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Category: writing

Friday, 18 November 2011

11:40 – I’m still working heads-down on the biology book, so I don’t have much to say.

One interesting thing. My editor, Brian Jepson, emailed me last night to say that O’Reilly/MAKE is getting ready to do a reprint of Illustrated Guide to Home Chemistry Experiments and ask if there were any changes I wanted to make before the book went to reprint. Although this book is what’s called an “evergreen” title–in other words, one that sells consistently for years–in the course of our discussion, I mentioned that at some point I’d like to do a re-write of the book to convert it to microchemistry kit-based. Brian said that was worth discussing in more detail, and mentioned that this would probably be the last reprint of the chemistry book.

Not that the book is going away. The reprint they’re about to do will provide a six-month or year’s supply, during which O’Reilly/MAKE will be transitioning to print-on-demand for this and other titles. That means they’ll no longer have to print thousands of copies and stick them in a warehouse while they wait for orders. Instead, they’ll just print as many copies as they need whenever they need them. And that’ll also make it a lot easier to manage updates, since we’ll no longer have to worry about having thousands of unsold copies that an update obsoletes.

The other nice thing about POD is that it decreases risk in publishing new titles. For example, we finished the Illustrated Guide to Home Forensics Experiments a couple of years ago, but it’s never been published because doing so is very expensive. With POD, that expense is reduced. There’s still the cost for layout and production, of course, but there’s no longer the risk of printing 10,000 or 20,000 copies of a four-color book and then finding out that it doesn’t sell as well as hoped.

12:16 – Here (h/t to Abbie Smith) is a worthwhile graphic that illustrates science-as-perceived versus science-as-reality.


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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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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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Friday, 11 November 2011

09:01 – Even the scummiest of politicians will sometimes tell the truth when it suits his own agendum. So, it was with no surprise that I read Eurozone collapse ‘will send continent into depression’

According to no less than Jose Manuel Barroso, the president of the European Commission, a collapse of the eurozone would instantly wipe out half the value of the eurozone’s economy, plunging Europe into a deep depression, the likes of which haven’t been seen since the 1930’s and reducing living standards to Latin American levels. Barroso has his own agendum, of course, which, as always, is “More Europe”. As with all statists, his motto is Never Waste a Good Crisis. And, in fact, he exaggerates. Living standards in the southern tier, including his own country, may in fact fall by 50% or more, but the effects on the FANG nations will be considerably less severe.

Someone asked me the other day why I am more optimistic about the future of the US, UK, Canada, Australia, and New Zealand than I am about the rest of the world, including other first-world countries that use other languages. Two reasons: first, and the importance of this should not be underestimated, we speak English, which is demonstrably superior to all other languages. As a rough guide to relative usefulness, I suggest cubing the ratio of the number of words in the English vocabulary to that of the comparison language. Second, and even more important, our women have equal rights and responsibilities. We don’t waste half our population. Of course, that’s also true of Europe, particularly northwestern Europe, but they have saddled themselves with inferior languages, which limits their competitiveness.

Still, Europe is in wonderful shape compared to most of the rest of the world, where women are treated at best as less-than-a-man and more commonly pretty much like livestock, if that well. (A woman, of course, is often cheaper than a cow, and easier to replace.) This situation applies throughout the entire islamic world, India, nearly all of Africa, and much of Asia, Central America, and South America. It’s no wonder that these are all third-world countries, and doomed to remain so.

And yet, people are often surprised to learn that I consider myself a feminist. In truth, I’m an elitist. I value hard-working competent people above others. I have no use for people who are lazy or incompetent, or both. If people are hard-working and competent, I don’t care what color their skin is or whether they pee sitting down or standing up. And I think that attitude is common in the first world and rare otherwise.

Work on the biology book continues. I’ve finished three microcosm lab sessions, leaving only one on observing Winogradsky columns in the to-do pile. Today, I’ll jump to a different topic altogether, although I’m not sure which one.

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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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