Tuesday, 29 November 2011

07:20 – UPS showed up yesterday with a whole bunch of bottles and lids. I shoved them into the spare room that used to be full of computer gear until I have time to move them downstairs.


When we ordered the Pentax K-r DSLR, I was hoping that the Live View feature would make it easier to shoot images through the microscope, and indeed it has. Here’s Aspergillus sp. at 100X showing conidia and spores.

It’s still difficult to achieve proper focus, but much less so than it was without Live View. Without Live View, I often had to shoot literally 30 or 40 images of the same view to get one in reasonably good focus. It’s near impossible to focus on an SLR focusing screen when viewing through a microscope. With Live View, I can generally get a pretty well-focused image by shooting three or four images and tweaking the focus slightly each time.

Of course, the real problem is that for most subjects there’s really no such thing as proper focus, because those subjects are actually three-dimensional. Although many appear to be two-dimensional, most of them actually have depth. It’s often a matter of 100 micrometers or less, but that still means that when one part of the object is in focus, others aren’t, particularly at higher magnifications. Even in this image, which is a thin section at only 100X, some of those tiny little spores are sharply focused and others aren’t. That’s because some of them lie above the plane of focus, and others below.

I’ve often wondered if I should use stacking software designed for astrophotography to shoot composite photomicrographs with everything is in focus. The problem in astrophotography isn’t focus–everything is at infinity–but turbulence in the atmosphere, which changes constantly and blurs parts or all of the object. With stacking software, you shoot many images–hundreds to thousands–and then process them with the stacking software. It finds the non-blurred parts, if any, of each individual image and then combines those into one composite image. Processing an image is, of course, resource intensive, both in terms of disk and CPU. Even a fast PC may need several minutes to many hours to complete the stacking process, depending on image resolution and the number of frames in the sample.

Of course, I wouldn’t shoot dozens to hundreds of photomicrographs separately. Instead, I’d focus the microscope as well as I could and then adjust focus one direction or the other until the image was clearly out of focus I’d then turn on the Pentax K-r video mode and capture 720p video for 30 seconds or a minute as I very slowly ran the focus in the other direction. It’d be an interesting experiment, but of course the results would be low-resolution (720p), probably not good enough for publication. Also, I just don’t have time to do this. Finally, using images that were in sharp focus across the entire field would raise unrealistic expectations among readers, i.e., “What’s wrong with my microscope?”


09:42 – Amazon says they sold four times as many Kindles on Black Friday this year as they did last year. Presumably the same held true yesterday for Cyber Monday. Of course, a lot of those Kindles are Kindle Fires, which I suspect most buyers intend to use primarily as tablets rather than e-readers. Reading ebooks on a backlit display is a miserable experience, as anyone who’s used both backlit LCD and e-Ink readers can tell you. So the reality is that e-reader sales have perhaps only doubled year-on-year, if you consider e-readers to include only devices that people actually use primarily for reading.

Sales of e-readers last December were high enough to cause catastrophic sales declines for print books, particularly MMPBs, which fell about 50% year-on-year. Sales of e-readers this month should be sufficient to pretty much kill MMPB entirely, not to mention driving another nail in the coffin of trade paperbacks and hardbacks. For now, trad publishers are hanging on, although they’re doing so by raping customers with $10 and higher ebook prices and raping authors with 17.5% royalty rates. That won’t go on much longer, as more and more people, both readers and authors, come to understand that even $2.99 is a pretty high price for just a license to read a book, and as more and more titles become readily available on torrents. By this time next year, I suspect a lot of people will be trading multi-gigabyte ebook archives in the same way they started trading MP3 archives years ago.


10:49 – I just got email from a reader asking which Kindle I’d recommend, and why. There’s no single answer to that, so here goes:

If you’re a serious (heavy) reader of novels, no question, the baby Kindle 4 is the best pure ebook reader. At only $79 ($109 without ads), this should be a no-brainer for any serious reader. It’s noticeably smaller and lighter than the other models, so nearly anyone can use it one-handed, and it just gets out of your way while you’re reading. If you take notes, play games, or otherwise use a keyboard or if you want to listen to audio books, this model is a bad choice, but otherwise go for it. The ads, incidentally, are not at all intrusive. You see them only on the screensaver and as a small pane at the bottom of the screen that lists your titles. As regular readers know, I hate and despise ads, and these don’t bother me even slightly.

If you’re a serious fiction reader who does need a keyboard or listens to audio books, go with the Kindle 3. It’s larger and heavier than the baby Kindle and some people will have trouble holding it securely with one hand, but otherwise it’s a match for the baby Kindle except that it has a physical keyboard and audio support.

If you’re looking for a cheap iPad and you intend to use it only casually for reading ebooks, go for the Kindle Fire. Just be aware that, although the Fire is probably about as good for reading ebooks as an iPad, in real terms that means it isn’t very good at all.

Finally, the bastard child, Kindle Touch. This might actually have been my first choice, if only Amazon had included physical page-turn buttons. They didn’t, which means to turn pages you have to move your finger and touch the screen, which really, really gets in the way of reading. Not to mention smearing up the screen. About the best I can say for the Kindle Touch is that its virtual keyboard, which is operated by touching the keys on-screen, is a lot better than the baby Kindle’s virtual keyboard, which requires moving the cursor around using the arrow keys on the controller button. Still, if you need a keyboard, in my opinion the original Kindle 3 (now the Kindle Keyboard), with its physical keyboard, is a much better choice.

Thursday, 17 November 2011

08:44 – Apparently, some people took one of my comments yesterday to mean that I was planning to abandon Linux for Windows. I’m not. What I may do is buy a low-end PC with Windows on it to do some stuff that requires Windows.

For example, right now I’m driving to the post office to mail kits. The USPS has a web site where I could print labels with postage and have the mailman pick up the kits at our home. That’d save me a lot of trips to the post office, but the problem is that I’ve never gotten that site to work properly on our Linux boxes. When I try to use it, it goes off into an endless loop. I think the problem is the version of Adobe Reader rather than Linux per se, but of course that still means it doesn’t work on Linux. And there are a few other Windows-only applications that might be useful for the business. I am and always have been practical about operating systems. They’re not a religious issue for me. If I need Windows, I’ll use Windows. If I need OS X, I’ll buy a Mac. I prefer to use Linux simply because it’s secure and doesn’t lock me in to a corporate walled garden, as the alternatives do.


And, speaking of kits, we just sold the last chemistry kit in stock. We had to increase prices on the new batch by $10 per kit. We’ll be assembling three dozen of those over the next couple of weeks. We’re still accepting orders for kits to be shipped the week of December 4th. With Christmas and the winter semester approaching, this new batch probably won’t last long, so I also need to get orders placed for the components we need to build another batch.


09:49 – Old memories. I used to do a lot of darkroom work, including processing color film, which was a big deal to do in a home darkroom back in the 60’s. There were kits available: E3 and later E4 for processing Ektachrome color slides, and other kits for processing color negatives and color prints. I ran through all of those, but was looking for a new challenge. So I decided to process Kodachrome at home.

Kodachrome is (was) utterly different from standard color films and papers. Those were called “substantive”, which meant they had the color couplers built into the emulsion layers. There was just one development step, during which an organic chemical in the developer reacted with each of the three color couplers to form the three dyes needed to make up the color image. Kodachrome, on the other hand, was actually a black and white film. No color couplers. Instead, it had three separate black and white emulsion layers, each sensitive to only part of the color spectrum. During processing (which, IIRC, involved more than 30 separate steps) the film was first developed in an ordinary black-and-white developer and then exposed individually to monochromatic light to fog the unexposed silver halides in each emulsion layer. After each layer was fogged to reverse it, it was developed with a specific developer that produced the appropriate dye for that layer. The final layer was fogged with white light and then color-developed. There were numerous intermediate steps.

I actually got recognizable results on my first attempt. Not good, but recognizable. So I wrote Kodak to ask them for some tips. By return mail, I got a very polite letter from Kodak, which basically said as inoffensively as possible that they didn’t believe I was doing what I claimed to be doing. So I mailed the guy back and told him I most certainly was. He then, again very politely, basically asked me to prove it by sending him a Kodachrome slide developed as a negative. So I did that.

It was a couple of weeks before I heard back from him, and when I did he was asking me if I’d like to come up to Rochester for a job interview. I replied, thanking him for his interest, but explaining that my parents thought it would be inappropriate for me to apply for a job with Kodak since I was still in junior high school.

Oh, yeah. The reason I was thinking about this is that we just sold the last kit in stock to a guy who’s a professor at Rochester Institute of Technology–sometimes called Kodak Institute of Technology–where I did graduate work. Of course, as I’ve mentioned before, RIT isn’t actually in Rochester, NY. It’s in South Henrietta, NY. I used to have a great t-shirt for the South Henrietta Institute of Technology.

Saturday, 1 October 2011

12:33 – It’s a standard Saturday around here, if a bit brisker than expected for this time of year. Barbara just finished cleaning house, and I’m doing laundry interspersed with working on the biology lab book.

I also need to get the table in my office cleaned up and set up for tabletop photography. Many of the images for the book are shot through the microscope, but many more are standard tabletop shots. And at some point I’ll shoot the cover for the book, which’ll probably feature a microscope, Petri dishes, and other biology-related lab stuff. I’ll take some pains with illumination for the cover shot, but I’m hoping that I can get away with quick-and-dirty flash illumination for most of the table-top shots, using on-camera flash with one or two slave flashes for fill.


17:50 – It’s been a long time since I studied Greek, and even then it was classical rather than modern Greek. But today I realized that Google Translate probably supported Greek, so I entered the name of the Greek finance minister, Ευάγγελος Βενιζέλος, into Google Translate and asked it for an English translation. The English version was, and I am not making this up, “Joe Isuzu”.

Well, okay. I am making it up, but not by much. All politicians lie pretty much constantly, but Evangelos Venizelos makes most US politicians look like paragons of honesty. I was about to say, “like Honest Abe”, but the truth is that Abraham Lincoln was a lying weasel like the rest of them. But not as bad as Venizelos. I’ve noticed that none of the images I’ve seen of Venizelos is in profile, presumably because his nose is about 10 meters long by now.

His latest porkie? After meeting with the troika, Venizelos says that Greece has met all of their terms, and is absolutely certain to get the next tranche of the bailout. I’m sure that comes as a surprise to the troika auditors, since Greece has met literally none of their terms, nor even come close to doing so. Nor even tried to do so. As to any assurance that the next tranche will be approved, Venizelos may be right, but if he is it has nothing to do with Greece meeting the terms; it’s simply overwhelming fear on the part of the EU and the IMF that a Greek default will cause the euro to collapse almost overnight. And that fear is well-founded.

Wednesday, 31 August 2011

09:20 – We’re well into the endgame for the euro. Even with the ECB buying huge amounts of Italian debt on the secondary market, yields on new Italian debt crept above 5% yesterday in the first auction since the ECB began propping up Italy. And one of the German heavy-hitters has finally publicly come out in favor of Germany leaving the euro. (Of course, he’s merely said out loud what most Germans are already thinking.)

German business chief calls for country to quit euro and join new currency with Austria, Holland and Finland

If (when) that happens, the Euro crashes and burns. Those holding euro-denominated debt are likely to lose nearly all of their investments. Without the northern tier backing it, the euro is backed only by countries that are already bankrupt, and will have no option but to inflate the euro into worthlessness. A 100 euro note may buy a cup of coffee, if you’re lucky. Of course, the upside is that Greece, Portugal, Ireland, Spain, Italy, Belgium, and France won’t have to default on their debts. They’ll simply pay them off in worthless euros, after which no doubt these weak economies will soon revert to their former local currencies. The other upside is that having devalued their currencies, these weak countries will be able to export much, much more to nations with stronger currencies, thereby allowing their economies to grow again after many years of zero or negative growth. That may be some consolation to their citizens, who won’t be able to afford to import goods from wealthier countries.


Barbara and I were watching something the other night in which one of the characters was pregnant and several of them were sitting around discussing what a horrible idea it was for a pregnant woman to drink any alcohol at all. This is one of those things that everyone knows that turns out not to be true. There is zero evidence that light to moderate alcohol consumption is dangerous for the mother or the fetus, and in fact there is some evidence that one drink or less per day is actually beneficial. Intuitively, it would seem to most reasonable people that heavy drinking is a really bad idea for a pregnant women, but then it’s a really bad idea for anyone else as well.

When I visited the Wikipedia page on Fetal Alcohol Syndrome, I learned that 30% to 33% of pregnant women who consume 18 drinks per day or more give birth to babies with FAS. I assume they meant 18 drinks per week; at 18 drinks per day the baby would be born an alcoholic. But perhaps they really did mean 18 drinks per day, because FAS is relatively rare, so perhaps a 30% to 33% incidence does require that much alcohol consumption.

Clicking around Wikipedia, I came across something that made me wonder if there are words other than “foot” whose plurals vary depending on context. Not usage; those are relatively common. Context. The phrase in question concerned someone’s height, which it gave as “five feet and eight inches”. My first thought was that the person who wrote the article was not a native English speaker, or at least not a native US English speaker. In US English, when referring to a person’s height, the plural of “foot” is “foot”, “and” is never used between the numbers, and “inches” is always understood rather than spoken. For example, if someone asked me how tall my friend Paul Jones is, I would reply “six foot four” (or just “six four”). Conversely, if someone asked me how tall the Washington Monument is, I would reply “555 feet, 5 inches”. So, are there any other words whose plurals are context-dependent? I can’t think of any.


12:28 – Barbara was playing around with the new Pentax K-r DSLR the other day, and shot a few images of Colin at 28 weeks old. Here’s a crop (about 4.8 MP from the original 12.2 MP file).

There’s nothing in the image to provide scale, but Colin is one huge Border Collie puppy. He’s about as large at 28 weeks as a typical adult male BC. We don’t have a scale, but I estimate his weight is in the 50 pound (23 kilo) range already and he can stand with his paws on my chest.

I may reconsider having the camera set to save both RAW and JPG by default. The JPG images it produces are fairly large (about 5.5 MB), and the camera’s processor does a very good job of compression. I looked at zoomed in portions of various images in RAW and JPG form. RAW has a bit more detail, but not much. So I’ll probably reserve RAW form for times when white balance or brightness range is likely to be a problem.

Tuesday, 30 August 2011

08:00 – The Pentax K-r DSLR showed up yesterday, along with its kit lens, a spare battery, and a memory card. When I opened the battery and charger, I plugged in the charger and plunked in the battery, only to see the indicator light green. I assumed that meant the battery was fully charged, so I installed it in the camera. It had a very low charge, so I resorted to reading the manual. As it turns out, the charger light is green as long as the battery is charging and goes out when the charge is complete. One interesting thing. The manual recommends not storing the battery completely charged, because that reduces its service life. That’s a new one on me. I thought storing a partially-charged battery was bad, but at least for the Pentax battery that’s the recommended procedure.


I’m still working on the biology book and kit. One thing I want to include is several different antibiotic resistance samples–amoxicillin, cephalexin, erythromycin, penicillin, tetracycline or doxycycline, metronidazole, and so on. The problem is, the things are ridiculous expensive to buy.

For example, Home Science Tools sells a set of eight antibiotic test discs–two each of penicillin, ampicillin, neomycin, and erythromycin–for $3.95. These discs are tiny. They appear to be about 3/16″ (4.8 mm) in diameter, about the size of the discs produced by a notebook 3-hole punch. And you only get two of each for $4.

I could buy antibiotic discs from a wholesaler for maybe $10 per hundred, but that’s still $0.10 each. That starts to add up if I include multiple discs of several different antibiotics. So I decided to make my own and supply them in the biology kit as 2X2″ (5X5 cm) squares, which the user can trim or punch to the desired size. With half-centimeter squares, for example, a 5X5 cm sheet would provide 100 test pieces, each 5X5 mm, or 5 mm circular pieces if they used a hole punch. (Sterility is not a major issue; even bacteria that are resistant to a particular antibiotic are typically resistant only to the levels found in blood plasma, not to the levels present in these test papers.)

I can buy filter paper in 8.5X11″ (21.6X28 cm) sheets, each of which will provide 20 squares, each about 5 cm square. I’ll run each sheet through the laser printer and print the type and concentration of antibiotic in small print repeated at frequent intervals. I’ll then sterilize the sheets with dry heat and absorb an aqueous solution of the relevant antibiotic into each sheet. Of course, the issue then becomes how to determine the concentration. To do that. I’ll weigh a sheet of the filter paper dry, soak it in water, allow it to drain, and reweigh it. Knowing how much water each sheet absorbs will allow me to calculate how concentrated to make the solution to reach a given concentration of antibiotic in a specified area of the filter paper. I love devising cunning plans.


09:35 – Well, no more site traffic stats for me. When I clicked on the site stats link, WordPress told me that the stats plugin now required installing and enabling something called Jet Pack and setting up an account on WordPress so that I could get to my stats in the WordPress cloud. I hate clouds. And site traffic doesn’t matter to me. I don’t care if I average 100 visitors a day or 10,000. I write this journal for myself, not for anyone else.


12:17 – I just assembled enough chemistry kits to fill the orders that have been outstanding since I ran out of kits on Saturday. While I was at it, I built a dozen extra kits and put them on the shelf. Final kit assembly goes much faster now that I have all the components organized and ready to hand. Assembling a dozen kits from subassemblies and individual components now takes less than an hour.

Thursday, 25 August 2011

08:22 – I’ve been thinking about unusual antonyms, ones that almost no one knows. Last night, I was thinking about writing something about the Euro crisis, focusing on the mistaken idea that the Eurozone is an “optimal currency area”. Far from it, the Eurozone is the opposite of optimal. So what’s the antonym for optimal? I had to think about for a moment. So, quickly and without looking it up, what’s the antonym?

Having thought of it, I did a quick google search on “optimal” and its antonym. The results were about 200 million hits on “optimal” and about an eighth of a million on the antonym, making “optimal” about 1,600 times more commonly used than “pessimal”.


In every one of my books, I’ve included one horrible pun, often quite subtle, and I just added the one for the biology lab book. I was writing up a lab session about the effect of nitrogen-fixing bacteria (rhizobium) on the growth of lima bean plants, touching on the ecological principles of mutualism and commensalism.

In mutualism, each species benefits from the relationship with the other species. In a commensalist relationship, only one of the two species benefits. The other does not benefit, but suffers no harm. For example, on one level the relationship between squirrels and oak trees is commensalist. The oak tree provides shelter for the squirrel by providing a secure location for its nest, but the tree does not benefit from the presence of the nest. (In another sense, the relationship is mutualist, because the squirrel benefits from acorns as a food source, while the tree benefits by having the squirrel bury its acorns far afield, where they can germinate.)

Rhizobium forms nodules on the plant roots, and converts atmospheric nitrogen into nitrates that the plant can use, an obvious benefit to the plant. But what is the benefit to the bacteria? Obviously, there must be some benefit to the bacteria from a close association with the plant, or the bacteria would be distributed throughout the soil, rather than forming nodules on the plant roots. Oh, yeah. The pun. I mention the plant providing the bacteria with a location for a nice, cozy nodular home.


09:09 – I just ordered a Pentax K-r DSLR with the kit lens from B&H, along with a spare Pentax battery and a Class 10 memory card. The AA battery adapter is back-ordered, so I’ll pick up one of those later. B&H is supposed to email me when they’re back in stock.

This is the first DSLR we’ve bought that can save image files simultaneously in RAW and .jpg formats, a feature that I’ll definitely use. For the last few years, we’ve always saved as RAW format and then I’ve used showFoto to convert to .jpg for printing at Walgreens and so on. Having the camera produce and save .jpg files along with RAW files will save some time and effort. Speaking of RAW, that raises another question. All of our past Pentax DSLRs have offered only the proprietary Pentax .pef RAW format. This camera offers the choice of saving RAW as .pef or .dng. Is there any advantage or drawback to choosing one or the other?


16:06 – As usual, good sense from Pat Condell, this time concerning the European Union.

Thursday, 18 August 2011

08:45 – Pity the poor European Central Bank, which has the tiger by the tail. Two weeks ago, the ECB began buying Spanish and Italian debt. That intervention worked, driving down Spanish and Italian bond yields from considerable more than 6% to the 5% range. That still isn’t good, but it puts off the crash a bit longer.

The problem is, having started, the ECB can’t stop buying Spanish and Italian debt because no one else will buy it. With Spain and Italy no longer having access to the capital markets, if the ECB doesn’t buy their debt, the yields will jump catastrophically. We saw this happen with Greece, Portugal, and Ireland, and it will most certainly happen with Spain and Italy. Rather than 5% yields, we’d soon see yields climbing into the 10%+ range, and eventually probably into the 20% range, as happened with Greece.

That means the ECB must buy essentially all debt offered for auction by Spain and Italy. Considering rollovers, interest payments, and new debt already scheduled to be auctioned, for the remainder of this year that comes to something like $50 billion per week. Call it $1 trillion between now and the end of the year.

And, in an incredible irony, Finland announced yesterday that it would require full collateral from Greece if Greece expected Finland to participate in the Greek bailout. In other words, Finland wants Greece to cough up enough cash to allow Finland to buy AAA bonds as collateral against Finland’s share of the bailout. Of course, if Greece had any collateral it wouldn’t need the bailout. Later yesterday, Austria, Slovenia, and Slovakia also announced that they’d require collateral from Greece before they participated in the bailout. The Netherlands is expected to require the same. In other words, all of these countries, and others likely to make similar demands, are running as fast as they can away from the Greek bailout, which means the Greek bailout may never happen.

The real irony, of course, is that everyone is pretending this is a liquidity crisis, when in fact it’s a debt crisis. And Greece is small potatoes compared to Spain and (particularly) Italy, and eventually Belgium and France. The simple truth is that these countries owe far too much to have any chance of ever repaying what they owe, and that bill is quickly coming due.


I have to order a new Pentax DSLR. The one Barbara took to work was damaged by a power surge, and her firm is reimbursing us for the cost of a new camera. The damaged camera still functions, but the power surge killed its USB port, which is essential for using it on a microscope. Her firm will keep the damaged camera, which still works for shooting images. It’s no problem for them to transfer images by removing the memory card and putting it in a card reader.

I plan to order a Pentax Kr, which is the nearest current model to the one we’re replacing. One thing I insist on is the ability to use AA cells. The Kr comes with a lithium-ion battery, but AA-compatibility is now optional, via the $40 D-BH109 adapter. I’ll order it with the kit lens, which is an excellent 18-55mm zoom. I’ll also order a fast memory card or two for it. I haven’t looked at memory cards lately, but I’m assuming that 4 GB and even 8 GB cards are pretty inexpensive nowadays. At 12 megapixels, a 4 GB card would probably give me roughly 200 image files in RAW format per card. The last time I bought a memory card, fast cards were roughly twice the price of slower ones, so I might be able to get a fast 4 GB card for what I’d pay for a slow 8 GB card. Any advice would be appreciated.