The Questionable Authority

Aaaaaannnnnnddddd... We're back.

Wed, 05 May 2010 19:40:22 -0500

It's been a while since I've posted, because I've been busy goofing off and having fun - I took a long European vacation (pictures and posts to follow). I'm back, mostly recovered, and almost back to my normal routine.

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Federal Judge Strikes Down BRCA1/BRCA2 Patents.

Mon, 29 Mar 2010 21:09:23 -0500

As of this morning, at least 20% of your genes were patented by someone other than you. The holders of the patents could quite literally forbid you to investigate large portions of your own personal genome. This afternoon, a federal judge in New York handed down a broad ruling that calls into question - thankfully - the entire idea that naturally occurring genes are patentable.

The ruling in question most directly affects the BRCA1 and BRCA2 genes, which have been implicated in hereditary breast cancer. Myriad Genetics patented those two genes, and has been jealously guarding those patents. This has restricted research into those genes, and has prevented the development of any alternative methods for tests involving those genes. The ACLU filed suit challenging the patents last year, and the ruling in question came in response to their request for summary judgement.

I'm still reading through the 156-page ruling, which can be downloaded from the ACLU's website (pdf), but I think I may have already found one of the quotes that - if the ruling survives the appeals process - is likely to have extremely wide-ranging effects on genetic research in the future:

Because the claimed isolated DNA is not markedly different from native DNA as it exists in nature, it constitutes unpatentable subject matter under 35 U.S.C. 101.

Myriad is sure to appeal the ruling, so the case is most likely far from over. But it at least gives cause for hope that research into human genetics will not be restricted by firms that claim patents on part of our very physical makeup.

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What the scientific community can (and should) learn from the pending UK rail strike

Mon, 29 Mar 2010 18:49:14 -0500

Next week, I'm going to be in the UK. My plans for the trip are centered on two things: the room I've booked in London for the week, and the 8-day rail pass I purchased a couple of months ago. This morning I hit the National Rail website to start figuring out exactly which trains I need to take to get to the destinations I've been planning to hit. After the third or fourth inquiry I ran, I began to notice a disturbing pattern: every train I might want to take had a little yellow exclamation point icon under "status". Clicking through to details brought up a notice that, "industrial action may affect this train" and a link for yet more detail.

Clicking through to that link, I was able to find enough context to figure out that "industrial action" translates as "strike" without needing to resort to my English-English translation dictionary. I have defended unions on this blog before now, so the brief rush of euphoria that was brought on by my linguistic prowess was followed by an almost pleasant diversion into the etymology of the phrase "hoist with his own petard".

Then I moved on and began to look into the details involving both the "industrial action" and the underlying disputes.

The brief version of affairs is this: unions representing railway signalers and maintenance workers have announced that their members have authorized action, and that if the disputes that they have with Network Rail are not resolved forthwith they will strike from Tuesday to Friday of next week. The maintenance workers will be on strike for the entire period, while the signalers will only walk off during the peak hours from 0600-1000 and 1800-2200.

The representatives of the unions point out that they are being kind enough to wait until (just) after Easter to stage their walk-out. The representative of the group of companies that run the trains has (predictably) called the planned action "deplorable", because the unions are not putting the passengers interests ahead of their own. The Daily Mail, noting that the strike is set to begin on the day when the prime minister is expected to announce the date of the next national election, called the unions' timing "blatantly political."

My own reaction to the strike plans, particularly given their potential impact on my own travel, is a bit complex:

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Remembering Megan

Thu, 18 Mar 2010 16:25:10 -0500

If it takes a village to raise a child, I was particularly lucky to grow up in the middle of a wonderful little village in the middle of the Bronx. All things considered, the village did a pretty good job with a whole bunch of kids, who have since spread out all over the place. Some have gone on to really cool editing gigs, occasional appearances with Keith Olbermann, and our own Wikipedia pages. Others have wound up working as lifeguards in Lower Alabama. But pretty much all of us came away from the village we were raised in with at least three things: a strong understanding of the importance of community, a strong sense of social justice, and the simple knowledge that the best way to make sure that a problem gets fixed is to get in there and fix it.

Those are not things that we know because someone sat us down and talked to us about them. They're things we learned by watching the adults who were around us, and important to us.

Today, we're all mourning the loss of one of the adults who loomed large in our lives. Yesterday, while bicycling to work, Megan Charlop was struck by an opening car door and forced into the path of a city bus. Her death leaves a gaping wound in many, many lives.

A couple of obituaries have already appeared, and I'm sure more will follow, because Meg was important to her community - her family - in so many ways. Chris Hayes described her as, "One of the most righteous, humane,compassionate human beings I've ever had the good fortune to know." The Bronx Borough President talked about her "tireless advocacy". My brother Dan talked about how full of life Meg was, "in every sense of the word." Philip Alcabes says that Meg "wasn't a maker of big policy. She was a maker of many small differences."

Meg Charlop showed me what love of neighbor really looks like, and how much of a force it can be. And so much more. I will miss her a great deal, and my heart bleeds for her family.

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Upcoming Travel - England, Germany, France

Wed, 17 Mar 2010 10:05:37 -0500

One of my many distractions lately is travel planning. After spending several months living in the wilds of Lower Alabama, I'm getting to take a bit of a vacation. Right now, face a 60-minute round-trip commute to get to the nearest bookstore (a marginally acceptable Barnes and Noble). If I'm going to make a longer trip to restock the larder, I might as well go the full Monty and hit the Waterstone's on Piccadilly Circus.

So I'm off to Europe for a few weeks at the beginning of April. I've got the rough outline sketched in, and I'm hoping that some of you can help me fill in some of the details before I go. Here's what I'm looking at so far:

Fixed Dates:
On the morning of 5 April, I arrive in London. I have a hotel booked in Central London for the following week. I also have a BritRail England pass, which gives me unlimited rail travel through England for that week. On the morning of 12 April, I depart for Frankfurt. I'll be staying with friends there for two nights, and heading on to Paris on the 14th. On the 15th, my wife and children will be arriving in Paris. We're planning to head to Normandy for a couple of days, then meet up with my parents back in Paris, head down to see some of my wife's family in Auvergne, and then get back to Paris on the 20th or 21st. On the 24th, I'm taking the train back to London, and I'll be flying home early on the 25th.

The gaps:
Right now, I've only got some tentative plans for the week that I'll be basing out of London. I'd like to make sure I get my money's worth out of the rail pass, and I'm very much open to advice on ways to do that.

The last time I was in the UK, I got out to Oxford, Cambridge, Stonehenge, and Down House. Here's what I'm thinking about for this trip, in order of priority:

Nottingham. This one's actually a bit of a priority for me. I'm a long-time Warhammer and 40K geek, and I'd like to get to Warhammer World, if only for a few hours. I'm probably going to do this on the 7th, and only for part of the day.

York. I'd like to see at least York Minster, the walls, and the Railway Museum. (Yes, I'm also a transport geek. In fact, I have lots of hobbies, and all of them are geeky in one way or another. At the moment, this is a very good thing, because it helps me compensate for the fact that I seem to have somehow wound up making a living in sports and aquatics.) I'm not sure if I'm going to go to Jorvik or not - if anyone's been there, and has a review, please let me know. I'm strongly considering DIG, or at least the Hungate tour. (Again, opinions from those who've done any of those are very welcome.) At the moment, I've tentatively decided to head to York on the 6th.

Dover. Dover Castle, in particular, has a lot of appeal, and I'd like to take an hour or two to walk along some of the paths that head toward the White Cliffs.

Canterbury. I've wanted to see the place since I read Canterbury Tales in high school, but somehow didn't get around to it last trip. I might stop there the same day I go to Dover.

Those are the places I've got the strongest feelings about, at least for the moment. I'm considering a number of others - Bath, Salisbury, Bristol, Liverpool, Manchester, Colchester - but haven't settled on any of them, or even tried to sort out which I want to get to most yet. I also wouldn't mind getting back to Oxford or Down House, but I don't know that I want to sacrifice going someplace new to get back to either of those.

London. This will be my third time in London. Last time, Matt Brown (who was then working at Nature Network, and is now at the Londonist) took us on a couple of fantastic walking tours that covered a good bit of the scientific heritage of the city. But, London being London, there are still a lot of places I haven't seen yet, and quite a few that I have, but want to see again. Suggestions here would be good - I've been to most of the major sights already at least once, but I'm open to any sort of suggestions here. About the only thing on my "I'm definitely not skipping out on again" list is Kew Gardens. Everything else is open.

Germany. I really haven't done much planning on this one. One of my local hosts was going to ask for advice on another blog. I'll link that when it goes up.

France. My family is doing most of the planning for this part of the trip. Since they're being nice enough to let me go off and explore on my own for 10 days, I'm not going to argue with them much. Still, suggestions, particularly for Paris, would be appreciated.

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The Illinois Poison Control Center Shows Us Why Poison Control Centers are Important

Tue, 16 Mar 2010 20:32:39 -0500

Via GeekDad, I just discovered the blog of the Illinois Poison Control Center. More specifically, I discovered the "Day in the Life of a Poison Center" feature they did last month. As medical blogging goes, this was brilliant. They posted very brief descriptions of each of the calls that came into their center in a 24 hour period. The Tweetable little descriptions capture the stress, fear, and humor that is an integral part of providing emergency health care.

Some of the calls were scary to read, even in two-sentence bursts. These were ones that contained the phrase "child got into" - or words to that effect. It's easy to forget just how much poison every home contains, and just how easy it is for even the most well-attended toddler to eat some of it when a parent turns away for just a second.

These are the calls that make me glad we've got poison control centers.

Unfortunately, the budget crunch that is facing governments all over the country is hurting the Illinois Poison Center. They've lost a million dollars of their State funding - 25% of their total budget - and are slated to lose more next year.

Fortunately, there's something you can do to help them out a little bit. They've been pledged a $1 contribution for everyone who becomes a facebook fan of theirs in the month of March.

If you want a little encouragement to click the link, I'm excerpting a few of the calls that came in to their hotline below the fold. I'm steering away from the more serious and tragic of the calls, and focusing on some that I found memorable for other reasons.

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More on the material and metaphysical: or, trying to unconfuse Larry:

Thu, 11 Mar 2010 20:57:15 -0500

In what seems to be a bit of a continuation on his earlier post (which I talked about yesterday), Larry Moran has another post up on the whole "is science ever compatible with religion" thing. At the end of the post, he asks a very good question - one that gets right at something that's very important:

So, what exactly are the limitations of science that we are supposed to adhere to? Earlier I criticized the concept of methodological naturalism because it seemed to rule out investigations of the paranormal as well as investigations of miracles. Robert Pennock, another philosopher, was asked about that during his testimony and he had a ready answer. See if you are convinced.

Q. Isn't it true that as we sit here today scientists are investigating what some people call psychic powers?
A. I know that there are a few scientists who did that I believe. Mack is one name, someone who's done this. So there are a few scientists who have done that, that's right, and what they do in that case is really the same thing. It's often misunderstood to think, to call something paranormal means that it is supernatural. Essentially what's going on in those scientific investigations is to say no, that's not so. We will again treat this purported phenomenon, ESP or telekinesis for example, as though this is a natural, still yet unknown, but ordinary causal process, treating it essentially in the same way we treat other things under the constraints of methodological naturalism, reconceptualizing it as a natural thing rather than a supernatural.

Cool. You can investigate the paranormal because it's not supernatural and you can treat it as a potential natural phenomenon. Presumably you will reach the conclusion that is is not a paranormal event.

But for some reason you can't do that for miracles and the role of God in theistic evolution. That's forbidden science.

Excuse me if I'm confused.

Actually, there are cases - quite a few of them, in fact - where theological statements can be investigated scientifically, and where they can, and have, been shown to be false. The circumstances that surround these cases are very similar to cases where ESP, ghosts, ghoulies, and things that go bump in the night have been investigated by science.

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A Weight Loss Plan That Works. (or: How I learned to stop worrying and love the gym.)

Thu, 11 Mar 2010 19:02:02 -0500

As you might have noticed, ScienceBlogs picked up a couple of new bloggers recently. Peter Janiszewski and Travis Saunders moved their blog, Obesity Panacea, over to these parts last week. Their move gives me an opportunity that's way too good to pass up - an excuse to present my latest excuse for a prolonged gap in blogging.

I've been too busy getting thin to post much.

OK, maybe "getting thin" isn't the most accurate description. But it sounds so much nicer than reality - which is more like "becoming merely overweight instead of downright obese". (For starters, it's a much pithier phrase.) The combination of the time I've been putting into weight loss combined with the 45 or so hours I spend without internet access during the course of the work week combined to drastically reduce my available free time. But I'll whine more about that another time.

Anyway...

Two months ago, I said that I'd be joining the ScienceBlogs fitness challenge. In my typical fashion, I then proceeded to do absolutely nothing about it for a week. It's quite possible that things would have stayed as they were for longer, but then an in-house version of The Biggest Loser kicked off at work. That was the little nudge I needed to get up and actually try to make the lifestyle changes needed to drop the weight.

It took some effort, and some substantial research, but I seem to have found a weight loss plan that really works for me. The evidence certainly seems to be pointing in that direction, anyway. Since late January, I've lost slightly over 32 pounds (or 14.5 kg or about two-and-a-quarter stone depending on your measurement system of choice). My BMI has gone from an atrocious 33.4 to a more reasonable (if not actually good) 28.9. My body fat, resting heart rate, abdominal circumference, chin count, and clothing sizes have all also seen corresponding drops.

My energy level is up, I feel better than I have in years, and I owe it all to this extremely simple, amazingly effective weight loss program I discovered:

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Cities, Solipsism, Scientism, and Spirituality

Wed, 10 Mar 2010 10:03:04 -0500

While reading Peter Ackroyd's London: The Biography, I came across something I hadn't heard of before - the "city hermits" that lived in medieval London. The concept struck me as odd - hermits (at least the non-crab variety) were something that I had always thought of as a purely wilderness phenomenon. A life of solitude? In a city? Really?

As I read on, I became less confused:

The figure of the hermit has another significance also; the stories of the city throughout the centuries have been filled with lonely and isolated people who feel their solitude more intensely within the busy life of the streets. They are what George Gissing called the anchorites of daily life, who return unhappy to their solitary rooms.
(p. 41)

That, I can relate to.

I've spent time out in wilderness areas by myself, but all of the times when I've felt the most alone, the most isolated from the rest of humanity, have come when I've been in the city. The bigger and busier the city, the more likely it is that I'll find myself feeling like the only man alive. Wandering through masses of anonymous people makes me see the appeal of solipsism like nothing else can.

At the same time, I've also found myself feeling more connected to humanity in the city than anywhere else - even when I'm surrounded by people I don't know at all. Some of those times have produced memories I treasure. Some of those times have happened in the same cities, on the same days, as moments when I've felt at my most solipsisist.

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Picture of the Day - 11 February 2010

Thu, 11 Feb 2010 15:37:42 -0500

The Sandwalk
Down House, Kent, England
31 August 2008
1/45 sec @ f/4; 18mm focal length

Technorati Tags: blogpix, darwin, Raw, sandwalk

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Verdict in Texas Nurse Trial - Not Guilty

Thu, 11 Feb 2010 15:18:00 -0500

The title on this one pretty much says it all - after less than an hour of deliberation, the jury in the trial of Anne Mitchell came back with a not guilty verdict. The civil suit against the doctor, hospital, sheriff, district attorney, and county will presumably now come out of the holding pattern it's been in while the criminal case was pending.

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The Texas Nurse Trial - How Did We Get Here?

Wed, 10 Feb 2010 22:33:40 -0500

The more I look at the circumstances that lead up to the criminal prosecution of a nurse in Texas for informing the State Medical Board of her concerns with a local physician, the more I wind up wondering just how things wound up where they are. It's easy - and far from inaccurate - to view this as a case of the good ol' boy network gone bad, or as an example of a quack doctor twisting the system to turn the accusers into the accused. The more I think about it, though, the more I'm starting to think that we've really been looking at part of the picture. We've been missing something that's probably just as important - the role played by the totally screwed up medical care delivery system in this country.

Let's start by taking another look at Dr. Rolando Arafiles. He graduated from medical school in the Phillipines in 1977. In 1994, he did an internship at Harbor Hospital in Baltimore. Two years later, he finished a residency in Family Medicine at SUNY Buffalo - but I can find no indication that he has ever been board certified in FP or any other specialty. In 2007, the Texas Medical Board restricted him from supervising physician's assistants because he had failed to properly supervise (pdf) a PA at a weight-loss clinic he worked for, and had failed to ensure that the clinic protocols met standards of care.

At the trial yesterday, Arafiles reportedly had difficulty even defining "standard of care". He said that diabetics heal as easily as anyone else. He was questioned about a number of medical errors he's made, and he explained that contrary to reports, he had not in fact intentionally sewn part of a suture kit to a patients finger, but had instead done so accidentally. According to the hospital administrator, Arafiles has been reprimanded for mistakes a number of times since he was hired in 2008, which was confirmed by a surprise state inspection.

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Picture of the Day - 10 February 2010

Wed, 10 Feb 2010 05:38:29 -0500

Remains of street sign embedded in pahoehoe lava flow.
Chain of Craters Road, Volcanoes National Park, Hawaii
4 November 2006
1/60 sec @ f/5.6; 55mm focal length

Technorati Tags: blogpix, lava, volcanoes national park

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The Winkler County Nurse Trial, An Alleged Massive Conflict of Interest, and Morgellons

Tue, 09 Feb 2010 22:32:04 -0500

As some of you might know, there is a very scary criminal case currently underway out in West Texas. A registered nurse named Anne Mitchell is currently standing trial. She's been charged with misuse of official information, which is a felony carrying a 10-year maximum sentence. She allegedly committed this crime by sending a complaint to the State Medical Board, because she was concerned about what she believed to be a pattern of sub-standard care and ethics on the part of Dr. Rolando Arafiles, a physician at the hospital where she worked.

Dr. Arafiles, according to the complaint filed by Mitchell and a colleague, engaged in a wide range of questionable activities. Even though he did not have surgical privileges at the hospital, he performed a skin graft in the emergency room. (The graft failed.) He sutured a rubber cap to a patients crushed finger to help protect it (yes, that's about as nutty as it sounds). He also repeatedly attempted to get patients to purchase - from him - various herbal remedies.

If you want to see the good Doctor at his questionable best, I just found (via a comment at another blog) some YouTube clips of an appearance that he did for something called "God's Learning Channel", which appears to be some kind of local access program. In this program, Arafiles is discussing Morgellon's - a condition which most physicians believe is nothing more than delusional parasitosis. Dr. Arafiles does not seem to share their view:

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