The Austringer

Diane and I are working on a personal project to put together an acoustic sampling system that could yield information about the activity levels of snapping shrimp. Whitlow Au and his group have done this sort of thing out in the Pacific. Of course, they’ve gotten research funding to do it. We’re looking to do this out of our pockets, at least for the first proof-of-concept.

Snapping shrimp are small crustaceans. They stun their prey using an oversized claw. Well, that’s just half the story. Any crustacean with a claw might grab or bonk a prey item using a claw. Snapping shrimp create a cavitation event with a snap of their claw. The resulting burst of acoustic energy is a natural disruptor beam (obligatory SF reference can be checked off now). There’s some cool high-speed video of snapping shrimp doing their thing that got published some years back.

Those cavitation events are loud. Until human shipping noise is added to the picture, the single biggest item in the tropical to semi-tropical littoral marine acoustic environment is energy from snapping shrimp snaps. Part of the challenge for my dissertation work on dolphins clicks was coding a recognizer that would include dolphin clicks but exclude snapping shrimp snaps.

Because their method of prey capture produces a signal that travels significant distances, their activity can be tracked for a particular location just using acoustic recording. Because snapping shrimp are so widely distributed and so abundant anywhere there is structure in the (relatively shallow) marine environment, this can be done just about anywhere of interest: seagrass beds, reefs, mangrove swamps, etc.

We’re thinking of snapping shrimp as an indicator species. The various factors of their life history and acoustic features makes them well-suited for this role. A drop in snapping shrimp activity that doesn’t fit the usual diurnal and seasonal patterns would be taken as an indicator of declining ecosystem health.

But to get there, we have to be able to sample those acoustics. This is a job that we’re hoping to accomplish with an instrument we’ve budgeted $200 for parts. This is pretty much penny-pinching taken to an extreme. Here’s the basic gist of where we’re going.

We’re hoping to base the instrument on the new Raspberry Pi platform. This ARM-based Linux system comes with an SD-card interface plus USB. It doesn’t come with a clock. For places with a network connection, NTP can handle setting the time. For other places, we’re hopeful that a cheap USB GPS dongle will serve to provide both time and location. The RasPi also has no sound input, so a USB sound interface is needed. The RasPi needs a power supply, as do whatever USB devices we want to use, so a powered USB hub seems the best solution. We’ll need a hydrophone. That’s something we can make out of a piezo disk, cabling, and some waterproofing method (epoxy, urethane, or perhaps even Plasti-Dip). And that will need a preamplifier. This is where we might bust our budget.

The RasPi is $35. The GPS with USB is $28. The sound interface is $29. The powered USB hub is $27. A piezo disk is about $0.50, and the Plasti-Dip for it might cost a buck.

Some time back, Diane worked with engineers at the University of Texas at Austin’s Applied Research Lab on a dolphin biosonar project. They set out to make a preamp that would provide flat response from a few kilohertz up to two megahertz. The result was a circuit they called the Universal Dolphin Preamplifier. Depending on the discrete components on the circuit, it could be configured for 0, 20, or 40 dB of gain. Even though our first pass at an instrument would be strictly human audio range, I had hoped to be able to construct one of these preamplifiers for use in the project. That was before I started pricing the integrated circuits used in it. There are three of them, and the prices are $37, $16, and $13. All told, I’m estimating about $86 for the cost of parts for one preamplifier circuit. Instead, I’ll be looking to use a more common — and cheap — audio-range preamplifier for our first instrument to deploy.

There are some other things that would be useful to add that may not make it, like some sort of LCD panel to indicate system status. We may just go with some LEDs.

There are consequences of being cheap. The peak frequency of the broadband transient that is a snapping shrimp click is upwards of 50kHz. There’s energy at frequencies within the human audio range, so recording at that range will allow detection of snapping shrimp clicks, but not any sort of spectral analysis that would mean anything. That means just getting measures of activity, like number of detectable clicks. Recording a single point likewise doesn’t tell us much about spatial distribution of snapping shrimp being recorded. We might group clicks by relative received amplitude as a proxy for distance from the hydrophone. And because we’ll deploy an uncalibrated hydrophone, we won’t be getting absolute amplitudes out of the samples, everything will simply be relative.

Doing this for the maximum amount of information would thus imply use of calibrated hydrophones, multiple hydrophones to allow for acoustic localization, and sampling rates high enough to capture the full frequency range of snapping shrimp clicks. A calibrated hydrophone from a vendor could easily run over $1000 each. A system for recording four simultaneous channels of acoustic data at up to 500 kilosamples per second could be done for about $1000 using the Tern Micro GR4 ADC units and a microcontroller. That complete system could easily run between $6000 and $10000 all told. So for the moment we’ll stick with the limitations of doing science on a shoestring budget.

I see from the news that our armed forces have had another bad encounter with dead combatants, this latest kerfluffle stemming from photos taken as military forces pose with blown-up suicide bombers. We end up with another round of apologies, the folks who are supposed to be our allies moving closer to our declared enemies, and more discontented members of the populace ready to be recruited by the opposition.

It seems that trying to explain why these kinds of stunts aren’t good just isn’t getting through to the troops on the ground. They are in a rough place trying to get the job done. It’s little wonder that a need to celebrate being alive when people who tried to kill you are dead results in, sometimes, these macabre recorded expressions.

But I have a possible meme to spread that might resonate with our troops.

We can’t use the “WWJD?” (What Would Jesus Do?) meme. Jesus would be at least a conscientious objector, if not a protester of war anywhere.

But we could use a “WWJBD?” (What Would James Bond Do?) meme. James Bond would totally get behind effective lethal takedowns of the enemy, even ones with a certain gross-out factor. Effective, professional accomplishment of the mission is completely within “WWJBD?” territory.

On the other hand, James Bond would not get behind unnecessary collateral damage. Would James Bond pose himself with dead body parts, smile, and upload the photo to Facebook? Not at all. Would James Bond pose with dubious iconography and send out a press release? Hardly. Would James Bond collect together a few bodies, set up the camera, and take photos while having a whizz on the bodies? Unthinkable.

Can we recruit the idea and image of James Bond for a more consistently professional American fighting force? I think it’s worth a try at this point. Hopefully the Ian Fleming estate would agree.

Here’s another way the acronym “ID” could be instantiated: idiots driving. I commute to work, and yesterday morning I was on I-275 northbound coming into St. Petersburg. I was in the right-hand lane, and a Honda Odyssey was in the left-hand lane. We were traveling at just about the same speed, and had been for a while. There was no traffic ahead of us for another quarter-mile or so.

The Honda was maybe five feet further ahead than we were as we approached 54th Ave. South. Suddenly, the Honda starting coming over to the right. As it crossed the line marking the lanes, I honked, expecting the driver to correct course and return fully to their lane. It kept coming right. I kept the horn going, but veered right and braked, too, to avoid a collision. It’s just as well, because the Honda driver apparently didn’t change their plan at all and simply completed their lane change. If I hadn’t been paying attention, we’d have had a two-vehicle mashup at 65 MPH on the interstate.

Diane was able to get a couple of photos just afterward. Here’s the back-end and license plate of the vehicle I saved from a high-speed crash:

And here’s one of the driver and passenger we prevented from coming to serious harm and injury:

I've been going through biosonar data and while the SciPy specgram method is serviceable, I was interested in a short-time Fourier transform (STFT) implementation. There are a couple of ad hoc routines on Stack Overflow and the like, but I've started off with the Google Code PyTFD module. There are others out there as well, at least two projects including an STFT implementation are aimed at extracting time and frequency data from musical recordings. I may have a look at one or both of those at some point.

In any case, installing PyTFD involves downloading the code via Subversion and then running the setup.py script.

Since I spent more time than I think was absolutely necessary getting a couple of examples done with the STFT, let me run through an example in the hopes that helps somebody.

OK, so there's a fair amount of things to be imported along the way. The first three items (lines 2 to 4) are specifically for setting up access to PyTFD's STFT method. Line 18 sets up the window function to use in the STFT. Line 19 actually does the work, getting the resulting multidimensional Numpy array with the STFT result given a Numpy array input and the window.
Line 20 sets up the extent array to express the size of the X range and the Y range covered by the STFT. Lines 20 to 24 puts the result in a subplot. There are some issues there. The STFT results are essentially a whole series of Fourier transforms, and those have both negative and positive frequencies, and are complex values to boot. So the "abs" function provides a magnitude for each point. The slice yields just the positive frequency range. Then the extent gets set to the range represented by the STFT. The "aspect" parameter is set to "auto" so that the X and Y ranges can be calculated separately by Matplotlib. The "origin" is set to "upper" to put the frequencies in the expected orientation.

Here's a couple of the outputs:

An op-ed piece by Mike Deering, the National Cattlemen's Beef Association Director of Communications, lays out an argument to let ranchers handle conservation of the sage grouse without involving the protection of the Endangered Species Act:

The wackos – as I still prefer to call them – have successfully weaseled their way to the front steps of BLM and the U.S. Forest Service. Late last year, the agencies released a plan to implement sage grouse protections on 45 million acres of federal lands with the goal of preventing the listing of sage grouse. While that’s a worthy goal, the plan fails to recognize that grazing is responsible for retaining expansive tracts of sagebrush-dominated rangeland, stimulating growth of grasses, eliminating invasive weeds and reducing the risk of wildfire. These services can only be provided by ranches that are stable and viable. Without grazing, sustaining and increasing the sage grouse population would be nearly impossible.

Grazing prevents fires. Fires cause death. Death equals barbecued chicken. It is that simple.

OK, let's posit that Deering is giving it to us straight for a moment. What does he say next?

Ranchers stand ready to work with the government to prevent the listing of the sage grouse, which has the potential to put public lands grazing to a complete halt (according to Dave White, Chief of the Natural Resources Conservation Service, March 7, 2012).

Hmmmm. This doesn't exactly inspire confidence that the NCBA is altruistically looking out for the best interests of sage grouse as a species. It sounds like a group that recognizes that a major resource may no longer be available to them and is taking steps to prevent losing that resource for their own use.

That line about "barbecued chicken" is an instance of rhetorical framing applied to sage grouse in the article.

"massive chicken barbecue"

"that barbecued chicken I mentioned earlier"

"the chicken debacle – officially called the greater sage grouse"

"ignore the chicken and set their sights on ranchers"

"not protect the chicken"

This isn't just what passes for folksy charm in the NCBA. Likening sage grouse to chicken blurs distinctions between a native species in undisputed decline and a ubiquitous introduced domestic species. How could something that is called chicken deserve protection under law, after all?

Now lets drop the notion that Deering's argument stands on its own. No, Mike, it is not "that simple" that ranching practices will produce a thriving population of sage grouse. The particular threat that Deering concentrates on, fire in sage habitat, is not always and everywhere a bad thing. Sage grouse need a particular mix of sage and other plants, and fire at a particular rate helps clear too-dense sage and restores a balance between cover and plants supporting forage for sage grouse. So a simple "no fires" policy is not a win for sage grouse.

Let's have a look at another part of Deering's rant:

I admit, those are some pretty inflammatory words. But these extremists deserve every ounce of it and I will back it up with one of many examples. Let’s hone in on that barbecued chicken I mentioned earlier. Extremists, for the most part, have refused any meaningful reform to the Endangered Species Act, which has resulted in a less than two percent species recovery rate over the past 40 years. Instead of looking at ranching as part of the solution, they spout rhetoric over facts. Look no further than the chicken debacle – officially called the greater sage grouse. Instead of working aggressively to prevent the listing of the sage grouse on the Endangered Species List, they are working aggressively to ignore the chicken and set their sights on ranchers. Say what? Yeah, their end goal is to end ranching; not protect the chicken.

Deering doesn't mention here what, exactly, constitutes "reform" of the ESA. One might take it to mean specific things that would improve its record on the metric of "species recovery rate", i.e., how often listed species become delisted. (A comment I've seen elsewhere notes that this is the wrong metric to use to evaluate the ESA; instead, one should look at the rate of extinction of listed species.) One would be wrong, though; the NCBA is on record with its list of proposed "reforms" to the ESA, and these have nothing at all to do with making the ESA more effective. They would, instead, guarantee less effectiveness of the ESA, putting in place automatic delisting criteria, providing exemptions that let certain classes of people off the hook for not following ESA regulations, placing even more burdens on those seeking to have a species listed, providing money to private property owners to implement policies, and adding logistical and paperwork burdens in the process of listing any species under the ESA.

I don't know why activists would want to 'aggressively prevent the listing of the sage grouse on the endangered species list'. Deering certainly doesn't inform us as to why an activist should consider that a bad thing. Nor is the claim that protecting sage grouse is not the aim of people urging conservation supported in Deering's rant by anything other than his assertion.

I'm not anti-rancher. But I am pro-sage grouse, and I think that preserving sage grouse is going to require more than stopping fires on grazing lands, which is the only thing I hear as a concrete policy coming out of the NCBA. The record of action on sage grouse conservation is a continual off-putting of listing as an endangered species, which is due to intense political action, not biological reality.

Time's web page has an article up by Jeffrey Kluger. Kluger is a lawyer and relates his reaction to the briefs filed in the case of David Coppedge v. Jet Propulsion Laboratory and Caltech.

Groups like the intelligent design community are not always free to pick their poster children, and it's unfortunate for them that Coppedge is one of theirs. It's true enough that employers and colleagues in a science-based workplace might be uncomfortable with the idea of a coworker who believes in intelligent design. But neither the Constitution nor employee-protection laws can regulate feelings — no more than they can or should regulate belief systems. They can, however, circumscribe behavior on both sides of that faith-divide. From the filings at least, JPL appears to have stayed well within those boundaries. Coppedge appears to have jumped the rails entirely.

Yes, even disinterested third parties get it now.

JPL's brief discusses a lack of self-awareness on Coppedge's part. The tone-deafness isn't just Coppedge, though. It permeates the DI and the IDC community. They are so intent on instantiating their myths that they cannot seem to wrap their heads around the idea that one of their own could be in the wrong. You'd think with all those lawyers in their camp that they would be better at this than they are.

I ordered a Raspberry Pi Model B computer from Newark, so now I'm waiting for stock to catch up with the truly phenomenal initial demand.

If you are wondering what the Raspberry Pi is, it is a small computer board based on a Broadcom System On Chip (SoC). The SoC is ARM-based, so the operating systems offered so far are Linux distributions. The board has a CPU, GPU, 256MB of Ram, an SD card interface, a USB host interface, audio output, Ethernet network port, and video output via composite or HDMI interfaces. And it costs $35.

The Raspberry Pi is the brainchild of a United Kingdom non-profit organization that aims to make a low-cost programming platform to re-invigorate interest in computer science among students. Since computers have turned into consumer devices rather than primarily being programming platforms, students don't have a low-cost way to spark an interest in programming itself. Until, the Raspberry Pi folks hope, now.

But the Raspberry Pi is just now starting to be distributed in quantity. As the device comes, it is just a computer board a little bigger than a credit card. It doesn't even have a case. So there is some shopping to be done to trick out your Raspberry Pi once you order it.

The first order of business is power. The way I've seen this discussed is to get a powered USB hub and micro-USB power cable. The Raspberry Pi's power plug is a micro-USB interface. That port only hooks up power, so there's no problem hooking that into a powered USB hub that you'll also use for peripherals.

You'll need an SD card and a downloaded image of an operating system to run. I see people talking about 4GB or larger SD cards. I found a SanDisk Class 4 8GB for less than $3:

Getting something on-screen requires either an RCA composite video card and monitor, or something that you can hook up via the HDMI output. I've got two DVI-equipped monitors here, so I'm looking to link my Raspberry Pi with a cable that goes from HDMI to DVI.

The rest of the items are peripherals that hook up via the powered USB hub discussed above. If you don't have a USB keyboard and mouse, or if you prefer a trackball, or if you want to add audio recording capability, that all happens by adding USB devices. Here are some items I located:

I've put the Amazon links in the sidebar.

Some time ago, I wrote about making a modular curriculum vitae in . Since that time, I've had to update the contents. Things change. Colleagues request current CVs to include in grant proposals, and given the current state of public sector employment it is no bad thing to have the CV ready to go.

But I'm now fighting a problem of separating content and presentation. There are different rules for formatting CVs and resumes, and I've done the wrong thing previously: I've copied and modified sections like employment history in order to change how the presentation happens. This is bad, because now any time I change something in my employment history, I need to make sure that every relevant copy gets changed. I needed some way to make it so there would be one and only one place where each piece of information would be kept, and apply that to different pieces of presentation code in the source.

The solution I found today is the datatools module for . This is a module that allows one to generate, read, and manipulate data stored in CSV (comma-separated-values) files. There is a lot of functionality in the module that I'm not using yet, but the ability to get data out of CSV and format it as needed is a big step forward for me.

I've created two CSV files so far, one to hold my education data and another to hold my employment data. The CSV files have more columns than will often go into an output format. For example, my education CSV has columns for my advisor name and my thesis title, even those don't appear anywhere in an output yet. This will allow me to keep all associated data together, whether or not it is currently used. Previously, I simply used comments to add this kind of information close to what it relates to in my source.

I'm using various sources of good resume formatting to get ideas. Here's the code to show my three degrees:

The "usepackage" line happens in the header. The "datatools" commands are only valid within the bounds of a document environment. I'm defining a macro "dtledu" to use in conditional statements. Within the macro, I skip an eighth of an inch down the page. I set the "datatools" package to emit a lot of debug information. The "DTLloaddb" command actually pulls in the contents of a CSV file. I first tried to use tab-delimiting, which is in the "datatools" documentation, but I couldn't get it to work. I eventually went with all default formatting: commas for delimiters, and double-quotes for separating fields. That means that any text that has a comma must go in double-quotes.

The actual work happens in the "DTLforeach" command. It uses the data that was read in. One line holds the assignments from data from columns to macros. Then a block appears where I can use those macros in conjunction with markup. Each line from my CSV is iterated over and formatted as I've defined it.

So this gives me a way to keep one place where my education information exists, and just one place for my employment information to exist. That information can be read in and formatted in different ways as needed for getting just the right output I'm looking for.

I ran across a link to a blog post from 2007 by Jeff Shallit. One of the commenters there took exception to Jeff's statement that the KvD case was primarily about religion, noting that a lot of the decision in the case discusses science. I was five years late to the party, but I felt that I needed to put my two cents in:

Sorry to have come across this so late. "analyysi" objects to the idea that the issue in Kitzmiller v. DASD was establishment of religion, saying that the decision discusses the topic of science a lot.

"analyysi" may be unfamiliar with the law here in the USA. The grounds for the complaint in KvD was indeed the establishment clause of the 1st amendment. The legal history will clarify why science is discussed at length in KvD. The Epperson v. Arkansas SCOTUS decision declared that one cannot prevent the teaching of science to privilege particular religious accounts, that science instruction has a valid secular purpose. Since Epperson, the religious antievolution movement has proceeded with a variety of dishonest efforts to characterize the same old arguments they usually make as science and to aid in this they offer new definitions of science. If they could convince a court that what they offer up for inclusion in a classroom is science, they would then have demonstrated a valid secular purpose in having it taught. And so in the KvD case you had the defense present lots of testimony from expert witnesses claiming that "intelligent design" was, indeed, scientific in character, at least as long as you allow them to also tweak the definition of science.

There are people who like to claim that Judge Jones could have completely ignored all the arguments made by the defense that ID was science and by the plaintiffs that, no, it wasn't. I think the decision would have been weaker if it failed to address an issue that both parties considered central to the suit. The reason that a discussion of the nature of science and whether ID meets criteria to be recognized as science appears in the decision is that both parties made it an issue and prior precedent made whether something is science an issue for determining whether something has a valid secular purpose in being taught. The point in law being addressed is still establishment of religion while the particular instance of argument concerned ID's lack of status as science.

Hope that clears that up for "analyysi".

At lunch at the Spoonbill Bowl on Saturday, I was privileged to volunteer with a group of students, faculty, and researchers. It was a long day. Lunch was provided, and I got to sit down with a colleague and a couple of faculty members from USF St. Petersburg. One of them posed a brain-teaser question. I followed up with broaching the Monty Hall problem.

Just to make sure everyone is on the same page, I'll briefly describe the Monty Hall problem. In the television game show, "Let's Make a Deal", host Monty Hall would offer a contestant an opportunity to win a major prize, let's say a new automobile. The stage would show three doors ("Door #1", "Door #2", and "Door #3"). The major prize is behind one of the doors. Behind the other two are booby prizes, let's say that they are goats. The contestant is allowed to pick a door. Rather than simply opening the contestant's pick, Monty would have a door the contestant did not pick opened to reveal a goat. Then, Monty would offer the contestant a choice: she could stay with her original pick, or she could switch to the other door that had not been opened.

The Monty Hall problem poses the question of strategy: Is it better to always stay with the original choice, to always switch to the other remaining door, or does it not matter one way or the other? This question was posed many years ago in a column hosted by Marilyn Vos Savant and gave her months of correspondence as people argued with her advice to always switch. Marilyn was right, of course. The problem and just how counterintuitive the result is has proven a popular topic since then, and Jason Rosenhouse even has authored a book about it.

Back to my luncheon discussion. Me bringing up the Monty Hall problem led to about twenty minutes of trying to explain to one of my lunch companions why always switching was the right choice. It was a microcosm of the entire history of the public history of the problem, and I found it frustrating that I wasn't able to more clearly and simply put it so that my companion could be convinced of the correctness of the answer. What finally made sense to my companion was that if one enumerated all the permutations, staying won in one-third of them, and switching won in two-thirds of them.

So I decided that I would make up a set of business cards to make future discussions of the Monty Hall problem go faster. Here is my graphic:

While I can't include all the text that I would like on something the size of a business card, I can use this to quickly demonstrate why switching is actually the better strategy. The card shows all nine possible ways that the game can be played. It also shows that in only three of those does staying with the initial pick work out to a win for the contestant. In the other six ways the game works out, the contestant only wins if they switched.

I think I'll put a version on a T-shirt.

Update: During lunch today, I tested out my card as a tool on a Monty Hall Problem-naive colleague. Her initial hunch was that staying with the initial choice was the strategy to pursue. I said that I would try to convince her that switching was the correct strategy and produced a card. I pointed out that every possible way the game could go was represented, and in only the top row did staying work out to a win. Within two minutes, I had convinced her of the correctness of the switching strategy. So that's one data point.

Also, I've updated the graphic here. I've changed the color scheme. Diane pointed out that it would be hard for color-blind people to distinguish differences in the original. I've also added door numbers to make it clearer that each block of three rectangles represents one set of doors. And I added drop shadows to the doors just because I think it looks better that way.

In looking at the Wallace biogeography flap, I came across an interesting passage in Wallace's 1855 Sarawak paper:

We shall thus find ourselves obliged to reject all those systems of classification which arrange species or groups in circles, as well as those which fix a definite number for the divisions of each group. The latter class have been very generally rejected by naturalists, as contrary to nature, notwithstanding the ability with which they have been advocated; but the circular system of affinities seems to have obtained a deeper hold, many eminent naturalists having to some extent adopted it. We have, however, never been able to find a case in which the circle has been closed by a direct and close affinity. In most cases a palpable analogy has been substituted, in others the affinity is very obscure or altogether doubtful. The complicated branching of the lines of affinities in extensive groups must also afford great [[p. 188]] facilities for giving a show of probability to any such purely artificial arrangements. Their death-blow was given by the admirable paper of the lamented Mr. Strickland, published in the 'Annals of Natural History,' in which he so clearly showed the true synthetical method of discovering the Natural System.

Hmmm, OK. What are the odds that one could manage to lay hands on a paper published about 172 years ago? Google search for "Annals of Natural History Strickland" placed an Internet Archive link high in the ranking. That page offers the text of the paper in several different formats.

So what does Mr. Strickland say about systematic work?

The postulate with which I commence the inquiry is, to let
it be granted that there are such things as species, distinct in their characters and permanent in their duration. This being admitted, we define the natural system to be the arrangement of species according to the degree of resemblance in their essential characters. In other words, the natural system is that arrangement in which the distance from each species to every other is in exact proportion to the degree in which the essential characters of the respective species agree. Hence it follows that the whole difficulty of discovering the natural system consists in forming a right estimate of these degrees of resemblance. For the degree in which one species resembles another must not be estimated merely by the conspicuousness or numerical amount of the points of agreement, but also by the physiological importance of these characters to the existence of the species. On this point no certain rules have yet been laid down ; for though naturalists in general admit, for instance, that the nervous system is superior in importance to the circulatory, and the latter superior to the digestive system, yet this subject is still in a very indeterminate state, and until our knowledge of physiology is much further advanced, disputes will always arise respecting the true position of certain species in the natural classification. Such differences of opinion, however, will continually diminish as our knowledge increases, and they are even now very few in comparison with the numerous facts in classification on which all naturalists are agreed. Much may be effected by education and habit, which impart to the naturalist a peculiar faculty (termed by Linnaeus a " latent instinct 5 ') for appreciating the relative importance of physiological characters to the satisfaction of himself and others, even in cases where he is unable to explain the principles which determine his decision.

Strickland devotes the bulk of his paper, though, to a thorough trashing approaches to systematics that proposes some ordering principle from without. Linear arrangements, numerological arrangements, and circular arrangements all come in for deconstruction and dismissal.

The best part I see, though, is Strickland's argument for why variety is and must be the aspect of nature that zoologists simply have to accede to.

2. It follows from the irregularity of external nature, as seen on the surface of the earth, that the groups of organized beings must be irregular also, both in their magnitudes and in their affinities. In proof of this it must be granted that the final cause of the creation of every animal and plant is the discharge of a certain definite function in nature, and not the mere occupation of a certain post in the classification : in short, that the design of creation was to form not a cabinet of curiosities, but a living world. Few, I trust, would hesitate to admit this proposition. If, then, the different modifications of structure which constitute the characters of groups were given solely with reference to the external circumstances in which the creature is destined to live, it follows that the irregularities of the external world must be impressed upon the groups of animals and of plants which inhabit it. The supply of organic beings is exactly proportioned to the demand ; and Nature does not, for the sake of producing a regular classification, go out of her way to create beings where they are not wanted, or where they could not subsist. Thus, for instance, the warm climate and varied soil of the tropics admits of the growth of a vast variety of flowers and fruits. The group of Humming-birds which feed on the former, and of Parrots which feed on the latter, are accordingly found to be developed in a vast variety of generic and specific forms ; while the family of Gulls which seek their food in the monotonous and thinly inhabited regions of the north, are few in species and still fewer in genera. Again, the variety of plants in the tropics admits the existence of a great variety of insects, and the family of woodpeckers is proportionately numerous; while the Oxpecker {Buphaga) % which seems to form a group fully equivalent in value to the Woodpeckers, is limited to but one or two species, because its food is confined to a few species of insects which only infest the backs of oxen.

It follows, then, that the groups of organized beings will be great or small, and the series of affinities will be broken or
continuous, solely as the variations of external circumstances
admit of their existence, and not according to any rule of
classification. If, indeed, we were to imagine a world laid
out with the regularity of a Chinese garden, in which a certain number of islands agreeing in size, shape, soil, and form of surface, were placed at exactly equal distances on both sides of the equator, we might then conceive the possibility of a perfect symmetry in the groups of beings which inhabit them ; but without some such supposition, I do not see how a class of animals or plants can be symmetrical in themselves, and yet be expressly adapted for conditions of existence which are eminently irregular.

This statement of Strickland's appears to express the concept of niche that Joseph Grinnell would be credited with some sixty-seven years later in 1917. There is the persistent difficulty in looking at almost all Victorian-era naturalist writings pre-Origin-of-Species that everything has to be couched in terms of some sort of creationary framework. But the citation of Strickland in Wallace's 1855 paper does show a nice progression in the history of ideas, where a concept of dependence of a species on a set of environmental conditions leads to the concept of biogeography relating species not just to particular constraints, but also to particulars of place and time in relation to parent and daughter species.

The particular proposal of Strickland's, to evaluate characters weighted in some way by importance to the species in order to assess affinities to other species, markedly differs from what is considered current today. The cladistic approach developed in the 1960s explicitly gets rid of "weighting" schemes and the notion that a few well-understood characters are better for assessing affinity than many characters simply noted as present or absent. So Strickland's actual proposal of what the true method of discovering the natural system would be hasn't held up, but several of his reasons for rejecting prior methods still carry weight, and his expression of this appears to have contributed to the development of biogeography as a topic.

There's a post on "PRUnderground" that takes delight in an alleged screwup by Prof. Jerry Coyne. Coyne is stated to have made a claim during a radio program about Alfred Russel Wallace:

In particular, Jerry was emphatic in claiming Alfred Russel Wallace never connected biogeography to evolution: “Wallace did not use biogeography as evidence of evolution. I mean, never!”

Given that "intelligent design" comes into it later, I'm suspicious about the veracity of any such quote. It certainly is a staple of religious antievolution argument to get things wrong. So I'll note that the basis for everything else is not verified and go on with the assumption that the author did manage to convey that claim of Coyne's in essence.

The article then goes on to discuss Coyne's claim, or, rather, to claim to discuss Coyne's claim:

That’s not how I remember this history, so I decided to check with Wallace biographer Professor Michael Flannery.

Professor Flannery: Well, he seems to really be unfamiliar with Wallace’s body of writing on that topic. The famous paleontologist and geologist, Henry Fairfield Osborn, he’s sort of an icon in the field, referred to Wallace’s Sarawak Law Paper as “A very strong argument for the Theory of Descent and a bold declaration from a strong and fearless Evolutionist.”

And actually if you’d like sort of an icing on the cake reference, Ian McCalman, who has written a pretty good book recently called Darwin’s Armada, refers to Wallace’s Sarawak Law paper as, “The first ever British scientific paper to claim that animals had descended from a common ancestor and then produced closely similar variations which have evolved into distinct species.”

What's remarkable about this is that the rebutting expert never directly addresses the question at issue. Did Wallace use biogeography to inform his discussion of evolution? Unless you already knew the answer to that, Flannery's response doesn't approach it at all. Rebutting Coyne's claim requires three elements to be shown: Wallace as source, evolution as topic, and biogeography as evidence. The Osborn and McCalman quotes address only the first two of these, leaving the critical component, biogeography, out entirely.

Flannery does mention in passing Wallace's Sarawak paper. Even a brief skim of the paper is enough to disabuse anyone of the notion that Wallace never used biogeography as evidence of evolution. But one would have to already know the content of the paper in order to decide whether Flannery's assertion carried weight or not. For completeness, though, I'll quote Wallace discussing that iconic example, the Galapagos Islands:

Such phænomena as are exhibited by the Galapagos Islands, which contain little groups of plants and animals peculiar to themselves, but most nearly allied to those of South America, have not hitherto received any, even a conjectural explanation. The Galapagos are a volcanic group of high antiquity, and have probably never been more closely connected with the continent than they are at present. They must have been first peopled, like other newly-formed islands, by the action of winds and currents, and at a period sufficiently remote to have had the original species die out, and the modified prototypes only remain. In the same way we can account for the separate islands having each their peculiar species, either on the supposition that the same original emigration peopled the whole of the islands with the same species from which differently modified prototypes were created, or that the islands were successively peopled from each other, but that new species have been created in each on the plan of the pre-existing ones. St. Helena is a similar case of a very ancient island having obtained an entirely peculiar, though limited, flora. On the other hand, no example is known of an island which can be proved geologically to be of very recent origin (late in the Tertiary, for instance), and yet possesses generic or family groups, or even many species peculiar to itself.

Back to the PRUnderground article...

Then, for nausea's sake, the folks go off into speculation and "intelligent design" cheerleading:

Alex Tsakiris: All this might seem like a lot of minor detail that no one cares about, but this little bit of history is actually quite important in the culture war debate over the theory of evolution. Why does an otherwise smart guy like Dr. Jerry Coyne say these things which are so obviously incorrect? What’s the real agenda here?

Professor Flannery: Well, my guess is that he is either just unfamiliar with Wallace’s work, although that’s kind of hard to believe… I actually think that it just doesn’t serve his purpose. When you look at his book, Why Evolution is True, one of the things he’s writing against is Intelligent Design. To bring Wallace into the picture becomes problematic for him because Wallace himself came to view evolution as being guided.

Blech.

Here's the response I entered in comments there:

Coyne was wrong about Wallace. Wallace was wrong about the concept of "intelligent design". Coyne not completely grasping the history of ideas isn't helpful, but it in no way can be taken as supporting IDC.

Professor Flannery also doesn't do well in forming his answer to the question of whether Coyne was right in his claim. Flannery's first try, invoking Osborn on Wallace's status as an evolutionist, doesn't even address the question. For the second, one has to oneself know the content of the Sarawak paper to know that the claim by Coyne is false; it isn't evident by the statement that Flannery makes. The quote he gives is remarkable for the complete absence of any geographical or biogeographical component.

Update: At Troy Britain's prompting, I've had a look at the Skeptico transcript of the Coyne interview and listened to the segment in the MP3 including the quote from Coyne that was at issue. The quote does fail to give the gist of Coyne's original claim. That claim is that it was Darwin who was the first to use biogeography as evidence of evolutionary change. Coyne rejects any discussion made by Wallace of both biogeography and evolution that occurs after 1859 as not being relevant to his claim. That makes Coyne's statement that Wallace "never" used biogeography as evidence for evolution a bit of hyperbole on his part, since his only interest seems to be in who got there first, Darwin or Wallace. Unfortunately, Coyne is mistaken on this point: the 1855 "Sarawak" paper by Wallace is quite explicit in using biogeography to undermine the idea that species are fixed. In 1855, Wallace did not have and did not produce a mechanism for speciation, but it is clear that he was talking about evolution and that he was using biogeography as evidence for it.

Giving Wallace appropriate credit for his innovations is not a concession to religious antievolutionists. Like I said before, Wallace was wrong in his advocacy of stuff that the "intelligent design" creationists have glommed onto. That doesn't make the good stuff that Wallace did less worthy of notice.

Have a look at this article on the BBC site.

There's just so much wrong. The mobile telephony companies are toting up projections of profit from SMS and MMS messaging and seeing a shortfall as a "loss".

"I think it's a growing threat which is manageable through the right tariffs and the right costing," Mr Barford added.

"People are still using the mobile networks to communicate - and they're willing to pay for that."

Yes, people are wiling to pay to communicate, but they are also going to look to find the best available methods. That evaluation is going to include cost. And the pricing telcos have artificially placed on SMS and MMS messaging simply is uncompetitive with other technologies now.

The buggy-whip manufacturers experienced a "loss of revenue" with the advent of the automobile. That doesn't mean they deserved to continue getting it, no matter what "tariffs and right costing" they might have contemplated. The only difference here is that the buggy-whip manufacturers were not also the only people selling and servicing automobiles.

As noted here before, I'm working through refreshing archived data, mostly from CD-ROM media. I've run into a whole batch of CD-ROM disks that are in good physical condition, but which mostly cannot be read. I'm trying some tools that I've seen recommended, but would be open to suggestions.

But the whole point of getting the archived data refreshed is to do something with it. And that's what I will aim to discuss here this time.

Over several years, there were a number of different technologies I was using to collect bioacoustic data. This means that I don't have one single type of data of interest. I have data that was recorded on audio cassette tape. I have data from a Racal Store V data recorder that was transferred to cassette tape. I have digital data from Keithley-Metrabyte DAS-1800 DAQ, Tucker Davis Technologies DAQ, and a couple of different National Instruments DAQ boards multiplied by at least two different multichannel scenarios. Plus, there's digital data transferred off of a Racal Storeplex unit via SCSI. There's mixed endian byte order issues, among other things.

I have a good software solution for two of these particular data acquisition scenarios. I wrote that between 1999 and 2001 using Borland's Delphi 5. In all, there's about 60,000 lines of code for data acquisition, reduction, analysis, and visualization. The original can handle multi-channel recordings taken from a single National Instruments board. A variant works on digitized audio recordings. That includes interactive data reduction with an automated click-picker whose choices can be refined with changes in parameters or by interaction with an oscillogram graph.

That still leaves a lot of data waiting for analysis. During my time at Michigan State University, I got into Python programming. There are a number of nice things about going after the rest of the data with Python. A big one is that Python is free, open-source software. I can have colleagues install it and not have to worry about breaking their budgets, which is a concern when one considers the well-established science and engineering scripting platform, MATLAB. While Python doesn't yet have all the "toolbox" capability of MATLAB, it has enough to move ahead with. For the scientific programmer, there are the Numpy, Scipy, and Pylab modules (I installed the Python(x,y) package on my Windows laptop, which includes those and more besides.) Numpy extends Python with a fast array and matrix manipulation capability. Scipy includes a variety of analysis tools. Pylab looks to put a wrapper on those two, plus the Matplotlib graphics module and the Ipython interactive shell.

I recently wanted to extract spectral information about dolphin clicks from one of the datasets that I hadn't previously examined. So I turned to Python to do that. The data was stored as raw binary, 16 bit signed integer samples. Reading that data was simply:

where "fn" is a filename pulled from the directory of interest. The "np" reference above resolves to "numpy". The three lines say to get an open file object, fd, by opening a file, fn, for binary read. Then, a Numpy array containing the data is returned by the Numpy static method, fromfile, given the file object and the specification of the data type as signed 16 bit integers. The third line closes the file object. If I had a problem with endian issues, there's at least a couple of ways to address that in Numpy. (Getting the wrong byte order should be obvious on visualization, but I've seen a professor merrily tout a new processing method for dolphin clicks when his slides clearly showed that he had a byte-order problem with his dataset.)

While it is better to handle DC offset problems at the time of data collection, sometimes you just have to deal with it at analysis time. This dataset handed me that problem. This problem is one where a time-varying signal should be centered at zero volts input, but instead centers at some non-zero voltage. Fortunately, it was a fixed offset, so a pretty simple approach worked nicely: find the mean value across the dataset, and subtract that value from each sample.

The use of a Numpy array for the data means that the one line above handles the element-wise addition operation. The Numpy array on the left is now a floating-point array instead of an integer array.

My Delphi program had a click-picking algorithm that took a while to craft. I haven't ported it yet, so I just went with a very simple approach in Python. That looks at chunks of the data, where the chunksize was selected to be a bit larger than the maximum click width, but a good deal smaller than the interval between clicks. Within each chunk, the maximum value and minimum value are found. If the maximum and minimum are outside a defined noise level, consider it a found feature.

Using the Numpy routines to find the min, max, and max location is pretty snappy.

Then, for each "click" located, I ran an FFT to get a power spectral density, and plotted that. I just used example code to add this functionality. (For underwater acoustics where pressure is measured, though, the conversion to decibels uses a factor of 20 rather than 10.)

So, for a quick and dirty script of less than three hundred lines total, I was able to:

* get a directory listing
* match to filename features to identify files to analyze
* remove DC offsets
* save new versions of the data
* scale the data according to field notes
* locate "clicks" in the data
* generate a PSD for each "click"
* collect PSD data
* generate and save oscillogram/PSD plots
* rank "clicks" on spectral features
* copy off plots of the highest-ranked clicks to a directory

My 2.4GHz dual-core Ubuntu workstation ran this script on 230 megabytes of data, producing over 1,400 graphs, and did it in eight minutes time. I've just located a calibration sheet on the hydrophone used, so once I've digitized that and applied it, I'll post an example with real dB numbers on the axis.

I don't know what other people got up to this weekend, but mine has been pretty well filled with computing projects.

I've been working with my friend Marc to try to get to the bottom of the Verizon FIOS connection foul-up. We each ran TCPDUMP on our respective machines while making a request that could be fulfilled (a small static HTML page) and one that could not be fulfilled (a dynamic page for webmail). We've sent the logs off to a networking guru friend of ours to see if he has any ideas. While I fully expect that this is a problem in Verizon's gear and processes, we are continuing to test any possibility that a fault in our gear could be an issue.

As I've mentioned previously here, I have data stretching back to the mid-1990s on CD-ROM. I've made a chunk of progress toward refreshing the archive by copying various of those to hard disk. It takes time, and needs manual attention every five minutes or so to unmount the last disk, load the new disk, mount it, and set up a copy process. Fortunately, most of the disks simply copy without error. I'm using ddrescue to go after the few files that won't copy cleanly.

I've also been going through some of the packed boxes to locate more disks to be refreshed. Along the way, I've been reminded that I also have a pile of video and acoustic recordings on tape to digitize as well. I do have a cassette tape deck set up to digitize to my laptop, but I haven't gotten my desk set up nicely to incorporate the video digitizing machine into a smooth workflow. From left to right, I have a Macbook Pro, a Viewsonic 24" LED monitor for a second screen for a laptop, a Gateway MT6458 laptop running Win7, an Optiquest 15" monitor for a desktop machine, plus keyboard and mouse for a desktop. Under the desk itself, I've got the video digitizing machine and the workstation/file server box. The video digitizing machine was built as state-of-the-art in 2001. It runs Windows XP, since the digitizing card doesn't work under anything more recent. It still does a nice job of pulling in analog sources in a DV video stream. The file server is much more recent, being built in 2007. It runs Ubuntu Linux 11.10. There's 4 terabytes of hard disk storage in that machine, which we use for our project files, personal files, multimedia, photos, and data. We're coming up to the limits on that, especially after this weekend's work.

I found a box of pocket notebooks, several of which have notes from our research data collection. But I did find one that has notes from the 1997 Discovery Institute conference on "Naturalism, Theism, and the Scientific Enterprise". I see from my notes that Michael Ruse classed approaches to "religion v. science" into "conflict", "accommodation", and "separation". I don't think "accommodation" was used by Ruse in exactly the same way that more recent commentary has gone, but I thought it interesting to see the word there, anyway.

I'm also working on some Python programming and a PHP/MySQL project. Between these things, that pretty well soaks up the time.

Dr. Eugenie Scott is giving a public talk Thursday, February 9, 2012, at the University of South Florida in Tampa. The topic is on the "critical analysis" legislative efforts that have popped up in Florida, and how these are part and parcel of the creationism movement.

The location is FAH 101 and the time for the talk is 7 PM. There's a reception at 6:30 PM, so getting there early would be a good thing. I plan to be there.

I have two new trouble tickets with Verizon FIOS as the connectivity situation continues to be nearly completely non-functional, as it has been since January 10th. The one entered from the Verizon Business FIOS side of things is TXP08R8CY. During the hour-and-a-half tech support conference call needed to get that one going, I happened to inquire about my previously-entered trouble tickets, and was told that they had been closed. Since the problem continues, I insisted that the tech set one up for my residential FIOS account, too. That one is FLCP08R8EN.

If you are a Verizon customer and have difficulty getting through to this site or other sites I run, be sure to reference the above tickets when you put your complaint in. Thanks.

I have a bit more information about the connection difficulties I've been having with my ISP, Verizon FIOS. I have a residential account in Palmetto, FL with Verizon FIOS. Mostly, it works fine. I can get to a host of web sites without difficulty, and the transfer speeds are great.

I do remote system administration on two servers in the Dallas-Fort Worth Metroplex. Those servers get their connection via a Verizon FIOS Business plan link. (Yes, Verizon, the servers are on an account where serving is usual and expected.) One server provides my regular email, the other serves a whole bunch of web sites via virtual hosting. And things there are mostly working, where the outside world can merrily get pages served on demand.

But...

As of sometime early last Tuesday morning, January 10th, Verizon FIOS stopped reliably talking to Verizon FIOS. I can tell the approximate time of the outage as the last email message my computer here picked up from the server there was at 1:09 AM CT. The problem is very likely to have manifested within a very few minutes after that. And the problem's characteristics are just plain weird. One expects most 'problems' with connections to be user error. Certainly that's the primary basis of Verizon FIOS's residential account tech support, who are ready to quit if the problem isn't solved by having the user clear their browser cache or resetting the router. This problem, though, is more complex and is not localized to my particular account. First, not all connectivity is gone, just *most* connectivity. I can use SSH to log in remotely and use commands that return small amounts of information. Once I try a command that would return a page or more of text, the connection drops with a 'Broken pipe' message. There's a web page that is static and is only a few hundred characters in size that I can successfully retrieve. But none of the web sites that rely on web applications (Drupal, WordPress, and IkonBoard) do anything but spin forever while the browser displays 'Waiting on ...'.

So let me jot down some things I've learned about this so far.

* It isn't a DNS issue, as 'nslookup' finds any of the domain names and returns the correct IP address quite rapidly.

* It isn't a single port failure. Ports 22, 25, 80, and 587 are, at a minimum, included in the affected list.

* It isn't a complete break, as connections on the scale of a single packet of data at a time work.

* Using traceroute for other websites shows three hops taken within the Verizon routing center in Tampa. Traceroute for the affected servers shows two hops taken similarly, but the third times out.

* My parents live in Lakeland, Florida, a goodly distance away from where I live, and have Verizon FIOS as their ISP. I visited there this past weekend and asked my dad if he had been able to check this blog recently. He said no, not for about the past week. I tried traceroute from their connection, and it behaved the same way as from my home connection. The problem is not localized, it affects other Verizon FIOS customers.

* I've heard from Texas where another Verizon FIOS user of the email system cannot connect to the email server. I don't have a traceroute result from them to compare.

I have two open tickets on this problem with Verizon, FLCP08NT6J and FLDQ090SXY. There are some other people who have posted to the web saying that they are having network difficulties with Verizon FIOS in the same time frame, but I haven't seen a report that exactly matches what I am seeing. I'm writing this post by the expedient of using a proxy for my browser, which is a nuisance. (While it is on, my Google search results tend to come back in German, which I can't read.) It's a bit of a Catch-22, since I'd like to get feedback from Verizon FIOS users, but if the problem is of the nationwide scale that I expect it is, this post will be unaccessible to them from that account. On the other hand, if it is accessible via Verizon FIOS elsewhere, that would be useful information to have. If you are a Verizon FIOS user, I would appreciate it if you could run traceroute from the Verizon account to baywing.net and copy the results into a comment here. I'll copy my traceroute results into a comment here shortly.

How to invoke traceroute:

Under Windows, open a command prompt. In the command prompt, type in the following:

tracert baywing.net > tr_baywing.txt

It will take a few minutes to complete if you also have the problem I'm having. The result ill be in a text file, 'tr_baywing.txt', in that directory. Copy and paste the text in a comment here if you aren't seeing the problem, or contact me if you are having the problem.

On Mac or FreeBSD, open a terminal window. At the command prompt, type in:

traceroute baywing.net > tr_baywing.net

On Ubuntu Linux, open a terminal window. At the command prompt, type:

tracepath baywing.net > tr_baywing.net

Here's my email, if you can't leave a comment here (remove spaces and convert to symbols as indicated): w e l s b e r r at b a y w i n g dot n e t

My connection to the servers in Texas from my home systems is unreliable. For the moment, my only reliable link to various of my web sites and my usual email is via my Android phone. Fortunately, I'm grandfathered into an unlimited data plan and have a Bluetooth keyboard. But that is still not a long-term solution. I have a trouble ticket in for my Verizon FIOS ISP that has been active since this past Wednesday without resolution. I just got a call from Marc saying that another email user is having much the same connection problem, so he's also putting in a trouble report from his side. The servers run on a Verizon FIOS business plan, so connection outages are a concern on that basis, too.