Monthly Archives: January 2005

A Late Birthday Present…

Our friend Greta Kaplan is moving. One of the things that she decided was not going to go with her has been handed to me instead: A Jackson/Charvel electric bass guitar.

Ok, one might ask, what am I gonna do with a bass guitar? It’s in that category of things that I consider “stress relievers”. It helps relieve my stress. It may not serve that purpose for anyone else in audible range, but, oh, well…

A little over a year ago, I bought an inexpensive electric keyboard for Diane. She can pretty much pick out a tune given sheet music. I’m hoping that we can come up with something simple that we can play together on the two instruments, though I’ll be starting pretty much from scratch.

Back when I was an undergraduate, I had an electric guitar, a Silvertone hollow body. I never got proficient, but I got a lot of enjoyment out of it. I loaned it to a friend, and somehow I never got it back.

When I graduated with the Ph.D., one of the things I was looking forward to was looking around for another electric guitar. But money has been tight, and it just hasn’t been something that there were any discretionary funds for. So this unexpected gift fills one of those long-term “I want that” bits. Thanks, Greta!

Bat Family Tree

Check out the article on tracing the evolution of bats. This relates some of the information from a publication in Science about affinities of microbats and megabats. Generally, the mibcrobats use biosonar megabats don’t. But picking out the family relationships has been a puzzle. This study asserts that the megabats “nest” within several of the microbat lineages.

While all this is cool stuff, including tracing the paleobiogeography of bats, there are some rough spots in the media hype.

“Bats are a spectacular group of mammals, with a combination of two remarkable specializations that you don’t see in any other land mammals: flight and echolocation,” Springer said.

Yes, bats are a spectacular group of mammals.

Yes, bats are the only mammals capable of sustained flight. Other mammals do have some pretty impressive gliding capabilities.

But Springer is off into the weeds with the claim that bats are the only terrestrial mammals to use biosonar. Shrews, rats, some badgers, and the aye-aye (Daubentoniidae) use forms of biosonar. Their use of biosonar is certainly less polished than that seen in many bat species, but they do use it. (Other species that use biosonar besides “the usual suspects” of bats, whales, and dolphins include oilbirds and cave swiftlets, showing that biosonar is not a strictly mammalian adaptation, either.)

There is a tendency in media reports for scientists to be quoted making statements that pump up the significance of their research. This is an all-too human quality, and perhaps we can’t expect reporters either to give all the caveats that someone might add to a statement that needs qualification, or to check out some of the sweeping claims that aren’t part and parcel of the actual data and analysis being reported. The simpler forms of biosonar noted in other species illustrate an important point, that this adaptation is not as limited in nature as Springer is reported to have stated.

It’s a Snap for the Venus Fly-Trap

Over on New Scientist, they have a short piece on the mechanism of the Venus Fly-Trap. The leaves that make up the trap change shape from convex to concave, and this change in shape produces the rapid snapping action that is able to catch flies.

This sort of action is called snap-through in other contexts. You probably know it best from the popping of tops in many canned goods, where if it doesn’t give a pop on opening, you know the can has been opened before. These changes in shape from one stable state to another happen rapidly, which is the basis of action of the common dog clicker, which in a click operation undergoes two of these deformations.

This still leaves the topic of how this mechanism evolved. I’ll have to check with Nick Matzke on this, for he’s looked at these carnivorous plants in some detail.

A Birthday

Yesterday, Diane and I had our planned outing. We headed over to the Lindsay Wildlife Museum, where we met up with Glenn Branch, his wife, Sujatha, and son, Vikram. Mark Isaak, John Harshman, Alan Gishlick and his s.o. Alanna were also there. We watched the raptor room and talked about their birds and our birds. One of the docents pressed us to demonstrate our raptor recognition abilities by naming the species of birds being taken out for a feeding session. Diane gave her the correct species for each and genders for some.

We went to the Left Bank restaurant afterwards, a place with good food and nice ambience. While most of the table had a rollicking discussion of cladistics, Diane, Sujatha, and Vikram had a talk about dolphins, whales, sharks, and Harris’s hawks. I had some 4×6″ prints with me to start discussion.

I ducked out to the van for a brief nap while the crew had dessert. Mark Isaak came out to say goodbye, and he got an introduction to Rusty, our female Harris’s hawk. Diane and I went off to a ravine where Farli and Ritka, our Vizslas, could run while Rusty and Glamdring flew around. While some quail and jackrabbits were sighted and chased, nothing was caught.

I did more standing and walking during the day than I had tried in a while. So today that caught up with me. I had a couple of short naps in between phone calls wishing me a happy birthday. My parents, Diane’s parents, JoAnn Griffin, Greta Kaplan, and Lissa Davis were among the callers. I also received birthday emails from John Wilkins and Troy Britain. Thanks to all of you. It was nice weekend. I’m glad to be here to see it.

Sugars, Stem cells, and Evolution

Carl Zimmer has a very nice post that examines research on an evolutionary event in the human lineage, the loss of a sugar that is ubiquitous in other mammals. The research points to loss of this sugar to an inserted Alu repeat between 1.6 and 3.8 million years ago. The link to stem cell research is that current embryonic stem cell lines cultured on media taken from other mammals. Other mammals have the sugar humans have lost, and the stem cells incorporate it into their cell membranes. So if these stem cells were inserted into a human host, the host’s immune system would be likely to tag them as foreign tissue and react to them, obviating one advantage that stem cells were supposed to provide for human medicine.

The kicker comes in that governmental policy dictates that researchers shall not fix the embryonic stem cell lines by starting over with a growth medium improved by our newfound knowledge; they either use the lines as they are, alien sugar and all, or find something else to do.

Please go give Carl’s post a read; it is well worth your time.

Impromptu Howlerfest: Walnut Creek, CA, Jan. 22nd, 2005

Just give me an excuse to announce a get-together… and I have two of them. Glenn Branch, my colleague at NCSE, has his birthday on January 22nd, and mine falls on January 23rd. So we’re having a joint outing/celebration, and thought we’d invite folks in the area to join us.

When: January 22nd, 2005, starting at 10 AM
Where: Lindsay Wildlife Museum, then the “Left Bank” Restaurant

Lindsay Wildlife Museum information:
Web site:
Hours: 10 AM to 5 PM
Admission: Adults $6; Seniors (65+) $5; Children $4
Directions: From I-680,

Take the Treat Blvd./Geary Road exit and turn left over freeway. Proceed three more lights and turn left on Buena Vista. Turn right on First Avenue. The museum is half-way up the block on the left.

Welcome to Lindsay Wildlife Museum, a wildlife rehabilitation and educational center that focuses on native California wildlife and natural history. The museum exhibits live, non-releasable native wildlife in Walnut Creek, California. Founded in 1955, the museum operates the oldest and one of the largest wildlife rehabilitation hospitals in the United States, treating more than 6,000 injured and orphaned wild animals each year.

Then on to lunch… we should arrive at the restaurant at noon.

The Left Bank Brasserie

From the North:
Take Highway 680 South. Exit at Gregory Lane and turn left onto Contra Costa Blvd. Turn right at Monument Blvd. into the new Pleasant Hill Downtown Center. Turn right at the first parking lot just before the fountain.

From the South:
Take Highway 680 North. Exit at Contra Costa Blvd. Turn left on Monument Blvd. into the new Pleasant Hill Downtown Center. Turn right at the first parking lot just before the fountain.

Lunch menu:

If you intend to come, let me know by Friday and I’ll set the reservation for the restaurant.
welsberr at antievolution dot org
will do nicely for a contact email.

Tangled Bank #19

Tangled Bank #19 is up for viewing. This is a collection of links to recent science blogging. The “Biosonar and Behavior” article below is among the entries. Give it a try…

The Weirdness of If

Over on Imago Dei, much is being made of the unfairness of logical asymmetry.

Once again, how can we have scientific evidence against the presence of something when we are not allowed to have scientific evidence supporting the presence of something?

This takes me back to teaching an artificial intelligence class some years ago. The answer to the conundrum lies in a basic asymmetry in propositional logic. One runs into it very quickly, because it has to do with that most basic of relations, implication. It is all about “if”.

If I make a statement A, and I say that when A is true, then statement B is true, I have just asserted that if A, then B.

OK, so what does a truth table for this look like?

A  B    (if A then B)
0  0            1
0  1            1
1  0            0
1  1            1

If we observe that B is actually true, that is consistent with A being true, but it is just as consistent with A being false. On the other hand, if we observe that B is in fact false, then we know that A cannot be true.

This is the basis for Popper’s procedure of falsification, and the reason why Popper so strongly asserted that no scientific theory could obtain absolute proof: while our observations can tell us which things are false, they cannot reliably inform us as to which things are true.

Progress on Writing

An activity that has been put off far too long due to the various health issues I had last year is getting papers published resulting from Diane and my dissertations. I’ve got three chapters to be made over; Diane has two. We have the additional constraint that we have to obtain clearance from the Navy Marine Mammal program for paper publications, which adds a set of reviews internal to the Navy before we can even submit papers to a journal.

Actually, my three chapters had been put in for Navy review last year, but only one seemed to come out the other end. The other two I’ve spent some time on recently and should be going back in shortly. Hopefully within a couple of months I’ll have the clearance and the opportunity to send them off to journals. There’s also taking care of the comments from the journal concerning the one paper that made it out of Navy review. One paper looks at simultaneous measurement of intranarial pressure and acoustics during a biosonar task in bottlenose dolphins, and reports on intranarial pressure differences between pressurization events that only have clicks and those that also have whistles. Another takes up what was learned about biosonar clicks when we had both intranarial pressure and acoustics. And the third concerns estimating the bioenergetic cost of pressurizing the gas in the bony nares of the dolphins.

Diane has been taking care of me and business this past year, so getting her chapters converted to papers is high on the to-do list. She has essentially two separate studies dealing with simple response time, both with bottlenose dolphins and white whales. One reports on simple response time in an auditory task when the subjects are given stimuli near threshold, and the other concerns response times when the stimuli are well above threshold. Once those are published, they’ll be the first papers to use a comparative approach to examination of simple response time across two species. Since simple response time work has been done ever since Helmholtz, this is a bit of a surprising novelty.

Beyond these, I have a few more to write up concerning the dissertation data. One will deal with properties of click trains and intranarial pressure. Another will examine a click classification system I used that was introduced by Houser, Helweg, and Moore in 1999. There’s a paper to be done on the apparent use of different biosonar task strategies between the subjects in the study.

Diane and I also have other data to be analyzed and written up. Probably the oldest set is the work we did on vocalizations of lekking male greater prairie chickens. The data goes back to 1994-1996. While we have various recordings taken of dolphins being rehabilitated at the Texas Marine Mammal Stranding Network, it’s more likely we’ll turn to some recordings of dolphins and white whales taken with gear giving good signal response up through 1 MHz frequencies. It turns out that dolphins and white whales are emitting significant energy in their clicks up to 400 to 500 KHz. A preliminary report was given by Tom Muir at the Acoustical Society of America meeting this past fall bringing this up. While the odds are that these high frequencies are an artifact of the sound production process, the fact of the matter is that no one has yet tested dolphin or white whale hearing at those frequencies. I was able to talk with C. Scott Johnson, the physicist who produced the dolphin audiogram in the 1960’s (and when I say “the” I say it advisedly) about his choice of frequencies to test. Basically, he tested to the limit of his electronic gear at the time, which meant 200 KHz or lower for tones and 100 KHz or lower for short-duration pulses.

So, if I feel like there’s nothing to do, I can just come back to this post and disabuse myself of the notion.

Biosonar and Behavior

On Sunday, Diane and I had a visit from Jennifer Pettis, who recently graduated from Georgetown University with a master’s degree in biology. Jennifer’s major professor was Janet Mann, and Jennifer did her research on the bottlenose dolphins at Shark Bay (Monkey Mia), Australia.

What Jennifer has done that is different from earlier studies of biosonar in the wild is to correlate behavioral states with the properties of click trains in bottlenose dolphins. Jennifer made audio recordings via a hydrophone while videotaping shallow-water dolphin activity and making voice notes on the video record. She then classified the behavioral state of the majority of dolphins in the study area from the video record. Click trains from the audio record were then analyzed and tagged according to the noted behavioral states. One of the clearest findings of her study was that click trains with low inter-click intervals (ICIs) were far more often emitted during the foraging behavioral state. She compared this tendency to the terminal buzz noted in studies of bat biosonar. Many bat species emit a series of FM sweeps, such that the intervals between sweeps is longest in the hunting phase, is reduced somewhat during the approach phase, and is greatly reduced during close-approach and capture. In dolphins, it has been noted that when dolphins are very close to a target, they will often emit a “buzz” or “burst pulse”, which is a click train with a very rapid rate (has low ICIs). Jennifer’s study goes beyond the anecdotal evidence of those earlier observations to a quantitative analysis that couples the click trains to behavior.

I’m happy to say that I was able to assist Jennifer a bit last year. She was able to utilize a program I had written to pull data from wide-bandwidth recordings of dolphin biosonar. This was a program written in Borland’s Delphi, essentially providing a computer-assisted means of recognizing and tagging click trains. Within it, I have a parameterized algorithm that runs through selected data and returns a list of offsets where it finds candidate clicks. The algorithm was based upon analysis of the trained state of a simple artificial neural system (specifically, Widrow and Hoff’s ADALINE model). By hand-tagging several click trains, I had made a training data set for the ANS. My method of running the ANS, though, was to present a fixed number of samples to the ANS, and then increment the starting position by one sample to prepare for the next presentation. While the ANS had nice accuracy in its recognition of candidate clicks outside the training set, running it was very slow. Therefore the switch to a parameterized algorithm utilizing the features apparently identified by the ANS.

I was myself surprised that very little needed to be done to shift between recognizing clicks in wide-bandwidth data (sampled between 400 and 5oo kilosamples per second) and Jennifer’s audio data (sampled at 44.1 kilosamples per second). My program is based on being a computer-assisted rather than completely automated system, so the picked clicks are presented visually for user review and editing. The user can adjust the indicated offset for a click, or delete a selection from the list, or add a new selection to the list of clicks. Something I added for Jennifer was a display of the power spectral density plot for a selected click. This was needed because in Jennifer’s data it was quite common for more than one dolphin to be emitting click trains at the same time. Fortunately, it was often possible to distinguish such overlapping click trains one from the other based upon the similarities of power spectral density plots within each click train, as well as the timing of intervals in each click train.

So it was gratifying to see the results from Jennifer’s analysis. She ran through her thesis defense presentation for us, and we also took a pass through a chapter in her thesis that she is now preparing for publication.

After that, we stepped out to do some jump-ups with the hawks (a sort of calisthenics where the hawk is encouraged to fly up to the gloved hand several times to receive a tidbit of food on an intermittent reinforcement schedule). Both Rusty and Glamdring readily came to Jennifer’s glove. Whether they had recall of the hunting outing we had with Jennifer last year or not is something I can’t tell, but they showed little reticence today. A bit surprising, overall, since the birds were basically fed free choice over the Christmas holiday and are currently still well over their usual flight weight. Usually, at these weights the hawks are in what we call “fat and sassy” mode, and not terribly responsive.

So Many Issues, So Little Time

Today, I found out there’s a crying need for me to write several essays.

I had a chat with a reporter about antievolution today; I need to put together a basic set of links and text to point the media in the right direction.

An antievolutionist made a wholly unsupported statement about the statistics of belief among biologists; I need to look up the actual polling results that apply so that the response is not baseless like the original conjecture.

I found out that a misapprehension about Darwin is being propagated through an essay at the TalkOrigins Archive; I need to track down the origins of this modern myth and expose it as such.

Another antievolutionist who didn’t like the recent National Geographic article on evolution was spouting nonsense about dolphin biosonar in a web article; I need to thoroughly critique the resulting mess. It’s not that often that antievolution intersects with my dissertation research.

If this keeps up, 2005 is going to be a very busy year for me.

Happy New Year!

Just a short note to say “Happy New Year” to everyone out there. I’m about to celebrate a belated Christmas with my parents and niece. I’m very glad to be able to do this in this new year. The various remaining medical issues are small potatoes compared to being able to appreciate life. I hope to have more to say in this coming year, so keep checking in.