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'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:

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.

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.

Upcoming television series on PBS: Inside Nature's Giants, begins January 18th at 10 PM.

Professor Joy Reidenberg is an unlikely TV star. She's a comparative anatomist with the Mount Sinai School of Medicine in New York. Physically, she is diminutive, dark-haired and dark-eyed, and not the sort of slender sylph in morphotype that TV producers seem to favor. But Joy has deep anatomical knowledge and a gift for communicating what she knows, and that led the producers of the documentary series, "Inside Nature's Giants", to feature Joy in their program.

Diane and I have known Joy for years as a fellow attendee of various biennial conferences hosted by the Society for Marine Mammalogy. At the latest conference, we caught up with her following the conference-end banquet. She spun us a fascinating tale of how she came to star in a television series. Joy said that she received a call from the producers early one Friday afternoon preceding a holiday weekend, asking her if she might be interested in dissecting a stranded fin whale for a television program. Sure, she said, thinking that they were prospecting and planning for a project that would be months, if not years, down the road. So the question following her "yes" response floored her: Could she be on the plane for Ireland at 6 PM? Maybe was the answer, as Joy told us that physically getting to each part of the transportation network she'd need to get her stuff and passport would stretch things. Her husband and daughter decided to join the expedition. To cut things short, Joy and family made it to Ireland, and despite various amusing misadventures, made it to the locality of the whale stranding on time. There, the documentary producers pressed her into service as liaison to the local health authorities, who had to be convinced that permitting a whale necropsy on the spot was the best way forward to safely disposing of the carcass. She also had to try to convince the police to keep people away from the body, and she reported less success on that front. In any event, Joy got to do the dissection there for the cameras, and her innate enthusiasm and ability to draw people into discussion of anatomy impressed the producers so much that she became a regular co-host on the series.

There was also the adventure of traveling back home. Diane and I have attended necropsies of cetaceans, sirenians, pinnipeds, and sea turtles, and one has to take fairly strong measures to deal with the remaining odor that clings to clothes, skin, and hair. Joy had to physically get inside a decaying whale there in Ireland, and that makes for a different scale of olfactory assault. Joy told us of taking a succession of showers with vigorous scrubbing, but in the end even her family opted to stay in a separate room at the hotel. On the plane ride back, Joy was shifted to the very rear of the plane by the flight attendants, who kindly told the other passengers that they were having trouble with the toilets to explain the stench.

The TV series, "Inside Nature's Giants", is slated to air six episodes on PBS, starting January 18th, 2012, at 10 PM. The series is all about charismatic megafauna, but concentrates on post-mortem anatomical examination. Check your local PBS affiliate to make sure of the schedule. Another regular on the series who should be familiar to readers is Prof. Richard Dawkins.

I'm attending the Society for Marine Mammalogy biennial conference this year. The location is the Tampa Convention Center, making this pretty simple to get to.

Saturday and Sunday are when various workshops are held. Today, I'm attending the Sirenian workshop. It is an all-day affair, with 33 speakers and over 200 attendees.

My early connectivity was best with my Facebook account (Wesley R. Elsberry), but I've gotten set up with synced Twitter (welsberr) and Facebook status updates, so most of what I'm noting as things proceed will be going out that way.

It's been a long time coming, but the paper on evidence for multiple sound sources in the bottlenose dolphin appears in the October 15th issue of the Journal of Experimental Marine Biology and Ecology. I've been told that the PDF will be freely available soon, hopefully in the next week or so.

The abstract is:

Indirect evidence for multiple sonar signal generators in odontocetes exists within the published literature. To explore the long-standing controversy over the site of sonar signal generation, direct evidence was collected from three trained bottlenose dolphins (Tursiops truncatus) by simultaneously observing nasal tissue motion, internal nasal cavity pressure, and external acoustic pressure. High-speed video endoscopy revealed tissue motion within both sets of phonic lips, while two hydrophones measured acoustic pressure during biosonar target recognition. Small catheters measured air-pressure changes at various locations within the nasal passages and in the basicranial spaces. Video and acoustic records demonstrate that acoustic pulses can be generated along the phonic fissure by vibrating the phonic labia within each set of phonic lips. The left and right phonic lips are capable of operating independently or simultaneously. Air pressure in both bony nasal passages rose and fell synchronously, even if the activity patterns of the two phonic lips were different. Whistle production and increasing sound pressure levels are generally accompanied by increasing intranarial air pressure. One acoustic “click” occurred coincident with one oscillatory cycle of the phonic labia. Changes in the click repetition rate and cycles of the phonic labia were simultaneous, indicating that these events are coupled. Structural similarity in the nasal apparatus across the Odontoceti suggests that all extant toothed whales generate sonar signals using the phonic lips and similar biomechanical processes.

This was a big undertaking, requiring the coordinated effort of a lot of talented and busy people.

Diane Blackwood designed and implemented our acoustic recording layout and the dolphin stationing device and biteplate, and made sure the amplifying equipment was operational and protected from incident. (Incidents with electronics in proximity to sea water are all too common.) I designed and wrote the software that acted as a multichannel digital data recorder, the data reduction program, and the analysis program. Bill van Bonn was our veterinarian who spent our data recording sessions lying prone on the dock as he placed, checked, and positioned the endoscopes and pressure catheters. Our principal investigator, Ted Cranford, operated the video side of things, including the high-speed video capturing the endoscope views. Sam Ridgway and Don Carder consulted with us, helping us with the use of the pressure catheters (which had previously been used in two prior studies they authored). Monica Chaplin and Jennifer Jeffress were the dolphin trainers on the spot during data recording. Tricia Kamolnick and Mark Todd were trainers who helped get the subjects prepared for our data collection process, and Mark Todd implemented the regular video system. It took between two and three hours each data collection day for us to set up, test, and calibrate all the equipment. Breaking down took somewhat less time, but I would still have to run a custom program to demux the data, produce images visualizing the data for each trial, and then shift the day's data off the hard disk and on to CD-ROM media.

Update: The Marine Mammal Center has put up the PDF of the paper.

I occasionally check out the Tern Micro website. They are manufacturers of controllers and expansion boards for embedded applications. Their controller boards use IAPx86 class CPUs and are programmed in C. A few years ago, I had checked with them about whether they had components suitable for a field acoustic recorder, and given the short time schedule we had, we decided to go with off-the-shelf components instead for that. Things have changed, though, as I found an expansion board of theirs called the GR4 on their page.

Let me set some context. Some years ago, Whitlow Au and Marc Lammers put together a four-element hydrophone array that allowed them to perform acoustic localization. If I recall correctly, their recording system was based upon a National Instruments DAQ card for CardBus hosted in a laptop computer and was capable of 500 kilosamples per second. When multiplexed across four channels, that's a max of 125 kilosamples per second per channel. With a multiplexed system, you have to account for time offsets between channels as you analyze the data for time-of-arrival estimates of signals. If there is crosstalk at the high acquisition rates, you might have to drop the total sampling bandwidth to give the multiplexing circuitry time to settle to the next channel's input level. That at least is how I had to work with an NI PCI-MIO-16-E DAQ card back in 1999. The solution to this problem is simultaneous-sampling, where all the channels of interest get their own sample-and-hold circuitry and the conversion is triggered off the same clock input. Simultaneous-sampling hardware is more expensive, since the main sets of circuits have to be multiplied for the number of channels. Around 2001, a project I was involved with bought a couple of simultaneous-sampling DAQ cards for the PCI interface, at a cost of a couple of thousand dollars each.

Of course, lugging a full-up desktop system into the marine environment is not a thing to be undertaken lightly. If one could instead reduce the field recording part to something that could be effectively shielded from the elements and work instead off of straight DC battery power, it would be all-around more convenient. The more remote the field work, the more convenient that gets.

So let's get back to the Tern GR4. This analog-to-digital expansion board is small, just a bit longer and wider than a business card. It can be provisioned with two ADC chips and 4 MB of memory (and that full configuration is what I'm talking about). The base price is $129, but with the additional features added the cost is $259. The GR4 boards are stackable. There are pin headers that form a communication and data bus with a controller card. Each GR4 permits simultaneous-sampling of two input channels. Each GR4 with two ADC chips aboard can record to its own CompactFlash card continuously by switching between ADC chips and FIFO memory, allowing the just-converted data from one FIFO to be streamed to the CF card while the other is collecting newly-converted data. Because the GR4 units are stackable, you can run several together at once. The Tern page shows a stack of four GR4s and a controller card. The maximum sample rate for the GR4 is 500 kilosamples per second. This means that each simultaneously-sampled channel can be recorded at that 500 kilosamples per second rate. It does 16-bit conversion, which gives good dynamic range to the recordings.

So the technical problem of getting to a four-channel field-deployable data recorder capable of capturing most of the acoustic information from a dolphin click has gotten both easier and cheaper with Tern's GR4. I had a chat with a technical representative at Tern going over what would be needed for this application, and basically got a recommendation for a couple of different controllers that could do the job with the addition of two GR4 units. Tern offers an evaluation package of a controller board plus the interface hardware and software needed for system development at $249. Add-on options are additional cost. For one of the boards, I'd be interested in an LCD 16x2 readout, RTC clock, CompactFlash interface, and switching regulator, which would add another $100 to the $249 evaluation kit price. So for $349 + 259 + 259 = $867, I'd have that part of the data recorder in hand. Of course, I'd still be looking at a variety of additional costs in development, but this makes contemplating the task that much more feasible.

There are some additional concepts that ought to be broached. For two GR4s, one has to provide CF cards for each. It is pushing the hardware to get continuous sampled data out to the CF card on each expansion card. Trying to move the data over the bus to the controller and out to its CF card just isn't feasible. There is no file system involved on the CF cards; the data is written to absolute sectors. This makes it a bit more interesting pulling that data off for analysis. In development, it will be up to the programmer to track which sectors go with which recording if multiple recording sessions are used. The signal input range for the ADC circuitry is 0-5V, which means that the output of many amplifiers will have to be conditioned to fit in that range. When recording two channels at 500 kilosamples per second, the total data bandwidth is 2 million bytes per second. So each CF card will receive about 7 gigabytes of data per hour of recording operation. A 32 GB card should be good for over four hours of data recording before needing to be swapped out. The Tern rep estimated that my stack of a controller plus two GR4s would pull around 500 mA of power at 5V while recording. The A-86-P controller at least has on-board power regulation so that it handles DC input from 8.5V to 24V and delivers regulated 5V power to its stack. I figure something like a motorcycle 12V battery would likely provide enough juice for a day's worth of recording. When not actively recording, though, the controller and its stack can go into a sleep mode that draws only a few mA, which saves a lot on battery power.

I was told by the Tern rep that the GR4 was developed for the needs of a research group doing field work on bat biosonar. It's no wonder that it caught my eye when I ran across its description.

I've been busy recently doing up figures for a paper on dolphin biosonar. One of the figures we ended up turning in earlier this week wasn't exactly as I wanted it, but deadlines don't wait. I put a lot of hours into trying to find alternative plotting for it, but just hadn't found the right approach for an alternative.

Now that we're done with that paper's submission, I think I've found the approach to use in the future.

Here's the problem: show the power spectral density (PSD) curves for all the clicks in a biosonar click train. What I was using years ago was my own code plotting a waterfall of PSDs on a bitmap. But I tied things too closely to the specifics of how I generated the PSDs, so for the 256-point FFT window I end up with each PSD's width as exactly 256 pixels. That's less than an inch for standard 300 dpi print resolution.

There are examples for "fence" plots in gnuplot and Python's matplotlib, but I wasn't able to get stuff that looked much better than up-res'd versions of my originals. Did I mention that I want to assign particular colors to each PSD in the click train?

Yesterday, I was thinking a bit more about the problem, and decided to look into Python's matplotlib again, this time going from the demo code on using a PolyCollection, that is, a collection of arbitrary polygons. That is looking quite promising. Here is an example of what I've got so far going along this approach:

The shapes are nicely done, I like being able to set a transparency value, I can output to a scale and file type I specify, and I can assign a specific color to each PSD in the series. (The colors are randomly set in this demo.) About the only quibble I have with the whole thing is that I'd like to run the "Y" axis in the other direction, so that the earliest clicks are plotted at the back of the plot, and the most recent are in the foreground. It's easy enough to flip around the list, but I haven't yet figured out getting the numbering to run the wrong way.

About the particulars of this click train... the X axis is in kiloHertz units (kHz). There are 24 clicks in the click train. It is apparent that the click train shows variation in the spectral content and amplitude of clicks, with a ramp-up to high-amplitude and high peak frequency, and followed by diminishing amplitude toward the end of the click train. For the highest-amplitude clicks, one may notice that there is some energy at the very highest frequency bins. There was anti-aliasing applied in the recording setup, but it evidently was not entirely adequate to the task. The B&K amplifier used has built-in attenuation of -3dB at 200 kHz, IIRC. The B&K hydrophone, an 8103, has roll-off at frequencies that high. So, if anything, the magnitude of energy in the highest frequency bins shown here is underestimated. That the high-frequency energy is correlated with the high peak frequency, high amplitude clicks is an indication that this isn't a general issue with background noise; this is part and parcel of the dolphin biosonar click output. There's some research that Diane did with the UT ARL group on such high frequency components in dolphin biosonar that I'd like to revisit sometime soon.

Update: A handy page over at StackOverflow put me on course to flip my Y-axis numbers. I've also fixed up assigning colors that way that I want them, so now the result is looking much better to me.

The colors correspond to a classification based on spectral features (all things related to the FFT taken) first proposed by Houser, Helweg, and Moore in the late 1990s. I don't process my transform in exactly the same way that they processed theirs, so the resulting classification is not necessarily identical to what they would have found if they processed the same click train. An extended discussion on that should be put off to another post.

Update 2: That was all too optimistic. There is a bug in "matplotlib". Actually, if you look closely at the figure just above, the red polygon toward the back is plotted over a blue polygon, and it should not be. Depending on the view angle chosen, "matplotlib" gets the render order of polygons wrong. I was able to reproduce this error directly in the example code provided on the "matplotlib" website. Here's the problem demonstrated:

I'm posting it here especially so that the "matplotlib" people can have a look. For my data and just 24 polygons, I can find angles where about a third of the polygons are rendered out of order. For other angles, everything renders properly. If you happen to like one of the correct-rendering angles, you can use the output. If the angle you want happens to be in the other range of incorrect-rendering, context does not seem to matter; no matter which direction you come to that view, it still renders incorrectly.

Back in graduate school, I wrote tens of thousands of lines of Delphi code in support of research projects I worked on. Well, it is several years later, and my colleagues and I are getting back to the job of writing things up from those projects. And with manuscripts, one also has figures. A fairly urgent task for my spare time currently is working up requested revisions of figures that were originally produced almost a decade ago. I've pulled a couple of things into Python and used Matplotlib for figures, but many things I did with heavy tweaking of the Delphi TChart component, and the simplest path to revised figures for those still lies within Delphi.

While it isn't exactly simple, the thing is that I can figure out where I was getting various things done. There is something to be said for Delphi's Object Pascal language, where even with some years intervening and a distinct dearth of comments (yeah, mea culpa), I'm getting the gist of things in fairly short order. For one scatterplot, the original had a color progression that went with the time of each click being plotted, so each click was represented by a dot of a hue indicating its position in time in the click train. Well, that wasn't wanted for print, so the request is for the same plot, but using a grayscale. The color progression doesn't simply translate, so it was back to the code to re-do the thing in grayscale. I just finished that one up this evening. The Delphi 5 IDE holds up as a usable development tool, but I've gotten used to later-generation tools like Apple's Xcode and Microsoft' Visual Studio 2010, and it does look dated compared to those.

I do want to eventually have a library of Python classes that will work with the dataset, and I've made some progress on that score. I've used the 'struct' module to parse various files composed of binary Delphi records and used SQLite to stuff the contents into a database. I have a partially-completed Python signal processing script to tackle going through all the original signal data I have and apply various techniques that I simply didn't have the compute-power before to try. Again, the sticking point is more that the time I can apply to any of these things is limited, given that so much remains to fix up in our fixer-upper of a domicile.

The Synthese special issue on "Evolution and Its Rivals" allows downloads of the full PDFs for all the articles, but only through 12/31, so you have just a day left to download them for free. After that, they go back to being $35 each or something of the sort.

Jeff Shallit and I have an article in it about Dembski's "complex specified information".

Quark Expeditions is having another popularity contest for a blogger to go on a trip, this time the destination is the North Pole. And I've entered again and am seeking votes.

Yes, that didn't work so well last time for the Antarctic trip, but I'm getting going sooner and the popularity contest isn't absolute: a Quark Expeditions collection of staff will select the winner out of the top five vote-getters. So go have a look, vote for me if you are moved to do so, and maybe pass along the word.

Miriam Markowitz has a piece in The Nation about George Price and the Price equation, a significant advance in mathematics for population biology. Along the way, she discusses this as resolving a problem left by Charles Darwin.

This conclusion left a paradox unresolved in Darwin's otherwise elegant theory. He insisted that natural selection acts on the individual, that it "tends only to make each organic being as perfect as, or slightly more perfect than" its competitors; it would "never produce in a being anything injurious to itself, for natural selection acts solely by and for the good of each." Yet his only explanation for the evolution of sterile insects was the good of the group.

The quotes used by Markowitz to substantiate her claim that Darwin had an insistence that natural selection acts on individuals do no such thing. Both quotes are found in the context of a passage where Darwin is trying to explain what natural selection does. I'm going to quote much more of the passage to make it clear how those parts lifted by Markowitz don't support her argument.

The foregoing remarks lead me to say a few words on the protest lately made by some naturalists, against the utilitarian doctrine that every detail of structure has been produced for the good of its possessor. They believe that very many structures have been created for beauty in the eyes of man, or for mere variety. This doctrine, if true, would be absolutely fatal to my theory. Yet I fully admit that many structures are of no direct use to their possessors. Physical conditions probably have had some little effect on structure, quite independently of any good thus gained. Correlation of growth has no doubt played a most important part, and a useful modification of one part will often have entailed on other parts diversified changes of no direct use. So again characters which formerly were useful, or which formerly had arisen from correlation of growth, or from other unknown cause, may reappear from the law of reversion, though now of no direct use. The effects of sexual selection, when displayed in beauty to charm the females, can be called useful only in rather a forced sense. But by far the most important consideration is that the chief part of the organisation of every being is simply due to inheritance; and consequently, though each being assuredly is well fitted for its place in nature, many structures now have no direct relation to the habits of life of each species. Thus, we can hardly believe that the webbed feet of the upland goose or of the frigate-bird are of special use to these birds; we cannot believe that the same bones in the arm of the monkey, in the fore leg of the horse, in the wing of the bat, and in the flipper of the seal, are of special use to these animals. We may safely attribute these structures to inheritance. But to the progenitor of the upland goose and of the frigate-bird, webbed feet no doubt were as useful as they now are to the most aquatic of existing birds. So we may believe that the progenitor of the seal had not a flipper, but a foot with five toes fitted for walking or grasping; and we may further venture to believe that the several bones in the limbs of the monkey, horse, and bat, which have been inherited from a common progenitor, were formerly of more special use to that progenitor, or its progenitors, than they now are to these animals having such widely diversified habits. Therefore we may infer that these several bones might have been acquired through natural selection, subjected formerly, as now, to the several laws of inheritance, reversion, correlation of growth, etc. Hence every detail of structure in every living creature (making some little allowance for the direct action of physical conditions) may be viewed, either as having been of special use to some ancestral form, or as being now of special use to the descendants of this form--either directly, or indirectly through the complex laws of growth.

Natural selection cannot possibly produce any modification in any one species exclusively for the good of another species; though throughout nature one species incessantly takes advantage of, and profits by, the structure of another. But natural selection can and does often produce structures for the direct injury of other species, as we see in the fang of the adder, and in the ovipositor of the ichneumon, by which its eggs are deposited in the living bodies of other insects. If it could be proved that any part of the structure of any one species had been formed for the exclusive good of another species, it would annihilate my theory, for such could not have been produced through natural selection. Although many statements may be found in works on natural history to this effect, I cannot find even one which seems to me of any weight. It is admitted that the rattlesnake has a poison-fang for its own defence and for the destruction of its prey; but some authors suppose that at the same time this snake is furnished with a rattle for its own injury, namely, to warn its prey to escape. I would almost as soon believe that the cat curls the end of its tail when preparing to spring, in order to warn the doomed mouse. But I have not space here to enter on this and other such cases.

Natural selection will never produce in a being anything injurious to itself, for natural selection acts solely by and for the good of each. No organ will be formed, as Paley has remarked, for the purpose of causing pain or for doing an injury to its possessor. If a fair balance be struck between the good and evil caused by each part, each will be found on the whole advantageous. After the lapse of time, under changing conditions of life, if any part comes to be injurious, it will be modified; or if it be not so, the being will become extinct, as myriads have become extinct.

Natural selection tends only to make each organic being as perfect as, or slightly more perfect than, the other inhabitants of the same country with which it has to struggle for existence. And we see that this is the degree of perfection attained under nature. The endemic productions of New Zealand, for instance, are perfect one compared with another; but they are now rapidly yielding before the advancing legions of plants and animals introduced from Europe. Natural selection will not produce absolute perfection, nor do we always meet, as far as we can judge, with this high standard under nature. The correction for the aberration of light is said, on high authority, not to be perfect even in that most perfect organ, the eye. If our reason leads us to admire with enthusiasm a multitude of inimitable contrivances in nature, this same reason tells us, though we may easily err on both sides, that some other contrivances are less perfect. Can we consider the sting of the wasp or of the bee as perfect, which, when used against many attacking animals, cannot be withdrawn, owing to the backward serratures, and so inevitably causes the death of the insect by tearing out its viscera?

The context shows that "being" in the above passage refers not to each individual in a population, but rather to species. I've bolded the original snippets quoted by Markowitz and italicized the further context that is either incongruous with or contradictory to the notion that what is under discussion is a property of an individual. One doesn't usually talk of individuals going extinct, nor of individuals "rapidly yielding" to introduced species.

Of course, Markowitz is not alone in making the mistake of taking the quoted parts as referring to individuals. She also quotes Richard Dawkins to that effect, and it isn't difficult to find Stephen Jay Gould using one of the same snippets to the same end in his book, The Structure of Evolutionary Biology. But common error is still error, and it is worth pointing out that the original source, when read for comprehension, is not making the claim of level of action of natural selection that some of Darwin's readers insist it does.

But, you might say, what about Markowitz's claim concerning Darwin and social insects? Does it show Darwin arguing the group selection line of "for the good of the species". Let's look at Darwin summarizing his response to the problem of "neuter insects" from the first edition of Origin of Species:

With these facts before me, I believe that natural selection, by acting on the fertile parents, could form a species which should regularly produce neuters, either all of large size with one form of jaw, or all of small size with jaws having a widely different structure; or lastly, and this is our climax of difficulty, one set of workers of one size and structure, and simultaneously another set of workers of a different size and structure;--a graduated series having been first formed, as in the case of the driver ant, and then the extreme forms, from being the most useful to the community, having been produced in greater and greater numbers through the natural selection of the parents which generated them; until none with an intermediate structure were produced.

Thus, as I believe, the wonderful fact of two distinctly defined castes of sterile workers existing in the same nest, both widely different from each other and from their parents, has originated. We can see how useful their production may have been to a social community of insects, on the same principle that the division of labour is useful to civilised man. As ants work by inherited instincts and by inherited tools or weapons, and not by acquired knowledge and manufactured instruments, a perfect division of labour could be effected with them only by the workers being sterile; for had they been fertile, they would have intercrossed, and their instincts and structure would have become blended. And nature has, as I believe, effected this admirable division of labour in the communities of ants, by the means of natural selection. But I am bound to confess, that, with all my faith in this principle, I should never have anticipated that natural selection could have been efficient in so high a degree, had not the case of these neuter insects convinced me of the fact. I have, therefore, discussed this case, at some little but wholly insufficient length, in order to show the power of natural selection, and likewise because this is by far the most serious special difficulty, which my theory has encountered. The case, also, is very interesting, as it proves that with animals, as with plants, any amount of modification in structure can be effected by the accumulation of numerous, slight, and as we must call them accidental, variations, which are in any manner profitable, without exercise or habit having come into play. For no amount of exercise, or habit, or volition, in the utterly sterile members of a community could possibly have affected the structure or instincts of the fertile members, which alone leave descendants. I am surprised that no one has advanced this demonstrative case of neuter insects, against the well-known doctrine of Lamarck.

Darwin's explanation of the problem of neuter insect castes was not, as Markowitz asserts, just "the good of the group", for if one reads the passage carefully, "community" in Darwin's passage is a reference to the fertile parents, and not just a fuzzy "group".

The "paradox" of individual action versus group selection attributed to Darwin is not supported by the examples purportedly showing such. One could charge Darwin justly with being somewhat imprecise for our modern tastes and reliance on jargon, but if one carefully reads what Darwin wrote, the concepts are clear enough.

This New Scientist article discusses some really cool results coming out of the Devolab at Michigan State University. In for particular attention was my colleague, Laura Grabowski, who defended her dissertation on memory evolving in Avidians shortly before I left MSU. She is now a professor at the University of Texas - Pan American in Edinburg, Texas, continuing her work on artificial life.

Rob Pennock and Jeff Clune also got attention in the article, and a paper of mine (with Laura and Rob) published last year got a link in the article.

There's an article in the Austin American Statesman about the ongoing Gulf oil spill. It talks about the effects of the spill throughout the water column. The massive use of dispersants at depth is noted as being experimental: nobody knows exactly what outcomes you get by doing that. Well, other than that less of the oil washes ashore where it is convenient for photographers to document the pathetic demise of many a bird and marine mammal because of the oil. It is a lot harder to get cameras on the pathetic demise of benthic, nektonic, and pelagic animals, but those deaths count no less because they pass unseen. Nor is most of the problem going to be at the level of charismatic megafauna, as the authors point out. This spill is disrupting the food web from the lowest levels right up to the top predators. Further, they note that the bacteria that are relied upon to consume the oil over time do so in the presence of oxygen. As they metabolize the oil, they deplete the oxygen. High levels of methane gas are not helping, either. It doesn't take much to make the inference that "dead zones" with low to no oxygen in the water will expand. What's worse is that given the toxicity of what we're dumping into the Gulf, they may well persist over time scales we have not experienced before.

It seems to me to be only common sense that off-shore oil drilling at any depth, if done at all, should be conditional on the principals demonstrating that they have the capacity on-hand to deal with even worst-case problems within a short time window. Turning loose the machinery and hoping for the best is no way to safeguard the public welfare.

As usual, this is only personal opinion.

I'm working on setting up a citizen scientist project to document where snapping shrimp (family Alpheidae) are active pre- and post-contamination by the oil spill in the Gulf of Mexico. In this post, I just want to introduce the basic concepts and provide an example sound file.

Snapping shrimp comprise a number of species, mostly distributed in tropical to temperate waters. They live in near-shore structured environments, including seagrasses, rocks, and coral reefs. They are predators on small, live prey, and they kill or stun their prey using a snap from a disproportionately large claw. The snap of the claw generates a cavitation event and, by the way, a high-amplitude, broadband transient sound that is also called a snap. The combined noise from the local population of snapping shrimp is a familiar feature not only to bioacoustics researchers, but to anyone who snorkels or SCUBA dives in areas with snapping shrimp.

Because of this noise and the role snapping shrimp play in the marine food web, they are an excellent candidate as an "indicator species", a species that can be easily monitored and which provides a measure of the health of that part of the marine food web. Better yet, the monitoring and assessment can be done acoustically, by sound recording, to get a measure for a local population.

If I had a chunk of money to throw at this, a sophisticated way to do this would be to make a baseline of calibrated sound recordings and be able to characterize tidal and daily cycle effects on snapping shrimp sound activity, and thus be able to statistically determine a reduction in activity post-contamination. I estimate somewhere around $10K would be needed to set up a portable data collection system from scratch with that kind of capability. Not having that in spare change in my pocket, I'm looking at a somewhat different approach that a lot more people can get into with minimal outlay of funds and just a bit of do-it-yourself drive.

Because snapping shrimp noise is broadband, you can hear it even in plain audio recordings, though the peak frequencies are actually ultrasonic. This means any sort of audio recorder can be used to find out if snapping shrimp are present in a location: cassette tape recorder, digital recorders, and even video cameras. The thing that any of those will need is a microphone input. What to plug in for that recording? A hydrophone would be great, but most people don't have those lying around. But one can also make a normal microphone water-resistant and use it. It is best to think of such a microphone as disposable, since better sensitivity also corresponds to the water-resistance being more fragile, and saltwater is great at destroying electronics. In another post, I'll describe making your own hydrophone or water-resistant microphone. If you already have a recorder, the additional cost is under $50 to be able to record underwater sound. I'm not looking for this sort of recording to do as much, simply to say whether a snapping shrimp population is active or not.

Below is an example of a simple recording I made last night that demonstrates the presence of an active population of snapping shrimp at one location and time. I'm still working on what additional information should be noted along with the recording, but I think what I provide here may be sufficient.

File: s_sunshine_skyway_201006241851_WS_30006.wma
Recorder: Olympus WS-320M, ST HQ mode, CONF mic sensitivity
Transducer: Salvaged hydrophone from a sonobuoy
Transducer depth: Approximately 2 feet
Recording made by: Wesley R. Elsberry
Date: 2010-06-24
Time: 18:51 EDT
Latitude: 27.586371°
Longitude: -82.620388°
Location description: South Sunshine Skyway Bridge on road to south fishing pier, at overpass over water, north side, toward east end.

I'll be posting more on this topic later.

I was looking for a particular post of mine, and ran across this one from back in 1999. "The Patterson Challenge" refers to a lecture given by Colin Patterson in which he asked his audience a question. This incident has become a favorite quote of antievolutionists.

I've been putting a simple question to various people and groups of people. Question is: Can you tell me anything you know about evolution, any one thing that is true? I tried that question on the geology staff at the Field Museum of Natural History and the only answer I got was silence. I tried it on the members of the Evolutionary Morphology Seminar in the University of Chicago, a very prestigious body of evolutionists, and all I got there was silence for a long time and eventually one person said, "I do know one thing -- it ought not to be taught in high school".

So when it popped up again in a forum I was participating in, I took the opportunity to answer the original question.

True things about evolutionary theory
Wesley R. Elsberry (welsberr@inia.cls.org)
Tue, 9 Nov 1999 11:26:29 -0600 (CST)

Art Chadwick writes:

AC>Those are fancy (and oft repeated) words. Let me issue you
AC>the Patterson challenge: tell us one thing you know for
AC>sure about the theory of evolution...other than that "it
AC>shouldn't be taught to high school students"

Patterson's challenge was broader, asking whether anyone knew any one thing about "evolution" to be true.

Let's see... true things about evolution. That would make an overlong list. I'll just give some of my favorites.

- Inheritance is particulate, not blending.

- Inheritance is not perfect. Changes can and do happen in heritable information.

- More organisms are produced than can be sustained under prevailing ecological conditions.

- Those heritable variations which correlate with differential survival of organisms tend to have higher proportional representation in the population.

- The distribution of traits in a population can be influenced by chance effects, such as population bottlenecks and sampling from a limited pool of variant.

- Fossils are the traces of organisms that were once alive.

- Fossil forms show that extinction of species happens. Certain fossils represent organisms common enough, large enough, and distributed in areas where if they were present through the present day could not have been overlooked.

- Fossils are distributed in a stratigraphic pattern indicating change in fossil assemblages over time.

- Fossil assemblages show that mass extinctions have happened at widely different times in the earth's history.

- The canonical genetic code is consistent with the theory of common descent.

- Patterns of differences in sequences of proteins and heritable information support the idea that these differences have accrued since the time of a last common ancestor.

- Evolutionary interrelationships have been used to advantage in medical research.

- The principles of natural selection have been used to advantage in computational optimization and search.

- Species have been observed to form, both in the laboratory and in the wild.

- A novel symbiotic association has been observed in the laboratory.

Well, that should get us started, anyway.

Wesley

The Consortium for Ocean Leadership's National Ocean Science Bowl is holding its national competition this weekend in St. Petersburg, Florida at the USF/St. Pete campus and FWRI. There is round robin competition on Saturday, then the finals will use a double-elimination tournament schedule that finishes up on Sunday.

I'm signed up as a moderator in one of the rooms on Saturday. I really enjoyed volunteering for the regional tournament, and I am looking forward to tomorrow's competition.