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Category: biology

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?

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Tuesday, 22 November 2011

11:38 – I’ve started placing orders for the biology kits. This morning, I placed orders for several thousand bottles and a couple kilograms each of agar and dextrose.

I’m still working heads-down on the biology book. I’m about to start a new group. I’m not sure if I’ll do the group on fungi or plants next.

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Sunday, 13 November 2011

10:32 – Still working on the biology book. I decided to stop trying to organize the protist stuff and just write labs. I’ll worry later about how to organize everything.

I also spent a couple hours on the chemistry lab kits. We’re down to a handful in stock. Making up the next batch will involve some changes, primarily a shift from using polypropylene centrifuge tubes as chemical containers to using a mix of dropper bottles and wide-mouth pharma packer bottles. That also means reorganizing the work flow and packing groups. We may end up being out-of-stock on the chemistry kits for two or three weeks, but that’s not a big deal at this time of year because orders are slow. I expect they’ll start coming in faster with Christmas and the winter semester fast approaching, so we want to have at least two or three dozen kits in inventory by early next month.

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Saturday, 12 November 2011

08:34 – Yesterday I started a group of lab sessions on protozoa/protista/protists, which is a very annoying topic. The problem is that p/p/p is a grab-bag grouping, basically “everything other than prokaryotes that isn’t a plant/animal/fungi”. That said, protists actually fall into three unofficial groups: plant-like (e.g. green algae), animal-like (e.g. amoebae), and fungi-like (e.g. slime molds).

It doesn’t do it justice to call this “group” polyphyletic. More like mega-super-ultra-hyper-phyletic. About the only thing they have in common is that they’re all eukaryotic, are unicellular or simple multicellular, and they mostly live in water or damp soil. Otherwise, they’re all over the map. Some are autotrophs, some heterotrophs, and some can be either depending on their environments. They use different motility methods (or none at all). They reproduce by binary fission or mitosis and/or conjugation and/or cyst formation. Try organizing that grab-bag into something.

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Thursday, 10 November 2011

09:02 – I’m so busy and the euro situation is so hopeless that I’m not going to bother to write about it any more. Merkozy are now talking openly about the breakup of the euro and the EU itself, and they’re talking about it as though it’s likely to occur sooner rather than later. Italian bond yields spiked to 8.1% yesterday, which is far past the point of no return. The 7% threshold is very real psychologically for the markets; once yields reach 7%, investors write off the issuer as so likely to default that it’s simply too risky to invest. That in turn causes bond yields to increase further in a vicious circle. So, Italy is gone, which means Spain and then France won’t be far behind. There’s nothing that can be done to stop the collapse–short of the ECB turning on the printing presses, which they’re not going to do–so it’s pointless to continue discussing it. The patient is brain-dead.

Work continues on the biology book. I’m doing a lab session right now on the effects of pollution on succession in microcosms. What fun. Build a tiny little world and then poison it. Forced selection and survival of the fittest.

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Wednesday, 9 November 2011

07:18 – So, how do I know when I’ve been writing too long? Here’s an example. By late afternoon yesterday, I was getting pretty tired, after more than eight hours of heads-down writing with only a few short breaks to walk Colin. I was writing a lab session about succession in pond-water microcosms, giving a detailed procedure for observing and documenting the microorganisms present in various parts of the microcosms. I mentioned adding a drop of methylcellulose, which is added to water to reduce the motility of some organisms. I actually found myself writing this sentence: “Some of these little fuckers are FAST.” (I actually intended to write “suckers” but I apparently experienced a Freudian slap.)

Now, it’s true that we’re often complimented on our informal writing style, but I thought that was a bit too informal even for us. After thinking about it, I left the sentence as is for then and decided to knock off for the day. I’ll fix it this morning.

08:34 – Ruh-roh. When I checked Italian bond yields this morning, I found they’d already touched 7.4% and seem likely to continue climbing. That’s very, very bad for a country that has about $3 trillion in outstanding sovereign debt, with about a sixth of that coming due in the next twelve months. About the only good thing that can be said is that, at six or seven years, Italy’s average maturity is longer than average for the eurozone. Still, there’s no way it’s sustainable to have to finance half a trillion dollars a year at the current rates Italy has to pay.

The fear all along, of course, has been that Italy is “too big to bail” and that fear is about to come home to roost. The ECB is legally prohibited from helping. In fact, their purchases of Italian and Spanish bonds are illegal, and the ECB is getting very nervous about that. Nor can the EFSF “bailout fund” help. Although it’s usually reported as having a €440 billion war chest, the fact is that it doesn’t really have any money to speak of. In terms of actual cash in the bank, it might have €4 billion. The remainder is in the form of promises from EU governments to commit funds to the EFSF. And one of the major guarantors of the EFSF is–you guessed it–Italy. Other EFSF guarantors include such already-bankrupt nations as Spain, Portugal, Ireland, and … Greece. The only currently-solvent nations backing the EFSF to any significant extent are France–which itself is likely to a bailout candidate–and Germany. In effect, the EU nations are cosigning loans to themselves.

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Saturday, 5 November 2011

09:08 – One thing about biology is that living things do things in their own time, and there’s little or nothing we can do to change that. That makes writing a biology lab manual a bit different from writing one for chemistry or nearly any other science. With chemisty, I could design self-standing experiments that fit in convenient cubbyholes. With biology, it’s often a matter of hurry-up-and-wait.

For example, as I was working on protozoa labs yesterday, it occurred to me that I needed to start a microcosm series of labs very early in the semester, both because the life cycles of microcosms run several weeks to several months, and because I could use those microcosms at various stages in their life cycles for lab sessions later in the semester. So I just added a group of labs in a chapter before Group I, which I titled First Semester Project. We’ll create two kinds of microcosms: open, aquarium-like microcosms where we’ll grow pond life, including protozoa that we’ll use later, and closed Winogradsky columns that we’ll observe over the course of the whole first semester, if not longer.

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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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Monday, 31 October 2011

08:44 – Edward P. Lazear in the WSJ points out something that should be obvious to anyone. The EU problem is too much government. Unfortunately, the only “solutions” they’re considering involve more of what’s caused the problem in the first place. It’s apparently impossible for politicians even to consider that government is the problem, not the solution. And the US has the same problem, albeit not quite as advanced.

Instead, EU politicians blame the market, the ratings agencies, and indeed anything else they can think of other than themselves. They’re now apparently seriously considering implementing a horrible idea that’s been simmering on the back burner for a couple of years now. A so-called “Tobin Tax” on financial transactions. Basically, the idea is that by making it more expensive for traders to trade they’ll reduce volatility in the markets.

Their problem is that, as Sweden found out in spades a few years ago, a Tobin Tax must be implemented globally. When Sweden implemented a Tobin Tax, the markets simply abandoned Sweden and moved their trading elsewhere. The vast majority of market activity in the EU already occurs in London, so implementing a Tobin Tax in the eurozone would simply cause essentially all of the little remaining market activity in the EU to relocate to London and New York, where it would not be taxed. The EU’s solution to this is to attempt to force the Tobin Tax on the UK (which has a veto over such things) and to lobby the US to implement such a tax. It’s not going to work, any more than any of the EU’s other “solutions” have worked. We’re really well into the endgame now.

10:51 – Hmmm. I just finished writing up a lab session on Mendelian inheritance, and realized that I might have a serious problem. Back when we were in school, everyone did the PTC tasting thing, but it was typically done with just the students in a classroom. This lab session is a bit different…

“Testing unrelated individuals provides some useful data, but ideally you want to test as many related individuals as possible so that you can follow inheritance of the PTC tasting and non-tasting alleles through generations of families. Testing both parents and their children is good; testing parents, children, and all four grandparents is better still. Best of all is testing the full extended family, with aunts and uncles and cousins.”

Most of my readers will immediately spot a very serious potential problem there, so I added the following warning:

Any human genetic testing, including this lab session, potentially has serious ethical implications. Many families have at least one “skeleton in the closet” that they’d prefer to keep hidden from the world at large. You are obligated—morally, ethically, and possibly legally—to maintain the absolute privacy of your test subjects by refusing to disclose the data you obtain to anyone else, including the test subjects themselves.

For example, in one of your family groups of test subjects you might find that both parents are non-tasters, as are all of their children except the eldest. You might conclude that that child was adopted or had a different father. Disclosing that conclusion TO ANYONE is a serious ethical violation, and may have direct and indirect consequences you cannot imagine. If you discover such an anomaly, KEEP IT TO YOURSELF.

Also consider this: you are not a geneticist, so you may be wrong.

12:02 – Jerry Coyne comments on Science publishing a new phylogeny of the mammals.

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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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