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Week of 11 October 2010


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Monday, 11 October 2010
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10:25 - Barbara dropped Malcolm at the vet on her way to work this morning. Malcolm had a urinary-tract infection, which the antibiotics seemed to clear up mostly but not entirely. He's still leaking a bit. When he's been asleep or resting, he'll be a bit damp underneath. The vet is going to do an ultrasound to make sure there's no bladder tumor or any other serious problem. It may be that the leakage is simply because he's 11 years old, and older dogs like older people sometimes have such problems. If so, there are several possible courses, including phenylpropanolamine, either short-term or long-term, or testosterone. We're hoping that Malcolm's problem won't require surgery. That's a lot to put an older dog through.



Scientists normally don't question the truthfulness of other scientists. When one reads a paper, one assumes that the author has reported his data accurately. The author may have used a poor methodology. His statistical analysis may be wrong. (It's not at all uncommon for working scientists--particularly those in the soft sciences--to have a very poor grasp of statistics.) His conclusions may be faulty, unsupported by his data. But one assumes that the scientist who wrote that paper was honest, that he reported his data accurately, and that he did not attempt to deceive the reader. It's not that scientists are gullible; it's that they have no choice but to trust other scientists. In theory, the data and conclusions of any paper can be reproduced and verified, but in practice there's simply neither the time nor the resources to do that for the vast bulk of published papers. So scientists trust other scientists.

The other side of that coin is that when it does turn out that a scientist has lied, either by falsifying or cherry-picking data or otherwise by intentional deception, other scientists consider those actions to be a crime against science. Everything the lying scientist has ever published is immediately cast into doubt. The fallout is not pretty, particularly because it can have a devastating effect on the careers of innocent scientists and grad students who happened to be colleagues or co-authors on the papers in question. Consequently, any scientist is loathe to even think about such scientific misconduct, let alone accuse another scientist of such. And that goes double when the paper in question is outside the area of expertise of the reader.

That's why the AGW crowd has been able to maintain this fraud as long as it has. When I first read about the AGW hypothesis (it's far from a theory, in the scientific sense) I reacted the same way that any scientist would. I assumed it was valid, or at least honest. These scientists presented data to support their hypothesis. It never even crossed the minds of anyone, including me, that those data might be faked. But things started to unravel quickly.

Real scientists expect to be challenged. Real scientists present their complete methodology and provide their raw data. Real scientists respond to questions from their peers and appreciate suggestions and corrections. Geez, for that matter, real scientists use error bars. The AGW crowd did none of that. They attacked and smeared any scientist who dared to challenge them. They attempted to prevent papers that did not share their point of view from being published. They refused to detail their methodology, and demanded that all of us accept their manipulated data, refusing to share the raw data upon which it was based or to explain how they had manipulated those raw data. They attempted to tar scientists who disagreed with them, questioning their credentials, and sometimes even trying to get them fired. These are not the actions of scientists; they are the actions of political zealots.

Through all of this, many real scientists have become increasingly uncomfortable, but still avoided the nuclear option--making accusations of scientific misconduct. Over the last year or two, that's started to change. Before then, many scientists with impeccable credentials, including Freeman Dyson, had expressed strong doubts about the AGW hypothesis, but most scientists kept their doubts to themselves. With ClimateGate, that really started to change. Any real scientist, whatever his field, must be nauseated after reading those papers, in which so-called climate scientists calmly discuss faking data, intentionally deceiving other scientists and the public, obstructing those who disagree with them, and suppressing dissent.

It's gotten to the point where many real scientists can no longer remain silent. Here's what one of them has to say. "I would almost make that revulsion a definition of the word scientist."

So, AGW is in the process of imploding, but that implosion is going to cause a lot of damage, direct and collateral. My one regret about this whole shameful mess is that it tars all of science and all scientists, giving more ammunition to creationists and antivaxxers and other anti-science groups. After all, if these climate "scientists" are a bunch of whores, who's to say that evolutionary biologists or physical chemists or astronomers or vaccine researchers aren't just as bad? The Left complains a lot about the Right's "war on science", and much of it is justified. However, with AGW the Left has probably done more damage to science than the Right ever could have dreamed of doing.


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Tuesday, 12 October 2010
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09:07 - Malcolm spent the day at the vet yesterday. They ran an ultrasound and found his bladder and urethra are fine. There's some minor thickening in the bladder wall, but Sue Stephens said it wasn't cancerous. They took a urine sample to be cultured and did some blood work. If things turn out as expected, Sue said the next step was to try phenylpropanolamine. It's possible that a short course of that may solve the leakage problem, or he may have to go on it permanently. If the PPA doesn't work, she said we could consider testosterone or PPA in combination with testosterone. Obviously, we'd like to avoid steroid therapy if possible.

Late afternoon, I picked Malcolm up to bring him home. He was surprisingly well-behaved during the ride home. He did have berserk barking spells twice when I forgot and used my turn signal. (Malcolm doesn't like the clicking of the turn signal, and goes berserk, literally bouncing off the roof of the truck.) And he did keep tossing the windshield sunscreen that was in the back seat over into the front passenger seat. But other than that he was well behaved, just riding along and watching everything we passed.



I'm placing more orders this week for the microchemistry kits, accumulating the stuff I need to put together the first three dozen kits. The bulk of it comes from two lab equipment wholesalers, but I have numerous small orders for individual items. Three dozen composition books (lab notebooks) from Costco, of all places. Three dozen purple Sharpie markers from another vendor. Three dozen 9V batteries from still another vendor. Three dozen snap-lid plastic shoeboxes from U-Line. And so on.

And I'm accumulating newspapers, which I'll shred and use for packing material. The SQE and ORM-D exemptions for shipping small quantities of hazardous materials without having to pay hazardous shipping surcharges have certain packaging requirements, including using sufficient absorbent material to soak up any leaks. Shredded newspaper meets the requirements, and is a lot neater than using vermiculite.

Work on the documentation progresses.


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Wednesday, 13 October 2010
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08:05 - I went to the dentist yesterday to have my fangs cleaned. While in the waiting room, I picked up a copy of a propaganda sheet from the ICR (Institute for Creation Research), a New Earth Creationist "think" tank. Of course, they don't actually do any research in the sense that anyone else uses that word, and they don't know how to think, but there it is. There was an interesting article about how christian "scientists" should interpret evidence only in the light of scripture. If the evidence and scripture appear to conflict, the evidence must be wrong or has been misinterpreted. The accuracy of scripture cannot be questioned. It is much more reliable than one's own eyes, because seeing something plainly is no proof of anything. These people are seriously twisted.

Pournelle keeps telling me that he doesn't believe there are actually any people in any modern first-world society who still believe Earth is only 6,000 years old. Well, they're all over the place here in the South, and my dentist is one of them. We had an interesting discussion about ape versus human chromosomes, transitional fossils, and so on. He knows he can't change my mind and I know I can't change his. Still, he's a nice enough guy and a competent dentist.



The news around here is dominated by the case of Zahra Clare Baker, the little girl who couldn't catch a break. At age 10, she hasn't had much of a life. She's deaf, has cancer, and wears a prosthetic leg to replace the leg she lost to cancer. Her home environment, by all accounts, was indescribably miserable, dominated by a wicked stepmother who made the wicked stepmothers in fairy tales look like sweethearts. Over the weekend, Zahra disappeared. An Amber Alert was issued, which made the national news.

Except that the police investigation has raised serious questions about exactly when Zahra disappeared, and why. It turns out that no one had seen her for quite some time before last weekend, and the police are now treating the disappearance as a homicide. Corpse dogs have detected the scent of human remains on two of the family vehicles. Her stepmother has been charged with felony obstruction of justice, and has admitted writing the ransom note she supposedly found. Although the stepmother hasn't yet been charged with murdering Zahra, it appears likely she soon will be. And all of us keep thinking about this little girl who never had a chance.



I'll surprise all my readers by coming out in support of a religious group. There's another story that's recently made the national news about a city park in King, NC, which is just up the road from us. There's a war memorial there, on city property. That war memorial had a Christian flag on display. The ACLU threatened to file a lawsuit, and the city attorney said the city didn't have any choice but to remove the flag. The flag was removed, and the city officials announced that they couldn't afford the estimated $200,000 cost of fighting the lawsuit. King is a small rural North Carolina town, and the vast majority of its residents are Southern Baptist. The removal generated a firestorm, and the city officials have reversed their decision and intend to fight.

I am as strong a proponent of separation of church and state as anyone, but this isn't really about separation. This is, after all, a memorial to King's war dead. Many of those who died were Christians, as are their families. Some, no doubt, were of other religions, or no religion at all. I'll go so far as to say that the government of King should not be installing or maintaining religious flags at the site. Fine. But nothing should prevent private citizens from installing and maintaining those flags, just as they place flowers at grave sites. All these people want is a flag to honor their war dead. I'm sure that they would be willing to pay for and maintain that flag themselves. I'm sure they would understand if others did the same for their war dead, raising flags with the Jewish Star of David or the Atheist A. As long as no government funds are spent to install or maintain these flags, why would anyone care?


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Thursday, 14 October 2010
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08:16 - Barbara mentioned an article in the paper this morning about a man who underwent a sex-change operation and is now suing to be allowed to play on the LPGA tour. LPGA rules say only women are eligible, and define a woman as someone who was female at birth.

I told Barbara I'd often wondered how the womens' golf and tennis tours are able to get away with what they do. There are thousands upon thousands of guys out there right now who could easily beat any woman playing on either tour, and yet the women playing on those tours make millions of dollars in winnings and endorsements, which without that artificial barrier would have gone to male players. US law prohibits employment discrimination on the basis of sex.

There are minor exemptions for situations where sex is a valid criterion. For example, a guy can't sue Hooters for refusing to hire him as a waitress. An actress can't sue because she wasn't considered for a male role in a TV show or film. And a man can't sue because a rape crisis center refused to hire him to counsel rape victims. In all of those situations, it's clear to any reasonable person that sex is a valid hiring criteria. But it's difficult to see how sex can be considered a valid criteria for participating in a commercial sporting event, particularly one in which ability is supposedly the sole criteria.



The search continues for the body of little Zahra Baker. Authorities are now draining a pond near her father's workplace. Serious questions are also being raised about the actions of the Social Services department, or rather its lack of action. Apparently, at least one person reported to Social Services that this little girl was being beaten routinely and was held prisoner, locked in her room, and allowed out for only 5 minutes at a time to eat. Social Services refuses to comment.

It's a pity that the neighbors didn't just call 911 and let the police sort it out. If they had, that little girl would probably still be alive. Of course, it's possible that the neighbors feared for their own safety. From the news reports, the stepmother is apparently a violent woman, one who doesn't hesitate to use her fists or threaten people with a gun. The real question is why she was walking around loose instead of penned up in a prison cell.



10:56 - Here is something truly disgusting. If Cristina Radacovici (AKA ZOMGitsCriss) has this right, and I have no reason to think she doesn't, these doctors are behaving unethically, to say the least.




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Friday, 15 October 2010
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07:52 - UPS showed up yesterday afternoon with my first order from United Scientific. The poor guy almost had a hernia carrying the box up to the front door. I've unpacked and checked everything in, and everything that was supposed to be there is there. There was also no tinkling sound of broken glass, which is always good.

So now I have a couple gross of test tubes, a thousand polyethylene pipettes in two different types, a bunch of reaction plates in two different types, a bunch of polypropylene centrifuge tubes in three different types, alligator clips, stoppers, spatulas, battery adapters, chromatography strips, stirring rods, and a partridge in a pear tree. I managed to get enough horizontal space cleared in the workroom to stow the stuff neatly, but this is only part of what I need to put together the first 36 microchemistry kits. Most of the rest of it will be arriving shortly from Ginsberg Scientific.

I'd planned to assemble these kits in batches of 100, which seems reasonable. I can certainly assemble 100 kits per month, if demand justifies it, and if pressed I could probably do 100 per week for short bursts. Now I need to do some serious thinking about detailed workflow issues.



Shortly after UPS showed up, the vet's office called with the results of Malcolm's urine culture. He has an E. coli infection that's resistant to amoxicillin, including amoxicillin with clavulanic acid, as well as most of the other common antibiotics. The count was > 100,000 per mL, so it's not a light infection. Barbara stopped by the vet's office on the way home from work to pick up an antibiotic to which the bacteria are vulnerable. He'll be on that for a couple of weeks, followed by a retest.



Show this compound to any chemist, and the first words out of his or her mouth will be "Jesus Christ!" or something very like it. That's assuming he or she isn't too busy running to say anything. Looking at the structure, my first thought was that this stuff would make nitroglycerin look inert. Nitrogen really, really wants to be free. It doesn't like to be bound up in compounds. Nitrogen atoms want to marry other nitrogen atoms--gay marriage, so to speak--to form stable nitrogen molecules and then frolick around with all their nitrogen-molecule buddies out there in the atmosphere. So, when chemists see a structure that contains eight(!) nitrogen atoms in a row and very little else in the molecule, they expect it to be unstable, to put it mildly.


As it turns out, though, this molecule is actually surprisingly stable, not just for a compound with so much nitrogen in it, but period. Despite what Derek says, though, I wouldn't get near the stuff. It might change its mind.



One of our neighbors is an elementary school teacher. She teaches math to the brightest fourth and fifth graders. I ran into her yesterday while I was walking Malcolm, and she asked if I had any ideas for a science experiment her students could do that involved a significant amount of math. I asked her if she had any budget, and she said whatever she needed she'd have to pay for out of her own pocket.

I thought about it a moment, and suggested she do Boyle's Law, which is the pressure-volume relationship of gases (for example, with the temperature constant, doubling the pressure halves the volume, and vice versa). She has several classes, each of 24 students, and they can work in groups of four. All she'll need is six oral syringes with caps, six small soda bottles, six two-liter soda bottles, some water, and a bit of vegetable oil to lubricate the syringes. There are no safety concerns, which is a big issue in today's schools.

I buy oral syringes wholesale by the bag of a hundred, so I can supply those. The kids will start with the syringes at full scale and the tip caps on. They'll then add water 200 mL at a time to the large soda bottles and use those bottles as masses to press down on the syringe plungers, noting the volume as more and more mass is added to the plunger. They'll have to calculate the surface area of the plunger from its diameter and then graph the volume of the trapped air at pressures from atmospheric to atmospheric plus 200 g, 400 g, 600 g, and so on, up to atmospheric plus 2,000 grams. They can then graph their results and compare their experimental results to the known actual values.


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Saturday, 16 October 2010
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10:09 - I cannot say enough good things about Netflix. Understand, from their point of view, I am the Customer From Hell. They lose money on me every month, and have done for years. In the last two years or more, they have been 100% efficient at sending discs to me. I receive a disc one day, return it the next day, they log it in the following day and ship the next disc, which I receive the next day. (The USPS also deserves kudos; they haven't taken even one extra day on even one disc in the last two years.) Netflix doesn't even mini-throttle me by shipping from remote distribution centers. I get an occasional disc from their Charlotte or Raleigh center rather than from the Greensboro center, but that's never taken an extra day. On my three-at-a-time plan, that means I'm averaging something like 25+ discs a month from them. All for $18 or whatever.

So, yesterday the mailman shows up. I was expecting two discs. Instead, I got just one disc and a cover sheet--the part you tear off and throw away from the Netflix mailer--for the second, stamped "Received without contents". The cover sheet was seriously mangled. I hope the disc survived somehow, somewhere.

So I went over to the Netflix website to report the problem. There was a choice on there, "Mailer received empty". That was the best description of the problem, so I clicked on it. Unfortunately, it wouldn't accept that. So I called their toll-free number, where I was put on hold for 17 seconds (literally; I timed it). Then I spoke to Kevin, who apologized for the problem and asked if I wanted a replacement sent for the missing disc. I told him I did, and he said it would go out tomorrow. He added that to make up for that delay he was also sending me the next disc in my queue.

Geez, I'm someone that, if I were Netflix, I'd be praying would stop being a customer. (Well, I wouldn't be praying, of course, but you know what I mean.) And they treat me like their most valued customer. Seriously, if you're one of the few people who hasn't tried Netflix, give it a shot. The price is beyond reasonable, the selection is gigantic, you can get both physical discs and unlimited streaming for the same monthly price, and the company simply could not get any better.



This is a long article, but it's well worth your time to read it. FTA:

“Science is a noble endeavor, but it’s also a low-yield endeavor”

Which is wrong. Science is the highest-yielding human endeavor. What he should have said was "low-percentage-current-yield endeavor". Probably not one in a thousand papers produces information that's widely and immediately useful, but that's not to say that those other 999 papers are failures. Many of them will provide the necessary building blocks for later discoveries, some of which may be hugely significant. If nothing else, many of these papers will allow future researchers to avoid wasting their time on blind alleys and dead ends that have already been explored.

It's often said that great discoveries are made only because the researchers stand on the shoulders of giants, but it's equally true that they stand on the shoulders of innumerable pygmies. If you want the great discoveries, the price you pay is to pursue all those studies that don't yield any great discoveries. Science is about false starts and failures. To lead the league in home runs, you have to swing for the fences, which inevitably means you strike out often. You can't have one without the other.



13:05 - Slashdot has an interesting poll up, asking readers where they'd draw the line for things robots are permitted to do. There's a slight bump at "... at letting them play with kids", but robots really run into the wall at "... at letting them run for political office", which was my choice. All of the preceding things seem like reasonable things for robots to do, but the last thing we need is an infestation of dishonest, lying robots.


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Sunday, 17 October 2010
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09:28 - I love it when I have to go back and re-write a lab session from scratch. Really. Yesterday, I was working on a session about doing a quantitative analysis of salicylate concentration in urine. One of the items I'd ordered from United was polypropylene centrifuge tubes in various capacities. I just ordered sample quantities of each to check them out. One of those samples was a bag of 50 mL self-standing centrifuge tubes, which struck me as ideal for urine collection containers.

Then, as I was sitting there playing with the centrifuge tube, my eye traveled down to the 1"x4" chromatography strips that I'm ordering by the thousands to include in the kits. Sure enough, those strips are an exact fit for the 50 mL tubes. I'd already written up the lab using a 250 mL beaker as the chromatography jar, but using the tubes is actually a faster and easier way to run chromatograms. So I'm rewriting that session accordingly.

In other news, I'd sent a preliminary pitch for a new home science book to Brian Jepson, my editor at O'Reilly, CC'd to Dale and Tim. Brian mailed me back last night to say they're interested, and asked me to send him a detailed proposal. So, assuming that comes to pass, between it and the science kits I know what I'll be doing for the next year.


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