Monthly Archives: September 2008

Who’s Fanti’s Coach, I Wonder?

Remember the Brunswick County (North Carolina) School Board and their stated intention to see about inserting creationism into the science curriculum? Apparently, they’ve gotten the word that what they proposed has a legal history, and is unconstitutional.

Remember how I said it could come to pass that antievolution advocates might contact board members and try to reform their statements to come into line with current labels for religious antievolution? Well, it looks like someone has suddenly had a complete reorientation of their rhetorical approach, but it was the citizen who urged the board to incorporate creationism, Joel Fanti.

Fanti said he learned about the court cases after addressing the board and now thinks the idea of teaching creationism as part of the curriculum will be crushed. But he plans to ask the school board to encourage “evolutionists” in the schools to talk about the strengths and weaknesses of their theory.

“Instead of making it a religious issue, let’s make it a scientific issue,” said Fanti, who identifies himself as a chemical engineer.

What are the odds that Fanti would suddenly come up with and adhere to the current DI talking points all on his own? Coincidence? Or will we see Fanti urging the board at the next meeting to adopt either “Explore Evolution” or “The Design of Life” as supplemental texts for the science curriculum? Stay tuned… we should know something more after the October 21st school board meeting.

Nor can Fanti dispose of the religious freight the arguments that he apparently would prefer as “weaknesses” carry.

The Supreme Court decision in Stone v. Graham will likely play a role in a future case over the latest re-labelings of religious antievolution. Part of the reasoning there was this:

The preeminent purpose for posting the Ten Commandments on schoolroom walls is plainly religious in nature.

The ensemble of arguments advanced as “weaknesses” or as “scientific information” under the misused “academic freedom” label is simply a subset of the old, tired, bogus religious antievolution that we’ve seen for decades if not longer. The preeminent purpose in pushing those as part of a science curriculum will never be secular, as teaching students falsehoods serves no secular purpose. One cannot “make it a scientific issue” when all one has is the same old false information presented under a new label, without scientific credibility or accountability.

Hat tip to John Pieret.

<> 10397 3720 >

Palin and the Case of the Dropping Polls

Sarah Palin’s approval rating dropped recently. How much? Well, that may be a matter of some discussion.

The Political Wire blog puts it like this:

Gov. Sarah Palin’s favorable/unfavorable ratings have suffered a stunning 21 point collapse in just one week, according to Research 2000 polling. Last week, 52% approved and 35% disapproved of the GOP vice presidential nominee (+17 net). This week, 42% approved and 46% disapprove (-4 net).

I’m certainly among those who would have been in the 35% last week and the 46% this week if anyone had bothered to poll me. But I have an issue with that “21 point collapse” figure. The problem is that while we are given poll percentages as our basic data, the net points, as they are called, are from a different scale. If someone had a 100% approval rating on one poll and somehow completely disgraced themselves and earned a 100% disapproval rating on the next, the net points tally would be -200. The net points count every person’s opinion twice, as it were, and thus don’t correspond to how the casual reader will first take the message that Sarah Palin’s approval rating took a 21 point tumble. At least, I was expecting far more dramatic changes in the percentage scores based on that first number presented.

How could the original statement be altered to make it correct? That’s rather simple.

Gov. Sarah Palin’s favorable/unfavorable ratings have suffered a stunning 21 out of 200 possible net point collapse in just one week, according to Research 2000 polling. Last week, 52% approved and 35% disapproved of the GOP vice presidential nominee (+17 net). This week, 42% approved and 46% disapprove (-4 net).

As it is, based on the percentage numbers, the net change from one week to the next was that 10% of the poll respondents became disapprovers of Palin, and apparently 1% of the poll respondents undecided about whether to approve or disapprove of Palin shifted to disapproving of her, though that last is beneath the usual stated resolution of such polling techniques and should not be relied on. But we don’t need smoky, mirrory math to describe that. One can find a real number that comes close to the 21 net points number, and that is in what proportion of Palin’s former approvers have jumped ship to disapproving of her: that’s a loss of 19% of Palin’s former approvers, as 10/52*100. That is a serious alteration of the political landscape. We could even call it stunning and not be relying on a technique illuminated in the classic, “How to Lie with Statistics”.

<> 11613 4264 >

Frontiers of Science Workshop

Last Saturday, there was a “Frontiers of Science” workshop led by Rob Pennock. This was part of a series of workshops given for secondary school science teachers on science topics, and Prof. Pennock took up effective lab instruction in evolutionary science as his topic. The featured subject was use of the Avida-ED software platform as a means of giving students an interactive laboratory experience in which they can observe an instance of evolution occurring as they watch.

The late dearth of posts was due to getting prepared for this workshop. Part of my tasks included the creation of a new lesson plan for use with Avida-ED to be given its first outing at the workshop. This took up the misconception that fitness is some property inherent to an individual, but must instead be thought of as a property that is defined relative to the conditions of its environment. Rob assigned me to lead the workshop on this new lesson plan. There were both good points and some procedural difficulties encountered, but overall it was well-received, and at least one attendee expressed her intention to use the lesson plan for her class. I’ll be modifying the lesson plan to incorporate improvements based on the experience.

In making introductions of workshop participants, many of the teachers expressed the concern that they quite often encounter students or parents who have the idea that evolution demands that one must choose between faith and science, either rejecting evolutionary science and accepting faith, or accepting evolutionary science and rejecting faith. In some instances, teachers related that they’ve told students to inquire of their pastors what their denomination’s stance is on the matter. For many students attending mainstream Christian denominations, they are told that their denomination does not hold to the “conflict model” so effectively sold by religious antievolutionists, and they can study without fear that they are somehow going against their church by learning the material.

For any science teachers tuning in now, you should be aware of the Clergy Letter Project and its message from over 11,000 Christian clergy that says that one can have a vital faith and not dismiss evolutionary science.

<> 11923 4164 >

The State of North Carolina Education Folks Know History

Not long following the Brunswick County School Board announcing plans to get intimate with creationism, there is a report that the state officials have clarified for BCSB and its counsel that, yes, the 1987 Supreme Court decision in Edwards v. Aguillard put paid to notions that evolution could be balanced with creationism in the classroom. It would still be reasonable to keep tabs on future meetings of the BCSB to make sure the history lesson is absorbed.

<> 9910 3581 >

Dolphin Biopsy Study Hits the Press

I suspect an editor at the Miami Herald didn’t get the picture from Cammy Clark’s report on Jennifer Lewis’s research on bottlenose dolphins, for it appears with the headline, “Dolphin researcher’s method decried as `cruel’”. Well, yeah, if you look hard enough for people ignorant enough, you can get that sort of reaction. It doesn’t seem like something a responsible journalist would do to saddle a solid article with an irresponsible yellow headline like that, but it does sound like something a partisan at the paper might do to a perfectly reasonable news story.

Lewis is using a procedure for biopsy acquisition developed by Richard H. Lambertsen in the 1980s. (The paper is one of the earliest that I assisted in the production of.)

Richard H. Lambertsen. 1987. A Biopsy System for Large Whales and Its Use for Cytogenetics. Journal of Mammalogy, Vol. 68, No. 2 (May, 1987), pp. 443-445.

The problem with Lewis’s procedure is that she is apparently collecting biopsy specimens from dolphins in view of people with misplaced sensitivities.

But the sight of someone shooting icons of cute nature is too frightening for many in the Keys, triggering debate.

”This is cruel,” said Sheri Sullenger, founder of the Florida Keys Wild Dolphin Alliance. “They could become infected and even die. And the dolphins appear like they are being hunted, and are starting to change their behavior.”

Clark’s report addresses Sullenger’s assertion.

Biopsies have the potential to harm or kill, said Keith Mullen, marine mammal program manager at the Southeast Fisheries Science Center in St. Petersburg and the person overseeing Lewis’ work under the federal permit.

”But done safely with training, the risk is very minimal,” Mullen said.

He said he knows of only one documented case in which a dolphin died after a biopsy sample was taken by a crossbow: in 2000, in the Mediterranean Sea.

”It’s amazing how quickly they heal,” Mase said. “They are adapted to recovering from shark bites.”

They could become infected, sure, but the risk, as shown by decades of practice, is pretty darn low.

”We have happy, healthy dolphins,” said Donna Fielder, who runs Captain Seaweed Charters. “If we were having sick or injured dolphins, and they were showing up dead and we didn’t understand what was going on, then absolutely come in and do the research to assist in solving the problem.”

I’m sorry, Ms. Fielder, but you have no clue about the health status of the dolphins in the area. You may see dolphins doing what you perceive as cavorting, but on the one hand that doesn’t even guarantee that those dolphins have the health status that you assign, and on the other it does not speak to a population’s health status. Purposely remaining ignorant until after a mass stranding is, well, idiocy.

Again, Clark’s report has the relevant rejoinder within it.

”People in the Keys are emotional about the dolphins and sometimes it’s hard for them to understand the science,” said Blair Mase, Southeast Stranding Coordinator for the National Marine Fisheries. “They don’t want any harm to come to them, and neither do we. But the amount of information we gain is so valuable to help us protect them better.”

So, why would the editorial staff undo the careful research of Clark with the inflammatory and pandering-to-the-ignorant headline they chose? It’s a mystery.

<> 12932 4541 >

Collecting More OAS Information

Given the comment on my earlier thread pointing out a surgical alternative to use of CPAP machinery, I’ve been doing some looking into treatment of obstructive airway syndrome (OAS). This evening, I came across another alternative, oral appliances (OAs). These are structures applied in the mouth that are supposed to provide an open airway mechanically, but without the need for a power supply, as CPAP devices require. OAs apparently don’t have as much research behind them as either CPAP or surgery, but it’s a good thing to have some acquaintance with the options before spending one’s limited time in conference with one’s physician. That way, discussion can move on to more substantive issues related to personal treatment rather than being taken up with the physician giving tutorial information about methods.

<> 14805 5029 >

Inside the Trailer, Doing a 360

A panorama, that is.

Given the pitiful wages that postdocs and adjunct faculty earn, the debt accrued through grad school for two, the further problems that my medical issues have caused to our finances, and the rapidly rising cost of living, we need to sell our trailer so we can take down some of the debt. In order to further that cause, we gave the interior a thorough cleaning in preparation for taking pictures. My previous experimentation with the Hugin panorama tool made me confident that I could do a 360 degree panorama to show most of the stuff in the trailer. And here is the first one:

And another, with the beds raised:

And another, configured for cargo (“toy”) hauling:

Hand-holding the camera for panorama stitching wasn’t completely satisfactory, so I looked into panorama heads. These are devices that allow you to mount a camera and lens such that the whole apparatus rotates around an axis that passes through the nodal point of the lens. When that happens, things that were in alignment in foreground and background remain in alignment. Unfortunately, panorama heads start at about $80 and quickly run up to a couple of grand. The device at the low end of the scale, the Panosaurus, seems reasonably engineered. There are, of course, things one doesn’t get that the more expensive heads deliver. However, even $80 is out of my budget at the moment. In making my online searches, though, I came across a cheaper alternative: do-it-yourself. I spec’d out the materials, and my father-in-law Sam sprang for the parts: 48″ of 1×4″ oak, 1/4-20 insert nuts, washers, and wingnuts. From that $16 purchase, I’m putting together two homemade panorama heads and will ship one to Sam.

The homemade job doesn’t offer adjustments like the commercial heads do, but if one is careful in measuring where the lens nodal point lies and physical dimensions involving the camera/lens combination, one can get good performance out of the setup. The trailer panorama was made with the homemade head, and Hugin reported a mean alignment error of 0.6 pixels, maximum 20.6 pixels, and pronounced the fit “very good”. There were a total of 19 pictures aligned and stitched to make that panorama. I also used the Qtpfsgui HDR software, so each of the 19 pictures is actually derived from three separate bracketed exposures that were tonemapped using the same settings. The one thing that I didn’t nail down that I should have was the white balance used; you can see that the auto white balance thought the cabinets on one side of the trailer were slightly different in color from those on the other side.

Now, on the slim chance that anybody reading this is looking for a trailer, here’s the summary. The trailer is a 2006 model Northwood Desert Fox SW-21. That’s a 21-foot “toy hauler” model bumper-pull trailer, total length of about 25′ from hitch to rear end. It has a bathroom with shower and tiny tub, refrigerator (propane and electric, with automatic switchover), gas oven and range, microwave oven, two beds with electric lift, 4 kilowatt Onan generator, gas tank and pump, central heat and air-conditioning, and completely enclosed tanks for water and wastewater. Besides the two queen-sized bed mattresses, the dinette bench seats fold to make another bed, and the couch seat folds to make another. This model has insulation and the tank enclosure for all-weather use; if the heater is run to keep the interior warm, it also keeps the plumbing from freezing. Diane got this model trailer in order to have a place in the field in Wyoming where she was doing research back in February through April, 2006, and it worked fine through the cold weather there. We’ve used the trailer as a guest room for company and an emergency shelter for times when the electricity has gone out at the house we’re renting in addition to trips to places where we’ve dry-camped. For those unfamiliar with the toy-hauler concept, this trailer’s basic reason for being was to transport one or two “toys”: motorcycles, dune buggy, ATVs, etc., to a place where the toy could be used in the great outdoors, and while on the spot, provide a place to sleep and cook meals. The back of the trailer is a large ramp that folds down, permitting the “toy” to be loaded in and taken out. One reason I like this design is that it has a high roof; I don’t feel like I’m going to bump the top of my 6′ 3″ frame into the ceiling while moving around inside. We don’t have “toys” of the sort that the trailer was intended to carry, but the floor comes equipped with a number of internal tie-down points for securing a load from shifting around. We use a 2005 Ford E-350 one-ton van to tow the trailer, which it does fine with a weight-distributing hitch. We’d consider selling the van and trailer as a complete package. We’re looking to get Blue Book value on the trailer or both. We’ll toss in the macerator pump with the trailer; that’s a handy device for being able to dump the blackwater tank through an ordinary garden hose to either a distant dump station or septic system standpipe. [Other features that I missed initially: indoor/outdoor stereo system with AM/FM radio and CD player, bedside light and stereo power switches, roll-up awning, 6 gallon capacity propane gas water heater, kitchen sink, bathroom sink, carries two propane tanks, two 12V deep discharge batteries, exterior light with switch by electrical and water hookups, outside shower, and space for a bar-be-que. We never got the bar-be-que, but I'm sure that could be high on someone else's list of amenities to acquire.]

Having the van and trailer got us to a campsite in the Smoky Mountains where I could get this picture of Ritka:

And here are a couple of pictures of the rig on the road.

<> 24273 7527 >

Another School Board Poised to Make a Mistake

A report in the Wilmington (NC) Star-News recounts interaction at the meeting of the Brunswick County School Board. It’s the same old religious antievolution.

When asked by a reporter, his fellow board members all said they were in favor of creationism being taught in the classroom.

The topic came up after county resident Joel Fanti told the board he thought it was unfair for evolution to be taught as fact, saying it should be taught as a theory because there’s no tangible proof it’s true.

“I wasn’t here 2 million years ago,” Fanti said. “If evolution is so slow, why don’t we see anything evolving now?”

The board allowed Fanti to speak longer than he was allowed, and at the end of his speech he volunteered to teach creationism and received applause from the audience.

Please, please, Brunswick School Board, if you do go ahead with this plan, do have it taught by Joel Fanti. I really have a desire to see Mr. Fanti cross-examined by Eric Rothschild or Steven Harvey.

Besides the school board members all being in favor in sticking religious antievolution into the classroom, the report classes their legal advisor among the incompetent:

Board attorney Joseph Causey said it might be possible for the board to add creationism to the curriculum if it doesn’t replace the teaching of evolution.

Unless Joseph Causey just stepped out of a time machine bringing him to the present directly from, oh, 1986 or before, no, one cannot simply add creationism to the curriculum. That was the basis of “equal time” and “balanced treatment” labels for religious antievolution arguments, and those had local failures in court from 1975 to 1982, and the 1987 Supreme Court decision in Edwards v. Aguillard quite clearly said “no” to inclusion of creationism.

Now, we might predict some outcomes in the case of the Brunswick County School Board’s consideration of creationism as a way to waste time in science classes there. Maybe Joseph Causey, Esquire will either buy or otherwise acquire a clue, and inform the board that what they are considering has been considered unconstitutional for over two decades. That could do the trick. If they check their insurance, they’ll likely be informed that attempting to defend creationism in the courtroom will not be covered by any provision of their insurance policy. However, we aren’t talking about these folks doing this in a vacuum. If I got the notice of this report, the Discovery Institute won’t be far behind, and is likely to be on the phone with one or more of the school board members posthaste. This is the sort of opportunity the DI doesn’t often miss having a go at. What we might see in that case is a sudden alteration of the rhetoric being spouted from advocacy of creationism to one of the trendier labels currently being pushed by the DI, either “academic freedom”, “critical analysis”, or “strengths and weaknesses” heading the list. Since it is a school board, I’d say that there may be a slight preference for “strengths and weaknesses”. “Academic freedom” seems to be what the DI offers to state legislatures so as to remove the possibility of a facial challenge to a law. So, come October 21st, we’ll see whether the Brunswick County School Board managed to get wise in the interim, or get taken by deceptionists looking to peddle the same old religious antievolution arguments under a different label.

If they do try the path of deception, I’ll note that judges seem not to take kindly to people trying to skirt rulings. The 1987 Supreme Court decision had already identified the essential untruth behind the urge to re-label what was plainly a religious doctrine, calling it a sham. The 2005 decision in the Kitzmiller v. DASD case cited that specifically, and noted the personal falsehood-telling ways of various principal actors on that school board as they tried to morph from being “creationism” advocates to being ‘intelligent design” advocates. The record caught up with them, and their strategies to deny the past failed.

OK, Brunswick County School Board, what you have said so far has been noted. I’m going to drop the reporter a note to make sure the documentation is preserved, so that there won’t be the unseemly behavior that we were treated to in 2005, when the Dover School Board advocates asserted that the multiple reporters who quoted them saying “creationism” must have invented it all. No, teaching creationism and evolutionary science doesn’t make everything peachy; that’s over twenty years out of date. Science is taught to students because it is important for them to know. Religious doctrines are not taught to public school students, because religious instruction should be a matter for parents to determine, not buttinsky school boards.

<> 32279 8088 >

A Critique of the McCain Health Insurance Plan

A press release points out a review of the likely effects of the plan proposed by John McCain to change health coverage. The results? They don’t look so good.

“Moving toward a relatively unregulated non-group market will tend to raise costs, reduce benefits, and leave people with less consumer protection,” says Sherry Glied, PhD, professor and chair of the Department of Health Policy and Management at Columbia University Mailman School of Public Health and one of the paper’s authors. “The system Senator McCain envisions is one in which many more — perhaps most — insured Americans would buy health insurance and health services in a national, relatively unregulated, competitive market. Because this is a radical departure from the current system, its likely effects deserve close attention.”

Well, I guess we weren’t expecting McCain to propose something that would be socially progressive on the healthcare front, and he apparently does not disappoint on the “let them eat cake” factor.

As someone who has benefited greatly from having health care group plans available through my employers (or Diane’s employers), I can be pretty confident in saying that if I had significantly less coverage, I wouldn’t be writing this, I’d have kicked it about the time my colon perforated in 2004. That was caught quickly because I was already hospitalized and had attending physicians who were paying attention to symptoms that were not at all obvious to me.

According to Dr. Glied, the elimination of the income tax preference for employer-sponsored insurance would cause 20 million Americans to lose coverage, but the effect could be much larger especially if employers are quick to drop health benefits in response to the McCain plan, or if employers drop coverage for low wage workers. She suggests that “while initially there will be no real change in the number of people covered as a result of the McCain plan, people are likely to have far less generous policies than those they have today.”

It seems to me that it is silly to spend billions per year for critical care treatment for the un- or under-insured and act like spending any part of that for preventive medicine for the same groups would be somehow un-American. Saving lives is un-American? Saving money is un-American? It sounds to me like the McCain plan simply shifts more people to having astronomical medical costs assessed against them personally, rather than having effective health insurance, or to being indigent non-paying patients crowded into hospital emergency rooms, our health poor-houses.

<> 23382 7460 >

My Next Medical Challenge

I shared a room with a colleague at the GECCO 2008 conference, and my snoring disturbed him. I brought this up with my primary care physician, who set me up to take a sleep study. This isn’t a new thing; I was experiencing daytime sleepiness back in high school, where my Spanish teacher was confounded by my frequent naps in class despite doing well on homework and tests (and that despite the rotating class schedule so that classes met at different times of the day through the term).

I arrived at the Sleep Center the evening of my study and was escorted to a room. The room was a fairly basic affair, much like your standard mid-America motel room: bed, end tables, dresser, TV, private bath (shower only, no tub). It had some other amenities not usually found (or not usually noticed) in your standard motel room: continuous positive airway pressure (CPAP) gear, IR camera, and various bits of data acquisition setup.

They had me watch a videotape that gave a little explanation of sleep study procedures and a lot of promotional information about a brand of CPAP apparatus. The assumption throughout was that patients would have obstructive airway syndrome (OAS) treatable with mechanical aids, to wit, a CPAP machine or one of the close variants with somewhat more capability.

But first things first… there needed to be a diagnosis. And for that, I needed to be rigged up with a variety of monitoring equipment. In order to assess what sort of stage of sleep I might be in and for neurological data, my nurse hooked up about eight leads for an electroencephalogram (EEG). They also wanted to see cardiac response, so I needed three more leads for an electrocardiogram (EKG). Because poor sleep states often involve excessive leg movement, I needed two leads on each leg for electromyography (EMG). Also, stress that is involved in some sleep deprivation is manifested in teeth clenching or temporo-mandibular joint (TMJ) tension, so I needed another six lines or so of EMG on my face. Pressure sensors at the nostrils would pick up nose versus mouth breathing. Two strain gauges on bands around my abdomen and chest would help monitor respiratory effort, an essential part of distinguishing OAS from central neural system causes of sleep disorders. And, last but not least, a pulse oxymetry device was installed on my right index finger. It took about fifteen minutes to get me tricked out in all the data collection lines. An illustration might help:

OK, after all that, I was supposed to get to sleep. Usually, I don’t have difficulty getting to sleep, even under otherwise challenging conditions. But I did have trouble that night. I also have issues with the aftermath of having had a colectomy. I usually am up once in the middle of the night to make a bathroom trip. That night, I was up twice for that purpose. I recalled awaking four times; I’m not sure how many times the instruments called it. I also recalled about four distinct periods of dreaming; again, I don’t have the details on how much REM sleep I was recorded having. So in the morning, another nurse came in to remove the various leads, leaving me looking ill-used:

I took advantage of the shower and then got out of there.

A few days ago, I got a call from the Sleep Center wanting to schedule my second visit. I hadn’t heard from my primary care physician, but apparently she had ordered the second round. I called in to find out what was up. Apparently, I do have a diagnosis of OAS, with observed episodes of sleep apnea and hypopnea, with my O2 saturation going down to 83% at one point. The second study will hook me up to CPAP and do a titration to figure out just how much pressure is needed to keep my airway open during the night.

I’m joining a common club. According to a survey, about 24% of men in the USA have some form of OAS, and 9% of women. Middle-aged men are more prone to OAS. OAS also has implications beyond the direct sleep-disorder thing: increased risks of heart disease, hypertension, arrhythmias, diabetes, obesity, and erectile dysfunction. Fortunately, I don’t have the laundry list of effects, but arrhythmia is among the things I have manifested. As far as I recall, my previous healthcare team working on what they called idiopathic atrial fibrillation events did not assess me for possible OAS as a contributing factor.

According to the promotional video, many of the people getting treatment for OAS find that a number of quality-of-life issues improve. I’m looking forward to seeing if I get any of those benefits myself.

<> 17146 6077 >

Evolutionary Computation and Astronomy

Back in 1998, I was suggesting the use of evolutionary computation to investigate alternative hypotheses concerning data about foraging in a certain species of bat that preyed upon a particular species of insect. Nature has a summary of a paper in Astrophysics Journal where the researchers used a genetic algorithm to look in a space of over a quadrillion possible orbits for a spiral galaxy and a dwarf elliptical galaxy, and come up with an orbital scenario that closely matched the observed characteristics of the pair. This is a somewhat different application of evolutionary computation, essentially to identify better explanations for an observed state, rather than to produce an approximate solution to a problem given a specific set of conditions. I have no doubt that more of this style of application of evolutionary computation will be seen in the future.

<> 13291 4712 >

Computational Chemistry and … Evolution?

Research at Florida State University in computational chemistry has uncovered evidence that an enzyme that initiates processes involving DNA and RNA does the job via two mechanisms, one of them slower than the other.

Wei Yang is an assistant professor in FSU’s Department of Chemistry and Biochemistry and a faculty member in the university’s Institute of molecular biophysics. Working with colleagues from FSU, Duke University and Brandeis University, he recently produced remarkable computer models of an enzyme that carries the unwieldy name of inosine monophosphate dehrydrogenase, or IMPDH for short. IMPDH is responsible for initiating certain metabolic processes in DNA and RNA, enabling the biological system to reproduce quickly.

“In creating these simulations of IMPDH, we observed something that hadn’t been seen before,” Yang said. “Previously, enzymes were believed to have a single ‘pathway’ through which they deliver catalytic agents to biological cells in order to bring about metabolic changes. But with IMPDH, we determined that there was a second pathway that also was used to cause these chemical transformations. The second pathway didn’t operate as efficiently as the first one, but it was active nevertheless.”

Why would an enzyme have two pathways dedicated to the same task? Yang and his colleagues believe that the slower pathway is an evolutionary vestige left over from an ancient enzyme that evolved over eons into modern-day IMPDH.

Now, that’s a pretty cool finding. I wonder how many other enzymes that we think we know everything about have alternate mechanisms for getting things done.

<> 10229 3600 >

An Example of a Difficult Patient

Michelle Mayer had to become a difficult patient to secure adequate health care for a misdiagnosed illness that actually turned out to be scleroderma. She has a blog, Diary of a Dying Mom, where she discusses her own case and the larger policy issues of how health care is managed — or mismanaged — in this country.

I’ve seen the necessity for being alert and my own advocate while hospitalized for the last part of my ulcerative colitis. There was the critical information that, at the time, seemed trifling: the acquisition of a sharp pain in my shoulder during a shower. What it suggested to my internist was something I had not considered for a moment, that my inflamed and weakened colon had perforated. Follow-up X-rays and a CT scan confirmed that, and set me up for an emergency complete colectomy. At another point, I requested the re-insertion of a naso-gastric tube to reduce the chance of vomiting during my recovery. At another, I refused to take a provided medication that didn’t match up physically to the shape and color of the pill I was expecting.

Mayer’s sojourn covers far more ground, though, as her case pitted her against the policies that make doctor-patient interactions fleeting and cursory. My own case had something of the inverse problem Mayer had. For Mayer, an early diagnosis of a more minor malady prevented the attention needed to make the real diagnosis of a major illness. For a couple of years, I had an internist who refused to believe that I actually had an ulcerative bowel disease, until I presented at a colonoscopy with a full-blown flare-up plus a Clostridium difficile infection on top of that. (“You’re sick,” was his simple admission that the previous five doctors had not gotten it wrong.)

<> 15598 5248 >

A Study on Whistles — And Only Whistles

There’s a study in the Journal of Comparative Psychology that comes somewhat up my alley.

Quick, Nicola J. and Vincent M. Janik. 2008. Whistle Rates of Wild Bottlenose Dolphins (Tursiops truncatus): Influences of Group Size and Behavior. J. Comp. Psych. 122(3):305-311.

OK, so what are the authors reporting as results? A lot of that is in the abstract:

In large social groups acoustic communication signals are prone to signal masking by conspecific sounds. Bottlenose dolphins (Tursiops truncatus) use highly distinctive signature whistles that counter masking effects. However, they can be found in very large groups where masking by conspecific sounds may become unavoidable. In this study we used passive acoustic localization to investigate how whistle rates of wild bottlenose dolphins change in relation to group size and behavioral context. We found that individual whistle rates decreased when group sizes got larger. Dolphins displayed higher whistle rates in contexts when group members were more dispersed as in socializing and in nonpolarized movement than during coordinated surface travel. Using acoustic localization showed that many whistles were produced by groups nearby and not by our focal group. Thus, previous studies based on single hydrophone recordings may have been overestimating whistle rates. Our results show that although bottlenose dolphins whistle more in social situations they also decrease vocal output in large groups where the potential for signal masking by other dolphin whistles increases.

I was right with them up to the part bolded in the above. Why am I not convinced that their paper delivers on what the abstract promises? Let’s have a look at the methods of the paper.

The distributed array consisted of three HTI–94–SSQ hydrophones and one HTI–96–MIN hydrophone (High Tech, Inc., Gulfport, MS) all with a frequency response of 2 Hz to 30 kHz +/- 1 dB, attached to tensioned 2m pieces of chain with waterproof tape. The four elements were then distributed around the boat in a box array to allow passive acoustic localization. Hydrophones were positioned at 2m depth and were placed between 160cm and 280cm apart. Recordings were made onto a Fostex D824 multitrack digital recorder (Fostex, Tokyo, Japan) during 2003 and an Alesis adat HD24 multitrack digital recorder (Alesis, Cumberland, RI) during 2004 (sampling frequency 48 kHz, 24 bit for the Fostex, 32 bit for the Alesis). Spoken tracks of the two observers, one detailing the surface behavior of the animals in the focal group and one the positions and behavior of nonfocal groups were also recorded on the multitrack recorder.

Anybody spot the trouble yet?

Sure you did.

First off, one simply isn’t going to get higher frequency response out of a system than that of the least capable component. Starting with the hydrophones, 30 kHz is near the top frequency one might be getting. There is the issue of roll-off, but generally there is pretty steep roll-off at the high end of a hydrophone frequency response curve. I didn’t find an accessible calibration curve for the Hi Tech hydrophones to find exactly what the roll-off would be. But even that is going to be truncated sharply by the recording gear. The Fostek D824 recorder is said in the methods to have a “sampling frequency [of] 48 kHz”, but that is ambiguous. One can report a sampling rate of, say, 48 kilosamples per second, or a Nyquist frequency of 24 kHz. The upshot is that the Fostek recording six channels, as stated in the methods, is capable of 48 kilosamples per second per channel, giving a Nyquist frequency of 24 kHz as the highest frequency that the recorder might manage to represent. So just from that, we know that no frequency data over 24 kHz was part of the set analyzed in this study. (We won’t go into the lack of specification of anti-alias filters in the equipment as it isn’t really relevant to my critique, but any serious acoustic analysis would need to take aliasing into account.)

Here’s something from the discussion…

In our study, whistle rates during socializing in groups of 6 to 10 animals was 0.53 whistles per minute per dolphin, for nonpolarized movement it was 0.27. Dolphins in Sarasota only whistled half as often in similar group sizes during these behavior patterns (Jones & Sayigh, 2002). In Wilmington, whistle rates during milling were the same as in Sarasota, but for socializing they were Increased whistle rates during socializing may be due to animals communicating information to social associates or using calls to maintain contact. According to our definition animals were socializing when they were within very close proximity, often rubbing body parts and touching (see definition in Table 1). Rates may be dependent on social bonds between the individuals present or may be a consequence of increased arousal due to contact with individuals and not be dependent on social relationships. Cook et al. (2004) showed higher signature whistle rates during socializing and suggest that this may function to maintain contact as other group members get more dispersed while individuals are engaged in socializing.

OK, this gets to the stuff that I just can’t handle. Remember that 24 kHz maximum possible frequency in the data set? (Due to practical considerations, it could be even lower.) Bottlenose dolphins have an upper hearing response over eight times as high as that. Bottlenose dolphins have peak frequencies in clicks over six times as high as that. The sweeping speculations about communication inherent in the abstract and the quote just above are made in complete ignorance of over 7/8ths of the acoustic sensitivity of the subject species, and over 5/6ths of the peak frequencies within the vocal repertoire of the species. We know that click-based sounds are used by dolphins in communication; the only experimental work on obligate acoustic communication between individual dolphins to perform a task revealed that the signals used by the subjects were click-based and not whistles. We know that recording lower frequencies does not necessarily secure any vestige of click-based vocalizations. There is absolutely no consideration in the study here given to any of those issues or the fact that click-based sounds could quite plausibly be used for some of the functions being discussed. In fact, the paper does not even contain the word “click” or the word “pulse”. As a result, the claim that dolphins “decrease vocal output” within this study is something that the authors cannot possibly support; they have no clue whatever what dolphin vocal output over 24 kHz might be. They can, at best, report that dolphins decrease whistle rates with increasing group size, but they need to leave the “vocal output” claim out of it, since there is so much more to bottlenose dolphin vocal output(*) than the puny amount of bandwidth that they actually measured.

Whistles do seem to have some importance in dolphin behavior and sociality. But just because whistles have traditionally been relatively simple to acquire by comparison to high frequency, broad bandwidth, narrow beam clicks does not mean that clicks in general or those higher frequencies can be ignored with impunity. Studies like the present one should make their speculations that take cognizance of this technological gap between what we humans can readily find out and what the dolphins are actually using.

(*) What to call dolphin sound emissions is a semantic issue. Personally, I don’t see the problem with “vocal” that some others do; the roots of the words were non-technical in the Latin, and one need not treat “vocal” as pertaining only to laryngeal sound production. Some offer “phonation” as an alternative, which so far as I can see simply grabs another non-technical Latin root that has as many issues and baggage from prior usage as the other. I went so far to avoid even getting into this terminological morass in my dissertation as to invent a neologism for emitted sound, and called them ensonds. For the purposes of this post, I’m simply accepting “vocal output” as sufficiently clear to move along with.

<> 19899 7536 >

The Tammy Bruce Factor

Tammy Bruce has an op-ed piece plumping for Sarah Palin, “A feminist’s argument for McCain’s VP”. Bruce apparently likes a inverted form of the genetic fallacy in which she seeks to gain approval for her arguments by identifying herself as liberal and feminist. Bruce sees things starkly, as befits a Fox News analyst. Between Hillary Clinton getting a raw deal from the Democratic primary process and the Republicans choosing a female VP candidate, Bruce assures us that the feminist response must be to embrace the true feminist-sensitive folks, shown in this election to be the Republican party. Those inconvenient statements from McCain and Palin on women’s reproductive health? Never fear, argues Bruce, they haven’t made those a priority in their past political lives, so we can be sure that they will not ever use their authority to push those issues. It’s utterly safe to vote for them this fall, according to Bruce.

I don’t think so.

I don’t know that I could call myself a feminist or sign on to various examples of twaddle that have passed for feminist commentary. I do know that I’d have had no issues on account of gender if Hillary Clinton had headed the Democratic Party ticket this fall, and my current opposition to the Republican Party ticket is certainly not premised on the gender of the VP pick there. But I don’t for a moment believe that gender is all it takes to inject an appreciation for equal rights into a campaign or an administration. Would Bruce argue in the same vein if McCain had picked Phyllis Schlafly, that most implacable foe of the Equal Rights Amendment, as his running mate? Unfortunately, I don’t have any evidence that would say “No”. Others have noted that Bruce’s words rarely, if ever, seem to corroborate her self-classifications. So far as social agenda is concerned, Sarah Palin has done nothing to distinguish herself as being other than a younger, less strident, and more attractive Phyllis Schlafly. Feminism is not an obligate stance of those who are physically female (or their exploiters), and Tammy Bruce is certainly making no sale on her argument with me.

<> 9538 3568 >

“Victory in Iraq” — What Does that Mean?

Sarah Palin’s acceptance speech at the Republican convention made a couple of mentions of a concept of victory in Iraq and how her political opponents didn’t want it or didn’t recognize that we are “close” to achieving it.

Which makes me wonder what, exactly, the victory conditions are for us when it comes to Iraq.

The new regime in Iraq is plagued by a number of problems, but the top one has to be that it cannot reasonably expect to secure itself from internal or external threats to its own continued existence. It requires the continued — and continual — presence of security forces to assure its own existence. Victory cannot mean that we will soon come to a point where we can hand over both control and responsibility to the new Iraqi government. If we want that government to continue, we have to either provide troops to continue to help secure it, or convince allies to do that in our stead. How long will it be before the new Iraqi government has even the poor prospects for stability of other middle-eastern governments? We are certainly talking years, and possibly decades, before that state of affairs is likely to come about, if it comes about at all.

Maybe Palin is talking about Iraq ceasing to be a magnet for insurgent forces and terrorist personnel. Again, this doesn’t appear to be anything that we can say will happen in terms of days, weeks, or months. The bungling of the Iraq war was inherent in its conception as a showcase for a high-technology, hands-off, stand-off sort of affair with minimal involvement of ground troops with irregular forces. That’s the war Rumsfield planned for, but you don’t get the war you plan for, you get the war your enemy makes for you. A problem in Iraq had to do with the fact that there wasn’t a singular enemy to be defeated; Saddam Hussein was simply the top of a regime that itself kept the lid on a number of factional disputes that had long been simmering. The removal of Hussein’s regime simply allowed all of those to come to the fore and start interacting with our forces, and since our forces had no intention of allowing them free reign to pursue each of those disputes, our forces became targets of them, too. There’s plenty of what-ifs to go around, but it seems certain that Rumsfield and the Bush administration failed to heed the old saw about quality, and bought a shoddy war thinking that they were getting a bargain. The USA gets to shell out for that spectacular failure in judgment, and will be shelling out for a long time to come.

It seems to me that what Palin is referring to as victory is simply a possibility that defeat is not immediately in the offing, as it seemed might be the case just a couple of years ago. Adding more US troops helped shore up the security situation such that the new Iraqi regime need not be described as teetering on the brink of collapse, but it hasn’t turned everything bright and rosy.

Considering moral issues instead of pragmatic politics doesn’t improve things. The conduct of the war has not distinguished our forces from the terrorists we claim to be our targets. We capitulated any claim to moral superiority early on, and have not acknowledged that there was a problem to be corrected since. The decision to devalue the lives of non-citizens did not proceed without damage to how citizens are valued by the agents of our government. The corrosive nature of this moral turpitude that we adopted is nowhere clearer than in the loss of personal freedoms for our own citizens, covered over with mistaken labels invoking patriotism. The Republican nominee, who should understand the basic injustice against human dignity that torture represents, failed to stand up for that dignity, and instead connived with our current administration in their attacks upon it. Candidates for various positions of both parties, though, have found it convenient to extend the current administration’s policy of denying — not merely failing to protect — the free speech rights of those who disagree with them. “Free-speech zones” are no such thing, as removal to where one will neither be seen or heard by those one disagrees with is straightforward denial of free speech.

Iraq’s future, rightly or wrongly, is now a responsibility that we as a nation have taken on. We may eventually, with massive expenditure of money and heartbreaking loss in lives, help ensure the security of the regime there that we made possible. But to reduce this complex issue to the jingoism inherent in Palin’s “victory” rhetoric is an insult to those who have given their lives in the war and to ourselves, our children, and very likely our grand-children, whose livelihoods have been yoked to the burden of paying for every advance made or defeat endured. We deserve leadership who can assess actual situations, not techno-fantasies as this war’s architects indulged in, and come to a sober assessment of benefits, costs, and risks, and be willing to abandon convenient political equations to secure our best interests. Sarah Palin’s speech shows a facile command of cheap rhetoric; it does not demonstrate the resolve or ability needed to fix the mess that she would be inheriting from the current administration.

PS: After writing this, I had a look around and found a similar topic in Slate

<> 10370 3984 >

Good News on Equipment Malfunction

Early in the summer, I noted a problem with my Canon S2 IS camera. It would intermittently show a black screen in camera mode, though the screen worked fine for playback. I was planning on arguing with Canon repair people, since the S2 did not have a service advisory out on it.

Well, I found out something since then. I procrastinated long enough on sending it in that I had to look again for forms to send it in for service. While I was doing that, I found that some other people had encountered this, and found a do-it-yourself fix. The problem wasn’t in the linkage to the sensor chip after all, as previous searching had indicated as the likely thing. Instead, various folks said that the iris sticks in a small-aperture condition. Further, by putting the camera in “Tv” or shutter priority mode and setting the shutter to 15 seconds, tripping the shutter release, then turning the camera off after seven seconds have elapsed, one can force the iris to open again. This process may need to be repeated several times, and the condition may turn up again. But regular use of the camera tends to reduce how often the finder blacks out due to the sticky iris. My S2 is working fine once again, and I don’t have to worry about a repair bill that I can’t afford.

<> 17005 6070 >

A Thirty-Year Interval

Back in high school (Santa Fe Catholic Regional High School, Lakeland, FL), I went to many of the football games as a photographer for our yearbook. One nice thing about football games is that people tend to be in good spirits, at least before the game commences. I don’t remember exactly which game the following photo was taken at, but Bill Robinson and I had arrived and five of our classmates turned up while we were getting photo gear organized to go in. Bill snapped this picture of the six of us arranged across the hood of the green El Camino I drove around at the time.

Now for the bad part… I don’t know that I can recognize everybody here, or even if I get all the names, accurately place them with the people. Beth Bordelon is on the left, Lee Pinner at bottom left. Jo Ellen Riley is in here, I think on bottom right. I think that might be Sharon Harrell leaning on my right shoulder. It is Jennifer Venable on my right shoulder (thanks, Teresa!). And it could be Linda Rushing leaning on my left shoulder. It is sad what thirty years can do to the memory. Any of you whose memory has not turned to mush, please help me with the corrections.

The exposure was skewed by the street lights in the background, so the negative was underexposed. The print above was the result of processing the negative a couple of times in chromium intensifier and still required a fair bit of dodging in the center to lighten two faces there. That is clearly seen in the scanned print, since I upped the gamma on the whole thing for this web version.

Time passes… a lot of it. This spring, Santa Fe had a reunion open to all graduates. My sister and I went; I had managed to get discount airfare via Allegiant Air from Lansing, MI to Sanford, FL. The first evening’s activities included concerts by Lake Mirror in downtown Lakeland, followed by more music on one of the streets downtown. There I got to meet up with four of the five classmates from the group shot above plus one more friend from the class of 1979. My sister snapped this group photo of us there on the street.

From left to right (if I have the names right), Lee Pinner (Strain), Beth Bordelon (LeCorgne), me, Linda Rushing (Kibler), Jo Ellen Riley (Gray), and Celeste Cooper.

Unfortunately, Allegiant Air is taking a break from the Lansing to Sanford routes, and I don’t have a budget that will stretch to regular airfare to make it to the 30th reunion of my Class of 1978 this coming October 4th and 5th. Have fun… I hope Ben McConnell gets plenty of great pictures at this one.

<> 10080 3882 >

Hawk-Killing Golfer Receives Sentence

Pro golfer Tripp Isenhour pled nolo contendere on the charges filed against him in the killing of a red-shouldered hawk. Here’s the sentence he got because of it:

Charged with killing a migratory bird and animal cruelty, Isenhour was assessed penalities that included a year of supervised probation, four hours of anger-management training, 100 hours of community service — with 40 of those hours being at an animal or wildlife shelter — and a $500 fine.

<> 10878 3949 >

Pledge to Learn Something About American History

Republican Vice Presidential candidate Sarah Palin answered some questions from the Eagle Forum back in 2006. One of them shows that Palin was sleeping through civics and doesn’t follow news of hot-button cases concerning the Pledge of Allegiance.

11. Are you offended by the phrase “Under God” in the Pledge of Allegiance? Why or why not?

SP: Not on your life. If it was good enough for the founding fathers, its good enough for me and I’ll fight in defense of our Pledge of Allegiance.

Is the Republican party aiming to reconstruct themselves as a resurgent Know-Nothing Party? They seem to have taken a large step in that direction. Of course, it could be possible that Palin has learned something about this in the intervening years. Maybe a reporter should give her a pop quiz ask for for an update on this.

archy has the remedial civics lesson for Palin. And a hat tip to GCT at AtBC for pointing this out.

<> 9620 3578 >