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Week of 15 December 2008

Latest Update: Saturday, 20 December 2008 14:53 -0500

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Monday, 15 December 2008
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08:47 - Barbara is much happier with her kitchen now, although I still haven't hung the cabinet doors. At least the cooktop vent hood is in place and working, and we've moved the old microwave cabinet and installed the shelves. I'm not sure why, but we always seem to have a major project going on at the same time the final deadline for a book looms. Oh, well. We're making progress on both.

Yesterday afternoon, we shot many of the images for chapter 4 (lab practices) of the forensics book, and a couple for chapter 5 (soil analysis). There are still half a dozen left to shoot for chapter 4, which we'll do tonight or tomorrow. I've been shooting most of these images as setups in my little mini-studio, but I need to get the lab cleaned up because many of the images for the lab session chapters will need to be shot in the lab itself. I'll probably use the roll of white background paper (which is actually disposable picnic tablecloth) to cover the counters for shooting images. Actually, it wouldn't be a bad idea to put some down semi-permanently with spray adhesive to protect the counters. There are already a few small stains on the counters, but most of them are iodine, which is easy to remove with sodium thiosulfate.

Today, I'm choosing images. I always shoot a bunch, at least half a dozen of each setup, and then pick the best to use in the book. That adds up fast. Yesterday, we shot close to a hundred images, which is about a gigabyte of files. I suppose I should just discard the ones I don't use, but I'm a keeper.


Tuesday, 16 December 2008
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09:47 - Poor Barbara. She's used to finding strange things in her oven or dishwasher. Yesterday, just in time, I finished shooting images for one of the lab sessions. This one was about collecting and preparing soil samples, and I had to dry the samples. If Barbara had arrived home only a few minutes earlier, she would have found her oven baking dishes of ... dirt. As it was, I got the soil samples downstairs in the nick of time and shot images of them. I left the oven door open so the nice earthy odor could dissipate.

And my mouse died yesterday. It was a Logitech cordless rechargeable with a docking station that was both the receiver and the charger. I really liked that mouse. I've been using it for probably six years or more. It's been through two or three sets of NiMH rechargeable AA cells and just kept ticking, but apparently it decided it was time to die. At first, I thought I needed to replace the AA NiMH cells, but when I did that it refused to charge. So I charged up a set in a separate charger and put them into the mouse. It worked after a fashion, but the cursor movement was jerky and then it just died as I was editing a document. Oh, well.

I fished around in my spares and came up with a Microsoft Optical Mouse 2.0 (Model 1008). Although I suppose I could use NiMH cells in it, it doesn't have a charging station, just a USB-connected receiver. I really don't much like this mouse, even disregarding its disgusting reddish-orange color scheme. The scroll wheel is mushy and hard to use, and middle-clicking it in Firefox doesn't always work. This mouse is unused, out of the box. I may try one of the other mice I have lying about.

Or perhaps it's time to try a trackball. I have a couple of those, including some new in the box. I've never tried using one seriously, but I suppose I may give it a shot.


Wednesday, 17 December 2008
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08:15 - Yesterday I finished the first rewrite pass through chapter 5, Soil Analysis, including deciding which images to shoot and putting in placeholders for them. I've already shot some of the images for that chapter, and I'll shoot the rest of the ones I can do without Barbara, who is my "hand model", today. I'll also start the rewrite pass on chapter 6, Hair and Fiber Analysis, which is a long chapter.

This book will have more images than the home chemistry book. So far, the equipment chapter has 30 images, the mastering lab practices chapter 26 images, and the first lab chapter 18 images (covering five lab sessions). For the chemistry book, I basically shot an image when I thought about it as I was doing one of the lab sessions. For this book, I'm planning the images and the setups ahead of time. That makes for more work and more time needed, but I think it's worthwhile. The images will also be better for this book. Not perfect, but better.


Thursday, 18 December 2008
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09:43 - Chapter 5 (Soil Analysis) is complete and posted for download by my tech reviewers and subscribers. It includes one image, Barbara using the Project Star spectrometer to view emission lines from a soil sample, that was shot at 1/3 second. She did amazingly well to remain steady for that exposure time.

I'm starting on Chapter 6 (Hair and Fiber Analysis), which is a long one. Eleven lab sessions, with many images needed. And my lab looks like Julia Child has been cooking it it. I just went downstairs to do a setup and found that I was out of clean glassware. There were 11 dirty Erlenmeyer flasks of various sizes, about a dozen dirty beakers, and scads of dirty test tubes covering all of the horizontal surfaces, and all of that glassware needs to be washed. Ordinarily, I wash up at the end of each lab session and put everything away. The last week or so, I've just been blasting through lab sessions, letting the dirty stuff accumulate.

Although I've always hand-washed labware, I'm seriously considering doing a dishwasher load of beakers and flasks. I'd rinse the stuff well first, of course. What I really need is a grad student working behind me to keep things clean and neat.


Friday, 19 December 2008
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08:03 - I'm working away on Chapter 6, Hair and Fiber Analysis. This is a long chapter. I may not finish the rewrite today, but things take as long as they take. I'd like at least to get all of the image placeholders positioned where I want them so that I can shoot some or all of the images this weekend while Barbara is available.

I also need to finish writing the January 2008 HomeChemLab.com subscriber supplement. That's finished except for one lab session I need to write up about isolating casein from milk and doing some quantitative analysis on it to test for nitrogen, phosphorus, and sulfur. Or, depending on the length of the write-up, I may pend the analysis for the following month. I'll also need to at least stub out the February issue, because each issue lists what's coming up in the following issue.

For that matter, I may actually finish the February issue. Until recently, I've tried to keep at least a month or two ahead, but when I sent out the December issue my inventory of completed future issues dropped to zero. That makes me uncomfortable.


Saturday, 20 December 2008
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08:25 - You know it's a long day when you carefully wet-mount a hair specimen on a slide with a frosted-glass end and then find when you attempt to label the slide that the frosted side is face-down.

By late afternoon yesterday, I'd finished rewriting chapter 6, Hair and Fiber Analysis, and added placeholders for images. I decided to shoot a few of the images that I could do without Barbara's assistance, and headed back to the bathroom to grab a specimen from my hair brush. I wet-mounted it, found that the only way I could label it was by holding it up above eye level and writing mirror-image characters on the bottom of the slide, and then stuck it under the microscope objective.

I found that my head hair has no individualizable characteristics. In fact, it looks like an artificial fiber. Perfectly smooth, of uniform diameter, and lacking any visible internal structure. At 100X and 400X, my hair shows no cuticle scales, no medulla, no ovoid bodies, no cortical fusi, and no pigment bodies. That last is why it looks gray. Gray hair isn't actually gray. It's transparent and colorless because there are no pigment bodies. It scatters the light and so in bulk it appears gray rather than transparent and colorless. So, under the microscope, my hair looks a lot like a polyester fiber.

14:53 - I finished the January 2009 issue of the HomeChemLab.com subscriber supplement. Each issue includes a list of the articles to appear in the next issue, so I had to come up with at least the titles of those February articles. Here they are:
Laboratory 24.2 uses the casein we isolated in the January issue. We'll hydrolyze it and run a paper chromatogram to separate the individual amino acids. We'll visualize the chromatogram with the ninhydrin solution we used to reveal fingerprints in the home chem lab book, and identify the amino acid bands by their Rf values. Pretty cool stuff, actually.

But it's Laboratory 24.3 that I really wanted to do. In the early 19th century, many chemists accepted the vitalism hypothesis, which held that some chemicals could be produced only in living creatures. That was the origin of the term "organic" as applied to chemicals. In 1828, Friedrich Wöhler, one of the early Titans of organic chemistry, drove a stake through the heart of the vitalism hypothesis by synthesizing urea, an organic compound present in urine, from the inorganic precursors silver cyanate and ammonium chloride.

Upon completing this synthesis, Wöhler wrote triumphantly to Berzelius (another early giant of chemistry), "I must tell you that I can make urea without the use of kidneys, either man or dog. Ammonium cyanate is urea." Wöhler went on to say that he had witnessed "The great tragedy of science, the slaying of a beautiful hypothesis by an ugly fact." Well, not so much. As it turned out, Wöhler had made two errors, one large and one small.

The large error, which is understandable given the complete lack of understanding of chemical structures at the time, is that ammonium cyanate and urea are two distinct compounds. They have the same empirical formula, (NH2)2CO, but the atoms are arranged differently in the two molecules. (It was urea that Wöhler synthesized, by the way, not ammonium cyanate.)

The smaller error, of which Wöhler may have been unaware, was that his silver cyanate originated from an organic source, so in that sense his synthesis did not disprove vitalism entirely. Vitalism was not discredited indisputably until 1845, when the German chemist Adolph Wilhelm Hermann Kolbe made a complete synthesis of an organic compound, acetic acid, from unquestionably inorganic precursors. Incredibly, even after Kolbe's proof, many chemists retained their belief in vitalism, including such respected chemists as Louis Pasteur. It wasn't until the early 20th century that all vestiges of vitalism disappeared.

At any rate, I wanted to reproduce Wöhler's synthesis of urea. The first problem was the silver cyanate, which is available but extremely expensive. It's the cyanate anion rather than the silver cation that's important, so I decided to substitute another cation. The most readily available and inexpensive cyanate is potassium cyanate, but even it's relatively hard to come by. HMS Beagle carries it, for example, although they charge $5 for a 10 g bottle. I wanted to do the synthesis on a somewhat larger scale, so I decided to make my own potassium cyanate, whence the first article in the February issue.

There are a lot of ways to synthesize potassium cyanate, including oxidizing potassium cyanide. Ironically, the easiest and cheapest way to synthesize it is by fusing potassium carbonate (available for a few bucks a pound as "pearl ash" from pottery supply vendors) and, wait for it .... urea. Urea is also cheap and plentiful--used in everything from cold packs to moisturizers to 46-0-0 fertilizer--so I decided to use urea to make the potassium cyanate we'll need to synthesize urea. Of course, that means our synthesis won't falsify the vitalism hypothesis, but then neither did Wöhler's.


Sunday, 21 December 2008
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