Wednesday, 30 November 2011

09:37 – It’s the last day of the month, and I’d scheduled the Fungi chapter to be complete today. I don’t think I’m going to make it, but I may come close.


13:24 – Good grief. The Fed, the Bank of England, and most of the world’s other major central banks are going to bailout the eurozone, with (of course) the US bearing a disproportionate share of the costs. Not that it will ultimately make any difference. The euro has a fatal design flaw, so all this latest initiative will do is kick the can down the road a bit farther. And, like all the other half-measures taken so far, the actual long-term benefit will be zero while the costs will be extraordinarily high. You can’t fix a rotten, collapsing old shack by slapping a fresh coat of paint on it, and euro makes that rotten old shack look like a concrete blockhouse.

In case it’s not obvious to everyone, this initiative has nothing to do with saving the euro, which is not savable. The only purpose is to kick the can down the road far enough to stave off the collapse until after the 2012 election. Obama is as cynical as they come. He’s obviously weighed the political cost to himself and the Democrats of committing hundreds of billions of dollars to an ultimately futile bailout of Europe and Europe’s banks against the political fallout if the EU collapses before the 2012 election and concluded that screwing US taxpayers is his best option. No surprise, I guess. That’s what he’s been doing since he was elected.

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.

Monday, 28 November 2011

07:02 – Barbara arrived home in the early afternoon yesterday. As usual, Colin and I did our happy dance. One of us was so excited, he peed. I’m not saying which.


I was working on the fungi/lichens chapter yesterday when I nearly took leave of my senses. The “standard” stain for fungi, which also serves as a mounting medium, is called lactophenol cotton blue or LPCB for short. It’s what I would use for staining fungi, no question. There are other stains that work, but not as well.

So, I decided I needed to include LPCB in the biology kit. I actually started tracking down sources for the chemicals and pricing everything. One of the components–phenol, AKA carbolic acid–is tightly regulated by DOT for shipping, so I made sure that I could ship under the small-quantity exemption, which indeed I could. Then I finally came to my senses. Phenol is truly nasty stuff, and LPCB is essentially a 20% solution of phenol in glycerin and lactic acid, with some water and a small amount of dye added. Phenol is highly toxic, absorbed through the skin, and corrosive. Making matters worse, phenol is a local anesthetic, so you don’t even feel it as it eats through your skin and poisons you. Not something I or any sane person wants an inexperienced 15-year-old student messing with.

So, turning lemons into lemonade, I decided to have students test the various other stains already included in the kit to determine their effects on fungi. Safranin O is actually not a bad alternative to LPCB, but I won’t tell them that. Let them find out for themselves.


14:05 – Yesterday I linked to a YouTube version of The British Grenadiers. The Grenadiers were and are scary guys, no doubt about it. Over the last 350 years or so, they’ve helped Britain win more than a few battles. But for some really, really scary guys, check out the Biochemist Grenadiers. These guys and their colleagues in the other sciences win wars and topple empires. You want these guys as friends.

If you’re not a scientist, you may find the lyrics incomprehensible. Don’t worry. It’s not just you. Here a few lines of the lyrics:

The moiety of glucose, in the succeeding phase
Is transferred to a ketose by an isomerase
Phosphofructokinase now, acts on that F6P;
Fructose 1,6 bisphosphate is the product that’s set free.

The kinase is effected quite complicatedly
And as you’ll have suspected it uses ATP;
FBP by aldolase is split reversibly
To phosphoglyceraldehyde, also DHAP.

It’s good to be a geek.

Sunday, 27 November 2011

08:56 – Barbara is due back this afternoon. Colin and I will celebrate. I will admit that I rewatched some stuff while she was gone. The final three episodes of Firefly, Serenity, and the fourth series of Blackadder. Right now, I’m doing laundry. A load of towels and a load of Barbara’s work clothes. The regular dark and white loads can wait until she gets home.

I’ve been trying to teach Colin not to chase cats. I’ve explained to him that they’re really pretty much just small, incompetent, ugly dogs and that he should feel pity for them rather than chase them. But this morning on our walk, Colin noticed a cat in the bushes only a couple meters from where he was standing. He went on alert, the cat bolted, and Colin was off in pursuit. Fortunately, I locked the leash before he’d gotten more than about two steps or he’d have pulled me into the bushes.

When we got home, I explained things to him: “Look, you’re a dog. A dog! Your natural prey is large animals. You and your buddies can drag down an elk or a moose and rip it to shreds, for heaven’s sake. Your jaws can bite a broomstick in half. That pathetic little creature you were chasing is a cat. It has tiny, weak little jaws. Its natural prey is mice. Even a good-size rat with an attitude is more than a match for it. Why do you think they breed three-kilo terriers as ratters? And you’re about ten times that size. It’s beneath your dignity to chase a pathetic loser cat.” Colin seemed to understand. We’ll see.


12:41 – The theme music of the fourth series of Blackadder started with a couple bars of The British Grenadiers, one of those marches that everyone recognizes when they hear it, but almost no one knows the name of. I, of course, sang the first couple bars in my basso profundo as each episode started:

Some talk of Alexander, and some of Hercules
Of Hector and Lysander, and such great names as these.

So I just searched YouTube for those lyrics, and got a hit. ARRRGHH. Whoever the guys are singing this, they mispronounce a significant portion of the lyrics. My favor is “toe, row, row, row, row, row”, which refers to lining up on parade (toeing the row), and should be pronounced with all long oh’s. Instead, they misspell “toe” as “tow” and then proceed to pronounce both toe and row as in bow-wow. Then they mangle “fusee” into “fuze” and manage to use the French pronunciation for “glacis”, glaw-zee, rather than the proper British, glay-siss. That’s particularly ironic since they made a politically-correct alteration to the original lyrics. We now hear “We throw them from the glacis, about the enemies’ ears” rather than the original “We throw them from the glacis, about the Frenchmen’s ears”, which doesn’t even scan. Geez.

Saturday, 26 November 2011

09:37 – Barbara is due back tomorrow afternoon, so tonight’s my last chance for wild women and parties. No luck so far.

I’m still working on the chapter on fungi and lichens. I’d forgotten how much I hate biological taxonomy. When Barbara and I were taking biology classes in junior high school, fungi were still classified as plants. Then in 1969 Whittaker proposed the five-kingdom system that put fungi in their own kingdom, which they richly deserved. For the next 20 years, everything went swimmingly well, until DNA analysis pretty much wiped out morphology-based taxonomies, which really messed everything up.

Imagine you had to classify four people under the old morphological taxonomy. Individuals A & B appear Nordic–very light skin, blond hair, blue eyes. Individuals C & D appear sub-Saharan African–very dark skin, brown hair, and brown eyes. Under the obsolete morphology-based taxonomy, individuals A & B clearly belong together, as do individuals C & D. But then DNA analysis comes into play, showing that individuals A & D are more closely related to each other than either is to either B or C, and that individuals B & C are more closely related to each other than either is to either A or D. So, in the new DNA-based taxonomy, individuals A & D are in one group, while individuals B & C are in another group. It makes sense scientifically, but it is non-intuitive to say the least. (Obviously, all four of these individuals are actually members of the same species and subspecies, but the point remains.)

In a more accurate example, fungi have always been considered more closely related to plants than to animals. In fact, most biology books, including recent ones, treat mycology as a sub-discipline of botany. But the reality, based on DNA analysis, is that fungi are much more closely related to animals than they are to plants. Geez.


Friday, 25 November 2011

09:44 – I got 28 sets of the hazardous chemical subassemblies made up yesterday, with about 90 minutes’ work. It was a nice break from writing. Barbara won’t be home until Sunday afternoon, so the remaining work involved in building those 28 kits will have to wait for the following weekend, but we will be ready to start shipping chemistry kits again the week of 4 December.

On the heels of Germany’s disastrous bond auction Wednesday, Italy held an even more disastrous bond auction yesterday, with yields averaging more than 7.2%. It’s now obvious even to the biggest euro proponents that investors–individuals, banks, and foreign governments–are no longer willing to risk their money in euro-denominated instruments. Death of a currency as eurogeddon approaches. If you have any assets in euro-denominated instruments or funds, get out now, today, while you still can. The collapse, when it comes, won’t be gradual. And it will come, sooner rather than later.


13:38 – It really is time for any sane person to get as far away from the euro as possible as quickly as possible. At this point, we’re talking about the euro becoming a smoking pile of rubble within weeks, if not sooner. Don’t be lulled by the idea that Germany might save the euro. In the first place, it won’t because it’s not willing to take on responsibility for the debts of the other eurozone countries. In the second place, even if it were willing to do so, it can’t. Even if Germany were willing to beggar itself to save the euro, it doesn’t have sufficient assets to do so. Nor will Germany form a currency union with Finland, Austria, and the Netherlands. Germany will ultimately have no choice but to revert to the D-mark. All of them, including Merkel, know this, and you can bet that Germany has been frantically printing new D-marks in huge quantities for the last several weeks, if not months.

Euro armageddon: David Cameron fills the sandbags.



15:03 – And I see that S&P just downgraded Belgium from AA+ to AA, which is preposterous. Not that S&P cut Belgium’s rating, but that it left it ridiculously high. The ratings agencies obviously didn’t learn their lesson after the Lehman crisis, during which they were still rating junk derivatives AAA literally days before they crashed. The same is true now for sovereign credit ratings. A credit rating is supposed to reflect the likelihood of a country defaulting on at least some of its debts. On that basis, only the US really deserves the top credit rating, because it will never default. It may inflate the hell out of the dollar, which amounts to the same thing, but it will pay off its debts in dollars, regardless of what those dollars are then actually worth. So, if you assume that the US deserves the highest credit rating among all the world’s countries, although that rating is in fact crap, where should the major EU countries be rated? Well, let me fix that for them, using the descriptions from Wikipedia:

UK: BBB (An obligor has ADEQUATE capacity to meet its financial commitments. However, adverse economic conditions or changing circumstances are more likely to lead to a weakened capacity of the obligor to meet its financial commitments.)

Germany, Finland, the Netherlands: BB (An obligor is LESS VULNERABLE in the near term than other lower-rated obligors. However, it faces major ongoing uncertainties and exposure to adverse business, financial, or economic conditions which could lead to the obligor’s inadequate capacity to meet its financial commitments.)

France, Belgium, Austria: B (An obligor is MORE VULNERABLE than the obligors rated ‘BB’, but the obligor currently has the capacity to meet its financial commitments. Adverse business, financial, or economic conditions will likely impair the obligor’s capacity or willingness to meet its financial commitments.)

Italy, Spain: CC (An obligor is CURRENTLY HIGHLY-VULNERABLE.)

I’m not sure why the three major agencies haven’t assigned these ratings to these countries, because that would reflect reality. It may be that the agencies, as usual, are behind the curve, or it may be that they are coming under immense pressure from the countries in question. Well, there’s no doubt they’re under intense pressure from the EU governments and the EU itself, but I’m not sure that fully explains their failure to assign accurate ratings. Note that, of this group, only the UK with its BBB rating can still be considered “investment grade”, and it’s teetering on the edge. Germany and all of the other nations rated BB or lower are actually “junk grade”. And, as we all know, changing a bond’s rating to junk causes all sorts of unpleasant things to happen, not least of which are mass sell-offs by banks and investment companies that are not allowed to carry junk bonds on their books.

Thursday, 24 November 2011

09:21 – Happy Thanksgiving to my US readers.

Peanut butter and jelly sandwiches for dinner last night, with Doritos as the second course and ice cream for my evening snack. And people say I don’t eat a balanced diet. I started to watch the second episode of Survivors last night, but it was so well done that I stopped. I really think Barbara would enjoy the series, so I’ll save it until she can watch it with me.

I’m going to spend some time today building chemistry kits. Although the product page says we’re out-of-stock and will begin shipping backordered kits the week of 4 December, I’m still uncomfortable having outstanding orders and no product to fill those orders. I have 28 sets worth of chemicals bottled and ready to package. It’s a couple hours’ work to get those 28 chemical subassemblies packaged up, so I’ll try to get that done today.


Wednesday, 23 November 2011

10:10 – Barbara took off this morning on a trip to Pigeon Forge, Tennessee with her parents, sister, and sister’s husband. They plan to spend several days going to shows and shopping at the outlet malls. They rented a Toyota handicapped-accessible van to make it easier to handle Barbara’s dad’s wheelchair. They’ll be back Sunday. I told Barbara I’d watch 20 or 30 episodes of Despicable Housewives while she’s gone and then tell her what happened when she gets back. The truth is, I probably won’t turn on the TV while she’s gone. I’ll work during the days and read during the evenings. Well, read and throw the ball for Colin. Over and over and over.

I’m still working heads-down on the biology book. I sent the protists chapter to my editor this morning, and am currently working on a chapter about fungi and lichens.

Meanwhile, during the last couple of weeks, the euro crisis has gone from desperate to catastrophic. Italy and now Spain are on the verge of needing bailouts to avoid defaults, and there’s no money there to bail them out. Belgium isn’t far behind, and France maintains its AAA rating in name only. The FANG nations are now the G nation, with Finland, Austria, and the Netherlands coming under the gun. The ECB has reached and passed its limit in terms of its willingness to buy Italian and Spanish bonds, and without that subsidy Italian and Spanish bond yields will skyrocket from their already-catastrophic 7% levels. Private investors are no longer willing to risk their money in sovereign bonds or private bonds from any EU country other than Germany, and they’ve begun to be leery even of German bunds. The IMF and the BRIC nations have basically told the EU that it’s on its own and it can’t expect any IMF/BRIC bailouts. The US has tossed diplomacy aside, told the EU not to expect any financial support from the US, and is now ordering the EU in no uncertain terms to DO SOMETHING. The trouble is, there’s really nothing to be done, and even if there were, Germany is not willing to pay for it. We’re watching the collapse of the eurozone and the EU itself, and the timeframe is now weeks rather than months. This is not going to be pretty.


13:42 – Oh, my. Forget what I just said about Germany being the last FANG nation left standing. Germany–Germany!–just suffered a failed bond auction. Germany offered €6 billion worth of bonds, but private investors were willing to buy only about 60% of them, leaving the central bank having to buy the rest. Granted, the interest rates were low, at about 2%, but even so. This was the worst auction of German bonds in the euro era. At this point, it’s clear that investors don’t want even German bunds, perceiving (correctly) that Germany is in deep, deep trouble.


14:38 – Actually, I think I will watch something while Barbara is away. We started watching the BBC series, Survivors, on Netflix streaming a couple of months ago, but we watched only the first episode. Barbara found it grim and depressing, and I could tell she really didn’t want to watch any more of it. But it’s still in our queue, and I should be able to get through the remaining 11 50-minute episodes while she’s away.


15:46 – Ah, I wondered how long it would be before this shoe dropped. After watching the concessions given to Greece, it was only a question of time before other bailed out nations demanded that kind of favorable treatment retroactively. The only thing I wasn’t sure of was whether it’d be Portugal or Ireland first. Well, it turns out to be Ireland. Can Portugal be far behind?

Monday, 21 November 2011

10:53 – Over the weekend, Barbara and I got a good start on making up a batch of 28 chemistry kits. The chemical bottles have to be divided into groups to comply with hazardous material shipping regulations. We finished up Group D, which contains the 26 unregulated chemicals. Those don’t require the caps to be taped or shrink-wrapped. All 26 of them simply go into a plastic bag–one of the kind used in supermarkets–which is then tied off.

Groups A (five strong acids), B (three strong bases), and C (four flammable liquids) each require the caps to be taped or otherwise sealed, and each group has to go into its own sealed plastic bag. Then one each of bags A, B, C, and D go into yet another plastic bag with a large scoop of vermiculite (to absorb leaks). Doing all that qualifies the kit to ship under section 173.4 (small quantity exemption), which means the kits can ship via USPS Priority Mail (air) rather than having to go ORMD Parcel Post (ground).


Barbara is getting ready to leave Wednesday on a Thanksgiving trip with her parents. She returns late Sunday. Colin and I are planning wild women and parties while she’s gone.