The Austringer

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.

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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.

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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.

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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 16×2 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.

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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.

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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.

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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”.

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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.

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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.

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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.

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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.

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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.

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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

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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.

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The Los Angeles Times reports on how the US Interior Department made a decision about sage grouse:

The Interior Department declared Friday that an iconic Western bird deserves federal protection under the Endangered Species Act, but declined to offer that protection immediately — a split decision that will allow oil and gas drilling to continue across large swaths of the mountainous West.

The department issued a so-called “warranted but precluded” designation for the greater sage grouse, meaning that the bird merits protection but won’t receive it for now because other species are a higher priority.

Yes, that’s right, sage grouse are an endangered species, but not so endangered as to have us do anything about it.

The “other species” bit is a particularly bogus piece of argumentation. The fact is that listing sage grouse as an endangered species would put most of the burden on developers, who would have far more stringent requirements to meet to show that their projects would not unduly impact sage grouse. Plus, I’d like to hear the list of endangered species that are getting better attention within the Department of the Interior because they don’t have to pay attention to sage grouse. That ought to be darkly amusing for a while as we contemplate what the Department of the Interior has done for them.

Now let’s have a look at what Department of the Interior head honcho Ken Salazar had to say:

“The sage grouse’s decline reflects the extent to which open land in the West has been developed in the last century,” Interior Secretary Ken Salazar said in an issued statement.

“This development has provided important benefits, but we must find common-sense ways of protecting, restoring and reconnecting the Western lands that are most important to the species’ survival while responsibly developing much-needed energy resources,” Salazar said. “Voluntary conservation agreements, federal financial and technical assistance and other partnership incentives can play a key role in this effort.”

Let’s see, Salazar correctly notes that the problem for sage grouse is one of habitat loss. Then, Salazar goes on to emit some bafflegab that doesn’t actually imply that anything will be done that has any effect on habitat loss. There’s already a history of “voluntary conservation” when it comes to sage grouse: I don’t think that the rate of habitat exploitation has even slowed due to this; I’d appreciate comments from people who have the numbers. The feds are broke, so there isn’t much that we can expect in the way of financial assistance there. The feds have given the technical assistance that would be of help (“If you build it, they will go away.”), and it has been ignored. I’m not sure what a “partnership incentive” is, but my suspicion is that it is merely pretty pettifoggery to try to obscure the fact that the Interior Department has decided that corporate interests are more important than the survival of the sage grouse as a species.

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The regional National Ocean Sciences Bowl, the Spoonbill Bowl, happens this next Saturday, March 6th, 2010. The location is at the USF Marine Sciences and Fish and Wildlife Institute (100 SE 8th Ave., St. Petersburg, Florida 33701). It gets going pretty early in the morning. This is a quiz competition with each game pitting two teams of four players against each other. There are two rounds of toss-up questions requiring fast responses, with bonus questions for correctly answered toss-ups. In between, there are two “team challenge” questions that give each team a set time to collaborate on answering more involved questions. The questions are drawn from topics contributing to marine science, including

1. Biology
2. Chemistry
3. Geography
4. Geology
5. Math
6. Physics
7. Marine Policy
8. Social sciences (including economics, history and human interactions)
9. Technology (including instrumentation, remote sensing, & navigation)
10. Current Events

The public is welcome to attend the event.

I’ve volunteered to help with the event, where I will be one of the moderators. I think that we are planning on running eight rooms for the round-robin initial phase of the event. The final phase will be run as a double-elimination tournament. I’m really looking forward to this. In April, the NOSB nationals will be held here in St. Petersburg, where teams winning at the regional competitions around the country will compete.

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Casey Luskin has decided to treat us to an agony in eight fits, wherein he will whine mightily concerning “information”. I don’t know how many of those I’ll be taking note of, but I might as well have a look at the first one.

It does not augur well for the series. Luskin leads with a lot of bluster, claiming that citations to the scientific literature on the topic of genetic information were “bluffs”. It seems dubious to me that Luskin will be able to do more than try to spin armchair philosophy stuff from William Dembski and Stephen Meyer as somehow putting actual research in doubt.

Here’s an example of Luskin innuendo, complete with scare quotes:

Virtually all of those “publications” mentioned by Judge Jones came from one single paper Miller discussed at trial, a review article, co-authored by Manyuan Long of the University of Chicago.4 The article does not even contain the word “information,” much less the phrase “new genetic information.” 5

Well, a publication is still a publication, and a peer-reviewed one to boot, even if it is cited in a review article, so it is unclear what, exactly, Luskin is trying to do with the scare quotes. Usually the Discovery Institute (DI) is all for counting any odd scrap of paper with print on it as a publication, even inventing meaningless phrases like “peer-edited” to try to put some cachet on obvious partisan near-vanity press dreck. Perhaps the DI respect for articles and books only goes so far as to cover those that toe the “intelligent design” creationism (IDC) party line.

One can see that Luskin managed to shoot himself in the foot in that sentence-as-paragraph. Notice the footnote. That goes down to this text:

[5.] The word “information” appears once in the entire article—in the title of note 103. Id. at 875 n. 103. See Manyuan Long, Esther Betrán, Kevin Thornton, and Wen Wang, “The Origin of New Genes: Glimpses from the Young and Old,” Nature Reviews Genetics, Vol. 4:865-875 (November, 2003).

So, Casey, how is it that you can get all huffy about someone not including a specific phrase of “new genetic information” when the title promises that the article is about “new genes”? Do you suppose that “new genes” are never associated with new genetic information? If you were that nit-picky about things being different you wouldn’t have been making those claims about the degree of “near-verbatim” passages in the Kitzmiller decision. It appears that the one trait that runs through both of the aspects of Luskin’s text discussed above is hypocrisy.

It gets worse from there.

But are Judge Jones’s, Ken Miller’s, and the NCSE’s bold proclamations supported? Does Long et al. actually reveal the origin of new biological information? Is Explore Evolution wrong? A closer look shows that the NCSE is equivocating over the meanings of the words “information” and “new,” and that the NCSE’s citations are largely bluffs, revealing little about how new genetic functional information could originate via unguided evolutionary mechanisms. This bluff was accepted at face value by Judge Jones, who incorporated it in his highly misguided legal ruling.

No, Casey, the equivocation about “information” comes from antievolutionists like your colleague William Dembski. As for “new”, this point can be found in the transcript of the Kitzmiller trial, where Scott Minnich was cross-examined by Pepper Hamilton’s Stephen Harvey. When asked about the evolution of a DNT breakdown system that evolved in bacteria, Minnich agreed that the multi-part system developed naturally, but dismissed it as an “adaptive response” rather than being evolution per se. But the IDC mindset comes through clearly there, as Minnich testified:

Q. And if you look on — at figure 1, which is on page 113. And Matt, perhaps if you can bring that up for us. These researchers, based on their own original data, have published the organization and evolution of the bacteria that breaks down DNT?

A. Right. This is an adaptational response.

Q. And that’s a DNT — this process by which these bacteria breakdown DNT, that’s a biochemical pathway?

A. Correct.

Q. So we do have published information in this scientific literature about the evolution of biochemical pathways?

A. Steve, you’re extrapolating from the data here. I mean, not all these enzymes evolved specifically to break down this compound. I mean, you’re mixing and matching enzymes, I’m sure, from pathways that had some other property.

It’s pretty simple, really. A gene is new if it was not there in the population before but is now. A system is new if it does something that was not done before. Evolution, if Luskin had paid attention in class (and I don’t know what excuse Minnich could claim), works by modification of what exists. And sometimes those modifications result in novel functionality.

As for the stuff we don’t see happening in living systems, as alluded to in Minnich’s testimony, the de novo injection of systems that had no precursors, that’s what is known as “special creation”. It’s pretty ironic that when trying to figure out what they want from evolutionary science, quite commonly the antievolutionists are really asking that biologists demonstrate that creationism is observed.

Casey Luskin again:

In fact the origin of new functional biological information is perhaps the most important question in biology. As origin of life theorist Bernd-Olaf Kuppers stated in his book Information and the Origin of Life, “The problem of the origin of life is clearly basically equivalent to the problem of the origin of biological information.”8

Now, I think someone introduced the word “equivocation” into the discussion. Right, that would be Casey. And here we see why Luskin introduced “equivocation” into the discussion: he’s projecting. There’s something a bit different between the processes that we see happening in the evolution of living things (the subject of discussion) and pre-biotic chemistry when talking about new genetic information. That would be that there is a system of inheritance established and operating in living things, something that is not available as an assumed starting position in origin-of-life research. So dropping origin-of-life into the discussion is simply a non sequitur, though one that has strong misleading properties.

Casey Luskin:

Judge Jones was not merely in error. Worse than any simple mistake, the misinformation he propounded in his ruling entered media and academic culture, becoming enshrined as a Darwinian myth, alongside many others. This myth holds that perhaps the most important question in biology has been solved, when really (as this series of 8 total posts will show), that is far from being the case.

This is what the lawyers call “an appeal to facts not in evidence”. In fact, parts of this have already been proven false just in the discussion above, and Luskin hasn’t even gotten around to much more than a quote-mine, some projection, and a double dollop of hypocrisy. Nor do I have any expectation that the parts yet to be published will do any better than Luskin’s initial poor showing.

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I have data on Compact Disks (CDs) from past projects. The technology was getting toward being affordable around 1996. CD writers dropped under $100 for the first time somewhere around there, and media started selling for less than $5 a disk. The amount of storage space on a CD was comparable to the size of hard disks available at the time, and optical storage seemed far better than tape as a medium. So now I have cases, drawers, and spindles of CDs dating right back to 1996.

No storage medium is perfect, so archived data is a commitment and not just a static collection. Last month, Sam asked me what I would like for my birthday. I said I wanted a disk for backing up data. After having a look at off-the-shelf external hard drives, it seemed that all the models I looked at had warranties of 1 year or shorter. However, if you buy an internal hard disk and a separate USB enclosure, the warranty on the drive can be much, much longer. Sam and I visited the Newegg site and picked out a Western Digital 1.5 terabyte drive and a Rosewill USB enclosure. The drive comes with a 5-year warranty. I can pair this with another 1.5 terabyte disk so that I can copy off my data from the CDs, then copy to the second hard disk.

Back when I was about to move from California to Michigan, I had a chat with a fellow who works for the Internet Archive. That is a project whose modest aim is to store the World Wide Web. All of it. You can browse sites as they were in 1995. Well, with a few caveats. My acquaintance said that the Internet Archive’s data storage was based on consumer-grade IDE drives. You can get them cheap and in quantity, and if you store things on multiple disks, the redundancy will help. That’s because disks fail. With an organization like the Internet Archive, they rack up lots of failures. They have to be swapping out bad drives and attempting to restore content from remaining copies on other drives. And they couldn’t, he said, quite keep up with the failures. Some data does get lost because failures occur before the redundancy can be exploited to restore some sites.

I figure for my purposes, the data I have is a copy of what my colleagues have, and for the hard disk copy, I aim to have two of those. I think that should be sufficiently paranoid. The process or workflow takes about six to seven minutes per CD to create a directory, copy the files, and mark the CD as copied. I’m working on the third page out of 32 pages in a CD case now. This will take some effort, but then I invested years of my life getting that data in the first place.

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A perfectly reasonable letter to the editor from Walter Kania elicited a response from Andrew Ricks with all the hallmarks of the concern troll.

I was moved to enter a comment there that I’ll share here. There was a 1000 character limit on online comments.

I read the previous letter by Walter Kania. The response from Ricks is overwrought and misguided.

There is open discourse in science, conducted in the scientific literature. The “intelligent design” creationists (IDC) mostly skip that, and have established a track record for premature promotion of their claims as something worthy of inclusion in the public K-12 science curriculum. The IDC advocates have not done the hard work of convincing the scientific community that they have something that works as science.

Efforts to undermine the effectiveness and rigor of science instruction anywhere are fully worthy of disparagement, denigration, and contumely. The religious antievolution movement, IDC included, has been engaged in precisely that for decades. It is precisely because we seek to curtail inappropriate indoctrination that IDC is opposed. If they want respectful discourse, they need to stop being charlatans pushing a sham.

Wesley R. Elsberry, Ph.D.

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From about 1992 to around 2002, I was a frequent commenter on the Usenet talk.origins newsgroup, contributing several thousand posts there. I’m going to do some recycling of content from time to time, and pull posts from the archives to bring into this blog. Here are a couple of posts from 1998 related to “puncuated equilibria”.

Continue Reading »

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