The Austringer

A gentle touch for better control, a quantum mechanical con, and milestone PRL papers

Gaming and gambling have inspired a number of advances in science and technology, going from Babbage’s fascination with horse racing through the invention of Unix to support a game of “Space Wars” to the upward climb in personal computing capabilities driven by video game performance. The article above finally shows that people are starting to think about exploiting quantum mechanics for the purpose of rigging games and winning bets off classically-thinking suckers.

The basic gist is that, in theory, particle-sharp Alice will fleece classic physics chump Bob by allowing him to examine one of two boxes. Bob’s task is to observe a particle in the box; he notes whether he does or does not detect a particle in the box he has selected. Alice’s pitch is that the particle is in one of the boxes, and that she will try to guess whether Bob did or did not observe the particle in his choice of box. Because Bob is thinking in terms of classical physics, he thinks it is a fair game; Alice should only be able to guess at chance levels, in this case with a fifty-fifty chance of being right. With many repeated plays, the number of wins for Alice and Bob should be about the same, or so Bob thinks. However, Alice isn’t about to let Bob leave with cash left in his wallet, and actually has three boxes. The particle at issue is set up before each round to have a quantum superposition such that it could be in any of the three boxes. Alice’s third box, though, has a detector in it, so if Alice checks after Bob attempts an observation, she either detects the particle, in which case she answers the Bob didn’t observe it in his look, or she doesn’t, in which case she answers that Bob did observe it, since Bob’s observation thus collapsed the superposition and means that there is nothing for Alice’s detector to detect anymore. Alice can win every time this way.

It’s good to know that quantum mechanics has finally made it out of the dull and boring role of providing the basis for modern electronics and stuff like LASERs, and now shows theoretical promise for displacing the three-card-Monty game in the back alley near you.

With advances in quantum technology, it may someday turn out that gambling is only risky for those of us who don’t understand quantum mechanics.

Part of the reason that gambling is risky has nothing to do with understanding the game at hand and everything to do with human cognitive wiring. Gambling tends to payoff on a variable schedule, and that happens to increase the frequency of the behavior via operant conditioning even more than fixed payoff schedules.

Oxygen depletion: A new form of ocean habitat loss

We take breathing for granted. And especially we take the availability of oxygen for granted. For air-breathing animals, things are relatively simple on the physics. If there is adequate ventilation, the air is comprised of about one-fifth oxygen, and only things like altitude really impinge on how well that can be utilized. The relevant principle for we air-breathing sorts is partial pressure, and for everybody but folks on mountains and those flying at high altitudes, it simply isn’t a matter of much thought or import.

Once one goes aquatic, though, things are different. Oxygen tension is highly dependent upon a number of factors, including salinity and temperature. Of the non-biotic factors, temperature is the most important. And temperature is the thing at issue when we are talking about climate change. Relatively small changes in temperature can trigger fish kill situations, though for most people large scale death of fish is most commonly associated with biotic anoxia through agents like algal and dinoflagellate blooms.

The research linked above looks at the abiotic issue of declining oxygen tension due to increasing temperature. And that, in turn, is linked to climate change.

Scientists confirm computer model predictions that oxygen-depleted zones in tropical oceans are expanding, possibly because of climate change

An international team of physical oceanographers including a researcher from Scripps Institution of Oceanography at UC San Diego has discovered that oxygen-poor regions of tropical oceans are expanding as the oceans warm, limiting the areas in which predatory fishes and other marine organisms can live or enter in search of food.

As the title says, this is yet another aspect of habitat loss. Where oxygen tension drops, fish may either have to leave or die, and over broad enough areas, leaving just isn’t an option. The study also discusses how low-oxygen tension waters can be carried into coastal areas, creating problems for all sorts of organisms dependent upon a continuous supply of oxygen in the water. As global warming progresses, the regions of low oxygen tension enlarge and more often are carried to coastal areas. This adds yet another stress to already decimated fisheries.

Oxygen is not omnipresent in aquatic and marine environments. As the temperature goes up, the places where enough oxygen can be found in the water for fish and other species of commercial interest goes down. Though the physics is more complex than for air-breathers, the situation just comes down to managing to keep in places where the oxygen stays high enough, all the time. It just will be getting tougher as the heat rises.

Friendly Atheist » Scientists Are Murderers

According to Ben Stein, at least.

Stein (speaking about the Holocaust): …that was horrifying beyond words, and that’s where science — in my opinion, this is just an opinion — that’s where science leads you.

Crouch: That’s right.

Stein: … Love of God and compassion and empathy leads you to a very glorious place, and science leads you to killing people.

Crouch: Good word, good word.

Reprehensible and insane seem to be the only adequate descriptors here.

Now we can see why Ben Stein was recruited for this job. I hope that someone on the spot is able to read out Stein’s statements above in the legislative sessions where “Expelled” is being touted as a reason to pass antievolution legislation. It would go some way towards informing the legislators as to just what they are signing themselves and their constituents up for.

Update: Check it out on YouTube.

Fishing throws targeted species off balance, Scripps study shows

Back on my birthday in 2006, I had a post about fishing as a cause of evolution in fish stocks. The linked article at the top of this post dances around the implication, saying that fishing makes the age structure of a population “dynamic” and “unstable”, but they keep a relentlessly ecology-only mindset on the issue. Nonetheless, the answer remains the same so far as regulatory policy is concerned.

Fishing typically extracts the older, larger members of a targeted species and fishing regulations often impose minimum size limits to protect the smaller, younger fishes.

“That type of regulation, which we see in many sport fisheries, is exactly wrong,” said Sugihara. “It’s not the young ones that should be thrown back, but the larger, older fish that should be spared. Not only do the older fish provide stability and capacitance to the population, they provide more and better quality offspring.”

If you want a population to produce bigger fish, you need to stop taking the very biggest fish available.

Warning buoys for right whales installed along Massachusetts Bay

Chris Clarke and the Ornithology Lab at Cornell University have an application for bioacoustics: right whale detection in shipping lanes. Right whales often make contact calls, called “up-calls”, and a series of ten deployed buoys with hydrophones and communications gear can pick up these calls for right whales within five miles of a listening buoy. Onboard processing does a first pass at picking out a “top ten” list of possible right whale calls, and those are uploaded to the Cornell Ornithology Lab for further processing. The system is computer-assisted rather than computer-automated, meaning that the computer processing narrows the things that would require a human decision, but it relies upon humans to make a final determination of whether a right whale call was present. If that is the case, the buoy is marked as having one or more right whales in the vicinity, and is tagged as having an “alert” status. This is reflected on a website that ship captains can access and, hopefully, reduce their speed while traversing areas where right whales have been detected. Right whales move slowly, travel near the surface, and ship strikes remain a major source of mortality for right whales. By highlighting where right whales are, Clarke hopes that responsible captains will take steps to reduce ship speed and post lookouts.

I heard a snippet on the radio, by Garrison Keillor if I heard it correctly, discussing an event leading to the discovery of the structure of DNA. The story is familiar, with Watson and Crick having been provided with data, specifically Rosalind Franklin’s photograph 51, that permitted them to leap ahead in the race to elucidate the structure of DNA. According to Keillor, once informed by the photograph, Watson drew a picture on a piece of newspaper while on a train with Crick. They utilized their physical model materials back in the lab to confirm the initial insight, and shortly afterward published their paper in Nature. Rosalind Franklin may not have been aware of the crucial role her own effort played in helping Watson and Crick steal a march on Linus Pauling. That aspect of this affair is arguable.

What isn’t arguable is that the specific way in which the structure of DNA was elucidated, at the time it was, was crucially dependent upon the excellent technique Franklin used in producing clear X-ray crystallography. There was plenty of X-ray crystallography of DNA to look at, but Franklin produced a better image, and to Watson at least this was sufficient to trigger the critical insight.

While much has been written about the role of chauvinism and feminism in denying Franklin a higher profile in the discovery, I instead want to explore another aspect of discrimination that I find no less deplorable. That aspect would be the common elitism that draws a line between the research roles of scientists qua scientists and “technicians”. In general, the way in which credit has been apportioned in the past has been that credit has been artificially restricted to a fraction of people who could claim a significant role in the production of knowledge. There are legitimate issues here, as in how to avoid a heap paradox (not everyone at a university need be included in the author list). But the cultural pressure here has less to do with such issues and more to do with aggrandizing the credit given to those who remain on the author list. This has something to do with lazy administrators who prefer simplicity in evaluation (”count up the number of single-author papers and multi-author papers separately”). One of the fields in which this trimming of credit has been curtailed to some degree is molecular biology and especially genomics, where the effort needed to produce a report of, say, the human genome simply cannot be trimmed down to one or a handful of researchers. Usually, though, critical or crucial contributions to scientific research have been relegated to notes in an “Acknowledgments” section of a paper, or omitted entirely, if the role of the contributor can somehow be construed as being that of a “technician”. This is something that I have personally observed happen time and time again, and can recognize in historical examples such as the diminishment of Franklin’s role in finding the structure of DNA. Being included in an “Acknowledgments” section of a papers earns someone pretty much nil credit for any meaningful review.

I think that a significant factor in the dynamic that shut out Rosalind Franklin has to do with classing her not primarily as a colleague in scientific research, but as a technician putting on airs. This is not to deny the chauvinism/feminism angle, but rather to give some consideration to yet another dynamic at work that has an impact on how credit for scientific work is apportioned — or excluded.

Bill Dembski invokes Stan Ulam as an antievolutionist. Pim van Meurs has a good response at Panda’s Thumb, noting a later publication from Ulam that diminishes or contradicts the attempt to turn him into an antievolutionist.

Well, given how the antievolution crowd really likes testimonial evidence and the “Were you there?” question, I thought I might relate my own experience. During my undergraduate college time, I worked as a staff photographer for the Independent Florida Alligator. This meant that I got assigned to get photographs of varius visiting celebrities and speakers at the University of Florida or Gainesville. I still have my negatives and some prints from the time. Despite having my newer USB flatbed scanner give out (which means I have a new entry on my wishlist), I still have an older HP OfficeJet that I can take a scan of prints with.

In the early 1980s, Stanislaw Ulam visited UF and gave a talk about his involvement in the Manhattan Project and later nuclear weapons production. Unlike some other speakers I covered, I had the opportunity to wander off after the talk with Ulam and his party. Here are a couple of my photographs from that day:

The McLean v. Arkansas case was current news, and I got to ask Ulam what he thought about the “scientific creationism” being promoted there. Ulam thought that the SciCre faction was peddling non-science and material that had no business in science classrooms. This has made me more than usually sensitive to misguided antievolution attempts to recruit Ulam’s authority as a prop for their socio-political program. I punctured pretentious antievolution misuse of the Wistar conference on “mathematical challenges” back in 1997.

I followed up on a comment left in the earlier comment thread about giving gnuplot a try. For some reason, I had difficulties getting it installed on the MacBook Pro, but I got past that hurdle and spent some time today working with gnuplot.

OK, for someone who has access to Matlab, what exactly is the attraction to command-line plotting tools like gri and gnuplot? It is precisely because these can be called as part of a batch process that I find them useful. In doing the work I do these days, I have replicates of runs. If I use an interactive tool, I’m going to be spending a lot of my time simply stepping through a process over and over. If I put in some effort up front, I can write myself some scripts to automate the process and let me spend more time in analysis or coding.

“gri” does permit the production of contour graphs pretty easily, but I was finding it a bit rough in trying to get a surface rendered instead. That’s kind of frustrating, because there are examples online that look like they are doing what I want to do. So I thought I would check to see whether it was any easier in “gnuplot”. As it turned out, it was.

gnuplot provides two basic graphing commands, “plot” and “splot”. “splot” is the feature of interest for me, and in gnuplot 4.0 and above, a further useful style of “pm3d” modifies that. I have to admit it took a while for me in playing around with gnuplot interactively to figure out exactly what had to be done. One of the big steps was putting the data in just the right format for gnuplot to handle. I could dump my xyz data into gri, and gri would figure it out for gridding. Not so with gnuplot. The xy coordinates have to be completely sorted. Further, gnuplot expects a blank line in between each column’s worth of xyz entries. Fortunately, there was a site online offering an awk script for adding those blank lines. A little extra work in my Perl script formatted x and y values with leading zeros so passing the file through “sort” gets it set for awk to do its thing.

Then there were the data points, irritatingly plotted with “+” symbols. It wasn’t at all clear to me that what I wanted in getting my surface plotted without distraction was to tell gnuplot to “unset surface”. The “pm3d” style handles the rest if I use “set pm3d at s”, which tells gnuplot that I want the color mapping of “pm3d” applied only at the surface. Other ways to specify pm3d action includes “bottom” and “top”. For myself, the “surface” option does fine on its own. Another thing I settled upon was using “set hidden3d”, which obscures parts of the projection that lie behind others.

gnuplot offers a large selection of “terminal” types, essentially how one wants the output to be presented. On Mac OS X, the “aqua” terminal is the default, putting a plot onscreen. For my batch processing, I can just “set term png” and I have output suited for figures in LaTeX via “pdflatex”.

I haven’t worked out all the labeling, but that will come soon enough, I think. Here’s a code snippet from my Perl script to output a gnuplot command file and launching gnuplot on it.

open(GPC,">${dataname}.gpc");
print GPC < < "EGPC";
#set term post
set pm3d at s
set pm3d scansautomatic flush begin noftriangles implicit corners2color mean
set palette positive nops_allcF maxcolors 0 gamma 1.5 color model RGB
set palette rgbformulae 7, 5, 15
set colorbox default
set term png transparent xffffff
set out "${resid}.gp.png"
unset surface
set hidden3d
splot '${resid}.grid.gp' w d
EGPC
close(GPC);
        # Call gnuplot
        $cmd = "gnuplot ${resid}.grid.gpc";
        system($cmd);

I make use of the Perl “here” document format, which makes it pretty simple to get Perl variable values into a block of text from another source. The funky command parameters were obtained by saving an interactive command session and using that to put together the script above; gnuplot came up with most of that.

Here’s an example output graph:

Obviously, transparency is better in some contexts than others. But basically I now have an alternative to firing up Matlab and interactively generating a color-mapped surface plot.

The PBS Nature series looks at the intersection between falconry and science with Raptor Force. The episode airs this evening, 8 PM ET.

Hat tip to Karen Spivey.

I hope to have some comments later when the program airs.

Update: They had a lot of nice photography on the show, though I think that they borrowed some film from the NatGeo “Wolves of the Air” program, or at least it was strongly reminiscent of scenes from that program when they showed Harris hawks in the desert. There were some problems here and there in statements, such as saying that Harris hawk “stacking” behavior has something to do with the top bird having a better vantage due to the few additional inches of height, and not saying anything about the work done that teased out the dominance hierarchies that underlie “stacking”. The other clinker I recall clearly was saying that the near-silent flight of owls was perhaps due to not interfering with the owl’s own hearing in flight, when a fairly obvious alternative explanation would be that they don’t wish to have the prey hear them coming. Or, rather, that noisy owls likely would less often surprise prey items than more silent-flying conspecifics.

I thought the technology tie-ins were fairly weak elements of the show. While military aircraft video certainly makes for guy-gripping TV, there really wasn’t much depth at all in explaining how raptor biology actually was part of some technology transfer to aviation. The whole bit about development of a raptor backpack-cam could have been condensed down to “our tech guys did a great job getting us this video”, rather than sucking up precious program time showing us a guy soldering circuits in his basement. I’ve been that sort of guy before, but even I recognize that that is not what makes for informative television.

All-in-all a better hour of television than most, but it could have been even better than it was without much more effort.

We’ve got a total lunar eclipse coming up here shortly. Friends are coming over, and we’ll pull out the telescope for viewing and our binoculars. I’ve already baked up a fudge cake for after; it is 11 degrees F out currently, and we’ll want something warm after that.

Diane says that the reports state that there may be moments when the moon appears tinted turquoise at the beginning and end of the eclipse. That is apparently due to the absorption spectrum of the ozone layer.

More later.

Update: Two pictures, one during totality, and the other as the eclipse was ending.

Antievolutionists make lots of claims about Charles Darwin, seeking to impeach the authority of someone born 199 years ago today. Given that science moves on and leaves no one’s ideas untouched, one would think that they would stick to negative claims that would stand up to some scrutiny. Again and again, though, we find that they continue to espouse negative claims that are just plain silly, at least to those with even the slightest familiarity with the actual record that Darwin left.

Today, I want to look at a common antievolution claim about Darwin, simply put, that Darwin considered the contents of cells to be “black boxes”, comprised of a simple or homogeneous protoplasm. This is expressed in similar ways by a number of antievolutionists. The following is just a sampling of the available instances.

Michael Behe:

To Darwin, then, as to every other scientist of the time, the cell was a black box.

And again:

Scientists use the term “black box” for a system whose inner workings are unknown. To Charles Darwin and his contemporaries, the living cell was a black box because its fundamental mechanisms were completely obscure. We now know that, far from being formed from a kind of simple, uniform protoplasm (as many nineteenth-century scientists believed), every living cell contains many ultrasophisticated molecular machines.

Casey Luskin:

There were other things that Darwin did not know. For example, Darwin assumed that the cell was like a primitive blob of protoplasm that could easily evolve new biological functions. As Behe explains, “To Darwin, then, as to every other scientist of the time, the cell was a black box. … The question of how life works was not one that Darwin or his contemporaries could answer.”

Nancy Pearcey:

To be fair to Darwin, he proposed his theory when scientists knew next to nothing about biochemistry. Living things were “black boxes,” their inside workings a mystery. The cell itself was thought to be nothing more than a blob of jellylike protoplasm. It was easy to draw large-scale scenarios about fins gradually turning into legs, or legs into wings, since no one had a clue how limbs and organs work from the inside. As Behe writes, it is as though we asked how a stereo system is made and someone answered, “by plugging a set of speakers into an amplifier and adding a CD player, radio receiver, and tape deck.”

That’s pretty rich, that “be fair to Darwin” phrase.

Jay Richards:

In addition, biochemists and biologists have discovered a microscopic world of mesmerizing complexity belying the simple blobs of protoplasm that Darwin imagined.

Jon Saboe:

Darwin must be forgiven, however, since he was limited by the science and paradigms of his day. Nobody then could have ever guessed the incredible complexity and information that resided in a living cell; something that was regarded as a ‘blob of protoplasm’.

“Do-While Jones”:

Biochemist Michael Behe says that modern science has made the Darwinian explanation of the origin of complex life forms much less believable than it was in Darwin’s day. In the 19th century, it was believed that a cell was just “a homogeneous globule of protoplasm.” 2 They did not know about DNA or the complex processes that go on inside a cell. Blood clotting, cellular transport, vision, and the body’s method of fighting diseases are “irreducibly complex systems” which could not possibly have evolved.

Jonathan Wells:

How living cells — which Darwin thought were mere blobs of protoplasm — actually consist of countless molecular machines that have all the hallmarks of design

Antievolutionists don’t go looking at the primary sources to come up with these nuggets; one of them creates a “magic bullet”, and the rest pass it around like a game of “telephone”, sometimes resulting in a garbled mess. As Casey Luskin’s contribution here indicates, the likely source of the BS in this case is Michael Behe.

Why call it BS? Because anybody can disconfirm the claim in seconds with a modern Internet search, and only moderately longer using the past technology scholars have long relied upon for substantiating claims about prior work.

An excellent recent source is the Complete Work of Charles Darwin Online website.

One finds there Darwin’s work on pangenesis, his hypothesis that there existed small particles that he called gemmules, each of which contained the heritable information for some particular trait, and which would combine, somehow, into the gametes. His continued advocacy of this wrong idea was a major failing on his part, but along the way we can see that even though Darwin was wrong about gemmules, he did hold an antithetical view to the claim that everything was simple at the most basic levels of life’s organization:

Notwithstanding the astounding complexity of the processes implied by this hypothesis of pangenesis, yet it seems to me to comprehend the several leading facts better than any other view. On this hypothesis we may fancifully look at each animal and plant as being compounded of many beings, in the same manner as a tree or coral is compounded of many similar beings; but in neither case have these so-called beings had a separate existence. Each of these beings, or parts, is supposed to be capable of throwing off gemmules, which whilst within the organism are capable of self-increase, and which can be separately developed at the part or organ whence they were derived, and can be united, as in the case of hybrids, with other gemmules into a single germ or bud, which reproduces the complete parent form. On this view, each organic being may be looked at as a little universe, formed of a host of different self-propagating organisms, almost as numerous as the stars in heaven, and as minute as they are immense.

Two papers by Darwin published in 1882 demonstrate Darwin’s readiness to experiment in resolving sub-cellular processes, using chemistry and microscopy to aid in the work.

Darwin, C. R. 1882. The action of carbonate of ammonia on chlorophyll-bodies. [Read 6 March] Journal of the Linnean Society of London (Botany) 19: 262-284.

Darwin, C. R. 1882. The action of carbonate of ammonia on the roots of certain plants. [Read 16 March] Journal of the Linnean Society of London (Botany) 19: 239-261.

These papers in the primary literature demonstrate vividly that Charles Darwin not only was aware that protoplasm was not homogeneous, but was at the end of his life working toward elucidating exactly what differences within cells existed.

The antievolution “magic bullet” intended to dismiss Darwin is a dud. Sub-cellular structure elucidation was another part of science in which Darwin was an active participant. Darwin’s own preferred hypothesis of heredity, though now discredited, presumed the sort of immense complexity at small scales that antievolutionists falsely claim Darwin had no “imagination” for. Many antievolutionists have willingly participated in passing along this falsehood and urging changes in public school curriculum policy based, in part, on their false and ignorant claims. I find it significant that I have yet to encounter any instance of an antievolution advocate pointing out the actual facts of the case and remonstrating with their colleagues, even though the disconfirming evidence is easy to locate and describe. I can only conclude that antievolutionists in general have no concern for the truth nor for fact-checking even the simplest of their claims. Trusting antievolutionists to help guide policy and form curricula for public schools would be malfeasance, plain and simple.

(While researching this, I found that Afarensis got here well ahead of me. Pfffbbbt. Visit that page to see some of the illustrations. I have more examples of clueless, unscholarly antievolutionists, though; so there.)

M-Audio has updated its handheld Microtrack solid-state recorder to the Microtrack II. The specs are attractive. It records in stereo to Compact Flash or MicroDisk format cards, in either WAV or MP3 formats. It can record at up to 96 kilosamples/second at 24 bits per sample. It has both 1/4″ and 1/8″ microphone/line inputs, and can provide 48V phantom power to microphones. Interfacing this unit to hydrophones should be a piece of cake. NCSE has one of the M-Audio Microtrack recorders for making high-quality podcasts or audio documents.

Back in 2005, Diane and I had to come up with a programmable field recorder on three weeks notice. We went with a PDA-based solution using Core Audio’s Compact Flash format audio input card, coupled with Core Audio’s microphone pre-amp/digitizer system. If you need progammability, as for making unattended scheduled acoustic sampling, that’s still a good solution. On the other hand, for interactive recording, the M-Audio Microtrack II offers the convenience of a smaller, discrete package to use, plus you only have to worry about one power supply. The M-Audio unit is about the same size as a standard PDA, though a bit thicker. Core Audio does sell the MicroTrack II, and sees it as aimed at a different market segment than their PDAudio system.

As with any pro-quality system, though, it is pricey. The MSRP on the Microtrack II is about $500. Sweetwater is advertising them at about $300. As such, it is out of range of our budget at the moment. That’s not a whole lot more than one might pay for a top-end media player these days, though, and I can always hope for a price drop.

While all antievolution depends upon previous expositions for the concepts and arguments, most of the time each new generation of antievolutionists takes up the burden, light though it is, of expressing past arguments in their own words. Like the game of “telephone”, this sometimes has the effect of adding novel distortions to the already-existing falsehoods.

Now, though, it looks like it isn’t enough to copy from stuff one published previously if one is an antievolutionist looking for a peer-reviewed paper credit. One may as well do some outright copying of the work of others, if it will help get a paper past the reviewers. This is, of course, behavior indicative of folks who cannot generate enough intellectual wattage to raise a spark of their own.

Enter the following publication, as cited by McDonald:

Warda, J, and M. Han. 2008. Mitochondria, the missing link between body and soul: Proteomic prospective evidence. Proteomics, Epub ahead of print.

They plump for “a mighty creator” as a “more realistic” cause of certain phenomena in proteomics. Along the way, they lift text from others without proper attribution.

P.Z. Myers announced the issue on the Panda’s Thumb recently, linking to this PDF that lays out just how much of the paper in question was acquired via copy-and-paste rather than research. It’s a lot. Where I got my doctoral degree, somebody turning in a term paper with that sort of plagiarism apparent in it would be out the door, with the assist of a large boot applied forcefully to their posterior.

So, is the corrosive moral influence of antievolution what drives these people to cheat like they do?

Why are we, at this late date, even thinking about extending a presumption of any sort of legitimacy to the antievolution movement? They talk big about “fairness”, but every time we turn around, they are pulling stunts like describing themselves as “top scientists” to congress, suborning bishops via public-relations firms, seeking “compromise” language that lets them slip in the same old arguments into classrooms, gaming university dissertation committees, gaming the Amazon review system, proposing kickbacks to schools to up the box office for movies, and getting editors to personally bring manuscripts safely through “review” processes. This does not sound like any sort of group with a claim to having a moral mission to accomplish, unless they think that more bad morals are needed in the populace at large.

I just did.

A PETITION TO THE FLORIDA BOARD OF EDUCATION FOR ADOPTION OF REVISED PUBLIC SCHOOL SCIENCE EDUCATION STANDARDS.
FEBRUARY 2008

WHEREAS: The current Sunshine State Science Education Standards have received an ‘F’ from the Thomas B. Fordham Foundation while the proposed revised standards have been graded excellent by one of the scientists who previously authored the report that gave Florida its failing grade.

WHEREAS: The revised standards address the scientific theory of evolution without equivocation or the introduction of nonscientific notions. Evolution is the central organizing concept that allows us to understand all biological sciences from medicine to forestry to entomology, and its principles are the theoretical basis that underlies major advances in all biological fields. Students must understand the current state of the science to be part of an informed citizenry.

WHEREAS: The economy of Florida requires the foundation of well educated citizens in order to compete and prosper within global competition. A solid grounding in the sciences is essential to providing a well educated labor force to the state’s employers.

NOW THEREFORE: We the undersigned urge the Florida Board of Education to adopt the revised Public School Science Education Standards as drafted by the duly appointed and authorized Department of Education Writing Committee.

Remember to uncheck the box about receiving notices of other petitions. This is hosted on an Internet petition site that will also beg for money. Ignore that if you don’t care to contribute, but if you have the ability to support the site, it seems that they are providing a useful service for many people who would not otherwise be able to organize an online petition.

You can add a comment, so here is mine:

I was born in Florida, and I care about the state of science education there. There are two main things that I want to say about antievolution and science education.

First, antievolution is not based in science, does not represent an alternative scientific understanding of the evidence, and it specifically conveys a narrowly sectarian religious doctrine. It is disruptive of the tolerance towards diverse religious faiths, or the lack of them, that help maintain amity and civility in our country. We are fortunate here to have avoided the deadly struggles over doctrinal positions that are common elsewhere and that have left their stamp on history. Antievolution efforts include attempts to rewrite the operating principles of science by fiat, and this alone should be sufficient to demonstrate that its promoters are not working for the common weal, but are bent upon achieving their own aims without regard for anything but their own satisfaction.

Second, science education needs to incorporate those concepts that have accountability, that have been proposed, argued, tested, revised, and that have by the record of empirical investigation and substantial engagement of criticism convinced the scientific community of the worth of the concept in question. Evolutionary science has met that high standard, and antievolutionary attacks upon it have no such claim to legitimacy. Science education should not be weakened by spending precious class time on material whose inclusion only serves the purposes of evading those stringent standards of accountability, undermining the principle of science’s ability to wholly reject hypotheses that predict false consequences, and gainsaying well-tested theories without substantiating a basis for such attacks.

It can do no one harm to come to an accurate understanding of what science is, and what has been discovered and supported through the scientific method. Please adopt the new science standards as written by your domain experts and experts in science education, and avoid the error of capitulating to the demands of the antievolution movement that evolutionary science be “balanced” with material that sows broad distrust of scientists and findings in biology, chemistry, physics, astronomy, and geology.

Bush allows Navy to continue sonar use (OneNewsNow.com)

President Bush signed off on an exemption so that the US Navy can argue for continuing to use mid-frequency sonar systems in training exercises off the coast of southern California. While there is still a court injunction, the article notes that this exemption strengthens the Navy’s position in pushing for use of the mid-frequency sonar during exercises, and everyone will be back in court soon to hash this out.

The article quotes the following:

“The president’s action is an attack on the rule of law,” said Joel Reynolds, director of the council’s Marine Mammal Protection Project. “By exempting the Navy from basic safeguards under both federal and state law, the president is flouting the will of Congress, the decision of the California Coastal Commission and a ruling by the federal court.”

The Navy has long held that its compliance with various and sundry rules and regulations is voluntary. Mr. Reynolds should know by now that the Navy’s end move is to tell everybody to get stuffed, and do what they were planning to do anyway. The real trick here is to advance, so far as possible, the cause of minimizing damage to marine mammal stocks due to Navy actions, while not doing so in such a way as to cause the Navy to stop listening altogether to environmental activists or more moderate voices for conservation. The rhetoric in the above quote isn’t helpful in this regard. The idiom about one may as well be hung for a sheep as for a lamb applies here.

And the long-standing tactic in environmental activism of confusing and conflating the different systems of sonar that the Navy uses doesn’t help with the current situation, either. While the general public may be impressed, the people in the Navy tasked with dealing with these issues certainly aren’t put in a good position when research results about one type of sonar are falsely used to argue that the Navy should stop using either other types of sonar, or all sonar systems. There has been some improvement on this score over the years, but things could be better.

There are real problems to be solved concerning the responsible use of military sonar. Getting to the point where solutions are possible is going to be tricky; the Navy does have a legitimate purpose for use of these systems that has not gone away, and there are also legitimate concerns about balancing the Navy’s use of these systems with the risk that they pose for marine mammal stocks. The viewpoint that the Navy might be somehow barred from use simply isn’t feasible, and the possibility that the Navy might stop interacting with civilian interest groups of various sorts to find that appropriate point of balance would be unacceptable.

Hat tip to Ed Brayton.

A comment came in not long ago that did not follow from the topic of the post, but I think that it should be seen, so I’ll make a thread for it. It comes from an author of an antievolution book, and handily demonstrates the “conflict model” thinking that is popular among religious antievolutionists and anti-religionists.

Why do scientists so readily embrace evolution in lieu of the written record of creation? The answer lies with a poll of select members of the elite National Academy of Sciences. The poll discovered a prevailing disbelief in God; in fact, only 7 percent of those surveyed held a “personal belief in God.” Of the balance, 72.2 percent held a “personal disbelief” and 20.8 percent were either doubtful or agnostic.

In effect, the sampling revealed that scientists hold a “near total disbelief in God.” (Poll by Peter Atkins and Richard Dawkins, published in Nature, Summer 1998.)

The reason for the rejection, and by assessment an intense hatred of God, is two fold. Firstly, evolution is accepted by an overwhelming majority of biologists and scientists - biblical histories are myths. Consequently, scientists unequivocally abhor any supernatural explanation of natural phenomena, as it questions their intelligence. Secondly, the scientific league refuses to accept a God who would allow all the evil, suffering, and pain that befalls both man and beast (due to sin entering the world through the man, Adam).

Matter-of-factly, anyone who professes belief in God is simply anti-intellectual. Hence, scientists succumb to the grave trusting that their fleshly beings will return to dust from whence they came: there is no God, no life after death, no hell, and no eternal separation from a loving God.

An amusing epilogue: When the results of the poll were first published, a lone dissenter in the U.S. House of Representatives, James Traficant (D-Ohio), complained from the House Floor, “Mr. Speaker, a new report says only 7 percent of scientists believe in God… And the reason they gave was that the scientists are super smart. Unbelievable…”

The scientific council and educators alike have played into the hands of Secular Humanists who view public education as the vehicle to move the citizen into a total secular, materialistic, godless society. According to the manifesto outlined in the journal of the American Humanist Association, The Humanist (1983), the “battle” for the minds and, it must be added, the souls of the innocents is to be “waged and won” in the public classrooms. The aspiration has gained strength by the endorsement of the liberal faction in the National Association of Educators and by teachers, many of whom believe in God but, nevertheless, have been subverted in their faith in that they may only teach the tenets of obstructionism as ruled by the Supreme Court.

The reader may be surprised to find that the expression, “separation of church and state,” is nowhere to be found in the seven articles and twenty-six amendments of the Constitution; yet, the phrase has gained sovereignty over the public schools, not by any right granted by the founding fathers, but by the repetitious manner in which it has been brandished about by those who wish to obstruct the truth. The lesson taught here is not new: “There is nothing new under the sun.” The obstructionist approach; that is, there is no God and, hence, no Son of God, dates back two thousand years to the New Testament epistle, 1 Timothy, penned by the apostle Paul unto Timothy, a servant of Jesus, the Christ. In the disposition, “the putting into order of the church’s affairs,” Timothy was warned to avoid the opposition of “science falsely so called,” or in the modern terminology, “religious obstructionism masquerading as science,” the real purpose of which is to undermine the faith of the people of God.

20. O Timothy, keep that which is committed to thy trust avoiding profane and vain babblings, and oppositions of science falsely so called;

21. Which some professing have erred concerning the faith. Grace be with thee. Amen.-1 Timothy 6

May God give the good people of Texas the courage and wisdom to rescue the innocents within the classroom from those who would preach the unprofitable theory of evolution.

C. David Parsons

For a moment toward the end, it seemed like Parsons was going to get it right, and take antievolutionists to task for falsely calling their arguments science. That certainly didn’t turn out to be the case.

Let me take up some of this more directly.

Why do scientists so readily embrace evolution in lieu of the written record of creation?

Quite a large number of scientists are both Christian and accept the findings of evolutionary science; I’m one of them. This fact has to be ignored by Parsons and others who wish to propagate the conflict model.

The answer lies with a poll of select members of the elite National Academy of Sciences. The poll discovered a prevailing disbelief in God; in fact, only 7 percent of those surveyed held a “personal belief in God.” Of the balance, 72.2 percent held a “personal disbelief” and 20.8 percent were either doubtful or agnostic.

In effect, the sampling revealed that scientists hold a “near total disbelief in God.” (Poll by Peter Atkins and Richard Dawkins, published in Nature, Summer 1998.)

Notice how the sampling effect of a poll directed only at the NAS is completely ignored and “scientists” is used thereafter. Nor is Parsons well-informed about such basic information as who conducted the poll in question. It was not Atkins and Dawkins who conducted the poll, but rather Edward J. Larson and Larry Witham. It was, in fact, the second phase of polling they did to replicate a poll taken in the early twentieth century. Parsons does not choose to inform his readers of the existence of part 1, where Larson and Witham found that the prevalence of disbelief in God among the general body of practicing scientists had remained mostly unchanged in the intervening decades, and was found in their poll to be about 60%. That means that about 40% of practicing scientists either do believe in God or are not predisposed to disbelieve, a rather different number than the one Parsons chooses to use. Another point Parsons does not bother to discuss is that even in the recent poll of the “greater scientists” of the NAS, Larson and Witham found that outright disbelief was less prevalent among scientists in the biological sciences, and more prevalent among physical scientists, though the biological scientists of the NAS also had the least prevalence of expressed belief.

The reason for the rejection, and by assessment an intense hatred of God, is two fold. Firstly, evolution is accepted by an overwhelming majority of biologists and scientists - biblical histories are myths. Consequently, scientists unequivocally abhor any supernatural explanation of natural phenomena, as it questions their intelligence. Secondly, the scientific league refuses to accept a God who would allow all the evil, suffering, and pain that befalls both man and beast (due to sin entering the world through the man, Adam).

As already noted, the “rejection” is by no means characteristic of all scientists. This is a common tactic among those who have to argue against reality: simply assert the state of affairs most congenial to their argument and there leave it. Here we have Parsons attributing “hatred of God” to an entire profession, where our best available data say only that about 60% disbelieve; Larson and Witham did not go into what feelings their respondents had about God, nor does it make much sense to attribute hatred to people who disbelieve in the existence of the being that is supposed to be hated. Nor is Parsons reliably informed about the reasons that scientists don’t accept supernatural explanations as science, which has nothing to do with “questioning their intelligence” or “hating God”, and everything to do with making sure that science works. When scientists began deprecating the use of supernatural causes as explanations in science back in the nineteenth century, the overwhelming preponderance of practicing scientists were also theists. These people certainly did not mold the modern rules of science because they thought the supernatural “questioned their intelligence”, and it is ludicrous to imply that they took the steps they did because they “hated God”. As for Parsons “secondly”, I’m afraid it simply doesn’t make sense; again, Parsons is attributing to all scientists a view that is only held by a subset of that group.

Matter-of-factly, anyone who professes belief in God is simply anti-intellectual. Hence, scientists succumb to the grave trusting that their fleshly beings will return to dust from whence they came: there is no God, no life after death, no hell, and no eternal separation from a loving God.

Again, Parsons is railing against a strawman of his own creation, that all scientists must be God-hating unbelievers. We know that premise is false. Matter-of-factly, some people who profess belief in God are anti-intellectual, and it appears that Parsons is arguing strenuously to be included in that grouping.

An amusing epilogue: When the results of the poll were first published, a lone dissenter in the U.S. House of Representatives, James Traficant (D-Ohio), complained from the House Floor, “Mr. Speaker, a new report says only 7 percent of scientists believe in God… And the reason they gave was that the scientists are super smart. Unbelievable…”

Rep. Traficant apparently understood as little about the poll results as does Parsons, since he makes the very same error of using the sample of “greater scientists” to pull a number he erroneously applies to the general population of practicing scientists.

The scientific council and educators alike have played into the hands of Secular Humanists who view public education as the vehicle to move the citizen into a total secular, materialistic, godless society. According to the manifesto outlined in the journal of the American Humanist Association, The Humanist (1983), the “battle” for the minds and, it must be added, the souls of the innocents is to be “waged and won” in the public classrooms. The aspiration has gained strength by the endorsement of the liberal faction in the National Association of Educators and by teachers, many of whom believe in God but, nevertheless, have been subverted in their faith in that they may only teach the tenets of obstructionism as ruled by the Supreme Court.

We here in the USA have a variety of different faiths and even non-faith. We are stronger if we do not engage in the sort of internecine struggles that ravaged Europe for centuries. We are best served if each person can pursue their faith (or do whatever they decide with their time if they don’t believe) in the private sector, and we are ill-served if some one or few doctrines are given the imprimatur of government promulgation. The Southern Baptist Church used to be in the forefront of First Amendment cases aimed at keeping government programs to strictly secular content, for the simple reason that if no religious doctrine is espoused by the government, it then is simple for the church to instruct its members without that interference.

The reader may be surprised to find that the expression, “separation of church and state,” is nowhere to be found in the seven articles and twenty-six amendments of the Constitution; yet, the phrase has gained sovereignty over the public schools, not by any right granted by the founding fathers, but by the repetitious manner in which it has been brandished about by those who wish to obstruct the truth. The lesson taught here is not new: “There is nothing new under the sun.” The obstructionist approach; that is, there is no God and, hence, no Son of God, dates back two thousand years to the New Testament epistle, 1 Timothy, penned by the apostle Paul unto Timothy, a servant of Jesus, the Christ. In the disposition, “the putting into order of the church’s affairs,” Timothy was warned to avoid the opposition of “science falsely so called,” or in the modern terminology, “religious obstructionism masquerading as science,” the real purpose of which is to undermine the faith of the people of God.

The reader may not be surprised to find people in the present who weren’t paying attention in civics class. The phrase, “separation of church and state”, appears in correspondence from Thomas Jefferson and is descriptive of the policies that do appear in our constitution and its amendments. That Parsons is apparently a fan of David Barton’s loopy stuff is no surprise at all. The purpose of keeping the government out of the business of telling people what to believe with respect to religion is to keep our internal affairs civil, and avoid all that stuff about hanging, burning, pressing, stoning, impaling, or otherwise managing to kill people who believe something either slightly or completely different from what many or most people in an area happen to believe. That purpose only undermines the faith of people who don’t value the lives and respect the views of their fellow citizens, in which case, yes, that ought to be undermined.

May God give the good people of Texas the courage and wisdom to rescue the innocents within the classroom from those who would preach the unprofitable theory of evolution.

Obviously, Parsons has no clue about the content of evolutionary science. “Unprofitable” is precisely the opposite descriptor that is actually required, since evolutionary science informs our medicine, our agriculture, our wildlife policies, and even aspects of engineering and chemistry which have picked up tools for getting things done more efficiently from evolutionary science. The Soviet Union and China adopted a teleological alternative to western evolutionary science, with the result of experiencing agriculture failure on a scale that killed tens of millions and produced long-term hardship for many more. We should take care to learn from their mistake, and not try to repeat it by politically mandating a non-materialist teleological ideology in place of good science.

All in all, Parsons’ performance here is less than inspiring. Even the simplest level of scholarship seems to be beyond him, he evinces no mastery of the topics he insists on criticizing, he deploys logical fallacies to the exclusion of reasoned argument, and on top of it all presents himself as a sanctimonious jerk. This doesn’t bode well for the book-length treatment that he has authored.

The following open letter from many biology professors in the state of Texas supports Chris Comer and criticizes the Texas Edcuation Agency’s action of forcing her resignation.

December 10, 2007

To Robert Scott, Commissioner of Education for Texas,

As biology faculty at Texas universities1, we are deeply concerned by the forced resignation of Chris Comer, the director of science curriculum for the Texas Education Agency (TEA). Ms. Comer’s ouster was linked to an email that she forwarded announcing a lecture by Barbara Forrest, a philosophy professor and distinguished critic of the intelligent design movement. A few days after sending the email, Ms. Comer was told she would be terminated. The memorandum she received from her superiors claimed that evolution and intelligent design are a “subject on which the agency must remain neutral”.

It is inappropriate to expect the TEA’s director of science curriculum to “remain neutral” on this subject, any more than astronomy teachers should “remain neutral” about whether the Earth goes around the sun. In the world of science, evolution is equally well- supported and accepted as heliocentrism. Far from remaining neutral, it is the clear duty of the science staff at TEA and all other Texas educators to speak out unequivocally: evolution is a central pillar in any modern science education, while “intelligent design” is a religious idea that deserves no place in the science classroom at all.

(more…)

State science curriculum director resigns

Chris Comer is out of a job. She was a nine-year veteran in the position of director of science curriculum for the Texas Education Agency (Texas-speak for the state’s “department of education”). The TEA administration essentially forced her resignation.

So, why would TEA do that? Comer forwarded an email from the National Center for Science Education announcing a talk by Dr. Barbara Forrest to several people with the following addition: “FYI”.

The call to fire Comer came from Lizzette Reynolds, who previously worked in the U.S. Department of Education. She also served as deputy legislative director for Gov. George W. Bush. She joined the Texas Education Agency as the senior adviser on statewide initiatives in January.

Reynolds, who was out sick the day Comer forwarded the e-mail, received a copy from an unnamed source and forwarded it to Comer’s bosses less than two hours after Comer sent it.

“This is highly inappropriate,” Reynolds said in an e-mail to Comer’s supervisors. “I believe this is an offense that calls for termination or, at the very least, reassignment of responsibilities.

How did that play out?

In documents obtained Wednesday through the Texas Public Information Act, agency officials said they recommended firing Comer for repeated acts of misconduct and insubordination. But Comer said she thinks political concerns about the teaching of creationism in schools were behind what she describes as a forced resignation.

Apparently, not being a team player in the The Republican War on Science is a firing offense at the TEA. Why forwarding an announcement concerning a talk whose topic is highly relevant to the conduct of science education by an internationally recognized speaker should cause TEA administrators a problem escapes me. One is forced to wonder whether Ms. Comer would be looking for a new job if instead she were forwarding emails announcing talks by DI fellows about “intelligent design” creationism.

(more…)

Scotsman.com News - Scotland - Spiky issue solved for Hamish the hedgehog

The fluffy, feel-good news story relates how a rail company in Scotland responded to a resident’s request to take into account access past the rail line for a hedgehog when performing maintenance on a wall. The company responded with a hedgehog-sized throughway in the new wall.

COLIN Seddon, manager of the Scottish Society for the Prevention of Cruelty to Animals’ wildlife centre at Middlebank, said it was becoming increasingly important to consider the effect on animals of human developments.

“We are moving further and further out into their territory so we have to do everything we can to make life easier for them,” he said. “We are invading their land, so we have to give something back.”

Well, the fact is that human development subdivides more than just lots in residential areas. As humans work out the most economical ways to connect things up, we arbitrarily restrict the movement of wild animals, and even plants. For each one-off solution to a noticed problem, we tend to overlook building in solutions to lots of unnoticed ones. This is a one-two punch for wildlife; first, there is the outright loss of habitat claimed by humans in development. Each time a home goes up, that plot of land is no longer available for the endemic wildlife to use. Second, when we connect together our separated developments with roads, pipelines for water and sewer services, rail lines, or separate apart property with fences, walls, ditches, mounds, and the like, we curtail the usual and normal means of access that wildlife has with other parts of the same population. “Habitat loss” is the usual term for the first, and it is easily remembered. The second part, though, comes under the daunting rubric of “vicariance biogeography”. Even though the term is a bit on the clunky side, the results from the science are pretty easily comprehended.

Vicariance refers to the events that split taxa. Vicariance biogeography takes as its field the geographical splitting of populations and the resulting patterns of phylogeny. A 1967 book by Edward O. Wilson and Robert MacArthur, “The Theory of Island Biogeography”, got things rolling, and a generalized appreciation for how barriers to intermixing of populations across geographical ranges impacts diversity followed. The short version is that introducing effective barriers that create non-mixing subpopulations reduces diversity and increases the likelihood that populations will go extinct.

On small scales, we see things like “mouse islands”, where interstate clover-leaf engineering puts small patches of green-space within a zone that is effectively lethal to mammalian predators that take rodents. Other than the occasional raptor, the rodents are fairly safe within the confines of a clover-leaf circle. But transfer of genetic material is strictly curtailed; even getting to the “mouse island” in the next clover-leaf over is a highly risky endeavor. These small micro-environments tend to support only depauperate diversity of wildlife, perhaps a couple of rodent species and whatever grass and plant species the road landscapers permit.

But there’s a lot of land that is not next to things like interstate highways. However, at the scale of highways, we see the same pattern emerging. Crossing those barriers is abnormally risky, so they create subpopulations with reduced gene flow on either side. These make for ready application of vicariance biogeography. In wildlife, it isn’t “divide and conquer”, it’s “divide and lose diversity”.

I’m sorry to put a damper on the holiday cheer for the resolution of the plight of Hamish the Hedgehog. The problems for wildlife created by both habitat loss and ignoring the lessons of vicariance biogeography are not the sort that have win-win solutions. Addressing either requires that humans do things that are costly to do. Fixing the problems we are experiencing is going to require addressing both. Making accommodations for an individual family of hedgehogs is a good thing, but we shouldn’t lie to ourselves that we have come to terms with our relationship with wildlife with these small gestures of limited scope.

Over on Ed Brayton’s “Dispatches from the Culture Wars”, Ed comments on NOVA’s attention paid to Behe saying that astrology qualifies as science under his definition of science. This is a comment I left there:

At the time when astrology was of a similar status to other live theories, it wasn’t called “science”, it was just a branch of philosophy. The philosophy of science has changed over time, which means that the things that once qualified as fitting within science may not do so at a later time.

It is within this understanding of science that Behe’s re-definition of science itself and the discussion of astrology can be usefully approached. Whether astrology might have been considered a live option historically doesn’t change the basic facts: a modern definition of science has no place for a mechanism-less “theory”, and Behe’s re-definition of science essentially reverts us back to a pre-19th century natural philosophy that can’t distinguish between explanations with testable mechanisms and those without.

IMO, that’s the real problem with the Behe/astrology issue, and I don’t think that it is readily amenable to sound-bite presentation on TV. It certainly wasn’t explained adequately in the program, judging by the commentary that has resulted.