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Week of 20 December 2010


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Monday, 20 December 2010
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09:46 - Over the weekend, I sent out the following email to my list of HomeChemLab.com subscribers:

I've just signed a contract with O'Reilly/MAKE to write Illustrated Guide to Home Biology Experiments, and I need your help.

Each of you subscribed to HomeChemLab.com. Your subscription included an answer guide for the questions in the book and a set of many supplemental experiments. What I need to know is this: did you subscribe mostly to get the answers to the questions in the book, mostly to get the supplemental experiments, or both equally?

I'm asking because the page count on the new book is limited to 350 pages, and the more questions I include in the text, the less room there is for actual lab procedures. My impression is that few readers care very much about the questions, so I'm considering dropping questions from the new book and devoting all of that space to additional lab procedures.

So, whether or not you're interested in the home biology book, please give me your opinion. Should I drop the questions and use that space for lab procedures, or keep the questions. Please also let me know if you're primarily a science hobbyist or a home schooler.

Thanks for your help.

I've gotten a bunch of responses so far, and they continue to arrive. The split is roughly 60:40 hobbyist:homeschooler. A trend immediately became evident, with the first dozen or more responses all favoring dropping the questions and devoting more space to lab procedures. Since then, I've gotten some that favor keeping the questions, but the ratio is still about 10:1 in favor of devoting all available space to lab procedures and related material.

I've also gotten quite a few suggestions about the content of the biology book. Interestingly, several people have made the same suggestion, which I'll paraphrase as, "Don't waste any space on dissections". I'll paraphrase the second most popular suggestion as "Do more DNA stuff."

Unsurprisingly, I've also gotten comments from home schoolers, some quite detailed, about the religious versus secular issue. For chemistry that wasn't really an issue, but for biology it can be. Many of the comments have been from (presumably) secular home schoolers, along the lines of "there are already plenty of religious home school biology lab books out there, but nothing secular aimed at home schoolers." A couple have been from religious home schoolers deploring the lack of rigor in current religious home school biology lab books and saying that an affordable, rigorous, secular biology lab book targeted at home schoolers would be great, as long as it doesn't go out of its way to offend their religious beliefs.

So, I've listened to what people have to say, and here's what I've decided:

As to the space allocation issue, I've always believed that questions are good because they make students think about the issues and figure them out for themselves. Nearly as good, though, is simply highlighting things I want them to notice and think about. In other words, "Note that ..." is just about as effective as "Why is ..." and occupies a lot less space.

I'd already decided not to spend any space on dissections. When I took my first biology lab class 40 years ago, we spent a lot of time on dissections, which I always thought were of limited value. I think we did so many dissections because scalpels and frogs in formaldehyde were cheap while in the 60's even student-grade microscopes were very expensive. Affordable microscopes are now widely available, so that's no longer an issue. So we'll start small, with a look at biologically-important molecules, and work our way up, looking at organelles, cells, tissues, and organs. In other words, the focus of this book will be on biochemistry, microbiology, and histology at the expense of gross anatomy.

We'll also do a fair amount of work with DNA. At the basic level, that's easy enough. We can extract DNA literally with items found in every kitchen. We can also do DNA separations via gel electrophoresis with a minimum of equipment and materials. More advanced work with DNA becomes problematic because the required equipment and materials become increasingly specialized (and expensive). Still, there are usable workarounds for items like ultracentrifuges, -80C freezers, and PCR thermal cyclers. We won't have the resources of a public school lab, let alone a university lab, but we can still do a lot.

As to the religious versus secular issue, I am a scientist not a preacher. That means this book will be firmly science-based. One of the responses pointed out that "You need to make clear that evolution is the unifying principle of biology". Well, yes. The great geneticist and evolutionary biologist Theodosius Dobzhansky, himself a religious man, famously said "Nothing in biology makes sense except in the light of evolution." It's simply not possible to understand biology without having at least a basic understanding of evolution, any more than it's possible to understand chemistry without having at least a basic understanding of atomic theory. Still, this book is a biology lab manual aimed at first-year and AP high school biology students and DIY bio enthusiasts, so evolution in its overarching sense will not come into play. I do plan one lab session that focuses on natural selection, a key mechanism of evolution, by culturing bacteria to produce antibiotic-resistant forms, but that is not a controversial topic. In short, the book will be rigorously scientific in approach and without compromise. If it somehow offends someone's religious beliefs, well better that than compromising the science.



Mary Chervenak stopped by yesterday. I pitched my cunning plan about the ultracentrifuge, and told Mary I needed her help. There's no moss growing on Mary. When I finished describing it, the first thing she was, "You're afraid it'll disintegrate, so you want me to turn it on for the first time..."

It was the first time we'd seen Mary since she ran the Baltimore Marathon. Barbara asked Mary how she'd done, and Mary said she hadn't been very happy with her performance. She started talking about her minutes/mile rate, how fast some of the other runners had been compared to her, and where she finished overall. Mary made it sound like her effort had been mediocre. Barbara finally asked, "But where did you finish in your age group?", to which Mary replied, "Oh, I won."

Mary, of course, is a woman. She's stellar at pretty much everything she does, but for a woman that's not good enough. A woman has to downplay her own achievements. It's almost a secondary sex characteristic. Barbara does the same thing, as does just about every girl and woman I've ever known. I just want to shake them and shout, "You're great! Take some credit for what you've accomplished."

I remember the story about the pickup softball game between the enlisted men and the officers. The enlisted men won, 10-0. The next morning, a poster appeared on the bulletin board, congratulating the officers on their great season, during which they lost only one game and finished in second place, and commiserating with the enlisted men for their poor season, during which they won only one game and finished next to last. That's the way guys look at things. I wish women would do the same.



We're waiting to hear how Kim is doing. Her mom called last night to let us know that Kim's back problem was causing her agonizing pain and she wasn't able to get up. Mary had already called her nephew, who is a physical therapist. She called us back later to say that her nephew had looked at Kim and said not to move her, so they called 911 for an ambulance.

Kim is retired on total disability from the US Postal Service. She badly injured her back moving heavy carts of mail, and has been in constant pain ever since. When I first met Kim about 10 years ago, she told me that there was surgery that might fix the problem, but the surgery itself was extremely dangerous and could leave her paralyzed. She told me then that she'd decided to wait until Jasmine had grown up and was off on her own before she risked having the surgery. With Jasmine heading off to college next autumn, I wonder if Kim will decide it's time to risk having the surgery.


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Tuesday, 21 December 2010
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08:26 - While Barbara and I were out walking Malcolm Saturday, I started to laugh. She asked me what was so funny, and I pointed out that our devoutly-religious neighbors had placed a naked anatomically-correct inflatable snowman in their front yard.


That was funny enough, but I didn't really start laughing until I thought about the autopilot scene in Airplane.



Here's something worth reading: A Holiday Message from Ricky Gervais: Why I’m An Atheist



I know I said I wasn't going to do any dissections, but I planned to do one this morning here. Last night, I read an article on Foxnews entitled "Report: Chromium-6 in Drinking Water". I was going to dissect that article to illustrate that what passes for science journalism nowadays is nothing more than advocacy dressed up as science. Alas, Foxnews apparently disappeared the article. A couple references to it remain on Google, but the article itself is nowhere to be found. I guess that's a good thing.

The article referred to a press release from the Environmental Working Group, who appear to be a bunch of green nutters. It claimed that chromium-6 had been found in the water supplies of 31 of the 35 cities that EWG "scientists" had tested. It also referred to a proposed California state standard of 0.06 ppb (that's 60 parts per trillion) with the implication that this was a reasonable standard.

The EWG also lied by omitting the "whole truth" part. It said that the EPA does not enforce any standard for chromium(VI). That's true insofar as it goes, but what it doesn't say is that the EPA enforces a standard for "total chromium", which is to say the combined level of chromium(VI) ions, chromium(III) ions, and elemental chromium. Obviously, any water supply system that meets EPA standards for total chromium must also meet that standard for chromium(VI). No, the EPA doesn't break out chromium(VI) separately. It doesn't need to. So EWG lies by telling "the truth" and "nothing but the truth", but leaving out that inconvenient middle part about "the whole truth".

Oh, yeah, about that proposed California standard of 0.06 ppb chromium(VI). The EPA publishes two values for many pollutants, including chromium. The first, and often higher, number is called the MCL (maximum contaminant level). This is an enforceable number. In other words, the EPA can take action against any water system authority if the water it supplies contains a contaminant at or above that level. The second, usually lower, number is the MCLG (maximum contaminant level goal), which is a target or goal for the maximum level. This is an "ideal" level, which takes into account the limits of technology and other factors. In the case of total chromium, the EPA MCL and MCLG are the same, 100 ppb.

The acceptable levels the EPA specifies for contaminants are generally at least one and often two orders of magnitude lower than the levels at which any harm has been shown to occur. In other words, there's at least a 10X and possibly a 100X safety factor built into that 100 ppb limit. But even that's not good enough for the scientific illiterates who proposed the 0.06 ppb limit in California. They appear to believe that the EPA limit is 1,667 times too high.

And that 0.06 ppb number is interesting in itself. I don't know, but I strongly suspect, that 0.06 ppb is simply the limit of detectability with practical test equipment. I checked the Winston-Salem water quality document, which is published annually. It doesn't list chromium levels, but it does say that the contaminants it does list are those that are present at "detectable" levels.

I didn't have time to check the 35 cities listed in the EWG report, but I'd bet money that none of the 35 exceed the EPA limits, which are themselves conservative. Of course, like all advocacy groups, the EWG isn't about to let the truth get in the way of their story.



11:45 - Thanks to D.R. Williams, who turned up this link to the original Foxnews report. It's been modified since I read it yesterday. The version I saw did not include the rebuttals featured in this version. This version does include one interesting number, the Cr(VI) level for DC and Bethesda, Maryland, which the EWG reported as having "contaminated" water supplies. The Cr(VI) level there was 0.19 ppb, less than 1/500th the EPA limit. Of course, the article spins that tiny concentration as:

"The study shows Bethesda and D.C. had .19 parts per billion of the chemical. That is three times the amount considered acceptable in California."

Is it really? Considered acceptable by whom? I don't think it's the state authorities. I understood the 0.06 ppb standard had only been proposed in California. Perhaps it is now a legal standard. I wouldn't put anything past those nutter legislators in California.



Speaking of elements, we watched an unintentionally funny segment on Grey's Anatomy the other night. Mark Sloan is an attending physician. Lexie Grey is an intern. They make a big deal about her so-called "photographic memory." In this episode they gave an example, which told me that the writers are absolutely clueless about memory.

Dr. Mark Sloan: So... a photographic memory, huh? ... Periodic Table. Go.
Dr. Lexie Grey: Hydrogen, helium, lithium, beryllium, boron, carbon, nitrogen, oxygen, fluorine, neon, sodium, magnesium, aluminum, silicon, phosphorus, sulfur. I can keep going.

I almost choked on my drink. That's not a photographic memory. Remembering the names and positions of the elements in the periodic table, particularly the parts above the transition elements, is ordinary good memory. Ordinary good memory is impressive; photographic memory is scary. Let me alter Lexie's response to what it might have been if she really had a photographic memory.

Dr. Lexie Grey: Hydrogen, atomic mass 1.008, shell configuration 1S1, melting point 13.8 K, boiling point 20.3 K, covalent radius 37 pm, Van der Waals radius 120 pm, Pauling electronegativity 2.20, ionization energy 1.32 MJ/mol, electron affinity 72.78 kJ/mol ...

(Yes, I had to look those values up, other than 1.008 and 1S1.)

They also had Lexie save a patient by remembering that she'd read an old and obscure paper that offered a fix for a very rare fatal condition. If her memory had been truly photographic, she could have retrieved a mental image of that paper and started reading it verbatim to the other doctors clustered around her. Instead, she just gave the cite.

I've often thought that we need to do much more research on memory. Computers can "remember" an entire library of books verbatim, along with all of the images in them at whatever resolution they existed in the book. Why shouldn't all humans have that same ability? No one is working on this, as far as I know.


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Wednesday, 22 December 2010
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11:38 - Pat Condell really knows how to celebrate Christmas. I think I'll use some of his tips this year.



I particularly like the islamic balloon idea. Wish I'd thought of that.



14:06 - Here is a stunning advance in DNA sequencing that raises the possibility that it will soon be possible to sequence an entire human genome in minutes at very low cost.

Robert Heinlein's Life-Line may be closer than we think. Of course, we should all remember what happened to Professor Pinero. Ultimately, technology like this may eventually obsolete health insurance as we know it. It's still a long, long way off, but as we gain a more detailed database of human genomes and correlate that with genetic diseases, the day may arrive when it's impossible to buy health insurance without submitting a DNA sample and accepting exclusions for genetic conditions to which you're subject. Why would any insurance company write a policy to cover a loss that they know is likely or certain to occur? That's like trying to buy fire insurance on your house when it's already burning down. In other words, we'll no longer have insurance in any real sense; at best we'll have pre-payment.

Such detailed knowledge of individual genomes would also change life insurance as we know it. It's unlikely that anything in our genomes would affect the likelihood of accidental death, of course, but you can bet that actuaries would use this information to calculate risks down to the individual level rather than in broad groups as they do now. Government will try to prohibit insurance companies from using DNA to calculate risks and premiums, no doubt. That's happening already, on both the insurance company side and the regulatory side. But it's going to become a much larger issue over the coming years.

Of course, two sides can play that game. A 35-year-old man whose DNA profile is clean may well decide to do without life insurance other than an accidental-death policy, and his wife may buy only a health-insurance policy that covers pregnancy and delivery costs. In short, the whole concept of insurance is about spreading risks. If the risks become known, there's no longer any point to insurance. It becomes a zero-sum game. Worse than that, actually, because the insurance company will have to charge a percentage above their expected loss experience to cover their own costs.

Again, this is all blue-sky for now, but the clouds are definitely gathering on the horizon.


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Thursday, 23 December 2010
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08:30 - I'm still cranking away on the biology book. My first milestone is two complete chapters, with a due date of 28 February. I'm going to try to have those submitted by 31 December, and I still have a lot of work to do on them. Accordingly, posts here are likely to be sporadic and short until next year.


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Friday, 24 December 2010
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08:39 - Ruh-roh. Barbara is off work until 3 January, and she's starting her annual Deep Clean today. My office and my workroom are on the schedule for today, which means I'm going to have to decide which old shit to throw out. Goodbye, old friends.



12:10 - The first pass on my office and the workroom is now complete. We got a lot of stuff out of my office and separated into various piles downstairs for garbage, Goodwill, and so on. Barbara vacuumed the floor, walls, ceiling, and blinds, muttering in disgust the whole time about how there were probably bugs in here. I told her that any bug foolish enough to wander into my office would be found lying on its back with all of its feet in the air. We also moved a folding table into my office, which I'll leave set up with lights, background paper, and so on for doing product illustration shots for the book and kits.

The next step I have to do myself. I need to clean off and organize my main desk and microscope desk. My main desk is a 3-0 solid-core 1-7/8" door, with an end table sitting next to it with the Brother monochrome laser printer. I've had a Brother color laser printer sitting on the floor of my office in an unopened box for several months, waiting for when I had time to deal with it. That'll go in the left corner of the main desk, which is currently home to a router, a couple switches, a wireless access point, and dozens of cables.

I've been trying to set aside enough time to migrate off my old main system to the hex-core system we built as the extreme system for the book. I think I'll basically do a cut-over, keeping old and new operating side-by-side until I'm sure I have the new system the way I want it. Then I'll shut down the old system but leave it untouched for a month or two, until I'm absolutely sure the new system is doing everything I want it to. Then I can salvage components from the old system. Other than my new main system, it's still the fastest system in the house, and by a long way. I'll use that motherboard and processor as the basis of Barbara's new system.

Once I get all that stuff done, it's time to go after my bookshelves. They cover one wall of my office, and hold about 80 linear feet (24 meters) of mostly reference books. Right now, they're organized for purely random access. That worked fine back when my memory was still trustworthy. I'd just stick a book anywhere there was space. If I needed that book months or years later, I'd remember exactly where it was. That no longer works as well as it once did. Barbara, being a librarian, has suggested a novel alternative. She proposes to organize the books by Dewey Decimal or LOCCCN. Probably the former, since I grew up with it and know almost instinctively where something should be, at least in the 500 range.

Oh, and Merry Christmas!



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Saturday, 25 December 2010
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09:43 - Merry Christmas!

I missed Santa again. I was lying in wait with the Atchison. As soon as I heard the reindeer hoofies on the roof, I cut loose and immediately ran outside to see if I'd nailed them. No joy. Now I have a bunch of holes in the roof that need to be patched.

It's just another working day for me, but Barbara is off to her sister's house to spend the day. Malcolm was outraged that she was leaving him with just me for company.

We had our first glitch last night with Netflix streaming. We were in the middle of watching something when the screen went black and the Roku buffering screen popped up. After 10 or 15 seconds, the program resumed just where it had cut off. Once in (I'm guessing) 75 hours of watching is acceptable. We probably get a DVD glitch that often.

One of the programs we watched was Nova's Dogs Decoded. People who haven't lived with dogs would probably find much of what they described unbelievable. Those of us who have lived with dogs just shrugged. They kept saying things like "Scientists were surprised ...". I kept rebutting that with "What they meant to say was "scientists who'd never lived with dogs were surprised..."".

Scientists have only recently really started to study dogs, and some of the studies have shown remarkable ignorance. I remember, for example, reading the abstract from one paper that claimed that dogs have only six distinct vocalizations. Bullshit. As I've said, Malcolm has distinctly different barks for the mail truck and the UPS or FedEx truck. (He obviously considers the latter two to be the same thing for all practical purposes.) Those barks are specific to those types of vehicles. Last Sunday provided some evidence for that. I was working at my desk when Malcolm started his mail-truck bark. It never occurred to me that he was mistaken or that I'd misinterpreted the bark. I walked to the front door. Sure enough, there was a mail truck just backing out of our driveway--on a Sunday--and a package on the front porch.

The USPS doesn't deliver mail on Sundays, ever. But last Sunday they did. The fact that I was perfectly aware that it was Sunday and that it couldn't possibly be a USPS truck was overridden by the fact that Malcolm was saying it was a USPS truck, Sunday or not. And it never occurred to me to doubt Malcolm.

One of the dog communications skills they didn't touch on in the segment is what I've deemed "thought waves." Malcolm uses those to control me. For example, if I'm sitting on the sofa eating a snack, he sits staring at me, sending out thought waves that demand I give him some. If I'm not consciously countering those thought waves, I find myself giving Malcolm part of what I'm eating. Often, I'm not even aware of doing so. Same thing happens when I walk into the kitchen to get a Coke. Malcolm sends out thought waves, and I find myself giving him a chew stick. Sometimes I ask him, "Didn't I just give you one of these a few minutes ago?" He denies it via thought wave and gets another one, even though I'm pretty sure he was lying.

They also showed tests that establish that dogs read human emotions from our faces the same way that other humans do, by looking left to focus on the right side of our faces. And the whole time they were talking about how dogs have evolved over the past tens of thousands of years to interact better with humans. What they never mentioned, but what I suspect is true, is that humans have also evolved to interact better with dogs. We are true symbiotes. As one of the scientists stated, if humans hadn't domesticated dogs, we'd probably still be hunter-gatherers.



11:48 - Here's some cheerful news. In a pretty amazing turnaround from 1985 figures, the UK is now a majority-secular nation (starting on page 70). More than half of those surveyed claim they have no religion. Even among those who consider themselves to belong to a particular religion, only about one in six attend services as often as once a month, and about three out of four attend services twice a year or less frequently.

And, of course, it's very likely that a large percentage of those who do attend services, even regular churchgoers, don't actually believe in gods. They treat church as a social event. To be fair, it's very likely that at least a few of those polled who reported themselves as having no religion do believe in gods. Still, that is probably a very small percentage. On balance, I think it's fair to consider these numbers evidence that the UK is now not just secular, but overwhelmingly secular. True Believers make up a very small percentage of the UK population. Some may argue that the UK is technically still a religious nation because it has an established church, but it's pretty obvious that UK citizens don't take that seriously.


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Sunday, 26 December 2010
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11:25 - Winston-Salem had its first significant snowfall on Christmas day in about 60 years. We ended up getting about 4" (10 cm) of heavy, wet snow. Malcolm is enjoying running around, snowplowing with his snout and licking the snow.

I did venture out this morning. We have several friends who are out of town for the holiday, in places ranging from Pittsburgh to St. Louis to Hawaii. I'm keeping an eye on their houses, picking up the mail and newspapers, and so on. The main roads have been plowed and salted, but the residential streets are still pretty treacherous. Nothing that 4WD and sane driving can't deal with. I did see a car that must belong to a Darwin Awards candidate. It was lying in the ditch along a main drag, nearly on its side. In the words of one of my favorite philosophers, "A man's got to know his limitations." With lows over the next several days forecast to be in the teens (~ -10 C) and highs to be around freezing or a bit more, this snow is likely to stick around through the new year. I'm sure there'll be many more accidents.

Barbara is doing her White Tornado thing, currently in our bedroom and bath. By the end of the week, she plans to have everything clean and sterile. My office looks a lot neater and cleaner than it did before, but there's still much work to be done. I haven't started on the transfer to the new PC yet.



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