand side. There are two ballistas in the center-left defending the fortress entrance, along with two rooms straddling the entrance to allow cross-bow wielding dwarves to defend the entrance. On the right hand side of the screen is a bridge (red double-tildes with outline) crossing a brook (blue tildes). A dwarf is chilling on the bridge. The middle portion of the screen contains three catapults with ammo stock-piles to the left of them.

The first thing you'll probably notice is that the game has an ASCII tile-set. If you're not used to ASCII games like NetHack, you might have a very hard time adapting. There are other tile-sets that are a little easier on the eyes. I personally don't mind the graphics so much as the limited view of the world. Many modern games use zoom mechanics to deal with complexity, but it isn't possible with Dwarf Fortress.

The game can be split into roughly three categories: building/mining/economy, combat, and history. I'll tackle the subjects one at a time to review the game

History

Dwarf Fortress keeps track of almost everything. The legends screens above about the dragon? One of those is created for each one of your dwarves, tracking the life events of the dwarf. Every sentient or large creature that your dwarf kills is tracked. Your dwarves can be happy, sad, or go crazy if their spouse dies. Baby dwarves can go insane if their parent dies. This, too, will be recorded.

The history system can be a bit overwhelming at times, but at the same time it feels as though the game you're playing has an epic quality to it. You're never forced to look at the history system, which I think is a big plus. Did a dragon just arrive at your fortress and take out half your population before one of your champions brought it down? You won't feel so bad after you look at the legend screen and find out that once upon a time that dragon killed the elven king.

However, if that dragon takes out your fortress, it is gone. Dwarf fortress is a one-way game with no mulligans. You can only pause the game and quit. You can never save the game, make a mistake, and then reload the game. If a dwarf dies, they're dead. This may make it difficult for some players, and if you like do-overs then this game probably isn't for you.

Combat

The combat system allows dwarves to train, equip specific weapons and shields, and become injured or die. The detail found in the history system also exists in the combat system. Axe-dwarves or sword-dwarves will lob off heads, while marks-dwarves (cross-bow wielders) will kill enemies by puncturing vital organs. You can find out (if you wish) that your marks-dwarf killed that fox by puncturing its spleen before the fox bleed out. Your soldiers will break bones that will take months to heal while doctors attend to them.

Overall the combat system is a nice balance to the economy, which I'll talk about below. One disadvantage with the system is that fights tend to be very one-sided. If a dragon shows up, your dwarves are either prepared or they're dragon-meat. There isn't really a delay-the-dragon-while-dwarves train option. Goblins will occasionally siege your fortress, which (again) isn't a problem if you're prepared.

Control with the combat system is probably the weakest link in the game. You can lump dwarves together into a squad, but if the squad leader is sleeping when the goblins attack you have to re-arrange the squad. I think it takes too long to re-arrange the military to respond to the threat. Controlling your civilians is also difficult; control is very coarse, only allowing you to shut off whether civilians or soldiers should stay underground. Additionally, civilians complain so much when they're forced to stay inside that it makes playing the game difficult during an attack. All you see is "civilian complains about going outside because civilian wants to do X." I think this area needs a little bit of work before the game can shine.

(above) Dwarves train in the barracks on the top left.

(above) Examining the wounds of a dwarf. The yellow text signifies a broken bone.

(above) Some goblins (purple and white 'g' characters) ambush and kill a bone carver (dead blue dwarf).

(above) An axe-wielding soldier (blue dwarf) is about to "axe"-xact revenge on the goblins.

(above) The goblins didn't have a chance.

Resources for the Economy

I love building games like Sim City or Civilization. Dwarf Fortress has a great building system. You start by ordering dwarves to mine out an area of a mountain, creating a safe haven from the outside world. You then can create areas for stockpiles of resources, and workshops to turn the resources into either goods or other resources. A trade system exists with caravans to trade for goods. There is a complex assembly line for some goods - for example, to make steel armor, first you'll need steel bars. To get steel bars, a dwarf needs to process iron bars, a flux stone, and charcoal at a smelter. The charcoal needs to be produced at a wood furnace, and the flux stone needs to be mined from specific types of minerals. Charcoal is also used in other industries besides metal-smithing, such as glass-making, so to optimize the resource through-put you have to lay out your fortress stock-piles and workshops correctly.

Creating an effective economy is quite difficult. The distance to the surface of certain industries, such as the wood industry, needs to be balanced against fortress defense. Some structures, such as farms, have restrictions on what type of soil you can build them on top of. Your dwarves need to eat and sleep, but they'll have trouble sleeping near noisy workshops or eating near garbage.

When I first started playing the game I found myself thinking in 2-D...but over time, I realized that highly optimized fortresses needs to be built in 3-D. The extra dimension really adds a lot to the game if you love building assembly lines or working with resource management.

(above) Fields next to a river.

(above) Quarters with a bed and a door for about 100 dwarves. A set of nicer quarters with smoothed walls is in the middle

(above) A stock-pile of furniture on the left.

(above) A set of workshops spread across two rooms to the left of the hallway. There is a nearly empty stockpile of wood below one row of workshops (empty stockpiles are denoted by "=" signs).

(above) A dining room to the left of the hallway, with a garbage dump on the right. A row of workshops is below the garbage dump. The purple cloud is a miasma cloud coming from decomposing waste.

One of the most novel features of the game is the trap and pump system. You can pump water, and then use pressure plates to activate or deactivate flood-gates or pumps. If you want to build an auto-filling cistern or an underground irrigation system, you can set it up so you only have to pull a single lever to get your pumps and flood-gates to do what you want. Are you having trouble with goblins attacking your fortress? Place ~~a puppy~~ some food outside as bait and then drown the goblins when they step on a pressure plate. If you prefer to catch the goblin, use the plate to slam doors shut or just use an old-fashioned cage trap. You could build an arena and then have goblins fight to the death! Or maybe start a goblin breeding program and use the baby goblins as a source of totems.

The building system, I think, is the strongest feature of Dwarf Fortress. The possibilities are endless - whether you want to build an arena or figure out how to build a computer, the open-ended system is one of if not the best I've seen in a game.

Overall

Dwarf Fortress is an old school ASCII game with a lot of promise. If you can look past some of the rough edges with the combat system and incomplete features (the game is still an alpha), the game plays out like Sim City meets tinker toys. Much like Sim City, there is some dead-time while you wait for things to happen, but there is a great reward for building that auto-filling cistern. Overall if you liked NetHack and Sim City I think you'll love this game; but beware the high learning curve almost mandates using a guide to help you out with the first few steps.

Tip About Airline Flights

2010-03-25T01:00:00.004+01:00

On my recent trip from Amsterdam to Boston to Iowa to Amsterdam, I needed to move my last set of flights forward a day because of an important meeting. I called up American Airlines, and because my Boston to Iowa trip had been delayed, AA didn't charge any money to change my flight to Amsterdam.

If you ever need to reschedule flights, AA will be very accommodating if you've had previous delays. This is probably true for other airlines. I hope someone finds this tip as useful as I did.

Grocery Stores in Iowa

2010-03-24T20:00:00.002+01:00

How can any store carry hummus but not pita bread! They even had the extra garlic type of hummus.

Well, I guess that is Iowa for you. Sigh.

A Little Bit of Dancing

2010-03-23T03:34:00.005+01:00

Congratulations to my big sister, who was married this weekend! There were some other photos that were shown at the wedding, but this one was my favorite; I think it sums up a lot of the past.

California Iowa Here I Come

2010-03-11T15:35:00.002+01:00

I'm on vacation for the next two weeks - woohoo! Looking forward to seeing you all.

Sorry about Anonymous Commenting Being Turned Off

2010-03-01T13:56:00.002+01:00

A loyal reader has informed me that anonymous commenting was turned off. My apologies, I've switched it back on.

Trust in Giant Corporations

2010-02-28T19:05:00.002+01:00

Nothing improves trust in a multi-national bank's online security quite as much as a directory listing for a home page.

It's The Small Things

2010-02-07T14:47:00.007+01:00

One reason I love VHDL is that the store operator isn't the equals sign:

IF (SHIFT = state_reg) THEN
    read_value <= next_value + read_value;
END IF;

Here is some (nearly) equivalent code in C:

if (SHIFT == state_reg) {
    read_value = next_value + read_value;
}

Both lines of code instruct that if state_reg is equal to SHIFT, read_value should be incremented by next_value.

In C the = sign doesn't actually mean equals - that is what the == symbol means. In C, as in most programming languages, the = symbol really means "store the right-hand value into the variable." This caused me no end of confusion when I started programming - if you subtracted read_value from both sides of "read_value = next_value + read_value" wouldn't you get "0 = next_value?" In reality the line instructs the computer to add next_value to the current value of read_value, and store this sum back into read_value.

In VHDL = means equals and <= means store. Unfortunately <= also means less than or equal to. I would have preferred VHDL to use the symbol <- for store. In the first programming language I ever learned, TI-86 BASIC, there was a single-character symbol for <-. I still find the first line below to be the most intuitive of the three:

sum <- element + sum
sum <= element + sum
sum = element + sum

I doubt programming languages will ever change from the equals sign to something else, but I would appreciate it. Every now and then my brain seems to go into math mode, and the = symbols still cause me confusion, but the <= is close enough to <- that I don't seem to notice. Oh well, maybe I'll never master C.

PyCharm

2010-02-03T16:24:00.002+01:00

I love PyCharm from JetBrains! I used Resharper when I was a C# monkey, and I am all ready much more productive with Python because of JetBrains. If you're a Python programmer you have to check out PyCharm as an IDE.

Software Fail

2010-01-26T16:53:00.005+01:00

My license is actually valid.

Just so you're aware, people use Xilinx FPGAs and the tool-chain for critical systems. I hope I'm not shaking your faith in that PET scanner, though. They're probably free from the issues associated with radiation therapy systems.

The End of an Era

2010-01-19T10:58:00.002+01:00

Tomorrow my @mit.edu account expires. It is about time, but I'll still miss it like crazy. The account was easily the best managed e-mail and file account I've ever had. I had over 12,000 messages in my inbox alone and nearly a gigabyte of files, capturing some of the best things I ever experienced, along with some of the most educational.

Farewell, account!

Officially Old

2010-01-07T06:37:00.003+01:00

With another birthday under my belt and the new year started, I am officially old. On the other hand, I've now been programming for more than 10 years! I dug up an old piece of my code, prime3b.java, which was last modified on July 14th, 1999. Technically, I've probably been programming for 12 or 13 years, but I don't think my self-taught, TI-86 programming should count as programming.

According to Wikipedia's Java Version Page, this program would have been created for Java 1.2. The program took a number, computed all the primes to that number, and could print out the calculated primes or number of primes.


import java.util.*;

public class prime3b
{
  public static void main(String [] args)
  {System.out.print("Would you like to print out all the primes?");
  String cond = KeyBoard.readString();
  boolean f = true;
  boolean d = true;
  if (cond == "no")  
    {f = !f;
  }
  System.out.print("Would you like to print out the number of primes?");
  cond = KeyBoard.readString();
  if (cond == "no")
    {d = !d;
  }
  System.out.print("Enter a number:");
  int x = KeyBoard.readInt();
  int a = 0;
  int b = 0;
  int []m = new int [100000];
  m[0] = 2;
  int z = 0;       
  int e = 0;
  int c = 3;
  int y = 0;
  long t1 = (new Date()).getTime();
  for(; c <= x; c = c + 2)
    {y = (int) Math.sqrt(c);
    for(z = 0; m[z] <= y; z++) 
      {a = c % m[z];
      if (a == 0)
        {b = 1;
      }
    }        
    if (b == 0)
      {e++;
      m[e] = c;
    }
    else
      {b = 0;
    }
  }
  long t2 = (new Date()).getTime();
  t2 = t2 - t1;
  z = e;
  if (f == true)
    {for (; z != -1; z--)
       {System.out.println(m[z]);
    }
  }  
  if (d == true)
    {e++;
    System.out.println("There were " + e + " primes at or below " + x);
  }
  System.out.println("Time is:" + t2);
  }
}

PS In case you're wondering about my instructor's feedback, he said that one day I would be a superb programmer, after I had been crushed by the complexity of a few systems (I don't think he said "been crushed by", maybe "grappled with?"). This would teach me discipline, actions like encapsulating code into functions, thinking about testing, using standard formatting, using better variable naming, checking inputs, checking boundary conditions, and learning that code was also meant for people.

I'm still hoping his prediction comes true.

PPS I think most programmers fall into two categories: OCD programmers who need everything perfect, constantly re-visiting and re-working, or ~~lazy~~ efficient programmers who do the least amount of work even if it means more code. I think the above firmly puts a younger me into the efficient camp.

Nature and Nuclear Reactions

2009-12-16T14:00:00.000+01:00

I've blogged about toilets evolving in nature, but apparently nature also created self-sustaining nuclear reactions:

Perrin and the other French scientists concluded that the only other uranium samples with similar levels of the isotopes found at Oklo could be found in the used nuclear fuel produced by modern reactors. They found that the percentages of many isotopes at Oklo strongly resembled those in the spent fuel generated by nuclear power plants, and, therefore, reasoned that a similar natural process had occurred.
...
Scientists think these natural reactors could have functioned intermittently for a million years or more. Natural chain reactions stopped when the uranium isotopes became too sparse to keep the reactions going.

It is amazing to me that the random motion of matter can create a self-sustaining nuclear reaction with an average power output in the 100 kW range. This interesting anecdote of a complex system arising from random processes is evidence that long time periods and random processes can create surprising, complex systems. Maybe even life?

Google Wave Invites

2009-12-11T15:49:00.002+01:00

Even after sending many invites, I still have a few left over. Let me know if you want one.

Auto-Pilot

2009-12-10T22:00:00.001+01:00

I'm sorry I haven't posted. I've been so stressed out lately that it has taken everything I have to focus on getting an iota of work done every day. I tried writing a long, thoughtful post about what is happening, but it just sounded lame.

I'm not dead, I know I'll eventually have things to blog about, but those things just aren't going to happen any time soon, at least not until I'm back in the states for vacation. You can check out today's PhD strip for a decent run-down on the current events in my life...only imagine someone who is convinced that working now will lead to laziness later, but instead this working is leading to more trouble with working. Or some other non-sense like that.

Rejection

2009-11-21T07:52:00.007+01:00

Last week I went to an astronaut's speech on the future of commercial space flight. The astronaut, Steve Smith, worked on the Hubble Space Telescope while it was in orbit. I got to meet and talk with him personally for a few minutes, and loved every second of it.

He had a lot of interesting anecdotes, but the one that I'm still thinking about is this: the space program rejected him as an astronaut candidate four times before being accepting him. You can only apply once every two years, so he was living in a state of space-program rejection for eight years before being accepted. I wish I had had the foresight to ask him whether this was normal for astronaut candidates, or if he was an exception. Either way, the fact that he keep reaching for his dream, even after eight years of rejection, is amazing and inspiring to me.

Chip

2009-11-07T21:38:00.003+01:00

My 2.5 by 2 mm^2 integrated circuit design was finalized yesterday. Maybe now I can stop stressing out so much?

Probably not.

Bleg: Books

2009-11-04T11:49:00.008+01:00

These are the books I'm thinking of buying for myself, with the up-coming holiday season discounts:

Non-Fiction:

Fiction:

Dying Inside

Any additional suggestions for books?

Randomizing a Coin Toss

2009-11-02T19:09:00.006+01:00

Way to report only the problem, Freakonomics blog:

But it may be that the the random coin toss isn’t so random. A 2007 study found that a vigorously flipped coin is likely to land on the same side it started on at least 51 percent of the time, possibly more depending on the person doing the flipping.

Say you have a coin with a bias that doesn't change from flip to flip. You can remove the bias by flipping the coin twice, and taking the first result if the second result differs from the first or repeating if it lands the same way both times.

Mathematically, if the probability of landing heads is P, then:

P^2 = Prob[HH]
P*(1-P) = Prob[HT]
(1-P)*P = Prob[TH]
(1-P)^2 = Prob[TT]

Since the probability of HT is the same as TH, taking the first element removes the bias.

Mad props to von Neumann for inventing this trick (publication was "Various techniques used in connection with random digits"), along with fundamental portions of the theory for quantum mechanics, cryptography, and game theory. They don't make mathematicians like they used to.

Temper

2009-10-14T17:35:00.005+02:00

I don't normally blog about personal things, because I think they're lame and I really hate putting personal information onto the interweb. But I figured I've got to try most things once and see how it turns out.

I lost my temper today. It was pretty bad. If you know me, I may not seem like the kind of person who loses it very easily, and in general I think I keep my cool pretty well. Today just wasn't my day.

Today at work, one of my officemates made a passing remark about gay people and how they were decreed to be killed in his home country. He was talking to another person at the time (not me), but I thought the way he phrased it was completely inappropriate. What I thought I heard was a statement supporting violence against people based on their sexual preference. What he probably said or intended to say was a factual statement about what happens in his home country because of the laws. In retrospect, as he isn't a native English speaker, the intention of the statement and what were said were probably different. I think the words "should," "could" and "would" are particularly difficult for non-native speakers to grasp. Even native speakers aren't clear with their intentions in everyday conversation.

Anyways, I then asked him if he would please keep the hate speech out of this country.

A large fight ensued where I lost my cool. He claimed the remark wasn't for public consumption, but at the same time I heard it and pointed out that other people use our room. When he makes remarks like the one he made, other people listen and he implicitly represents our group, and hence me in such remarks. We ended up taking the issue to our adviser, who as head of our group is mostly responsible for our group image.

My adviser agreed with me about our room and our remarks being public. My adviser warned my colleague to be more careful with his words in the future. My adviser told me I needed to be less strict in my interpretations of what people, especially non-native speakers, say, and that I shouldn't assume their intentions from their speech. He also said not to overreact so much. I think I agree with him on all statements. I lost my cool, and need to be more understanding of the slipperiness in communications.

I would be lying if I said there hasn't been a build-up to this, or to the other times I've lost my cool. The way my officemate structures his speech would be extremely rude in Iowa. I've tried explaining it, but so far without much success. Maybe the problem is with me? I don't know. Things aren't really great between us. He accused me of being a spy today (I don't think he knows what the word means), and I think I've burned too many bridges to try and explain to him how he is subtly insulting me. He probably wouldn't believe me anyways - I'm a spy, right?

I'm been having some problems with my temper lately (when I say lately, I mean over the past two years, since leaving university). At my last job, I had pretty big issues with how long it took to accomplish things. I'm a pretty ~~lazy~~efficient person, and when I do work I want it to matter. I get angry when it doesn't, or if I did unnecessary work. Making sure I take the right approach to getting things working is very important to me, and I think it makes me a good engineer. I know I can focus my anger when things don't go well. I distinctly remember times in middle school when I did poorly on a test and studied non-stop because I was angry about it, and the next tests always came back with high marks. At the same time, it seems over the past few years my temper has starting to get in the way of getting things done in the most efficient manner. I should have asked my officemate to clarify his statement, not immediately assumed a bigoted intention. I should have known that getting things done quickly is different for a very constrained university assignment than for work in the corporate world.

I thought I'd share this moment of anger with you. While writing about it has been a bit cathartic, I'll still be fuming for the next few days.

How are Our Children Going to Get Out of Bathrooms?

2009-10-12T18:00:00.003+02:00

It was roughly 2 am on a standard night at MIT. Pacing the hallways with my trusty football, I asked a few people if they wanted to hit up a local shop for some late night chocolate milk and Italian subs. Receiving an affirmative, I told them I'd be back in a moment. I really had to go to the bathroom.

Having finished my business and washed my heads, I went to unlock the bathroom door. The knob turned, but the latch did not retract. I looked at my football. We were stuck in the bathroom.

After yelling and attracting the attention of some local residents, I asked if they had any bright ideas. One suggested re-locking and unlocking the door, which had allowed her to escape a similar situation several days ago. Alas, it did not work. I looked at my football again. Still stuck in the bathroom.

But wait! I had my trusty Gerber multi-tool with me! Holding my football a bit steadier, I whipped out the mini-screwdriver, took off the doorknob casing, had some friends help take apart the rest of the doorknob, pulled out the latch, and escaped the clutches of the bathroom (EDIT: this sentence was modified to properly attribute work to people missed on the initial post).

Today, the NYTimes ran an article on schools punishing children for carrying multi-tools. I want to know from these multi-tool nay-sayers: Who is going to get our children out of the bathrooms at 2 am? Because I don't think it is going to be you.

The Invention of Google Wave: A Play in One Act

2009-10-12T03:02:00.003+02:00

Date: roughly one year ago. Two twenty-something google engineers (both decked out in blue google t-shirts and jeans) sit on their fitness balls. One sips some strange coffee-like concoction while the other downs an Odwalla drink. Engineer one checks his e-mail.

One: That jerk Larry from HR keeps top-replying to my emails. Seriously. Who the h#** uses top-reply these days?

Two: Everyone but nerds uses top-reply. Didn't you talk with new girl? She was an M$ intern last year, and apparently M$ mandates top-reply in their emails.

One: And what if you want to respond to multiple points in the e-mail?

Two: I think Outlook would have crashed by then.

One: Seriously, this is non-sense. We need to get some giant conspiracy going to make bottom-reply the default.

Two: I have an idea. How about we claim we're merging IM functionality with e-mail. But in reality we'll just be forcing people to use the indent-reply conventions nerds have been using for the past 40 years, and give people too stupid to setup IM notifications of email events the chance to get e-mail instantly.

One: That sounds awesome. We'll dress it up to look fancy, so people aren't so intimidated by the less than signs that would normally occupy the start of the line.

Two: I know. Heaven forbid people learn how to use conventions, or look at plain text.

One: Oh, and we can put in annoying features that geeks would hate! Maybe we can have it immediately show the person's reply, while they're typing! Heaven forbid people think before they respond, like us introverted nerds do with emails, so the hundreds of people getting our emails don't have to sit through our mistakes. We can cut out the subject line, too - it isn't like people use that to its potential.

Two: Those sound like exactly the sorts of nerd-hating features that'll launch this project into the big time! Let's get coding.

Curtains close as furious keyboard pounding commences.

Tape-Out

2009-10-11T14:00:00.001+02:00

If you've talked with me lately, I've probably told you how stressed out I am about something called a "tape-out." The phrase refers to production of an integrated circuit. According to my adviser, 20 or 30 years ago, before the internet was around, circuit designers would send physical tapes to the chip manufacturers. Hence the term tape-out. Thus when an electrical engineer is creating an integrated circuit, (s)he uses the term tape-out to describe the process.

Today I thought I'd share a little bit of the designer process, so you can understand what I'm talking about when I say I've been staring at colored polygons all day. Circuits perform a lot of tasks, from the main processing in our computers, to capturing images in some of our cameras, or detecting events in the world around us.

To create circuits to do all these things, engineers start simple and build up. The basic unit in an integrated circuit is the transistor, which acts as a switch in digital logic. The switch is on or off depending on the electrical signals we send to the transistor. I've taken public domain pictures from Wikipedia that shows the behavior when the transistor is off (first picture) or on (second picture).

The basis for transistor construction is the placement of materials with different characteristics. The "n" and "p" labels above are on materials with different elements. Placing these materials at proper distances from one another is critical to proper operation of the switches.

When electrical engineers create circuits, we need ways to control where the materials go, and then we can control the behavior of the circuit. Thus when I talk about colored polygons, I am talking about visualizing the locations of different types of material that determine a circuit's operation. I've labeled the drawings above with the colors of the layers, and including a screenshot of what I look at when I am using software to "create" a transistor. The wikipedia images are from the side, whereas engineers view things from the top.

The red polygon, representing the gate, interfaces with the control signal for the transistor. The green layer represents the 'n' implant into the 'p' type silicon. The blue layer is a metal routing layer on top - there are other metal layers for routing, along with via layers such as the teal layer above that connect metal layers to other layers.

You'll notice I don't specify all the layers. The silicon dioxide layer, dashed in the figure, doesn't have a corresponding polygon. Some layers are auto-generated from other layers; this can create problems when you want to do something fancy.

Starting from these simple layers, we can quickly build up complicated devices. I didn't mention this before, but there are actually two types of complementary transistors on most integrated circuits. This is the basis for the term CMOS, or complementary metal oxide semiconductor. The next picture shows both types of transistors. You can check out the CMOS Wikipedia page if you're interested in the two types.

The structure you're looking at is an inverter, as it outputs the opposite of the input signal after some time. If you're confused by the layers, follow the red polygon (the gate) to the green areas - the overlap area would be the two transistors. The yellow and white dotted layers help describe which type of transistor is to be created. The big orange box around the top portion would change the material in a large area, and is required for one of the two transistor types. The teal / cyan squares are vias that connect the metal to other material. Though vias only connect to the green layers in the transistor I showed above, they can also connect to other layers.

There are additional metal routing layers than the metal one I've shown so far. The next picture shows a custom structure I have made. This structure includes yellow and white polygons, which represent metals at different heights than the metal in the previous images.

The purple and orange squares represent vias between the various metal layers. The structure that you're looking at is a variable-delay buffer. It takes a control signal and an input signal, and outputs the input signal after a delay which is set by the control signal.

I've included measurements on the side of the structure in microns, or one-thousandth of a millimeter. A micron is also one-millionth of a meter. When you hear people talk about different integrated circuits production processes, they'll usually use the minimum accuracy of the gate size as a first-order statement of how advanced the process is. This is a 0.35 micron process, meaning that the minimum gate size is 0.35 microns, or 350 nanometers. The current processor in your computer is probably a 45, 90 or 130 nanometer process.

You might ask why people care about the construction of the circuit - don't we really just care about the behavior? Digital engineers do tend to care more about the behavior than the construction itself, and they usually don't lay out circuits by hand. They usually specify the behavior using some type of code, and run this code through a bunch of fancy tools to get the material locations.

However, if you work with sensors, it is often more difficult to specify the exact characteristics of the structures than simply laying out the structures by hand. This is the case for most of the work my group does.

There is the additional problem that messing up means the entire circuit might not work. This is why I'm constantly stressed out - while one mistake can cost a software person months of their life, simple things are enough to easily prevent this. This often isn't the case in hardware, as creating the circuit takes months, and you're stuck with the circuit.

Well, I hope you enjoyed my post on tape-outs. I cannot post pictures of my more complex structures, as a lot of the cells I work with are proprietary, and the man would come after me. I'm finished with this tape-out in early November, and then it will be a few months before I know whether it was a waste of time. I'll probably be drinking a lot of egg nog at xmas time.

Worst People

2009-10-10T07:00:00.000+02:00

I'm beginning to think Google is out to get me.

Architecture around TU Delft

2009-10-05T21:42:00.000+02:00

The weather was nice a few weekends ago, so I went out and snapped a few photos. Enjoy!

This is a picture from the window of my new apartment. I now have a view of the canal. Sorry for the tilt, my head isn't on straight so it looks normal to me.

TNO is a large defense contractor in Delft.

A south view from my building.

A west view from my building, towards the part of town with the high-rise apartment buildings.
I've circled a bunch of the high rise buildings. As I've previously described, most of the development in Delft occurs on the outskirts of town. This preserves the town center as is.

You can see that along the canal there are a lot of industrial type buildings. A lot of heavy freight is shipped along the canals instead of roads, which means that the roads require less maintainence.

Some apartments near the university. You can see part of my building in the background.

Some apartments near the university. They stand over a pond.

Due to all of the bicycle traffic, it can be difficult to know whether a bicycle is supposed to go on a path or not. The people who designed the park in the middle of campus included environmental cues to help. First, the rocks are close enough together that a bicycle would have trouble going between them. Next, the gray sections of the path are rough; riding over the alternating path sections feels unnatural on a bicycle. The path goes down a few steps out of sight, so it is important that bicyclists don't go on this path. People don't seem to like signs here, Delft has a lot of these environmental cues around the city to help bicyclists with whether or not they belong in certain places.

The main bicycle path next to the mechanical engineering building. Exposed stairwells are very common here, I think architects like them.

My building.

The civil engineering building, which also contains administrative offices. Another building with exposed stairwells.

A set of dorm rooms are by my building.

Two Hogeschools (or vocational schools) have opened up next to TUDelft. When they were building this school, they had water in the lot that is now under construction. This building looked like one of those beach buildings on stilts. The empty lot will soon contain housing.

Another vocational school. This one is interesting because it contains a parking lot on the roof!

Dracthen

2009-09-28T01:42:00.009+02:00

The town of Drachten in the northern part of the Netherlands took its main traffic intersection and changed it drastically in 2003 -- all traffic signs and lights were removed! Below are pictures from before and after the rebuilding of the city square.

My favorite note from the summarizing report is that respondents think the traffic situation is less safe now (appendix 6c from the report), whereas the number of accidents has fallen to under 20% of previous levels. I think something called the Peltzman effect is behind the discrepancy between the increased safety but decreased view of safety. When human beings feel safe, they might engage in riskier behavior. By playing on the fears of people, the intersection has (so far) been much safer. I have previously blogged about this effect in a post on condoms.

Oddly enough, people ranked the "quality" of the re-designed space much better than before, even though they thought the re-design was less safe. In addition, the transit times across the intersection improved.

I think this effect has strong implications for how we can misunderstand our own rationality, and helps explain why it is important to study information objectively by examining accident rates and transit times, getting a full picture of how our emotions steer us in all situations.

Tip of the hat to reddit for still providing signal, even though most of your links are now noise.

Copyright note - the publication with these pictures didn't include explicit copyright information, but did contain a logo for a sponsoring institution, a Gemeente, meaning they should be in the public domain. If you are a random visitor with more information, please let me know if you are aware of the copyright situation of these photographs.

Drawing the US

2009-09-20T01:00:00.000+02:00

As a follow-up to my earlier post, I drew the U.S. today. I managed to get all the states, though a few have some major issues. I colored in what I meant to draw, and I'm not really sure what happened at the MO / IL / KY border...hmmm...

If you think you can do better you should give it a shot!

Farewell, Norman Borlaug

2009-09-13T16:44:00.003+02:00

Norman Borlaug has died:

Norman E. Borlaug, the plant scientist who did more than anyone else in the 20th century to teach the world to feed itself and whose work was credited with saving hundreds of millions of lives, died Saturday night. He was 95 and lived in Dallas.

In high school biology class, we had a population unit that included articles on Borlaug. As a fellow Iowan, Norman Borlaug was the center of several important discussions, especially his premonition that "If the world population continues to increase at the same rate, we will destroy the species."

There are a lot of slow, dangerous effects that we hear about every now and then - I think that people, myself included, don't think enough about the drastic increases in population that will come with better health-care and nourishment in every part of the world.

High SNR Sentences: Identifying You in Data

2009-09-08T17:42:00.004+02:00

It was found that 87% (216 million of 248 million) of the population in the United States had reported characteristics that likely made them unique based only on {5-digit ZIP, gender, date of birth}.

The sentence was from a CMU researcher working in 2000 on 1990 census data. Unfortunately the paper is behind a wall, but a different, available paper with a decent methodology puts the number at 63%. I was not comforted by the lower estimate. Tip of the hat to Ars Technica for an interesting discussion on "anonymizing" data.

Drawing the US from Memory

2009-09-06T12:47:00.003+02:00

I used to challenge people to draw the US from memory, it was usually hilarious when people who weren't from the mid-west tried to draw the region. I can do a respectable job, I almost always hit all the states and the shapes aren't too bad...but holy cow, Al Franken, you're my hero.

Timing Properties of SPADs

2009-08-30T19:00:00.004+02:00

I've gotten requests for more technical material, so here ya go:

Today I'm going to talk about some applications of SPADs. If you want a reminder of the basics of SPADs, you can read my introductory post or my post on noise. SPADs are single-photon detectors that use feedback systems in conjunction with one another to accurately time the arrival of single-photons. Accurately timing a photon's arrival time is important in many applications, but today I'll be talking about rangefinding.

In rangefinding applications, such as laser-based rangefinding for land surveying, a laser fires a pulse of photons and a detector times the difference between the pulse and the photon detection time. Photons, being light, travel at the speed of light. You'll usually here the speed of light quoted as 300,000,000 meters per second, but optics people prefer to quote the speed of light as

30 centimeters per nanosecond
300 millimeters per nanosecond
300 micrometers (microns) per picosecond
30 millimeters per 100 picoseconds

We use these values because modern electronics usually have around 100 picoseconds of accuracy. In the future, I think the 300 microns per picosecond value will become more common.

Anyways, we have to accurately time this photon arrival so we can determine the time of flight. The timing inaccuracy is termed jitter; we use various metrics to quantify the jitter, but most of these metrics just capture the usual case. For SPADs, the jitter depends on a few things.

First, the temperature is very important. In a silicon integrated circuit, increasing the temperature increases the ambient energy available to electrons, the main information carriers in the circuit. The introduction of additional energy modifies a carrier's behavior, and thus changing the temperature will change the characteristics of both the fast and slow feedback loops in SPADs.

Next, the color of the light is also important. Different colors of light have different wavelengths. The wavelength describes how frequently the energy moves around in space. Since silicon has a repeating structure, the wavelengths will help determine how likely it is that the light interacts with the crystal, producing the primary electron that could cause an avalanche. It turns out that blue light is optimal for the current generation of SPADs - the optimal wavelength is a balance between how far light usually penetrates into the silicon and where the avalanche region is (remember that we moved the region away from the surface to avoid the noise-causing irregularities at the surface).

Within the avalanche region, the build-up time of the avalanche is obviously important. During the initial portion of the positive feed-back loop, when there are very few carriers active, the variation in each carrier can change the build-up time. Current understanding is that it takes between 0 and 15 picoseconds to generate enough carriers to average out these variations, though this build-up process depends on characteristics like the temperature and strength of the applied force (the electric field).

So what is the end result? Well it depends on what you need and what you have available. If you have a lot of area available on a silicon chip, you can use more complex current detectors to get the jitter as low as 15 or 20 picoseconds. On the other hand, if you're short on area you can raise the jitter as much as you like, but you'd be hard-pressed to raise it above nanoseconds and still have a viable application. Keep in mind that you'll be changing how close the SPADs are, so the cross-talk will change.

When you're making a range-finder, you might care only about one specific range, or you might be trying to acquire a bunch of ranges to get a 3D pictures. If you only care about one range, you can use a lot of area to achieve the 20 picosecond resolution. This corresponds to an uncertainty in space around 6 millimeters. If you have an array of SPADs and timing circuitry, you're more likely to have an error in the 100 picosecond range. 100 picoseconds corresponds to an error of 3 cm in space. You can lower this uncertainty by taking multiple measurements, and since the measurements are so fast the accuracy can easily be one millimeter or less.

Anyways, I hope this post helped you understand about the timing uncertainty in SPADs. The uncertainty affects other applications besides rangefinding, things like quantum-based encryption algorithms, biological imaging, and cancer detection, but those applications are a bit more complicated to explain! I'll be attempting in future posts, and we'll see how it goes.

Another Airbrushing Site

2009-08-30T14:01:00.002+02:00

I stumbled across a really interesting airbrushing site today...I can never click through enough of these to remind me how much people are mis-represented in print and online media. (earlier post)

Question

2009-08-27T13:12:00.001+02:00

Why are TVs and computer monitors horizontally long, but paper is vertically long? I suppose it makes sense that monitors and TVs are horizontal, as this matches our visual field, but then why is paper tall, rather than wide?

Firsts

2009-08-17T23:30:00.002+02:00

It has been a year! Here are some of the things I've done in the past year:

1) Forgot / lost passport, had to travel 3 hours to get it back
2) Setup an experiment using somewhat dangerous radiation while I was suffering a headache from lack of sleep
3) Was the last person on a plane, having nearly missed it (this experience is over-rated)
4) Laid out a portion of an integrated ciricuit that (if it works, crosses fingers!) will have 5.12 GBps going through it
5) Lost PhD topic
5.5) Lost PhD topic
6) Found PhD topic (errrr.....I think?)
7) Went all-in and won a poker pot, went all-in and lost a poker pot, successfully spotted a bluff at a poker table, successfully set a trap at a poker table
8) Gone to one of those fancy European clubs in Paris (it was worse than I thought and I will not be returning)
9) Bought plane tickets, booked a hotel, flew on plane and checked into hotel within 5 hours of one another
10) Successfully found apartment in a foreign country and moved into it from another apartment
11) Gotten a first-hand view of how difficult it is to be an immigrant
12) Earned the title Expatriate

Things I haven't done:

1) Successfully had a conversation in Dutch (I haven't had many successful ones in English over here, either)
2) Joined a choir
3) Written a paper (I'm working on one right now, and I have two in various stages of the paper pipeline)
4) Used tools to go from VHDL to ASIC

By the numbers:

Guitars purchased - 1
Bicycles purchased - 1
Haircuts - 2
"Original" research ideas that someone else had actually tried but adviser didn't know about - 3
Canned hot dogs consumed - 4
Moose seen - 4 (two real, two mascots)
Shoes purchased - 6
Countries book was purchased in - 5 (6 if you separate England and Scotland, 7 if you include online purchases)
Countries "visited" - 7 (Scotland, US, Canada, Switzerland, Ghana, France, Belgium)
Passport resources used - 27 boxes from stamps, 2 pages from visas
Train tickets purchased - ~100 (I go through about 8 a month)
PB&J Sandwichs consumed - ~150 (they have this awesome sour cherry jam over here)
Emails sent - 2,088 (more than I thought, 25 were to myself)
Emails received - 2,698 (fewer than I thought)
Most lines of code written in a single day - ~3,200 (most of it was test code...firmware test code can be pretty massive to go through the appropriate states)
Lines of code written overall - ~16,000 (again, around 14,000 lines are test code)
Heartbeats - ~37,000,000 (the heart is a work of art)

And finally:

Dutch postcards sent - 0 (yeeeeeeeah...I still owe a lot of people postcards.....)

$500 for a Bicycle

2009-08-17T19:25:00.005+02:00

The Freakonomics blog has a great post on the cost of bicycles in bicycle-crazy Portland:

Yeah, the bike guy answered, he had something super-cheap for me ... I could have it, he said, for $475.

So I went to another store. Same deal, more or less. There was one bike for $275, but it was a girl’s Raleigh from the 1960’s with a wicker basket.

...

At Portland’s Costco, meanwhile — on the outskirts of the city — you can buy a brand-new Schwinn Midtown city bike with Shimano shifters for around $200. But, according to the clerk there, those Schwinns aren’t moving.

I bought an inexpensive, new bicycle in Delft for just over $500, though the university reimbursed most of the cost through a travel program. I was expecting to find a nice, new one for around $250.

We don't have CostCo here, and sadly Ikea doesn't sell bicycles. I'll just keep dreaming.

A Test for Rental Scams

2009-07-23T22:30:00.003+02:00

I'm looking for an apartment, and I seem to get an awful lot of e-mails from people that have beautiful apartments for low, low prices but for whatever reason they won't show me the places. Or they say they'll meet me and when I show up a confused woman answers the door and says, "No, there is no apartment for rent here."

Today I'm going to describe to you how you can check if you are being scammed. Go into your email client and turn on all of the headers (in Thunderbird, this is View->Headers->All). You'll see a giant chain of "received" headers that look like:


Received: from [216.252.122.218] by n75.bullet.mail.sp1.yahoo.com with NNFMP;
          22 Jul 2009 20:09:46 -0000
Received: from [67.195.9.83] by t3.bullet.sp1.yahoo.com with NNFMP;
          22 Jul 2009 20:09:46 -0000
Received: from [67.195.9.105] by t3.bullet.mail.gq1.yahoo.com with NNFMP;
          22 Jul 2009 20:09:46 -0000
Received: from [127.0.0.1] by omp109.mail.gq1.yahoo.com with NNFMP;
          22 Jul 2009 20:09:46 -0000

At one end of these headers will be your e-mail provider, while at the other end will be the IP address of the computer that sent the email address:


Received: from SRV502.tudelft.net ([131.180.4.18]) by ...
...
...
...
Received: from [41.205.182.125] by web111904.mail.gq1.yahoo.com via HTTP;
          Wed, 22 Jul 2009 13:09:45 PDT

Sometimes the address of the originating computer is listed a bit differently:


Received: from BLU116-W26 ([65.55.116.72]) by ...
X-Originating-IP: [62.173.35.6]

The person might have masked the IP of their computer, but this is complicated and most scammers are idiots. Anyways, you can take this IP to a handy geolocation look-up service and find out the originating location.


IP: 41.205.182.125
Host: dial-pool07.ab.starcomms.net
Country: Nigeria

Every now and then the country won't be listed, but the host name you get back has information you can use to determine the country. For example, 62.173.35.6 resolves to 35-6.rv.ipnxtelecoms.com but the geolocation service doesn't give a country for this IP. ipNX Telecom has its headquarters in...Lagos, Nigeria.

I suppose in the future I'll have to screen any email about apartments. Sometimes I really hate people.

EDIT: Your email client actually uses the same method I describe above to label some emails as being probable scams. Usually IP blocks assigned to certain ISPs and sometimes even entire countries are labeled as suspect.

Sentences that Make Me Laugh

2009-07-23T16:03:00.004+02:00

If we ignore (thing one), (thing two), (thing three), (thing four) and assume (thing five), then the problem becomes tractable using only elementary results from field X.

Sadly I wrote the sentence...though it was followed by:

Subsequent sections will discuss the effects of (thing one), (thing two), (thing three) and (thing five), cumulating with results from a simulation including all these effects. The authors plan to revisit (thing four) in later work.

Planning to revisit something is a total cop-out.

CEOs and Pay

2009-07-22T19:00:00.001+02:00

While I was home the issue of executive compensation came up several times. I'm a person who thinks that a CEO could easily deserve tens of millions a year or more. The main reason behind this is two-fold.

First, I've worked at a company that has undergone restructuring at a management level. From personal experience, small changes in strategic direction have a massive impact on people at the bottom of the "job-food" chain. It is easy to lose months, probably even years of work because someone above you made the wrong call. Since a CEO helps determine the strategic direction of the company, it seems reasonable to me that the pay of the CEO should scale with the sum pay of every other member of the company.

Second, there are a few studies which show a CEO's personal circumstances can have a percentage-point effect on a company's performance. A great example is a study of the effect on profit by a death in the immediate family of a CEO. Excerpt:

Sorting by the number of children we find the biggest effects on firm profitability in cases where the CEO only has one child. Specifically, one-child death shocks correlate with a 5 percentage point decline in firm profitability irrespective of the age of the child.

The study goes on to show that the deaths of a spouse or child are significant events for a firm. I think the study underscores the importance of choosing the correct CEO. Though the study doesn't show the variation in profit during standard circumstances, to me it seems like a reasonable conclusion that variations in a CEO's ability to carry themselves through tough times will have a large effect on firm profit. For a company with hundreds of billions in profits per year, like an oil company, the CEO's personal circumstances could have an effect in the billion dollar range, meaning if the CEO themselves only received a fraction of this pay it would still be in the tens of millions range.

My math is a bit fuzzy here, but as always you're welcome to disagree in the comments and point out any mistakes I've made.

It's All About the Teachers

2009-07-21T12:30:00.001+02:00

I've been on vacation for the past, well, month, and I had a lot of interesting conversations. Aside from the very personal ones, the most engaging ones were on the topic of teachers. I had lunch with an old class-mate who is now a teacher at a high school. We talked a little bit about evaluating teachers. There isn't really a coherent point to this post, but if there was it would be that there is enormous room for improvement in the way we allocate resources to educate and invest in our next generation.

There is a lot of interesting quantitative data in how we invest in students. My class-mate and I talked about how too many smart people opt out of teaching. As the feminist movement has matured, a lot of really smart women no longer become teachers and the quality of teachers has suffered. I think the take-away is not that the feminist movement is bad, but rather we as a society don't have a great understanding of the importance of good teachers.

Another subject we talked about was the politics of teaching. If you haven't heard it, I suggest the TED speech of Bill Gates, the education portion begins at about 8 minutes. He talks, amongst other things, about how it is illegal in New York to use performance-based data to evaluate a teacher's performance. Coincidentally my old class-mate was for qualitative data like committees but against quantitative performance-based data. She claimed the quantitative data would have too much variance. I think I dissuaded her from this stance, but I do agree that quantitative data is not perfect. Any one metric can be taken advantage of. As an engineer, however, I have more faith in a well-designed system with numbers than a well-designed system with committees.

Finally, we went over the cost of education at private schools. There is a huge debate about whether private schools outperform public schools. The debate is quite contentious, especially when trying to account for socioeconomic and ethnic diversity factors. She said that public schools are critical to integrating immigrants into society. I do not have a great link to summarize this stance, as I haven't seen anything like this online - please comment and send along a link if you have one. I said that I thought public schools were wasteful due to the political pressure and lack of transparency into the teachers.

Anyways, I think the high level take-away is that evaluating teacher performance is a complex problem that has to touch politics and statistics, though a lot of information suggests there are inefficiencies. It would be interesting to attempt to evaluate schools, but creating a non-partisan report that accurately represents the facts seems to be near impossible. The only thing I know for sure is that I don't have a clue how parents choose schools for their children.

Big Pimpin'

2009-07-05T06:17:00.004+02:00

Sometimes it helps to remember your fashion roots.

Only a select few can go pantsless with combat boots and diapers. I am one of these few.

Sometimes, though, you've got to break out those whale pants.

When I was big in the 80's, I wore jump suits for a while. I think my life-long relationship with red started around this time.

I also tried the grunge scene in the 80's. Or the potato chip scene. They were kinda the same thing.

After the grunge scene I classed it up a little.

Speaking of classy, nothing says classy like gray shoes and a bow tie.

Sometimes it was hard being with other people who didn't get it. Going as a mouse to Halloween was so last year. Being a pre-schooler was where it was at.

Toilets Evolved?

2009-06-16T15:32:00.004+02:00

How awesome is evolution?

Using isotopic analysis, they estimate that shrew feces deposited in N. lowii’s pitchers are a significant source of nitrogen for the plants...Tree shrews visit the plants to eat nectar that oozes from the bowl’s open lid, positioning themselves directly over the bowl

Nature, how about you evolve me a starship? I promise I'll provide it with nutrients.

Errrrr, maybe I'll just build it myself.

Also, this is at least my fourth post on toilets, and those are just the ones I've tagged. How disturbing.

Shushing Doom

2009-06-11T19:53:00.003+02:00

According to space.com, the military is shushing incoming space objects:

A recent U.S. military policy decision now explicitly states that observations by hush-hush government spacecraft of incoming bolides and fireballs are classified secret and are not to be released, SPACE.com has learned.

I'd like to think they're trying to keep the location of orbiting platforms secret, but I know it's really a cover-up of a secret government program which has angered aliens previously posing as Gods who have sent a giant ball of explosives (posing as an asteroid) to wipe out our solar system and only an oddball team of four individuals (one carrying such an alien himself) can prevent the asteroid from hitting Earth by traveling to it and having their simple scheme fail while they'll still save the day with a more complex, 1 in a 1,000,000 chance scheme. Whew.

Mixed Nuts

2009-06-08T20:06:00.002+02:00

Sometimes you end up at the strangest pages on Wikipedia:

Modifying words like "fancy" or "choice" have not historically carried any legal meaning in the United States, and they remain absent from the current regulations.[1] In a 1915 federal case against "fancy mixed nuts" that were argued by competitors to be an inferior grade, U. S. v. 25 Bags of Nuts, N. J. No. 4329 (1915), the court declined to accept a trade standard.

Most Useful Undergraduate Classes

2009-06-08T17:30:00.000+02:00

Today I was thinking about how small the knowledge intersection has been between my undergraduate courses and my jobs. I made a list of all the classes I found directly useful at either of my two jobs, and it was shockingly small.

Classes I found useful at my previous, finance job (in order of usefulness):

1.  6.111 - Digital Design Lab / FPGA-based design lab
2.  6.001 - Intro to ComSci with LISP

Classes I've found useful at my current, graduate school job (in order of usefulness):

1.  6.111 - Digital Design Lab, or FPGA-based design lab
2.  6.004 - Computation Structures, or Build a CPU
3.  6.002 - Intro to Circuit Design
4.  17.477 - Technology and Policy of Weapons Systems
5.  6.001 - Intro to ComSci with LISP
6.  6.041 - Intro Probability

I think a lot of the other classes I took, such as the math classes and signal processing courses, have had a large impact on how I think and approach problems, but I haven't used this knowledge directly in my day to day life. I was shocked that 6.046, my algorithms course, isn't on the list. I haven't used any of the important concepts from 6.046 in either of my jobs. Just the other day I wrote a one-liner for bubble sort when I needed to sort data.

I'm not sure why there are so few classes on the lists, but I was thinking yesterday about why my design class, 6.111, was so high on both lists. I think it has to do with the design project, which was the first "real" design project I ever had. In 6.001, the programming introduction course, there was also a design project, but 6.001 worked on the principle of building up proven components. You wrote something and checked that it worked. Building bigger things meant building up the system one proven component at a time. When you were handed code, you read through and tested the code to check that it worked.

Unfortunately real life is more messy than this. Components are usually too complex to verify for yourself, and sometimes you have to work around interfaces that were designed for another task. My 6.111 project had to deal with these issues, along with the issues found in building up a proven and known system. My team created an electronic version of Labyrinth, the old tilting maze game wherein one tilts a board to guide a ball through a maze to a goal, avoiding hole traps along the way. Not only did we create a pretty big custom system, we also had to interface our system with a lot of 3rd party components, including tilt sensors, circuits that converted the tilt sensors into something understandable, a VGA controller and an LCD.

This was the first time that something I created had to work with sloppy, complex components. The components we interfaced with included complex but standard interfaces, like the LCD, and sloppy and non-standard ones, like the components written by the teaching assistants for the course. I still remember, four years on, that the tilt sensors could enter an error state during the read-out. This error state required a lot of hand-holding to work correctly. I also remember fighting for a week with the start-up sequence because of nuances with the timing.

It makes me sad that none of the theory courses I took actually have anything to do with my job, but the theory courses that I took don't really have much to do with anything. I indirectly use this theoretical knowledge every know and then, but rarely directly. Whenever I do digital circuit design, for example, my tools use the graph algorithms that I learned in 6.046, but this is abstracted away from me. I don't think I've used a single academic thing I learned in my senior year. What a waste of money. Sigh.

"He Thinks the Lavatory in his Cell is Fantastic"

2009-05-20T14:41:00.004+02:00

Or so swoon Somali pirates about Dutch toilets.

I think civilized people have a different opinion.

Let's Really Be Equal Here

2009-05-07T22:00:00.003+02:00

Insurance companies claim that women, especially child-bearing ones, use more health care than men, and hence pay higher premiums. Of course some people think this reason is non-sense, among them some law-makers introducing legislation to equalize the payments:

Senator John Kerry today introduced legislation that would improve health care benefits for women in the individual market by preventing insurers from charging them more, denying or limiting coverage based on their pregnancy status or delivery method, and ensuring comprehensive maternity coverage.

In related news, it was noticed that women live longer than men. Senator Kerry plans to fix this with a bill which would kill off specific women, equalizing the average lifetimes. He hasn't talked about his plans to equalize the "unmentionable parts of the human body."

Feeling Good About Being Stupid

2009-05-06T10:08:00.004+02:00

I wish I had some people's tolerance for their own ignorance:

Second, we don't do a good enough job of teaching our students how to be productively stupid – that is, if we don't feel stupid it means we're not really trying...Focusing on important questions puts us in the awkward position of being ignorant.

Aside from the isolating nature of graduate school, constantly feeling stupid is probably the hardest thing to adapt to. I still haven't found a good way to focus in the face of infinite possibilities.

Oh, right, I read reddit to help me focus. Nevermind.

The Best Game on Graph Theory This Year

2009-05-05T12:59:00.002+02:00

Sneeze!

Children are your future. Via NYTimes.

Quotes

2009-05-02T00:40:00.002+02:00

I've been staring at colored polygons for the past month, so I don't have anything interesting to say. You know the stress is getting to you when you run across random quotes on the internet and they bounce around inside your head. Enjoy the memes...or, rather, let the memes enjoy you.

Since its foundation nearly two decades earlier, Nato had had its headquarters in France. Now Nato would have to move. Furthermore, de Gaulle added, it was his intention that all American service personnel should be removed from French soil. "Does that include," [Lyndon B] Johnson is said to have replied, "those buried in it?"

When I was in the military they gave me a medal for killing two men and a discharge for loving one.

My father told me I had three career options. I could be a doctor, an engineer or a failure.

...any competent programmer, if given a chance to learn on the job, can become productive in a new software technology within a few weeks... [FYI I strongly disagree with the spirit of this quote, though the meaning is a bit truthful]

We hold these Truths to be self-evident, that all Men are created equal, that they are endowed by their Creator with certain unalienable Rights, that among these are Life, Liberty, and the pursuit of Happiness—-That to secure these Rights, Governments are instituted among Men, deriving their just Powers from the Consent of the Governed, that whenever any Form of Government becomes destructive of these Ends, it is the Right of the People to alter or abolish it, and to institute a new Government, laying its Foundation on such Principles, and organizing its Powers in such Form, as to them shall seem most likely to effect their Safety and Happiness.

Life is good, everyone just overreacts. Even me.

Accidentally Posted

2009-04-24T16:06:00.001+02:00

I seemed to have accidentally posted a draft before it was ready, I apologize to anyone who saw the post, "Firsts." It wasn't supposed to go up yet. Maybe in August.

(oops)

Ears Making Noise?

2009-04-20T15:02:00.004+02:00

Did you know your ears make noise? And people want to use the noise as identification?

Called otoacoustic emissions (OAEs), the ear-generated sounds emanate from within the spiral-shaped cochlea in the inner ear. They are thought to be produced by the motion of hair cells within the outer part of the cochlea.

My hearing and speech class at MIT, 6.551, went over this phenomenon. Your ear contains an active amplifier that can also create sound. Under normal conditions the emissions are very pure tones that occur at frequencies specific to each ear. The 6.551 professors had a few interesting anecdotes about the OAEs - one knew a conductor who memorized the frequency of one of his OAEs, and used it for "perfect pitch."

IIRC, though, not everyone's ears have OAEs. Aside from the problems mentioned in the article above, the Wikipedia article goes over a few details that could hamper using OAEs for biometric passwords. Another, small issue is that your ears have different OAEs, so you'd have to calibrate any system for both ears.

Naturalization

2009-04-06T09:00:00.002+02:00

I have been a bit surprised about the topics in my Dutch language courses. My previous foreign language courses were in high school, and American high schools avoid controversial topics. My Dutch courses tackle the difficult topics head-on. Our most recent lesson, "Are you married?", briefly went over some of the differences between marriage in the Netherlands and elsewhere. Weak English translation:

Dutch teacher: Do you have children?
Female student: No, after all I am not yet married.
Male teacher: Must you be married before you can have kids? Do you really need that? Is it really necessary?
Female student: Maybe not in the Netherlands, but in my society that is absolutely necessary.
Male teacher: What happens if a women is expecting a child while she isn't married?
Female student: Then you must immediately marry. Preferably with the father of the child.
...
Teacher: Not so long ago that also held for the Netherlands...the last 30 years, though, have seen many changes to marriage. People still marry, but frequently they'll live together first...You can also register with the government as "living together." Then you will be treated almost the same as if you are married, and it is a bit easier.
Another student: What is the difference between marriage and living together in the government's policy.
Teacher: That is indeed small, it is mostly the vows you've taken.

Aside from marriage, the book also goes over the population policy of the government, parties, alcohol, the police, and how the Dutch are friendly but difficult to know really well. I do not believe the policy on drugs is mentioned.

I'm not sure what to think about mentioning controversial topics with public opinions in the language course. They are only a small part of the course. I also think it is critical for immigrants to know about government policies and the values of the people. I think it is important that people make informed choices about where they live, the values of the people they live with, and what policies they support with their tax money. People are given a chance to share what their own country values during the discussion classes.

On the other hand, language courses are required for the spouses and other family members of any long-term immigrants. No one knows enough Dutch to explain the complex ideas behind the social values. It feels a bit like the government is forcing public opinion down the throats of minorities.

In the bigger picture, though, the language courses are one of the least controversial aspects of immigrating. Dutch law requires most new immigrants to watch a social orientation video containing gay men kissing and women on a crowded top-less beach. The video is so racy that an edited version of it was made specifically for Middle Eastern countries.

(I'm waiting for the sequel before I see it. I hear there is going to be an action sequence involving sheep)

Sleep Deprived Random Information

2009-04-01T23:02:00.003+02:00

Dutch phrase that doesn't translate so well: krab mijn rug.

Radioactive Ball

2009-03-28T11:00:00.005+01:00

I thought they were talking about a dance, not a deadly pile of Cs137:

Officials told the BBC that they had detected what may be the missing Caesium-137, adding that it may have been melted down...The BBC's Quentin Sommerville in Beijing says China has an appalling record on industrial safety - there are around 30 cases of radioactive material being lost every year.

Earlier I posted about how radioactive sources are used in construction sites and old factories. I think this instance is interesting because the Chinese government controls the media, and I'm confused why they would admit something like this. I don't think an incident like this is very dangerous, but people panic when they hear the term radiation. Did the government decide it wasn't all that dangerous, and it would gain the trust of its citizenship if it gave out the information? Was there a leak? Are they worried about keeping quiet and something blowing up in their face? If you controlled the media, would you admit that someone lost a "ball" of radioactive material?

[Insert snarky joke about radioactive balls here]

Blame Condoms or Human Nature?

2009-03-19T22:00:00.006+01:00

Do condoms spread HIV? Some recent comments by the Pope are causing quite a stir. But the Pope might be right. At play is something called the Peltzmann effect or risk compensation. When humans feel safer, they sometimes engage in riskier behavior. With the "safety" of a condom, people almost certainly engage in sex they would not normally have. Too much safer sex can be more dangerous than a little risky sex. Safer sex still has risks.

I wish I had time to dig into this, but I'm hosed.

EDIT: The exact comments under question are that HIV/AIDS in Africa is:

a tragedy that cannot be overcome by money alone, that cannot be overcome through the distribution of condoms, which can even increase the problem

The part about condoms sounds reasonable to me. The part about money is pretty non-sensical. He asserts a bit of wackoness right after, when he claims:

the traditional teaching of the Church has proven to be the only failsafe way to prevent the spread of HIV/Aids

That is bull$#!+.

Follow-up: Inches Overseas

2009-03-13T09:00:00.001+01:00

Europeans measure the strangest things with inches:

... wearing six-inch heels confirm ... with four inches becoming the norm ... wore a five-inch-high pair ...

Does America really export that much fashion?

Earlier I posted pictures showing how monitor sizes are still quoted in inches.

Rants on Media Continued: Misleading Graphs

2009-03-10T10:00:00.002+01:00

USA Today has a very misleading graph on the change in the American, Catholic population. The graph is meant to show the change in regional catholic population, but I found two problems between the graph and its mission. For the first problem, take a second and think about the circled states:

California and Texas have large increases in their Roman Catholic populations, and Florida has a sizable increase. These three states comprise 25% of the population of the US. This graph, which was supposed to represent growth in various regions, instead portrays a very inaccurate picture of overall growth. Yahoo! News breaks it down correctly:

Nationally, Catholics remain the largest religious group, with 57 million people saying they belong to the church. The tradition gained 11 million followers since 1990, but its share of the population fell by about a percentage point to 25 percent.

Would you have guessed, after looking at the graph above, that the Catholic population in the US increased? Or that the percentage of Catholics in the population dropped one percentage point, which is a drop in the portion of the population of roughly four percentage points (26 to 25)? By focusing on the four percentage point drop in the population portion data (even making this drop appear larger than it is), the graph misses both overall growth and the one percentage point drop in the overall population. USA Today's article text doesn't even mention the overall growth.

Forgoing the big picture to explain a less important point is the second problem with the graph. How would you visually show the information from the quote above? The more I have to create visual data, the more I'm struck by how much a sentence can communicate.

(Yahoo! News even links to the study. I still stand by my last rant, however.)

Short Rant: Lack Of Transparency in Online Media

2009-03-06T09:00:00.002+01:00

Some Japanese scientists think that riding motorcycles is good for you. The study sounds pretty suspicious to me...funded by a motorbike company? Studying only twenty men? The other group rode either bicycles or cars? Only looking at whether scores go up, not starting levels?

So I want to call b$#!+ on this study....except I cannot find it. I googled "Kawashima motorcycle", but not one of the top five Google results links to the study or reports where the study is published. Kawashima's publication pages currently lack the study (hopefully this will change later on).

It drives me crazy when the media reports the results of a study without linking directly to it (or at least stating where said study was published). How can people state a conclusion without offering insight into the supporting process and information? This "internet" thing lets you link to the original data if it is available. At the very least there could be a link to a gated version.

Shame on Yahoo! News for failing to leverage the transparency of the internet.

And stay off my lawn!

Lost in Translation

2009-03-03T12:34:00.007+01:00

Last weekend a few friends and I went skiing / snowboarding. I got up early to make pancakes, as there appeared to be pancake material available, but the pancakes tasted like cream of wheat. On close examination the "baking powder" looked a bit odd:

Perhaps I should have looked harder at that first word: mais-stärke.

100th Post

2009-02-25T09:00:00.001+01:00

I made it to post 100. I think I have been posting too much, so I'm going to roll back my expectations for myself to four posts a month, with one of them a big post. Otherwise I think I will end up posting too many secondary links.

Things that I've learned:

- writing long posts is hard, but it has been good practice for my writing abilities
- most random links I still email to one person only. It has been tempting to post them to the blog, but I am happier when I don't
- comments are really rewarding, I now find myself leaving comments at other blogs (though I only rarely post a link back to my own).
- there was a lot to say about my big move at first, but I don't have much to say anymore
- I still have a few mementos ("I'll write about this later") that I haven't gotten around to researching. I thought I would find out about these things, but they haven't sprung up in conversation
- I now schedule a lot of my posts rather than write them on the spot.

Some Ugly Truths about Human Trafficking

2009-02-24T09:00:00.003+01:00

The UN's Office on Drugs and Crime released its annual Global Report on Trafficking in Persons a few weeks ago.

The Dutch fared poorly. A uniform comparison across countries is difficult since reported data varies by country. Countries provide some sub-set of people prosecuted, convicted, investigated or suspected of trafficking. A quick look through the data suggests that the Netherlands is either much better at prosecuting people, or that human trafficking is a problem for the Dutch. Conviction and prosecution rates per capita in Holland were eight times as high as the UK. The UK has roughly four times the population of the Netherlands, but the UK prosecuted and convicted less than half the number of people that Holland did.

Another interesting anomaly was the gender breakdown of convictions in Eastern Europe. In Latvia, for example, women are convicted of less than 10% of all crimes, but they account for over half of human trafficking convictions.

Anyways, the big picture is very dim. Sometimes it is easy to forget that it is 2009.

Reddit Round-Up: Photoshop, Gender Biases when Rating Teachers, and Nuclear Reactors

2009-02-22T18:12:00.007+01:00

Some interesting photoshop examples (EDIT on 2009-06-09: link is borked, my apologies). Who knows if they're real - maybe they were reverse photoshopped?

Apparently high school students like male physics teachers more, even when the numbers say something else.

Iran is starting computer tests for its budding nuclear reactor at Bushehr.

On Dirty Bombs and Construction Sites

2009-02-20T09:00:00.004+01:00

Last week I got to play around with dangerous radiation, which was fun. But what was even better was talking to the people who work with the radiation. Apparently the Swiss government has a radiation "SWAT" team. I talked with a guy who was on the team about what they did, and he told me some crazy tales.

He said that he was routinely called to construction sites to deal with radiation problems. Apparently radioactive materials are commonly used on construction sites, especially in equipment that surveys the ground (sends waves into the ground and reads back the results). Bulldozers will sometimes accidentally drive over this equipment and expose the radiation source(s).

He told me the horror story of a factory worker in Chile who picked up an iridium source. Old factories use radiation sources for a variety of things, including flow meters, density sensors, and heating of all things! The source looked like a pen, and the worker picked it up. He tossed it from hand to hand (because it was so hot), and then put it in his back pocket.

At this point my colleague's story diverges from the internet. According to the IAEA, the worker showed the source to a few other people before some of them started to be sick. According to my colleague, the worker walked into a cafeteria and dosimeters of workers started going crazy.

They flew the worker to a French military hospital and immediately amputated a giant sphere (~10 cm diameter) of flesh from his butt, close to where he had the source. The French doctors used stem cells to treat him, and managed to save his life.

It was pretty fun to shot the breeze with this guy, especially on the subjects of dirty bombs and terrorism. We talked about how the current generation of bomb detectors at the borders was absurd. Shielding a uranium bomb from the border detectors or sneaking a bomb through under a common false alarm condition (hide the bomb in a truck with kitty litter and old electronics like CRTs) are not difficult feats of engineering. We talked about dirty bombs, and whether Cs-137 or Co-60 would make better "dirt".

The crazy part of my work with radiation is that now I feel a lot safer at Delft's nuclear facility than at a random construction site. If something horrible did happen, the people at nuclear facilities have the know-how to clean it up. Also, there are stringent regulations at the nuclear / radiation facilities I have been to.

If you need further proof of safety, just look at the moat at Delft's facility. Sadly the architect couldn't convince the university to spring for the draw-bridge option.

Don't Rub Beryllium Tools on your Skin

2009-02-16T09:00:00.001+01:00

Cool fact: beryllium scissors, screwdrivers and pliers are used near MRI machines since the metal doesn't react (noticeably) to the magnetic field. I looked into getting some Be-tools, but apparently the metal is highly toxic and the tool sets are really expensive. $4,000 a tool-set expensive. Weak.

No French Hamsters?

2009-02-13T11:15:00.006+01:00

I was wandering around Lausanne and saw an odd movie poster for "Volt", the translated version of the American movie "Bolt". I suppose hamsters are American, with their obesity and refusal to translate things:

I'd Focus Her Ion Beam

2009-02-13T09:00:00.001+01:00

Over the past week I've been doing a bunch of stuff in Lausanne, Switzerland. Unfortunately most of it failed. Sigh.

But I got to play around with EPFL's focused ion beam (FIB) for another project. EPFL's FIB is a combination of an electron microscope, a platinum depositor, and a Gallium microscope/etcher.

What was I doing with the FIB? I was fixing integrated circuits. One fixes circuits by etching away parts of the chip (the equivalent of cutting a line), and then using the platinum depositor to short other lines. This re-routes the signals, and fixes your design mistake. The etching is performed by the Ga microscope. Normally the number of Ga ions does not drastically effect the surface, but if you use a lot of Ga ions, then you can etch away parts of the chip. The etching occurs even when you're using the Ga microscope as a microscope - in other words, if you use the microscope for too long, you etch away the entire surface off the chip. As far as I know electron microscopes don't have sufficient energy to etch the surface, but it wouldn't surprise me if a high-energy electron microscope could also etch a chip.

The etching is mechanical, so the etched atoms spray above the chip. The etching is performed in a vacuum so that these atoms don't (hopefully don't) end up on the surface of the chip and interfere with surface electronics.

Anyways, that is enough theory. One of the other groups has been having trouble properly simulating a design, so they wanted to use the FIB at EPFL to test something. Since I was going to be in Switzerland, I oversaw the FIB use.

A high level overview is that we needed to re-route a grounded signal. A line was shorted to ground, and we needed to short it to the power rail instead. I'll call the line we're working with line "Q". First, we had to cut line Q. Next, we exposed line Q a distance away. We then exposed the power line. Finally, we shorted line Q's exposure to the power line's exposure. Well, at least we think we did. No one has tested the chips yet.

You might ask yourself why we didn't just short the power line to line Q's cut directly. The platinum (Pt) deposition isn't easily controlled (we're working with nanometers of distance), and we would have risked shorting both sides of the cut to the power rail if we tried to short the power rail to Q at the cut. Risking a power rail to ground short is bad. Very bad.

First up, we cut line Q. Here is a picture:

The hole near the bottom-middle of the L-shaped objects is the cut. I believe the L-shaped and square objects are support patterns on the surface of the chip. Silicon foundries yell at you if you don't use a minimum amount of metal for each layer. Something like a third of the layer must be used. I'm not sure if it is an issue with the lower layers supporting the upper layers or the implant process, but either way it is easier to put patterns on the un-used parts of the chip than having the foundry yell at you. You can see some lower layer patterns in the cut, they're the twelve or so little dots. We use different patterns for different layers, ostensibly for better chip support. Or something. I'm not 100% sure about reasons behind the patterns, so take everything I saw about them with a grain of salt.

Anyways, next up we needed to expose the Q line farther down:

I've circled the exposed Q line, which runs vertically. Ga ions interact differently with conductors, and the results is that conductors show up more brightly in pictures from this Ga microscope. If this pictures doesn't convince you that we hit the line, I wasn't convinced either. Due to the support patterns, the Ga ions etch through the chip at different speeds, and it was impossible to get a picture-perfect exposure. Also, please keep in mind that the line is about 500 nm wide. This was the best result of several failed attempts on previous chips.

Similarly, we found the power supply line, which ran horizontally:

Finally, we used the Pt depositor to short the two:

As you can see, some of the surface material was sucked into the hole when we deposited the Pt bypass. I don't know if the material melted or was pulled down from a mechanical force.

As I previously said, we haven't tested these chips. Even if they don't work, it was a very interesting event to see. Please feel free to ask any questions, though I'm not sure I'll be able to answer them. Single bypass surgery on integrated circuits isn't my specialty.

Things Going "sssshhhom" in the Middle of the Day

2009-02-10T17:29:00.002+01:00

Sometimes, when I'm away on a trip, I log into my workstation and eject / retract the CD tray. Just to mess with my office-mates.

# eject
# eject -t

I'd ding the terminal bell, but I don't want to over do it.

Google Translate, You're Killing Me Slowly

2009-02-07T08:00:00.001+01:00

I think English good?

On a Few Things Sewage

2009-02-05T09:27:00.005+01:00

The city of Oslo plans to run 200 of its buses on biomethane created from sewage. If this sounds interesting to you, I suggest you check out Rose George's book, The Big Necessity. In one of its chapters, the book goes over a similar use of sewage in China. The Chinese use "digesters" to create biomethane from pig and human excrement. Farmers use the biomethane for cooking and heating, and use the processed manure as fertilizer. Previously the farmers had spread the manure directly onto their crops, spreading disease. During the processing stage, the pathogens are partially broken down and the disease risk is mitigated. Not only does the digester create methane to heat homes, it also creates safer fertilizer for crops. The costs are the one-time construction time and materials of the digester, along with the recurring human cost of running the digester.

Footnote: The biogas link is via /. via EarthFirst via WorldChanging via IWA. Perhaps the blogosphere needs to come up with better linking customs.

Quick Hits: Blast from the Past

2009-02-02T14:10:00.004+01:00

At lunch today I mentioned the bizarre, Japanese balloon attacks on the American homeland during WWII. My Japanese colleague was unaware of them. Quote:

Improbable though it may sound, from late 1944 through the spring of 1945, the Japanese launched more than 9,000 balloons from their nation's eastern shores...One balloon, for example, managed to cut through power lines leading from the Bonneville Dam on the Columbia River. A resulting power outage that was quickly restored may sound insignificant; however, that particular dam provided power to a factory in Hanford, Wash., which was secretly manufacturing plutonium for use in the atomic bombs destined for Japan.

Though I dislike censorship, I think the evidence supported it in 1945.

Quick Hit: Massachusetts and Coddling Young'uns

2009-02-01T17:26:00.006+01:00

Requiring a helmet while sledding is one of the dumbest ideas I've heard:

... some people are pushing for a law that would require children, 12 and younger, to wear a helmet while sledding ... Panagiotakos argues that a state that requires children to wear helmets while bicycling - as Massachusetts does - should mandate the same equipment for sledding.

Seriously Massachusetts? Should we all wear bright orange jackets when crossing the street so cars see us, too?

Daylight

2009-02-01T17:00:00.006+01:00

As I go slowly insane while analyzing data, I find myself wanting to analyze more data. Thanks to the efforts of the U.S. military, I can fulfill these caprices. I have concocted a few graphs to illustrate daylight in the different places where I've lived. These graphs do not include the effects of weather. Note that southern CT is not included, as it has roughly the same longitude as Cedar Rapids, IA.

First up is a graph of minutes of daylight per day versus time of year.

Delft gets over 1,000 minutes of daylight per day in the middle of the summer. Or, rather, the cloud-layer over Delft gets this daylight. Boston and Cedar Rapids only have small differences in daylight per day.

I was wondering how much less daylight Delft gets per year than Iowa, and to my surprise, Delft gets more daylight!

The second graph is a zoom of the previous graph. As you can see, Delft gets roughly one more day of daylight each year than Cedar Rapids and Boston.

I am looking forward to the days following the Equinox here. One thousand minutes of daylight. Sounds like a novel.

Experimental Data

2009-01-28T23:01:00.003+01:00

We have some data that is supposed to be quadratic in nature. What does it looks like?

Great parabola to start with, but what happens? An interesting new phenomenon? Oh, nope, just a crappy cable.

Sometimes I hate you, science. Could you make pursuing you a little easier? You don't have to be such a @#*$( about random crap ruining good data, you know?

From the Department of "Brings Tears to My Eyes"

2009-01-24T09:26:00.002+01:00

A man laments the good old days he had with a BSD box:

...but I always kept a screen(1) session running with you.

Worst...Defect...Ever

2009-01-23T17:27:00.003+01:00

I just got screwed by a metastability issue. I thought it was a bunch of non-sense to scare second year undergraduates. I guess when you're looking at lots of events (more than 10^15 or 2^50 in my case), one synchronizing flip-flop is not enough. Especially when you're feeding a wide adder in high temperatures. Sigh.

-10 engineering points

Laptop-Less

2009-01-16T23:47:00.004+01:00

I'm running a campaign of long experiments (4 days or more per experiment) at work that require my laptop, and I won't be able to access my laptop. Anyways, I probably will be absent for a small amount of time.

(No, really, I'm not going on a bender, I just really have to use my laptop)

(Yes, I am going to be without access to the internet at home for over a week)

(Yes, everything is fine)

(No, I'm not seeing things. What frog? What are you talking about?)

What I've Been Reading

2009-01-16T09:17:00.009+01:00

Fruitless Fall: Honeybees are fascinating little creatures, and this book discusses their recent trials and triumphs. The book follows the attempts at diagnosing colony collapse disorder (CCD) in the honeybees of North America. The book goes on to talk about the difficulties of scaling complex, biological systems to meet our food requirements. Overall, I found it an interesting examination of several complex systems and organisms, and would suggest this book to any engineer or scientist. Or anyone who wants motivation to buy fancy honey.

Pride and Prejudice: I never had to read this book in high school, but figured I should probably pick it up at some point. I was pleasantly surprised by how good the story was, but I was disappointed in how little Austen examined Darcy's motives. Also, very few of the main characters perform any sort of work, they just seem to talk, think and feel a whole lot. Overall it was worth the read, but I don't see myself reading it again. I think Wuthering Heights has better stood the test of time.

Reaper Man: Terry Pratchett's Death is one of my favorite (dare I say favourite) personifications. I love reading his novels on airplanes, the humor is enough to keep me focused during the distracting flights. In between hilarious stories involving wizards chasing shopping carts and an undead support group, Pratchett manages to make a point about humans misinterpreting the natural force of death. If you want some light reading with serious undertones, a good read. If you're looking for something a shade darker, there is always Soul Music from the same author.

I'm excited about lots of books in my unread queue, though they're all non-fiction. I'm looking forward the most to The Big Necessity, which discusses the history of human waste and sewage.

Quick Hits: Old Unix Feature Hits the Big Time in Windows 7

2009-01-15T21:59:00.009+01:00

A new feature in Windows 7 is that when another program prevents you from moving a file, you receive the name of the program. This feature has been in *nix as the "lsof" command since, well, probably around the time I was born. Though it isn't as pretty as the 7 version will be, it is just as functional:


root@hammer:~# lsof /rainbows
COMMAND   PID     USER   FD   TYPE DEVICE      SIZE    NODE NAME
cat     14484 liamliam    1w   REG    8,1 227082240 9723906 /rainbows
root@hammer:~#

There is an lsof in BSD, but I'm not sure about Mac OS X.

EDIT: BlogSpot, you break my heart by clipping pre-formatted text which is bigger than your box. You break my heart.

EDIT: I upped the window size. I apologize to any readers with an 800-pixel wide screen.

What is It?

2009-01-10T15:17:00.002+01:00

I came across a strange object on Google Maps. Ketelmeer (Kettle Lake in English) is the surrounding body of water. Any ideas of what it is?

Tale of the Dueling Bugs

2009-01-09T08:21:00.005+01:00

One of the things I love about software is the completely bizarre cause and effect chains. I recently found one of these chains when I inherited a data acquisition system. The system consisted of firmware sitting on a custom printed circuit board (PCB), and PC software which reads out the data from the motherboard. The firmware had a known defect in it, so the first thing I did when I inherited the firmware was to fix the defect. Most people call defects "bugs," but I do not like the word "bug." Bugs are cute. Defects are not cute.

Anyways, I fixed the firmware problem and all went back to being okay in the world. I didn't see the communication timeouts and corrupt data from the defect. However, I couldn't get the data from the previous experiments out of my mind. The issues with the data didn't quite match the conditions of the defect, which occurred randomly and independently. The data had holes at regular intervals. These multi-day experiment have a lot of data, and when something looks wrong to me in a lot of data I have a hard time explaining what looks wrong. I have to play around with data to figure out what looks wrong. So I graphed it, and then I made some histograms, and then I did crazy things like graph every other sample.

Indeed, it turns out there was *another* defect, but this one was in the C++ software. This defect cropped every half hour, and it caused continuous communications issues, different from the firmware defect. I immediately tried running with the new firmware. The system didn't work at all after half an hour, right when the C++ defect cropped up.

Suddenly what had happened came into focus. The firmware defect occurs randomly, but it would always be an isolated incident. However, after half an hour of standard operation, the C++ defect occurred and continued to occur. The communication would be completely messed up until the firmware defect randomly occurred. This would reset the C++ code, and the system would go on as normal until the cycle repeated in half an hour.

I asked if anyone had performed a control experiment or a long-running test, and no one had. While I look on this incident as additional evidence for the importance of testing, I think it also displays the importance of running control experiments. If someone had run a control experiment, they would have discovered the issues before it ruined a portion of the data.

The person who wrote the software is no longer here, but he was a very hard worker. He worked a lot of really late nights, usually troubleshooting issues with the code. I think this is an example of how a Puritan attitude is a bad thing in a programmer. Lazy people constantly ask themselves if there is a better way - spending a day thinking about a month's worth of work is reasonable to me. Or maybe he made the right decision, which was to get enough data to graduate and leave the problems to the next guy.

Your Device Can Perform Faster

2009-01-08T09:52:00.003+01:00

Thank you, Windows Vista. You've made my day.

Closed on the Sabbath

2009-01-08T06:06:00.005+01:00

I've never heard of a web-site being "closed" on the Sabbath, but apparently the Dutch political party SGP has a site that is only open during the days of work. Crazy. Anyone know of other websites with similar quirks?

The SGP was involved with Islamic oaths (or rather the lack thereof) for Dutch public officials.