Soda as a dietary supplement

Last year I signed up for Arivale’s beta program. They’re attempting to quantify participants’ state of health through DNA sequencing, gut microbiome sequencing, FitBit tracking, interviews, and periodic saliva and blood tests. I’m enjoying the experience so far, and very much looking forward to analyzing my own whole genome (just as soon as my BAM is finally available…)

So far I’ve had two blood tests: one last November, and one a last month. There’s not enough data to establish a real trend yet (particularly since they switched lab service companies between samples). But it’s still fun to see extensive blood work results mapped out on a nice easy-to-read chart.

This month my personal coach pointed out that my homocysteine and overall cholesterol levels look a little high. Previously my homocysteine level appeared quite low, which might be due to a bunch of factors.

homocysteine levels

Changing labs between samples means that direct comparisons are less meaningful. My coach wanted to know if my diet or habits have changed significantly since the last draw. Six months is a long time to account for, but I really couldn’t think of a significant change on my part.

She recommended taking a B12 supplement to help offset the rise in homocysteine.

That’s when it hit me: there was a subtle shift in my diet since last winter. I may have been inadvertently supplementing my diet with B vitamins after all.


One of my shop mates sprung for a case of Red Bull last year. It had been sitting around the shop for a while, and after a few long nights slaving over a hot SEM power supply, I started drinking the stuff. And eventually bought a second case.

Red Bull is, of course, quite high in B6 and B12.

About halfway through the second case I was starting to have trouble sleeping and generally felt overcaffeinated, so I completely quit drinking the stuff.

Neither I nor my counselor (a nutritionist) are doctors, but the Mayo Clinic indicates there is some scientific basis for lowering homocysteine when used in combination with other B vitamins. The overall affect on cardiovascular health seems to be an open question leaning toward “probably not relevant”.

I’m still not sure whether the amount I got from a Red Bull or two every other day would account for the shift in levels, but it’s a fun theory. It’s the first time I’ve ever had the thought that soda might be good for me.

But don’t worry, I’m switching from Red Bull to a B12 supplement with significantly less sodium, sugar, and caffeine.

AmScope upgrades

I designed a 3D-printable eyepiece holder that mates a Raspberry Pi camera to a popular inexpensive stereo inspection scope. This lets me send 5MP images from my AmScope straight to the network, without the need for a laptop!


The design files are here on Thingiverse.

I’m also using this awesome Raspberry Pi case with a chunk of Misumi extruded aluminum to hold the Pi in place.


An external button from an old joystick is wired to the GPIO lines. Using Adafruit’s Retrogame GPIO keyboard emulator, this hits the enter key to tell raspistill to take a photo every time the button is pressed. It’s connected to an old LCD monitor, giving me a nice big view of what’s under the scope.

Glad to know my microscope is running a pre-empting kernel…

The pi automatically logs in on the console at boot, and saves its images to a folder watched by Bittorrent Sync, which then pushes it out automatically to the WiFi.

Turn it on, hit the button, picture lands on the network. Perfect!

More photos


SEM back online

A couple of months ago, Milly started having beam issues. At the time it seemed like emitter trouble. New emitter modules run about $3k, so I took the opportunity to look into manufacturing my own.

But that’s a long story for another time.

8mm across, 1mm high, 0.1mm thick. And the tip is just a tungsten atom or two.
8mm across, 1mm high, 0.1mm thick. And the tip is just a tungsten atom or two.

The short version is that I’ve learned a lot in the last couple of months:

  1. Cold cathode tungsten emitter tips are really, really tiny. I knew that of course, but you don’t truly have an appreciation for something until you try to make one.
  2. Spot welding tungsten is harder than you might think. It has the highest melting point of any element (3422 C) and gets quite brittle after heating.
  3. Before jumping right into emitter maintenance, be sure to check all of your fuses.

In the end, it turned out that I had blown two fuses in the electromagnetic lensing power supply. This was the cause of the beam trouble, not the emitter itself.

Why two fuses? This circuit uses two 10A fuses in parallel. Each half is supposed to carry 7A.

Why two fuses in parallel instead of a single 20A fuse? I have no idea. The original manufacturer thought it was a great idea. But with fuses in parallel, whenever one blows the other one does too, often in a spectacular fashion.

After changing the fuses I decided to put the original emitter back in place. One 24 hour bake later, she’s back online.

Some random junk that happened to be under the beam.
Some random junk that happened to be under the beam.

She’s not quite 100% yet… There’s a little trouble with the noise cancelling pre-amp, and I need to take the time to properly realign the column. But thankfully she’s up and making images again.

More on my DIY emitter adventure in a future post.

Cheap digital optical microscope

I recently picked up an AmScope SE400Z inspection scope. It’s a handy desktop microscope that sells for under $200. The large area under the objective lens leaves plenty of room to work, and the 10-20x magnification is plenty for most of my needs.

While they do supply some nice looking USB eyepiece cameras, the price is a little high considering that they need a laptop to function.

I happened to have a Raspberry Pi camera lying around, and thought that it might be handy to turn the AmScope into a digital scope.

Frankenstein is actually the name of the eyepiece, not the microscope.
Frankenstein is actually the name of the eyepiece, not the microscope.

The Raspberry Pi has a plastic case that includes a flush mount for the camera. It is mounted directly to the eyepiece with some high-tech laser cut plywood and gorilla tape.

I use it with a cheap WiFi dongle so it has connectivity wherever I happen to need it in the shop. It runs raspistill in full screen mode, with HDMI feeding to an old monitor. The USB keyboard makes taking a photo as easy as hitting enter, though I’m considering making a simple button / foot switch for that. Photos are automatically sync’d to the network with BitTorrent Sync as they’re taken.

If microscopy teaches us anything, it's that there's a whole universe down there. A filthy, nasty universe that you can't unsee.
If microscopy teaches us anything, it’s that there’s a whole universe down there. A filthy, nasty universe that needs a good scrub.

With the 5 megapixels provided by the camera, you end up with an effective zoom of about 50x.

Those lines on the right are millimeters.
Those lines on the right are millimeters.

Do a science, hit enter, publish. Handy!

Puss in Boots

Puss... in Boots.
Crouching tiger, hidden Walken. Hypnotic, isn’t it?

If you’ve never seen Christopher Walken in Puss in Boots, add it to your queue right now. That’s him as Puss, craftily stalking a bird for supper.

Spoiler alert: it’s among the more terrible children’s films of 1988. But every scene that Walken is on screen is comic GENIUS.

I made the gif directly from Amazon video. They don’t implement freeze frame, but hey, it’s a web player. Time to fire up the JavaScript console!

(To all the jQuery haters in the audience: no, you don’t need jQuery to do this. But since Amazon thoughtfully included it on the page, why not use it?)

Open a browser console. Click on the console prompt but hover over a video to show the video controls. Then run the following:

jQuery('.playIcon').click(); setTimeout(function() { jQuery('.pausedIcon').click() }, 30);

Each time you run it in the console, the video advances one frame. Grab a screen shot and away you go.

All that glitters…

Gold particles on carbon at x50,000
Gold particles on carbon at x50,000

Here’s an image of a gold calibration target. To give you an idea of the scale, that line representing 100 nanometers is roughly the diameter of the HIV virus.

In other news, I posted wav2tiff to Github. I made the above image with Milly, an audio cable, a 10k resistor, and that script.