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Category: dogs

Tuesday, 10 January 2012

08:00 – With three weeks until deadline, I’m in the home stretch on the biology book now. I’ve allocated the rest of this week to finishing up two lab sessions that are now in progress, one the vertebrate survey and the other about the life cycle (cell division/mitosis). Once those are complete, I’ll spend a few days doing a quick run-through of all the lab session chapters, cleaning them up and making them consistent before I send them off to reviewers. Then I’ll finish up the Preface and Introduction chapters and start incorporating comments from the editors.

Someone on the Well-Trained Minds forums posted a query yesterday about scanning her old color negatives to produce digital image files. She’d found the Epson Perfection V300 Photo Scanner on Amazon.com for $80 and asked if that would do what she needed. My old Epson 3450 scanner died some time ago, and I’ve had replacing it on my to-do list since then. I checked and found that the V300 is Linux-compatible, so I replied and told her that I’d just ordered one and if she wanted to hold off for a while I’d test it by scanning some of our old color negatives and let her know how it worked.

Barbara is mad at me because of my reaction to a story in the newspaper this morning. Apparently, she was talking about it with her friends at work yesterday. Some woman couldn’t find her dog, so she went and looked in her neighbor’s window–which I’m sure is what any of us would do if we couldn’t find our dogs–and saw him having sex with the dog. They got a DNA sample from the dog, which they had a vet analyze. The DNA matched, so they arrested the guy. When Barbara told me what had happened, I started to laugh. She was not amused. “This isn’t funny!”, she said. “It’s disgusting.” The more I laughed, the more trouble I was in. Must be a girl thing.

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Tuesday, 3 January 2012

08:00 – I see that a jogger in Chicago was savagely attacked by two pit bulls, which persisted in their attack despite the attempts of a bystander to drive them off with a baseball bat. The cops eventually shot the dogs. What surprised me was that the article mentioned that this was not normal pit bull behavior, and that the dogs must have been abused.

Pit bulls have a horrible reputation, of course, but the truth is that they’re normally sweet, gentle dogs, at least toward people. Pit bulls were bred to fight other dogs, and I would never trust a pit bull around other dogs. But they were also bred to remove any aggressiveness whatsoever toward humans. That was crucial for the safety of the handlers, who had to handle dogs coming out of the pits after fights, when they were injured. Any dog who showed even the slightest aggressiveness toward humans, even if the dog was injured, was ruthlessly culled.

I’m still working heads down on the vertebrates chapter. I’d planned to do a lab session on animal behavior using a couple of mice. Barbara says she won’t have any mice around here. I offered to give them to Colin to play with afterwards, but she still says no deal.

Not that Colin would hurt the mice. I remember the time Duncan caught a chipmunk out in the yard. It had strayed too far from its burrow, and Duncan pounced. He came up with the chipmunk in his mouth and pranced around for a while, showing off his prey. I yelled at him to let the chipmunk go and–I am not making this up–he carried it back over to its burrow and dropped it. At first I thought it was dead because it didn’t move, but apparently it was just stunned. Duncan snouted it towards its burrow a couple of times and it finally woke up and scampered into its burrow. My best guess is that Duncan considered the chipmunk to be a very small sheep.

13:38 – I’m sure all of us are eagerly awaiting the results from Iowa. There’s one thing I don’t understand, though. According to all the political commentators, Iowa is so important that if Romney wins it’s game over for Paul and the rest of the Republican hopefuls. But if Paul wins, which seems about equally likely from all the polls, it doesn’t matter. Huh? A little biased, are we?

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Monday, 2 January 2012

08:50 – I sent off the chapter on arthropods yesterday and got a good start on chordates, although I decided to change the focus from chordates to vertebrates. Right now, I’m shooting lots of photomicrographs. I’m using lots of images to minimize the need for readers to have complete sets of prepared slides. The images are not a perfect substitute for slides by any means, but they’re better than nothing, which is what many readers will have.

If I were doing this book again, I’d start by finding a high resolution video camera, say 6+ MP, and shooting video of all the slides, tweaking the focus as the video was captured. I’d then use stacking software to build composite images to eliminate depth of field problems. Of course, that would have added a lot more work, both in the shooting and the processing. Even on a fast six-core system with gobs of memory, processing a large stack of high resolution images into the composite could require many hours of processing per image.

After nine days at home, Barbara just headed back to work. Colin, of course, is now used to having her at home, which means he’s likely to be demonic for the next few days. He’s sitting outside my office door whining right now. I’m taking that as a warning.

The good news is that Colin may get to see snow before much longer. We’ve had shirt-sleeve weather for a couple of weeks, but the high today is to be only 41 °F (5 °C), with the low tonight 23° (-5°) and the high tomorrow 35° (2°). There’s supposedly a 10% chance of some snow tonight. It’s always fun to watch a puppy experiencing snow for the first time. They all instinctively spread their toes, making what Barbara and I call “snow paws”, to get better traction and avoid sinking into the snow. Then, when they come back indoors, they lie there chewing and spitting on their paws to get the ice out from between their toes.

Someone at the house down on the corner just called 911 for the second time in about a week. An elderly woman lives there with (I think) her grandson, who’s maybe 12 years old. According to the neighbors, the kid is a perv. I’m not sure if he’s officially a sex offender or what exactly he’s accused of doing. Something like exposing himself to little girls, I think. At any rate, the fire truck just showed up, followed in quick succession by the police and ambulance. Last time, I waited until the ambulance hauled her off. Jasmine told me later that she has severe asthma, so presumably that’s what caused the 911 call this morning as well.

That got me wondering how (or if) 911 calls are billed by the city. Does each person get a certain number of free 911 calls per year with additional calls being charged for? It seems strange to bill for emergency calls if there’s a true emergency, but on the other hand I know that 911 is often abused. So do the fire department and police and ambulance just keep responding to frequent calls from one home, or do they start charging after X number? Or do they judge whether a reasonable lay-person would have considered the problem to be an emergency worth calling 911 for? I would imagine they have to show up no matter what, given the potential consequences, not to mention lawsuits and bad publicity. But there has to be some kind of boy-who-cried-wolf option for declining service to serial 911 abusers, doesn’t there?

09:44 – We’ve had some discussion here recently about free will and my arguments that it does not exist. Jerry Coyne has an interesting post up this morning, which links to his full article in USA Today. If you still believe that free will exists, which of course you must if you’re a Christian, read this article and think about it.

14:19 – Also found on Jerry Coyne’s site: a baby Linux getting a tummy rub.

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Friday, 30 December 2011

08:23 – Barbara picked up some new “tennis balls” for Colin at the pet store the other day. Boy, I wish these had been around when I was playing tennis. They look just like standard tennis balls, but they aren’t. A standard tennis ball weighs 2 ounces (58 g) and, when dropped onto concrete from a height of 100 inches (2.54 meters), bounces about 60 inches (1.5 meters). These “tennis balls” weigh 3.7 ounces (105 g). I didn’t actually test the bounce, but I’d guess that if I dropped one onto concrete from 100 inches it’d bounce about 2 inches (5 cm). With no bounce to speak of, a hard flat serve would come up only a few inches from the court surface by the time it hit the fence.

Poor Colin. Now that I have a mixture of real and fake tennis balls on the foyer table, he’s never sure what to expect when we go out the front door. He always rushes two or three meters down the walk, turns, and waits for me to toss a tennis ball onto the walk so that he can pounce on it. The first time I used one of the bounceless ones, he over-pounced and it rolled under him. Once he got used to scooping bounceless ones off the walk, I switched to a regular one, which bounced over his head. Being a Border Collie, he quickly figured out that there are two different kinds of balls in play, so now he tries either to grab it in mid-air before it hits the walk or to short-hop it.

13:45 – Here’s a sensible young woman. I confess that I was only vaguely familiar with Kelly Clarkson’s name and had no idea what she does. Clarkson is taking heat for endorsing Ron Paul, whom some pretend to believe is racist, sexist, and homophobic. He’s not, of course. The only basis for these accusations are some articles that appeared in a newsletter decades ago. Paul has said repeatedly that he did not write these articles and that he never made the statements in question that were attributed to him. No one has presented any evidence whatsoever that he did write those articles or make those statements. His record as a congressman and his public statements as a presidential candidate for both the Libertarian Party and the Republican Party should be enough to convince any reasonable person that Paul has been the victim of a smear campaign. Of course, most people are not reasonable, and most of the other Republican candidates are exploiting that fact to harm Paul’s candidacy. He scares them, and rightly so. Paul has integrity, which none of the other major Republican candidates does, particularly Gingrich. Integrity? He’s heard of it.

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Monday, 19 December 2011

08:16 – All of my Saturnalia shopping is done, such as it is.

Yesterday, Barbara picked up an early Saturnalia present for Colin, not that he much likes it. It’s a snout twister collar. It has a running loop, one end of which is connected to the leash, with the loop around his snout. If he attempts to pull on the leash, it pulls down and to one side on his snout. It does indeed stop him from pulling, but it does little or nothing to stop him from leash-fanging. He grabs the leash in his fangs and works his way up the leash, usually getting it wrapped around him in a big tangle, and sometimes wrapped around me. At one point when he was much younger (and lighter), I ended up with him hanging completely airborne like a hooked fish from the handle of the leash.

Unlike all our other Border Collie pups, Colin is rather timid. Duncan and Malcolm, for example, started going up and down the stairs to the basement the first day we had them home. It took Colin weeks to get up the nerve to go up the stairs, let alone down them. If I threatened Duncan or Malcolm with a rolled-up newspaper (which I call a dog beater), they’d yap at me, look me straight in the eye, and say, “I’m not afraid of you!” Colin, conversely, cringes and pulls away.

We’ve never abused him or done more than tap his rear end with the dog beater, but sometimes Colin acts afraid of me. For example, I’ll offer him a treat and he’ll follow me to the treat jar in the kitchen. But as I’m getting the treat out of the jar, he disappears. I’ll find him at the end of the hall or in the bathroom acting as though he’s afraid I’m going to hit him. So we decided to stop using the dog beater and just speak sternly to him when we need to adjust his behavior.

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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.

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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.

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Monday, 14 November 2011

08:15 – Another Monday, which means Barbara is at work after a weekend, which means Colin is expecting me to play with him all day long. I can’t blame him for pestering constantly. He’s a nine-month-old Border Collie pup, and his priorities all involve constant work, which requires my involvement as well. If I try to ignore his requests he whimpers. If I ignore that, he starts climbing up on the arm of my chair and pawing me. If I ignore that, he takes my arm in his mouth (gently), and starts pulling me toward the front door. My only option is to use a baby gate to pen him outside my office. The problem with that is that I never know what he’ll get up to when he’s out of my sight. Usually something I don’t want him doing.

11:52 – Well, I’ve been trying to avoid this, but enough is enough. OpenOffice writer keeps hanging, and if there’s one thing I can’t tolerate while I’m writing, it’s an unreliable word processor. That was what motivated me to abandon MS Word for OOo Writer long before I converted to Linux.

My main system is old, really old. If it’s any indication, I’m currently running Ubuntu 9.04, which hasn’t been maintained for quite a while now. The system drive is a 500 GB Seagate Barracuda and the second hard drive is a 750 GB Seagate Barracuda that I installed before they were officially released. There used to be two of those 750 GB drives, as DATA_1 and DATA_2, but DATA_1 failed a couple of months ago. I should have stopped what I was doing then and built a new system, but I didn’t have time. I should stop what I’m doing now and build a new system, but I have even less time. So I’m going to nuke the current installation, run detailed scans on both drives, and (assuming they pass) re-install Linux.

The question is, which Linux? Ubuntu has gone off the rails, with Unity and Gnome 3.0. As ESR recently wrote, it’s not even worth messing with. He switched to KDE. Others have switched to Linux Mint. I think I’ll go with Kubuntu 11.10. Of course, that’s a major undertaking itself, just getting all my stuff migrated over. Don’t expect to hear from me for a while.

14:11 – I’m up on my knees at this point. I ended up pulling the original drives and replacing them with an old but unused 1.5 TB Seagate Barracuda. Kubuntu 11.10 is installed and updated, and I’m currently copying several hundred GB of data from an external backup drive. At this point, basically nothing is configured. I’m writing this in the default Kubuntu browser, which is called rekonq. I’ll install Firefox and/or Google Chrome when I get a moment. LibreOffice is installed by default, but I have a dozen or more key apps I’ll need to install before this system is really usable. Stuff like digikam, for example, not to mention one or more video-editing apps.

There are also a lot of minor annoyances to deal with. Sound isn’t working at all, for example, which is probably just a matter of finding and fixing a configuration setting somewhere in the KDE GUI. I’ll also try to find time to get my old Epson scanner working. It used to work perfectly and then one day it just stopped working. I don’t think the problem is the scanner, but just something that got borked on my increasingly cluttered Ubuntu 9.04 setup. We’ll see if a clean Kubuntu 11.10 will recognize and use the scanner.

I made a conscious decision to leave a lot of data behind. Stuff that I’ll never use again, such as hundreds of GB of raw .DV video files. When I finish transferring data, this 1.5 TB drive probably won’t be more than about half or two-thirds full. Barbara, being the thrower-away of the family, will be pleased that I, being the keeper of the family, have decided to throw out all this old stuff. We watched an episode of House, MD not long ago that featured a hoarder. During the scenes of the guy’s house, Barbara kept muttering, “Just like you…” Now, it’s true that I sometimes save things that nearly anyone would consider eminently throw-outable (such as burned out lightbulbs or dead alkaline cells), but there really is method to my madness. (In the first case, I wanted a small specimen of tungsten; in the second, I wanted to dissassemble the alkaline cells and compare them chemically to a new cell.)

Geez, I wish this copy would complete so that I could get back to writing. Once again, I’ve reorganized something. I had algae in with the Group VII lab sessions (protista), which is where they are categorized in some classification systems. But it’s equally valid to put algae in with plantae rather than protista. In fact, I think it makes more sense to do it that way, considering that grouping algae with plantae turns a polyphyletic grouping into a monophyletic one. So I moved algae into the Group IX lab sessions (plantae), immediately following Group VIII (fungi). Now if only I could start writing about them.

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Friday, 4 November 2011

08:27 – Here’s the final front cover image for the biology book. There may be a few changes to the text, but otherwise this is pretty much what it’ll look like. Thanks to Mark at O’Reilly, who took the cover image I shot and did his Photoshop magic on it to get rid of the lighting flaws and other artifacts.

About the only change I suggested other than minor tweaks to the text was the background color. The chemistry book uses blue, and I thought it was obvious that the biology book should use green. And the forensics book, once we get around to actually publishing it, should be red (or at least maroon). Physics, when we eventually do that one, should be black.

Barbara worked a full day yesterday, and was delighted to do so. Unexpectedly, Colin was no worse than usual. True, he did pester me constantly to go out, but there was nothing new there. Colin did disappear briefly while we were on a walk. Like all Border Collies, Colin wants to herd anything that moves. This time of year, on breezy autumn days, he has his work cut out for him, herding blowing leaves.

The incident occurred as we were returning from our walk, approaching our house. Our next-door neighbors have a huge pile of leaves at the curb. As we approached it, Colin took off in pursuit of a blowing leaf. He went airborne just short of the leaf pile, and plunged into it. So, there I stood, holding a roller leash that extended into the leaf pile, with no dog visible at all. After a moment, the leaf pile started to ripple and shift, and a Border Collie pup burst out the other side. In his mouth, he carried one leaf. I can’t swear that it was the same leaf that he took off in pursuit of, but I suspect it probably was.

I was working on a new group of lab sessions yesterday, and I couldn’t decide what to name the chapter. As I mentioned to Barbara later, as a librarian she’s used to a well-defined taxonomy that doesn’t change other than to make room for new subjects. Biological taxonomy, on the other hand, changes like dreams, particularly with the advent of DNA analysis. A species may be moved from one genus to another, or indeed may be assigned as the sole member of its own new genus. A genus may move, in whole or in part, from one phylum to another, and even phyla may be moved from one kingdom to another. Even the framework changes. What is a kingdom in one taxonomic system may be a sub-kingdom or even a phylum in another. For that matter, some scientists make a convincing case that the whole kingdom system is invalid and that if we are to have a valid taxonomy it must be on a monophyletic basis. But the real problem is that life is messy and doesn’t fit itself into a convenient two-dimensional matrix. I suppose it might eventually be possible to classify all life in an n-dimensional matrix, but I sure wouldn’t want to attempt it.

Oh, yeah, my chapter title. It started out “Investigating Protista”, changed to “Investigating Protozoa”, and then changed again to “Investigating Protists”. I finally settled on “Investigating Protista/Protozoa/Protists”.

14:45 – I’ve sometimes posted Pat Condell videos here, often noting that I generally agree with Pat but that he’s a bit mealy-mouthed for my taste. Actually, I’m sure that Pat hates and despises islam as much as I do, as evidenced by his latest video.

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Sunday, 30 October 2011

08:11 – Barbara goes to the doctor for a follow-up visit this week. She’s really hoping he’ll approve her to drive and return to work. She’s still in some pain, but she’s stopped taking the oxycodone and is now taking tramadol. If I were her doctor, I’d approve her to return to work.

The blizzard that hit the northeast didn’t make it this far south. But we had cold rain Friday night and yesterday morning and lows last night about a degree above freezing, so we just missed it. As has been true of all our Border Collie pups, the cold weather invigorates Colin, not that he needs any invigorating. For the last couple of days, he’s been charging around disregarding his leash, sometimes nearly pulling me off my feet. We use a long roller leash, and Colin learned very early exactly how long it was. Ordinarily, he knows he’s about to run out of leash and stops before it jerks him to a stop. Lately, he’s been ignoring that.

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