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Category: writing

Saturday, 29 October 2011

10:04 – Barbara continues to improve. She’s even taking Colin for short walks down the block and yesterday while I wasn’t looking she rolled the trash cart back down the driveway. She goes to the doctor next week for a follow-up visit, and I suspect he’ll approve her to drive again and return to work. She’s going stir-crazy here. Of course, Colin is going to be a problem because he’s now used to having her home all day every day.

Yesterday I finished up the group of lab sessions on microorganisms and started on a group of lab sessions on genetics. Right now, I’m working on a lab about Mendelian traits and inheritance. There are actually relatively few pure Mendelian traits in humans, but one of them is a classic. The ability to taste phenylthiocarbamide.

Fortunately, I also did a self-sanity check. Beginning biology students often make the false assumption that dominant and recessive Mendelian traits correlate to the percentages of individuals in a population that exhibit the dominant and recessive phenotypes. In other words, a high percentage of individuals exhibit the dominant phenotype and a much small percentage the recessive phenotype. A moment’s thought establishes that’s not the case, at least for anyone who’s aware that Huntington’s disease is a dominant Mendelian trait.

But I made that exact false assumption with regard to Colin and his prick ears, assuming that floppy ears in dogs are Mendelian dominant and prick ears recessive. In fact, floppy ears are a recessive Mendelian trait. The fact that probably only one in ten thousand Border Collies has prick ears doesn’t indicate that prick ears are recessive, but merely that Border Collie breeders have selectively bred a population of Border Collies that are almost entirely recessive with respect to ear conformation. (Not that they were selecting for ear type specifically, but sometimes something you don’t care about one way or the other is part of the package that you’re breeding for.)

Now the only problem is that I don’t remember either Colin’s mother or father having prick ears. Hmmm.

10:42 – Duncan was a giant among Border Collies, standing about 4″ (10 cm) taller than other large males and weighing half again as much despite the fact that there was no fat on him. When Duncan was two or three years old, we took him to a Carolina Border Collie Rescue event held at a farm owned by one of the volunteers. There was a large open field and a herd of about 100 Border Collies running around in it. We could pick out Duncan instantly because he towered above all of the other BCs, except one who was even larger than he was. (Despite the fact that Duncan was registered purebred, we always suspected that he might have some English Shepherd in his bloodlines.)

Barbara just got out a photo of Duncan standing on our front porch that showed the line of his back was at the line of mortar above the seventh row of bricks. She then took Colin out on the front porch while I stood back to see the level of his back relative to the bricks. At eight months old, Colin is already taller than Duncan was as an adult. He’s going to be a very big boy.

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Friday, 28 October 2011

08:48 – One thing that’s always struck me as strange about Netflix practices is that they don’t allow non-members to browse or search their catalog. One would think they’d want non-members to be able to see what they’re missing.

I just downgraded our plan from streaming + two discs to streaming-only, which took effect Wednesday. With the exception of the final disc of series four of Sons of Anarchy, there was nothing left in our disc queue that we cared that much about seeing, so I planned to go streaming-only for a few months to give Netflix a chance to add more discs that we wanted to watch and then bump up our membership to include discs. But, as of yesterday, I can no longer see anything that has to do with discs. Our disc queue is now invisible, although I understand that Netflix keeps it archived for two years. Not that that matters, since I did a screen capture of it before I changed to streaming-only.

But I can no longer search for discs, nor do search results even include series or seasons that are available only on disc. For example, series one and two of Sons of Anarchy are available on disc or streaming, but series three is disc-only. When I search for Sons of Anarchy now, all I see are the two seasons that are available streaming. Not even an indication that series three is available on-disc.

Given that Netflix is trying very hard to force people toward streaming, I wonder if the converse is true. If I had a disc-only plan, would they let me see what’s available streaming even though I couldn’t watch it? It seems to make sense for them to do that.

Actually, Netflix has made things easier for me. Rather than keeping an eye on new disc-only material, I’ll just wait six months or so and then upgrade our plan to include discs. There certainly ought to be at least a month’s worth of new discs we want to watch by then. Not that we’ll have to wait six months to see the last two episodes of Sons of Anarchy S3. Our friends Paul and Mary subscribe to both discs and streaming, and they tend to let discs sit around for extended periods. I asked Mary the other day if she’d mind getting SoA S3D4 for me, and she readily agreed.

Work on the biology book continues. Right now, I’m working on a lab session on culturing drug-resistant bacteria. Once I finish that session, I think I’ll jump over to a different group for a change of pace, maybe the genetics group or the life processes group. Or maybe even one of the survey groups. I’m also down perilously low in chemistry kit inventory, so soon I’ll have to set aside a day or so to build more chemistry kits.

14:55 – Well, that didn’t take long. In the first real test of the “solutions” reached at the EU crisis conclave Thursday morning, Italy has failed miserably on today’s bond sale. The yield was catastrophic, 6.06%, and Italy was unable to sell all of the bonds it offered. To knowledgeable observers, that’s sufficient evidence to declare the latest crisis summit a complete and utter failure. Not only did the non-actions taken at the summit not reverse the collapse of EU finances, they appear not to have even slowed things down. Contagion continues, unabated.

Of course, none of this crisis kabuki really had anything to do with Greece and not much more to do with the euro or the EU. What it’s really about is an attempt to shore things up until Merkozy can get past the next elections–not that either of them has much chance of being re-elected–and, even more importantly, the continuing push by the EU elite for “more Europe”. They’re actually loving this financial/debt/liquidity crisis, because it supports their long-term anti-democratic plans to consolidate Europe as a single political entity, ruled by them. Fortunately, I believe the FANG nations will refuse to go along with their cunning plan, leaving eurocrats holding the empty bag of the southern-tier nations only. Let them see what they can do with that motley collection.

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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.”)

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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.

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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.


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Saturday, 8 October 2011

09:37 – Our friends Mary and Paul dropped by for a visit yesterday evening. I asked them if they were attending the sunrise service this morning. They both use iPhones and iPods, you see, and this morning is the third day. Steve is risen.

Paul has drunk the Kool-Aid more than Mary, I think. He commented that he liked his iPhone, but he really liked his iPod. Where else, he asked, could one get a pocket-size music player? Barbara and I pointed out that she had one connected to her car audio system right now, a Sansa model. Yes, he said, but where can you get music to load on it? Barbara pointed out that she had several thousand tracks converted to MP3 that she’d ripped from her CDs, about a thousand of which were on her Sansa player at the moment. I added that if he wanted to buy music on-line he could visit Amazon, which has a huge selection with often better prices, and has never had copy protection.

I really don’t understand all the eulogizing. Not only did Jobs never do anything to help the advance of personal technology; much of what he did hurt it. He went from selling overpriced, underpowered PCs to selling overpriced music players and tracks to selling overpriced cellphones. Everything he ever did was aimed at pillaging his customers’ wallets and locking them into his “walled garden”. And, no, I haven’t forgotten the Apple ][, which deserves at best an asterisk in PC history.

Laundry this morning, with work interspersed on the biology lab book. Right now, I’m working on the chapter on cells and unicellular organisms. I’m just starting a session on making culturing media and filling Petri dishes and slant tubes with agar gel medium and test tubes with broth medium. We’ll use the Petri dishes in the following session to culture bacteria, after which we’ll isolate selected species and grow pure cultures of them in slant tubes and eventually broth tubes. We’ll then flood Petri dishes with broth culture to grow bacterial “lawns”, which can then be used for antibiotic sensitivity testing.

I’ve thought seriously about recommending that readers avoid culturing environmental bacteria and instead purchase pure cultures of known-harmless bacteria from Carolina Biological Supply or wherever. The issue is that there are a lot of pathogenic bacteria floating around in the wild. Ordinarily, they’re harmless, because our bodies defenses can deal with small numbers of them. But culturing them produces large numbers of them, so one must take care to avoid being exposed to them. With proper technique, the danger is nearly non-existent, but some danger does still exist. We’ll minimize that by using a simple beef or chicken broth and sucrose nutrient mixture and culturing at room temperature rather than body temperature. Those factors favor growth of bacteria that prefer the lower temperature, which is to say not most pathogens.

Of course, we’ll subsequently be using forced selection to breed antibiotic-resistant bacteria from those original cultures, and if you don’t want wild pathogens floating around the room, you really don’t want drug-resistant wild pathogens floating free. Of course, we could temper that risk by using antibiotics that are not usually used in humans, such as neomycin, sulfadimethoxine, and so on. We can also take steps to minimize exposure risk, including wearing an N100 mask, misting the area with Lysol spray and so on. On balance, I think I’ll do the lab with environmental bacteria, but warn readers that for complete safety they should purchase a known-harmless culture as their starting point.

Colin is still very much a puppy. Barbara had dinner out yesterday, so I made myself a bowl of tuna shock. Except that I didn’t have any tuna or any shock, so I just put a can of olives (less the can and lid) and a can of Costco chicken chunks (less the can and lid) in a big bowl and then added a large glop of mayonnaise. I’d eaten about a third of it when the doorbell rang. I got up to answer it, first warning Colin not to touch my food. When I got back a moment later, he had his snout in my bowl. Fortunately, he hadn’t eaten much of it, so I finished the rest.

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Tuesday, 4 October 2011

08:25 – Barbara had another scare last night, when her sister called to tell her that she was taking their mom to the emergency room. She’d hurt her leg that afternoon while volunteering at the hospital, and of course at her age there’s always concern about broken bones. All turned out happily, though. Barbara’s mom had only sprained her knee. The emergency room docs put a brace on it and allowed her to return home.

I got email last night from my editor, Brian Jepson, with great news. O’Reilly has decided to do the biology book in four-color. Every book has a budget, based on expected production costs and projected sales. The only way Brian had been able to get this book approved originally was to put tight limits on page count (extra pages cost money) and printing costs (four-color costs a lot more money). So we went into the project with a strict page-count limit and a center section of full-color plates. Before long, I asked Brian if I could trade the color section for more page count, to which he agreed. I really didn’t want to give up color images completely, but I really needed the extra page count.

But apparently the cost of four-color printing has come down somewhat, and Brian said that when he was discussing things with his colleagues they commented that it makes no sense to do a biology lab book with monochrome images. I suspect the sales history of the chemistry lab book also might have had something to do with it. That book is what publishers call an “evergreen” title. That is, it continues selling steadily for many years. That’s in stark contrast to most titles, which sell 90% or even 99% of their total lifetime sales within a few months of publication. The biology lab book should have a similar sales trajectory to the chemistry lab book

10:15 – I just checked my Netflix disc queue and found that there isn’t much disc-only material that we care about. When I upgraded a couple weeks ago from streaming + one-disc to streaming + two-disc, our disc queue was jammed with 30 or 40 discs that we wanted, most of which are series that Barbara likes and that were initially disc-only. Several of those quickly changed to add streaming, including the most recent seasons available of Army Wives, Brothers & Sisters, and Grey’s Anatomy. As soon as that happened, I pulled them from our disc queue and added them to our instant queue. So we’ve gone from 30 or 40 discs we want down to four Sons of Anarchy S3 discs and a handful of others.

Meanwhile our instant queue now totals 94 items, including a dozen or more series that between them total hundreds of episodes. We are not, to put it mildly, short of things to watch, even without discs, particularly since Netflix is adding more streaming titles every day. Our anniversary date is the 26th of the month, so in three weeks I’m going to downgrade our plan to the $8/month streaming only option. We’ll do without discs for the next few months while we catch up on streaming material, if we ever do. Once there are a reasonable number of disc-only titles we want, I’ll bump it back up to include discs for a month or three and then drop back to streaming-only.

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Monday, 3 October 2011

10:25 – The first weekday of what may be Black October. Or, perhaps more fittingly, Red October.

Greece is near collapse. Not just the economy; the country itself. Greece did not meet the requirements of the troika, so if the troika auditors follow their own rules they will recommend against releasing the final tranche of the 2010 bailout. Most people, including me, think they’ll ignore their own rules and release the final tranche just to stave off collapse for a few (or a couple) more weeks. If it were up to the EU and the ECB, that tranche would be released, period. But the IMF also has a vote, and it’s possible the IMF will stick to the rules. If so, Greece will default within days; if not, it may be a few more weeks. But it’s as certain as can be that Greece will default by the end of this year.

Several weeks ago, I mentioned rumors that Germany was already printing Deutsche Marks, and I’ve since heard the same rumor from several independent sources. It’s hard to keep something like that quiet. The current rumors say that Germany has placed a rush order with the printers, presumably to make sure it has new notes available when Greece defaults. Of course, that doesn’t mean that Germany will leave the euro, at least not immediately. This may be simply a contingency plan. But, contingency plan or not, I expect to see Germany re-introduce the DM sometime within the next few months, if not weeks. I don’t think there’ll be much choice.

I’m still working hard on the biology lab book. I have a couple of dozen lab sessions complete, other than images, with many more in progress. I’m getting more worried about sticking to my page count budget, but at this point I’m just continuing to add new lab sessions, and sometimes expand existing ones. By the time we get to 100% completion (scheduled for 31 December), I’ll probably have more lab sessions than we have room for in the book. If so, I’ll probably self-publish them as a supplemental set.

I also need to run or re-run some lab sessions to verify things. For example, yesterday I finished writing the lab session on extracting, isolating, and visualizing DNA. I’ve done that lab many times before, but always using 95% ethanol or 99% isopropanol. So the lab session is currently written using 95% ethanol, but I want to see how (and if) it works using 70% ethanol or 70% isopropanol, both of which are cheaper and easier to find than the 95%/99% varieties. The potential problem is that DNA is relatively soluble in water, but extremely insoluble in pure ethanol or isopropanol. During the isolation phase, one gently pours alcohol into the test tube that contains the aqueous DNA solution. That alcohol forms a layer on top of the aqueous layer, and DNA precipitates out at the boundary layer. If the alcohol contains significant water, I’m not sure how well that precipitation and the subsequent spooling of the DNA goop will work.

I could just specify 95% ethanol or 99% isopropanol, but I want to make it as easy and inexpensive as possible for readers to do the labs. So I’ll spend some time checking.

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Sunday, 2 October 2011

10:04 – It’s a standard Sunday around here, and most certainly cooler than usual this time of year. We finally turned on the central heat, because it was down to 66F (19C) in the house, and falling. The high today is to be 59F (15C) and the low tonight 41F (5C), so it’d get a bit chilly in here without the furnace running. I fired up the gas logs to test them. As expected, they burned for a couple minutes and then went out. Time to blow out the oxygen sensor with canned air.

Barbara and Colin are out in the yard blowing leaves and enjoying the cool weather outdoors. I’m working on a couple lab sessions about extracting and visualizing DNA and doing gel electrophoresis, enjoying the warmer weather indoors.

12:04 – This article summarizes the current euro situation pretty well. In short, no matter how bad you think it is, it’s actually far, far worse. If anything, I think the article is overly optimistic. I don’t think we have months left before the crash. We may not have weeks.

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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.

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