Corrosion --now in 3D

In reference to my previous treatise on battery terminal corrosion, you can now view a 3D image of a corroded battery terminal at the Lytro site here.

OK, probably, you don't want to do that. It's more fun than it sounds like, but still....

Padding

Here is the outer (leftmost) brake pad I recently pulled from my front Avid BB7 disc brake caliper. The part of the pad closer to the hub is at right in the picture. The "top" of the pad furthest from the hub is at left.

The top of the pad still has some material left on it, so should I have let the pads go longer? No. Look at the second picture, below. This focal plane shows more clearly that the pad has not worn evenly, to the point that the copper "panhandle" that sticks out of the caliper has obviously been hitting the rotor during braking. Oops. So yeah, it was time to change the brake pads. (Both of these images are from a single picture from a Lytro camera.)

Measuring with a caliper, the top had about 1200µm of pad left, and the bottom had at most 300µm left.

Interestingly, the inner pad is worn completely differently. The inner pad wore evenly top-to-bottom, but the front edge had had 950µm and the trailing edge 1100µm. So the inner pad wore almost flat by comparison, except the leading edge wore a bit faster.

Why did the pads wear unevenly? Well, I'm not sure.

Maybe I didn't set the brakes up correctly? BB7s mount with spherical fixing bolts, so that you can align the caliper in two axes with the rotor. Avid's old instructions and Park's current instructions for this are laughably incomprehensible, so I figured out a simple way: put in new pads, set the pad distance. Squeeze the caliper shut on a trued rotor. Tighten the fixing bolts. So maybe that's wrong? I checked the Avid site. Avid's new instructions are pretty much exactly what I did. So that's not it: AFAICT, the caliper was set up with the caliper coplanar with rotor. There isn't much play in the caliper inboard and outboard, but even if there were, the caliper is designed to compensate for that by adjusting the pad positions. This is necessary, since hubs vary in exactly how outboard from centerline they mount the rotor.

Maybe I had let the pad positions get out of adjustment? The BB7 has two knobs to adjust the pads inwards as they wear. The outer pad is on a piston that pushes it towards the fixed inner pad. Obviously, the rotor makes an angle as it's bent, and obviously the force of the rotor is going to be higher on the top of the outside pad and the bottom of the inside pad. But that's the opposite of the wear pattern on the outside pad, and the inside pad wore evenly. So that seems unlikely.

Maybe the pads aren't coplanar? I doubt the caliper body is bent, since it's so stout that I find it hard to believe a blow hard enough to bend it wouldn't throw it completely out of alignment. The piston that pushes the outer pad in obviously has more play in it than the fixed holder on the inner side, so maybe this is just as good as it gets. One way to look at it is, I got 3 winters off of a set of brake pads that cost me less than $20. (The rear pads will probably last a couple more winters yet.)

Hmm. If you have any experiences or ideas, or interesting things to measure, I'm all ears.

The Tomato Diaries

Sven is endlessly curious about math and frankly I'm a little worried that school next year won't give him enough to bite into. So he's signed up for 8th grade math in the fall and we've been doing a little math over the summer to make sure he had all the 7th grade bases covered. (He tested into 8th grade math, but these things aren't linear.)

I bought the school district's math book, Everyday Math and it's, how do I put this politely? A steaming pile of crap.

So we've pretty much had to write our own math book. The first unit to cover was probability and statistics. Everyday Math had a table of actual US immigration data and a series of measurements of an (imaginary) girl's head. The reader was expected to understand that one set of measurements was dominated by noise, whereas the other had inconsequential measurement error. I'm not sure why 8th graders are supposed to intuit this, given that many scientists have trouble with these concepts. But more importantly, all of the problems were boring.

So we decided to make some measurements of our own, so we'd have some data that we had a real feel for. What to measure? I figured nuts from the store, but a pine nut weighs around 3 grams, and our scale reports only to the whole gram. So we would have been overwhelmed by measurement error, which isn't normally all that much fun.

Sven thought of tomatoes from the garden. Much better. More variation than pine nuts anyway, and a light tomato is 25g. So good.

At right is our combined data from the first two harvests, conveniently of exactly 12 tomatoes each. X is tomato weight in 5g buckets. Y is count per bucket. Sven is predicting the third harvest will drive up our average weight and standard deviation. We've been looking at the data to see if it has an approximately Gaussian shape. We'll get more formal about that in a little while.

Corrosion

[UPDATE: see a 3D image of the corroded battery terminal here.]

AA battery packs are cool, but check for corrosion.

If your bike is transportation, or if you like endurance bike sports, you need bike lights. Hikers, climbers, spelunkers, and other outdoor sportsters also often need lights or other battery-powered devices. AA NiMH batteries are a cheap, effective solution. Damp weather and vibration can corrode contacts and degrade performance. Damp combined with vibration degrades performance faster.

The picture at right shows a corroded spring contact in a battery holder. This contact is at the bottom of the holder, and the spring at the top of the holder was not noticeably corroded, so moisture was the main problem here. (Leaking batteries cause corrosion too, although not in this case.)

GPS units that take AA batteries are notorious for vibration problems causing arcing, resulting a sort of electro-fretting that damages contacts on both the battery and the GPS. This is noticable because the GPS tends to reset whenever it loses power. The same problem happens with battery-powered lights, it's just hard to tell when it is happening. But the damage is serious. You can sand the corrosion off the contacts, but spring contacts are usually plated to combine long fatigue life with good electrical performance. Once the plating is corroded, the contact will never work as well again. Many GPS units now build Li-ion batteries into the device, eliminating this problem. Garmin makes a kit for their older GPS units with an extra tension spring to increase the spring force on the batteries. If you have this kit, I strongly recommend using the tension spring. It looks like an extra bit of hassle, but it is actually very useful.

One advantage of battery holders: replacing the battery holder also replaces all battery contacts. For example, DiNotte make nice lights that provide several hours of operation from a pack of four NiMH AA batteries in a standard "BH343" battery holder, shown at right. The holder has a connector like a 9v battery and cost $1-$2. Good NiMH batteries like Eneloops cost $3 each and a 4-pack will hold 10-12Wh.

I tape the batteries into the holders with electrical tape and use a battery pack charger (popular with RC enthusiasts) as I explain here. Taping the batteries seems to eliminate vibration problems. (Otherwise, the batteries will sometimes slip all the way out of the holder, a serious vibration problem!) But you then have to use a pack charger, which is very convenient anyway.

A battery pack is only as good as its weakest battery, so it's even more important to use good quality NiMH batteries when pack charging. I notice that after about two winters, battery life seems to get much shorter. So I tear the battery packs apart and recondition them with a La Crosse BC-700 battery charger.

Actually, a battery pack is only as good as its weakest link. I started scrutinizing the battery holders when I noticed that they would eventually crack, which reduces spring tension, and the connector to the light would also loosen, and would need to be (carefully, without shorting!) re-crimped once in a while. Then I started noticing corrosion. Once I started looking for corrosion, I started to find a lot of it.

I think 2 Seattle winters is probably all one of these battery holders is good for. After that, it's time to break down the battery pack, and recondition the batteries. The BC-700 tells me what the reconditioned capacity of each battery is. If it's over 90% of new, I put them into a new battery holder and give them another 2 years. Otherwise they get relegated to less demanding applications and eventually recycled. Either way, I now only use the battery holders once.

Opener for the gate

The gate latch needed an opener for the other side. Has needed for a couple of years.

After some thought, I decided to use a bicycle shift cable that was plenty strong for this application, but had some minor damage that made me not want to put it on a bike. Putting the shift cable in a left-over piece of housing allows someone to pull down on the cable from the other side, pulling up on the catch for the the gate and opening the gate.

I cut a piece of dowel to use as a handle and threw in a carriage bolt I had lying around. Perfect. I used CATV brads to tack the cable housing to both sides of the gatepost.

Except, there is a problem with these latches: if there is even a very small upward force on the attachment, it keeps the latch open, so that the gate never closes. The cable moves very smoothly in the housing, so even a very light handle will drag the latch open. So now the gate has an opener, but the opener kept the gate from closing.

I thought a bit, and realized the solution was quite simple: remove the brad holding the housing on the inside of the gate. The housing springs outward, pulling the latch closed. Pulling down on the handle on the other side pulls the housing towards the latch, then pulls the shift cable through the housing, opens the latch, and opens the gate.

It's probably lucky I decided to use shift cable and housing. Modern shift cable housing is quite stiff compared to typical brake housing, so brake housing may not have been springy enough to work.

A broken spoke: four views

DT Swiss straight gauge 2mm spoke. Velocity deep-V rim. Rear wheel, single-speed disk hub, so spoke tension is essentially the same on both sides. The spoke came just far enough through the nipple that I could cut a slot with a hacksaw and back the spoke out. The spoke was about three full turns from bottoming out the nipple. These pictures are of the piece of the spoke that was in the nipple.

Spokes break at the elbow. Everybody knows that. Why did this spoke break in the nipple? Manufacturing defect? Damage during wheel building (by me)? Some random damage from falling into one of Seattle's piano-swallowing chuckholes?

From the pictures, it looks like a fatigue failure from some damage near the end of threading on the spoke.

I took these pictures with the Lytro camera Aki gave me for Christmas. Not really a useful camera for portraits, but actually pretty good as a macro camera. Being able to take pictures with multiple, very thin focal planes is pretty much ideal for this kind of picture.

Thanks to Chris Heg for insights into what fatigue looks like.

Traffic Hazard

This pole used to have a sign on it. The sign was either removed or stolen. Now there's just a pole. This pole is in the sidewalk approach to the Fremont Bridge southbound, where as many as a thousand bikes and (literally) uncounted pedestrians pass. (Bikes are directed onto the sidewalk here, to avoid the open bridge grating that motor vehicles use.)

At this point, traffic narrows to go over the bridge. Depending on traffic coming the other way, a bike rider or pedestrian may want to move near to where this sign is to give oncoming traffic a wide berth. (Pedestrian with dog, bike with trailer, drunk with attitude, etc.) This could easily cause an accident. Any sidewalk users could be affected, but it's obvious how this could be dangerous for a bike. The pole is hard to make out from the background, particularly on a cloudy day. Hanging up handlebars or a trailer on the poll could easily result in getting thrown from the bike, into bridge traffic.

It's a matter of time before something bad happens, and somebody rushes out to fix this.

[Update: I submitted this as an incident on Bikewise.org]

Refactoring the Human Genome

I I am pleased to announce my participation in a bold new effort to refactor the human genome. This effort is without a doubt the most ambitious project ever seriously attempted to ameliorate the long term burden of human disease. The potential benefits are vast.

The team behind this project is a biology A-Team that I'm honored to be a member of. Heading up this effort: noted evolutionary bioinformaticist Dan Graur. The core team also includes renowned bioinformaticists Yichen Zheng and Nicholas Price, talented genomic architect Ricardo B. R. Azevedo, and population geneticist Eran Elhaik. Advisers include Larry Wall, fresh off the successful Perl 6 project; noted computer language theorist Edmund Arranga, and celebrated biostatistician and data analyst Lawrence Sanna. Beyond the specific technology, important philosophical guidance was provided by Francis Galton. This project makes use of important work by Francois Pinard, although he is not directly involved in the project.

The thesis of this star-studded group is simple, but like many simple things hidden in plain sight, it takes a true genius like Graur to realize the potential that lies before us, within reach. When you ask Graur why nobody has proposed such a project before, he just smiles wryly and shakes his head. "The human genome is rife with dead copies of protein-coding and RNA-specifying genes that have been rendered inactive by mutation. It's time we stopped passively accepting this situation and did something about it."

Our project: refactoring the human genome. "Refactoring" is a term from computer science, meaning to reorganize the internal structure of a code base without changing the (intended) external behavior. This term has been borrowed into bioinformatics, where the meaning is equivalent: the reorganization of the structure of a genome without changing the behavior of the organism. As Graur eloquently observed, at least 85% of the human genome is plain junk. Most of it is not transcribed, and even much of which is transcribed is by definition nonfunctional, because it is not subject to purifying selection.

Why does this matter? Even though it is not important to our normal genomic lives, this junk DNA is an important source of disease. Most obviously cancer, but also genetic disorders such as converse errors that can cause acute adhominem ataxia.

From an evolutionary viewpoint, a function can be assigned to a DNA sequence if and only if it is possible to destroy the function by removing the DNA sequence. Put another way: by definition, eliding nonfunctional DNA does not change the organism's function. Since 85% of DNA is nonfunctional, suppressing it has no effect on normal biology. Why is it worth eliding? Studies by Graur's colleagues show that transcription of junk DNA is highly active in immortal cancer cell lines. The implication is obvious: the key to curing cancer is to attack it at the root: junk DNA.

Thus our project, dubbed RECODE (short for "Refactoring to Eliminate redundant non-CODEing regions") will use well-understood recombinant gene technology. The result will be a human genome that is between one third and one sixth the present size. The project is ambitious. The benefits clear. The savings in file storage alone amount to millions of dollars a year, and will only grow as genome sequencing becomes more common.

Technically, the project is straightforward, although the bioinformatics is a challenge. The hardest part, and the part I'm personally most excited about, is ensuring backward compatibility of the new genome which we've taken to calling "H. sapiens 2.0" with the present "H. sapiens 1.0" genome. Personally, I'm not sure backward compatibility is actually essential, but politically, it's probably indispensable. For one thing, there is the installed-base to think of.

As often happens, backward compatibility will involve compromises. In particular, rebalancing chromosomes will probably have to wait for a future "H. sapiens 3.0" project. But an elegant implementation of backward compatibility gives humanity a smooth upgrade path to a genomically more healthy future.

This project is so new, it doesn't even have a proper web site yet. However, basic information is available here.

Return of the road spikes

The city puts these spikes in the street to hold down air hoses for traffic studies. The spikes are supposed to be pounded flush with the pavement after they aren't being used any more. But as I've found (over and over and over) they are often not pounded flat.

This spike is on N. 34th in Fremont. It's on the south side of the street, maybe two meters from the curb, near the Sunday Market marker for stall 47, about where the new steel towers carry the new high-tension line cross the street. The Burke building is on the south side of the street here.

This is a busy bike route, with several bikes a minute passing through this way during rush hour. On Sundays, this is a very busy walking route, with people packed along the street in good weather.

If these spikes are not pounded down, they can cause a bike flat tire or even loss of control. Eventually they work their way loose. The resulting spike is several inches of hardened steel that can cause a serious injury to a person, a flat tire on a car, and other damage. This is why it's Seattle policy that these spikes get pounded down. Yet it doesn't happen. Now somebody has to take time out of their day to come back out and pound the spike down. It would have been better to do it right the first time.

Weight, Wait!

Another lead wheel weight on my commute. This one is a biggie. Feels like at least half a pound of lead. Well weathered. Probably heavier when it fell off. I've been finding a lot of these on Seattle streets, even though putting them on cars is now illegal. Do we have to let them all fall off and get ground into dust?

Today's Debris Haul Weighs on Me

Today's haul of debris in or near the bike lane was substantial.

That big hunk of steel is a tire puncture waiting to happen, as are the screw and the masonry anchor. And the battery, while less toxic than the old days, is still not something that should be in the street.

But far more impressive: four lead wheel weights. These can get knocked off when the car wheel goes in a pothole, and Seattle has plenty of potholes, but Dexter was repaved only about a year ago, so it's not potholes. Mostly, I reckon, people knock one of these weights off when they hit the curbs a bit hard while parking.

Rain will wash glass into the storm sewer, but lead weights are too dense for that to be likely. Streetsweepers clean Seattle streets infrequently if at all, so the weights hang around, getting run over, bouncing around near the gutter. All that abuse wears off lead as dust, until eventually the weight breaks up and gets washed into the storm sewer, where I suppose it eventually ends up in the Sound.

This grieves me. Heavy metal pollution is one of the least-fixable pollution problems in the Sound. But moreover, where does that lead dust go? Into our yards, and homes, and into us. As a recent article makes clear, our current lead exposure, while much lower than in the past, is still far higher than is healthy. Moreover, lead persists in the environment for a very long time.

So why are lead wheel weights still legal? At the very least, weights on the outside of the rim, which probably fall off as often as not, should not be allowed.

But if we can't outlaw lead wheel weights just yet, maybe we at least ought to sweep them up before they pollute our city?

Update: My friend Geoff Hazel points out that installing new lead wheel weights is already illegal in Washington State, as well as California and a few other states. Of course, it will take a while for these lead weights to disappear, and it will take much, much longer for the lead dust in the environment to go where it's going to go. But this is progress.

Clothes Moths

The shame of wool moths. Nobody likes to talk about it, but let's face it: many bikers, especially randonneurs, own their share of wool, and that wool is not always stored clean. These conditions favor wool moths. What I've learned might be useful to others, and if anyone has more knowledge to share I'd like to learn more.

We had a wool moth infestation. It probably traveled up with me from Portland, lay dormant for years, and resurfaced in 2004 or so. I thought we cleaned the problem up, but I have now learned the measures I took were probably entirely ineffective. The moths came back last summer. (Or, it may have been an infection from a wool item bought used. Now I quarantine wool that comes into our house, regardless of whether it was bought new or used.) I threw out some expensive suits and one very nice wool hiking sweater. I took measures. The problem abated, but has not entirely gone away.

When the problem recurred last winter, I found moth damage on the sweater and two wool suits. I threw out the now hopelessly damaged items and started researching.

There are two problem moth species: the webbing moths and the casemaking moths. The casemaking moths are rare here, and the casings they leave behind are obvious. You can get pheromone traps for the webbing moths. The "Pro-Pest" ones seem to work well and are available via Amazon and etc. The traps attract male moths, which then get stuck to the trap. They are supposed to be good for 3 months, but seem to still be pretty effective after 6 months, at least at room temperature.

When I discovered the moths, I ordered some traps, and looked into what wool moths liked and what killed them. Clothes moths like dark, warm places that smell like humans. They lay their eggs in wool that has human sweat, urine, or the like on it, as this is what the larvae eat. Apparently they don't need the wool to live so much as our blood, sweat, and tears, so to speak. So clean wool is usually safe. Besides wool, moths will sometimes infect silk, down, and in rare cases even cotton.

Dry cleaning kills the moths, so everything dirty that was dry-clean only went straight to the cleaners. (Washing and drying clothes does not reliably kill moth eggs.)

Cold kills moths, but slowly. Suddenly taking clothes from room temperature to a cold freezer and leaving them there for a week should do it, but I am not super confident in this method.

Heat kills moths. Half an hour at 120 degrees should do it, so I cranked the sauna up to 140 degrees and put the remaining clothes in for about an hour. This method is more difficult than it seems. I used a radiant thermometer to find out what temperature the clothes were really at. Just because the room is 140 degrees doesn't mean the clothes are.

Permethrin kills moths. We have plenty of permethrin around. It's an insecticide. We treat clothing we are going to wear in areas where malaria is endemic. Once it dries on the clothing, it's almost entirely non-toxic to people. Also, permethrin repels bed bugs. We've never had bed bugs, but we visit a variety of hotels, so I treated our luggage inside and out with permethrin to discourage bed bugs from hitching a ride on our luggage. And, permethrin kills clothes moths. So I put on a respirator and the big rubber gloves and sprayed down all of the seams and crevices of all the closets that had had wool in them.

The permethrin and sauna treatments were hot, sweaty jobs, but seemed to work. I put the moth traps in the closets, and, well, moved on.

But I did some more research. I found out two interesting things:
- Moth speed of development is highly temperature dependent. This means that they are more likely to emerge in the summer.
- Carbon dioxide kills all life stages of moths.

A CO₂ concentration of as little as 15% should kill moths eventually, and higher concentrations should kill them in a few days. I decided that, to be sure, I'd shoot for a CO₂ concentration of over 95% and hold it for a week.

My first test was with a more-or-less airtight plastic storage box that I put the skiing woolens in at the end of ski season. I put about half a pound of dry ice wrapped in a rag at the bottom, put a heavy book on the lid, and left the latches open. As the dry ice sublimated ("melted"), the CO₂ gas would collect at the bottom, and displace air at the top. At the time, I didn't have a real way of measuring if it worked, but recently I found out it had. It doesn't take long doing this to realize that you can smell really high concentrations of CO₂. It's the smell of getting a fizzy drink up your nose, without the wet part. So, when I opened the box of winter woolens recently, I could smell the CO₂ that had been there since spring. I have to think that any moths or moth eggs were long dead.

I had decided to treat our woolens once or twice a year, just to be safe. My method was to buy Space Bag storage bags. These bags seal air tight, and they have a vacuum port. (Several of these bags are shown in the picture, above.) Put the woolens in the bag with a chunk of dry ice wrapped in a rag. Suck all the air out. Close the cover on the port until the bag starts to inflate. Open the port. As the pressure inside the bag rises, it will push air and CO₂ out the port, until the final CO₂ concentration will be quite high. Leave for a week. It works great. I know, because after I open the bags after a week, I can smell the CO₂ in the bag quite easily.

But a funny thing happened, just as I was about to embark on the Space Bag project: I had been checking the moth traps every week. Never a moth. I decided to Space Bag treat the woolens at the end of an unusually warm and dry August.

Literally as I was collecting the woolens to bag them, I checked the traps one last time. They all had moths, in some cases, quite a few. So now I know the traps work.

Where did the moths come from? I don't know. I literally checked all the wool and silk in the house, including carpets. Nothing. No holes, no dead moths, no webbing, nothing. Did they come from outside the house? Maybe. They might also have come from some bulky wool sweaters where damage might not be obvious.

Actually, none of my theories for where the moths came from are all that persuasive. So I don't really know. I treated with CO₂. Most of the woolens are in airtight storage now, and almost all of the rest will be soon. I ordered fresh traps. I plan on treating the woolens twice a year until we go two years with no moths in the traps.

To be continued....

My First Patent

Insilicos was issued a patent for diagnosis of cardiovascular disease. This is the first issued patent that I have been an inventor on. It's exciting, since the patent actually matters for our diagnostic work. The method is for analysis of proteins carried by HDL particles. It's directly related to our ongoing clinical study to predict heart attacks in advance from a blood test. I'm really excited about the potential for this test to be a breakthrough in diagnosing CVD. You never know for sure until you have the data in hand, but I'm optimistic.

We launched a new cloud service

My company Insilicos has formed a joint venture with the University of Washington to further develop and commercialize the Rosetta molecular modeling software developed in David Baker's lab. The product is Rosetta@cloud, a cloud-based service for protein modeling and similar services.

We've been working on getting this project going for most of a year. It's nice to see some real customer activity!

Haleakala

Last week, I rode from Wailea up to North Maui and then back south to the top of Halekala. 57 miles, 10,023' elevation gain. Aki and Sven met me at the top. It was a nice ride. Started in moonlight, rode up through mostly good weather, and finished in the spectacularly harsh landscape of the peak.