Month: October 2011

Friday, 21 October 2011

09:55 – Barbara seems to be fully recovered from the episode on Tuesday. I’m still keeping a closer-than-usual eye on her while she’s in the shower and so on, but I think the risk of a repeat episode is pretty small.

I seldom do breaking news, but I figured I’d make an exception in this case and report the results of the EU crisis pre-summit scheduled for this coming Sunday and the EU real-summit-between-Germany-and-France scheduled for next Wednesday. On Sunday, the press release will say that the major parties have agreed to agree, and that the crisis will be defused at the following meeting. After the real meeting, the press release will say that major steps will be taken to address the crisis. If a particular step is to be taken soon, no details will provided about what exactly is to be done. If details are provided about what exactly is to be done, those actions will be promised only for the distant future. On Wednesday and Thursday, mainstream news sources will report that decisive actions have been taken, and the markets will breathe a sigh of relief. On Thursday and Friday, everyone will realize that exactly nothing came out of the summit meeting, and the crisis will return and intensify.

Remember, you read it here first. My new slogan is “Breaking News, Before it Happens”.

Thursday, 20 October 2011

09:37 – Barbara is back to using her regular cane. She used the walker frame on Tuesday, my four-foot cane yesterday, and declared last night that she was ready to start using her regular cane again. She took the final anticoagulant shot yesterday, and started this morning on one 325 mg aspirin daily, which she’ll continue for a month.

I see the Greeks are revolting, for what good it will do them. Most of the MSM are calling it “protests”, but throwing rocks and Molotov cocktails at the police is a bit beyond protesting. Attempted murder, say. It seems that most Greeks are blaming the EU and IMF for their problems, and the socialist government is near collapse. No one knows what will replace it, but the Communists are pushing hard. I expect we’ll see the current rioting devolve into actual revolution if things don’t greatly improve soon. And things are likely to get much, much worse, not better. As the infection spreads and other southern-tier countries default, we can expect to see similar violence as governments teeter and then topple in Italy and Spain and Portugal and Belgium and France. Not Ireland, thank goodness, nor the northern-tier eurozone countries. Unless they’re foolish enough to commit their economies to subsidizing the southern tier.

Unfortunately, the US is on the same course, albeit probably five or ten years behind. And there’s no one to bail us out.

13:32 – Barbara went to the doctor this morning, just to get looked over and have a few tests done. Her doctor didn’t seem too concerned about her brief loss of consciousness Tuesday. He seems to think it was caused by her severe pain immediately before the event, which caused her body to be flooded with adrenaline. He’s going to keep an eye on her low hemoglobin levels, but for now he basically said to take an extra multi-vitamin tablet every day and be sure to drink plenty of fluids. He also said that she was doing extremely well in terms of knee movement and so on, especially for only two weeks after her surgery.

Here are a couple of articles that caught my attention. First, despite the Guardian’s early report that a consensus had been reached before Sunday’s upcoming crisis summit for a huge effort that would finally resolve the euro crisis, it soon became obvious that not only had no such consensus been reached, but that Germany and France were farther apart than ever. This article sums things up pretty well. Franco-German deadlock over ECB’s role in rescue fund

Then we have Who Will Bail Out the Rescuers?, which starts by talking about the inability of France to contribute to bailouts and then goes much farther afield. I’m not entirely sure, but I think the article recommends stocking up on firearms and ammunition to shoot back at rioters. And police.

15:04 – Okay, this is interesting. I’ve had Sons of Anarchy S3D1 at the top of my queue since several weeks before it released, which has been a month or two. The status has never shown anything except “very long wait”.

We’re on the two-discs-at-a-time plan, and my DVD queue is getting down to the dregs. Other than Sons of Anarchy S3, Netflix just shipped us the last disc I really care about today. Our anniversary date is next Wednesday, and I’d already put a reminder in my calendar to downgrade our account to streaming-only and wait a few months for more DVDs we wanted to become available. And then this email arrived.

Re: Arriving Later: Sons of Anarchy: Season 3: Disc 1
From: Netflix
To: Robert Bruce Thompson
Date: Thu Oct 20 13:43:20 2011

NETFLIX – Shipping update

Dear Robert,

“Sons of Anarchy: Season 3: Disc 1” was not available from your local shipping center. Fortunately, it was available from a shipping center in another part of the country. It’s on its way and should arrive within 3 to 5 days.

You’ll notice we also recently sent the next available DVD from your Queue to enjoy while “Sons of Anarchy: Season 3: Disc 1” makes its way to you.

Your Queue now shows this extra DVD rental. Enjoy.

-The Netflix Team

Wednesday, 19 October 2011

09:56 – Barbara’s recovery continues. She had a minor problem yesterday during physical therapy when she felt faint. Fortunately, her physical therapist is 6’8″ (203 cm) and about 300 pounds (135 kilos), so he just caught her and sat her down.

Barbara’s blood pressure is normally on the low end of the normal range, and she’s been giving herself daily injections of an anticoagulant that lists low blood pressure as a side effect. She gives herself the shot early in the morning, and until yesterday the physical therapist had been visiting in mid- to late afternoon. Yesterday, he came in the morning, not long after she’d taken the drug. We’re convinced that the problem was due to the anticoagulant. Fortunately, today was the last day for that. Now she’s supposed to take one 325 mg aspirin tablet daily for the next month.

Tuesday, 18 October 2011

09:15 – Barbara’s recovery continues. She’s doing better than anyone could have expected. The nurse made her final visit yesterday, and said that the incision had healed completely. Now it’s mainly a matter of Barbara continuing her exercises to rebuild strength and mobility in her knee. She’s getting along fine with her cane, and has pretty full mobility inside the house and out in the yard. She’s not doing stairs yet, but I suspect she’ll begin doing that before long. We went to the grocery store yesterday, and she was able to cruise up and down the aisles picking out items.

I’m still working hard on the biology book, including a lot of re-write to take into account the change from monochrome images to full-color. The fact that the book is now full-color means that it’ll be a lot more illustrated than it would have been, because I can now use images where it would have made no sense to do before. For example, when we’re doing Gram staining, the original draft had no image because showing a monochrome image of Gram+ and Gram- bacteria was useless. (“The violet-stained Gram+ bacteria are visible in Figure 3-8 as gray, and the pink-stained Gram- bacteria as … gray.” or “The green chloroplasts are visible in Figure 4-12 as … gray dots.”)

Monday, 17 October 2011

09:27 – Someone emailed me yesterday to say that Europe wouldn’t have to inflate the euro because the EU €440 billion bailout fund could cover any shortfalls. Where to begin?

First, the ESFS €440 billion reserves aren’t really €440 billion. After accounting for monies already allocated to Greece, Ireland, and Portugal, they’re actually under €300 billion. And that only potentially. Second, the size of the fund is sufficient to cover only a small percentage–less than 10%–of at-risk EU sovereign debt. Third, this so-called fund exists only on paper. There aren’t stacks of gold bars in a vault somewhere. The EFSF has the right to issue bonds–to borrow, in other words–to make up that €440 billion total. And investors are not lending to Europe now, or for the foreseeable future. Even if they were, they sure wouldn’t be buying EFSF bonds. Why? Because those bonds are backed in large part by the sovereign economies they’re intended to bail out. It’s true. Spain and Italy, both on the brink of default, are major guarantors of the EFSF bonds. As are Belgium and France, both of which are little better off than Spain or Italy. None of these nations can pay their own bills, let alone someone else’s. That leaves the FANG nations, none of whom are willing to pay off the bad debt of the rest of the EU. So, while the EU authorities talk about building a bazooka to firewall Spain and Italy, what they have right now is barely a firecracker. And no prospect of getting anything bigger.

Barbara is recovering very well, better than anyone could have expected. She just showered by herself, using the walker frame in the shower for stability. Which, oddly, made me think of Steve Jobs, that supposed marketing genius. Barbara mentioned that she’d shaved her underarms and legs, which made me think of a true marketing genius, King Gillette. His primary market, men, was saturated, but Gillette wanted to sell more razor blades. So, in a stroke of genius, he somehow convinced American women that leg and underarm hair was undesirable. Were it not for his times, he’d probably also have gone after their pubic hair. To this day probably 98%+ of American women shave their legs and underarms, and no small number shave their pubic hair as well.

13:44 – I see that Greece is almost shut down, and this before the 2-day general strike that’s set for Wednesday and Thursday. The unions can protest and riot all they want, but that won’t change anything. Just to be clear, no one, and I mean no one, other than the Greeks themselves, is even slightly concerned about “saving” Greece. Greece is unsalvageable, and everyone is fully aware of that, including many Greeks.

The fundamental problem is that Greece is not even remotely competitive with first-world economies, including the northern tier euro nations. For the last decade or more, Greeks have enjoyed a standard of living similar to those of the citizens of Germany, Holland, and the other productive northern-tier nations, while producing only enough to enjoy half that standard of living. In reality, Greece is a third-world nation that’s been living as a first-world nation on borrowed money. So, assuming that Greece is able to maintain its current productivity, for the next ten years or more it’s going to have to get used to tightening its belt. And not just to half the previous level, but to more like a quarter. Once Greece defaults, it will be left to its own devices. And the unions will just have to get used to that.

Sunday, 16 October 2011

10:18 – It would be amusing if it weren’t so disastrous. Back in late July, the EU authorities announced after the crisis meeting that Greek bondholders would have to take a “voluntary” 21% “haircut” (read writedown). That number has been climbing steadily recently, first to 33%, then 50%, now 60%. The reality, of course, is that there’s nothing voluntary about it. One cannot get blood from a stone. And, when the dust settles, the actual writedown is likely to be nearer 90% than 60%. Call it $450 billion, just on tiny Greece. And that’s assuming a “structured” or “organized” default. If Greece declares full default, which is not at all unlikely, the writedown will be 100%.

That’s what the EU is struggling desperately to avoid. They’ll do anything, including spending trillions of dollars of IMF (read US) money, as long as they don’t have to spend their own money. The problem is that when Greece formally defaults, holders of Greek debt, including European banks, will have to write down that debt to face actual value, which is to say nothing. Right now, they’re all carrying those worthless Greek bonds at full face value on their balance sheets. If they’d already written down the bonds to current face value, every bank in Europe would be bankrupt. Which, of course, means that every bank in Europe is actually bankrupt right now.

But it gets worse. A lot worse. When Greece defaults, investors’ attentions will immediately turn to the next dominoes, Portugal, Ireland, Spain and Italy. Those four countries are already bankrupt or nearly so as far as investors are concerned. The market won’t lend to Portugal or Ireland at all, and even with the ECB buying Spanish and Italian bonds to keep yields down, the yields on those bonds are now approaching the levels they reached before the ECB began to intervene. (Italian bonds were at 5.71% the last I looked, just short of the 6% panic level.)

Spain and Italy both need to sell tens of billions worth of bonds between now and the end of the year, just to roll-over maturing debt. When Greece defaults, selling those Spanish and Italian bonds will go from almost impossible to utterly impossible. Spain and Italy will be locked out of the markets, and will have no way to pay interest on current bonds, let alone redeem maturing bonds. In other words, they will default. And, although many have spoken of this as a domino effect, in reality what will happen more resembles an avalanche. As that tiny Greek snowball rolling downhill gains momentum and mass, it’ll take the rest of the EU economies down with it.

Of course, the EU does have one remaining solution. The ECB can simply print a boatload of new euros. And I mean “boatload” literally. They’ll have to print many trillions of new euros. Enough new euros to reduce the actual value of outstanding sovereign debt to a small fraction of what it is now. Right now, one euro buys about $1.35. To make EU sovereign debt sustainable, particularly among the PIIGS nations, the ECB would have to print enough new euros to reduce that exchange rate to one euro buying about $0.25, if not less. The result of that would be widespread defaults in all but name, as sovereign debts were paid off at $0.20 on the dollar. The standard of living throughout the EU would decline dramatically, but that’s going to happen one way or another. The euro is nothing but a gigantic bubble, and all bubbles eventually burst. Not that I’m suggesting massive inflation, which is the worst possible solution. But I think political realities mean it will be the only possible solution.

Saturday, 15 October 2011

11:43 – This guy makes a pretty good argument on why he expects Greece to default on 28 October. Of course, the Greek government hasn’t yet gotten its grubby little hands on the final bailout payment, so that may give them pause. But it’s not like the EU/ECB/IMF are actually handing over suitcases full of euros, so the reality is that the Greek government really doesn’t get its hands on bailout payments anyway.

As things stand, the Greek government has no intention of ever repaying any of the money it owes other than in the sense of paying back a little bit to get a lot more. And everyone else is fully aware of this. If the EU/ECB/IMF actually does pay the last tranche, it’s only to prop up Greece for a few weeks longer, buying time for them to do what they can to prevent the inevitable Greek default from starting the row of dominoes falling. At this point, that’s pretty much a foregone conclusion, with Portugal and Ireland toppling soon after Greece, followed soon after by Spain, Italy, Belgium, France, and, eventually, Germany itself. I just hope the UK, US, Canada, and other first-world economies can minimize the damage to themselves.

In writing our books, we try very hard to keep the costs of doing home science as low as possible. That means using cheap or free items as much as possible, rather than requiring purchased items. But I’m going to make an exception for the series of lab sessions I’m working on now, which are on culturing bacteria. I’ve done these labs in the past. I used environmental bacteria, but then I’m not an inexperienced high-school student. The risks of culturing environment bacteria, particularly at room temperature, are pretty minimal, but not non-existent. A dropped Petri dish, for example, could put large numbers of pathogenic bacteria into the air.

So I decided to specify a purchased culture of bacteria intended for use by students. There are still minor risks involved, but they’re much smaller than those of culturing unknown bacteria. I’m going to specify a mixed broth culture from Carolina Biological Supply. It’s $17 plus shipping, but it contains three types of bacteria that are useful for learning purposes, and it’d be pretty hard to get into trouble with them.

The three bacteria are Bacillus subtilis (Gram+ rod), Micrococcus luteus (Gram+ sphere), and Rhodospirillum rubrum (Gram- spiral), which gives us all three bacterial shapes and both Gram types. They’re also large enough to be visible without an oil-immersion objective, and they form colonies that are easy to discriminate visually from each other. Finally, they’re reasonably robust, pretty easy to culture on standard nutrient agar or in nutrient broth, and grow reasonably well at room temperature.

We’ll use these bacteria over the course of several sessions. We’ll do a standard agar plate culture to grow and identify colonies of each of the three species. We’ll isolate each of the three and grow pure cultures in broth. We’ll then reculture on agar to grow bacterial “lawns” of each of the pure cultures. Finally, we’ll test the susceptibility of each species to various antibiotics. We may also re-culture resistant bacteria repeatedly to produce a resistant strain.

We don’t want anyone to have to re-purchase the mixed culture because the first one died off, so we’ll probably also experiment with re-culturing in refrigerated nutrient broth and/or phosphate-buffered saline to maintain a live culture over the course of several weeks. I haven’t done this with these species, so I’ll order one of these mixed culture tubes from Carolina to run that part of the procedure myself.

Friday, 14 October 2011

09:22 – Here’s the working cover that we’ll use for marketing materials and so on.

Mark Paglietti, the cover designer, commented, “Far be it from me to suggest filling in some white space, but there is a huge hole in the middle that could use some additional items… But, it works fine for our immediate purposes.” I was trying to come up with something to fill in that white space. I thought maybe a hand-drawn and labeled DNA molecule would be a decent background when it finally hit me. Duh.

My actual microscope workstation is a large desk that makes an “L” with my main office desk. Sitting at the back of that microscope desk is a wooden shelf organizer that’s full of bottles of stains and other reagents, spare slides and coverslips, a microtome, and other microscope accessories. So I just shot a quick image of that to send to Mark and Brian to ask what they think. If they agree, I’ll set up that organizer as a background for the microscope and other stuff in the current image, positioned to leave white space for the “Includes” column down the left side.

11:09 – Someone asked me what’s in the tubes stoppered with cotton balls. They’re broth culturing tubes. Ordinarily, they’d contain some sort of nutrient broth, such as LB or diluted beef broth with sucrose or glucose added. In this case, they contain a special culturing broth made up of tap water to which I added five drops of red food coloring and one drop of green. The advantage is that it doesn’t need to be autoclaved; the disadvantage is that nothing actually grows in it.

Barbara went out on the front porch for a few minutes after dinner last night. While we were out there, Melissa and her husband drove by and waved. She was about due to have her baby, so I walked down to see if she’d had it yet. She did, on October 5th, a little girl to go with her pair of very active little boys. I was quite proud of myself because I went through a mental checklist of things women always want to know about new babies. Name? Scarlet Gray. Check. Sex? Female. Check. Dimensions? 6’8″ and 18 pounds. Check. (When I told Barbara, she said it was highly likely that I’d confused the dimensions, which she thought were probably 6 lb. 8 oz. and 18 inches.)

While I was standing talking with Melissa, she asked what I was up to with the biology book. (She’s a biologist.) I told her I was working on a group of lab sessions on bacteria culturing, and the conversation went something like this:

Her: Oh, what species are you culturing?

Me: I have no idea.

Her: Well, where did you buy them?

Me: I didn’t buy them. I just used environmental bacteria.

Her: (horrified) So you have no idea what you’re growing?

Me: No, other than from the color and morphology of the colonies. I have one that’s a beautiful golden yellow color. (implying that I might have a colony of S. aureus, a dangerous human pathogen.)

Her: Well, you better dispose of those carefully.

Me: Sure, but before I do that I’m going to use them in some other lab sessions. I want to use natural (forced) selection to develop a multidrug-resistant strain by repeated culturing of the survivors in a broth with antibiotics added.

Her: (really horrified) Which antibiotics?

Me: Well, obviously, amoxicillin, tetracycline, ciprofloxacin, sulfamethoxazole, metronidazole, and all the other mainstream antibiotics. I also have some vancomycin, linezolid, and daptomycin, so I’m wondering if I can develop a strain that’s immune to all known antibiotics, including the last-ditch ones.

Her: (speechless)

I finally told her that I was practicing my straight face, and that, no, I wasn’t going to breed multidrug-resistant pathogens. I actually expected her to hit me (women do that a lot), but she just seemed relieved.

And, speaking of saying outrageous things with a straight face, Mary Chervenak told me that if there was anything at all she could do to help while Barbara was recovering just to say the word. I was going to tell Mary with a straight face that I really needed her to clean our house. Fortunately, I have a finely-honed survival instinct. I feared Mary’s Fist of Death even when she was on the other side of the planet during her run around the world, so I’m certainly not going to risk the FoD when I’m standing face-to-face with her.

Actually, that’s not fair to Mary. If she really thought I was serious, I have no doubt that she’d come over here and clean house for us. Wearing a respirator, because she’s deathly allergic to dogs.

Thursday, 13 October 2011

09:43 – Barbara continues to do very well. She’s using my four-footed cane now, other than when I use it while walking Colin or while she’s taking a shower, when she uses the walker frame. She came back to bed around 0600 this morning. I guess sleeping on the sofa is getting old. The only reason that concerns me is that we have a 25+ kilo puppy that loves to jump on people.

Brian Jepson, my editor at O’Reilly, emailed me to ask if I had an image suitable for dummying up a cover. I told him I didn’t have anything suitable, and suggested they might use a stock photo until I have time to shoot a real cover image. That needs to be portrait orientation, with a white background and items placed to take text placement into account. I’m not sure what I’ll include in that image to suggest “biology”. A microscope, certainly. Maybe a test tube rack with some test tubes stoppered with cotton balls, perhaps a couple 50 mL centrifuge tubes hand labeled and with some leaves and chlorophyll extract in them. Some dropper bottles of stains and other reagents. Perhaps a box of microscope slides and a couple of Petri dishes. I’ll work it out, I guess. If I’m going to go to the trouble of setting this up, I’m not going to do it to shoot a dummy image. I’ll shoot real cover image candidates, which means devoting some time to it.

12:46 – Here’s what I just sent Brian as a first sample. I shot it handheld and without paying any attention to lighting or color balance, but I wanted to give him and the cover designer some idea of the “stuff” we could include in the actual cover image. Obviously, there’s way too much stuff, and I paid zero attention to composition for leaving areas clear for text. But at least this gives us a starting point to get a real cover image put together.

Wednesday, 12 October 2011

10:05 – Colin is really a Fearsome Predator now. This morning, he caught a chipmunk. Six times. The first time, the chipmunk froze. Colin pounced on it, and came up with it in his mouth. I shouted, “Drop it!” and he did, whereupon the chipmunk ran for its life. Colin gave it a headstart (seriously) and then overran it in about five steps, again coming up with it in his mouth. Again, he dropped it and it ran under a pile of leaves. He grabbed it again. This went on until he’d grabbed it six times. I’ve heard it said that Border Collies have had all the kill instinct bred out of them, and it’s obviously true. Despite the fact that he had it in his fangs repeatedly, he never bit down on it. The last time he dropped it, the chipmunk staggered away slowly and I dragged Colin away from it. I hope the chipmunk was just stunned rather than injured, but I’ll go out and look for it later.

Barbara is doing extremely well. This morning, she tried using my four-footed cane, which I need only for balance, particularly at night. I’ll borrow it back when I take Colin for a walk, but otherwise she’s welcome to use it. She’s still sleeping on the sofa, and will keep the walker frame for use at night if she needs to get up and also as a physical barrier to keep Colin from jumping up on her.

I just officially transferred my Kindle to Barbara. I connected it via USB and deleted dozens of titles I knew she wouldn’t want to read, but that still left her with 140 titles to sort through and decide whether or not she wants them. Most of those are free or $0.99 ebooks that I downloaded from Amazon because they sounded like something she might like. If she finds some authors/series that she enjoys we’ll buy the rest of the titles in that series, assuming they’re not outrageously priced.

Overall, I think the Kindle is nearly perfect. The exception is that its file management sucks dead lifeforms through a small tubular object. The fundamental problem is that Kindle uses a flat file structure unless you use its incredibly awkward organization tools. I should be able to create a directory structure on my hard drive and copy individual titles into that directory structure. If I then copy that directory structure to the Kindle, the directories should show up as top-level categories that contain the individual books. It doesn’t work that way. If, for example, I create a directory called “Downie, Ruth”, copy her four Medicus books into it, and then copy that directory to the Kindle, the four books show up as individual titles at the top level. In order to categorize them, I have to create a category named “Downie, Ruth” (or whatever) with the Kindle’s tiny little keyboard, go find each book, and manually transfer it to the new category. That takes lots of keystrokes and lots of time. It sucks. Nor is calibre any help. I can use it to organize the titles with no problem, but according to the calibre docs, Kindle makes no provision for transferring that organized structure via USB. The only consolation is that the Nook is just as suckful. Apparently, the only company that gets it is Sony, whose ebook readers support transferring organized structures. Still, I’ll never buy a Sony product, so there’s no use worrying about it.

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