Monthly Archives: March 2006

Salmon Trouble: People Just Don’t Get It

An article by Dennis Cuff in the Contra Costa Times today reports that a federal panel is considering closing the salmon fishing season this year from Monterey to northern Oregon in order to protect Klamath river salmon.

The salmon are not the focus of the story, though they do get some mention.

Because Klamath salmon mix in the ocean with salmon from other rivers, regulators say they need to restrict fishing along 700 miles of coastline to protect the Klamath salmon.
Experts expect healthy salmon runs on the Sacramento River this year but a low run on the Klamath for a third consecutive year.
In defense, a federal fishing regulators say they are trying to protect a public resource. They said they want to bring back Klamath salmon before they become threatened or endangered.
The Klamath River suffers from interconnected problems of plant water quality, low flows, old hydroelectric dams that block fish migration and parasites that kill baby fish.

The article spouts generalities about “experts”, “regulators”, and “federal panels” without ever bothering to get a statement from any specific person. Contrast that with Cuff’s central figures in the story, people associated with the fishing industry. This is the story lead:

Duncan MacLean has weathered stormy seas, lean years and competition from fish farms to stay afloat in the West Coast’s shrinking commercial salmon business for 30 years.
Nature’s bounty has been good to him.
But now he fears the government’s failure to manage a river environment 600 miles away could put him and other California salmon fishermen out of business.

Here’s something we all need to know about MacLean:

“If I don’t fish for a season, I’m dead. I’m history,” McLean said this week aboard his fishing boat, berthed in Pillar Point harbor nestled in the moon-shaped bay 20 miles south of San Francisco.

The only others quoted in the article were Peggy Beckett, a party boat trip arranger and former salmon boat captain, and Yogi Adams, a charter fishing boat owner.

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Catching Up

Last Thursday, my sister, Emily Kay May, arrived from Australia. She came in via a military transport hop to Travis AFB near Fairfield, then caught a BART bus to reach the Pleasant Hill BART station. At the time she telephoned me, I was at the Kaiser Permanente medical offices in Walnut Creek talking with my gastroenterologist about the abdominal pain I had about three weeks earlier. I told Emily I’d be there in about half an hour.

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Digital Photo Post-Processing

There are a number of ways in which I handle post-processing digital photos.

The first issue is that if the original photo is in JPEG format, then one wants to be careful to preserve the original file. All editing and modifications, save lossless rotation, should be performed on a copy of the original. This is because JPEG is a “lossy” format, and each time a JPEG image is resaved, some more of the original detail is lost. I wrote an application some years back to rename multiple files at a time; several programs now offer similar capabilities. My usual approach now is to name a directory by the date certain photos were taken, and also to give a very short description of the contents of the directory in that name.

If I just want to edit individual photos, I use an editor like GIMP or Corel Photo-Paint. Adobe Photoshop is the canonical tool, but I was using Corel products way back when, and never really got into it. GIMP has a lot of features, and is free, though you will likely want to purchase a tutorial book if you decide to use it. Corel’s products are definitely commercial, but if you are willing to use versions one or two steps behind the latest one, you can get the graphics suite pretty cheaply.

When I want to print a digital photo on my own printer, the essential tool is QImage. This package has a number of features that make it well-suited to batch processing and printing of digital photos. One of the best of these has to be the ability to set an image crop with the right aspect ratio for a selected print size: no guessing about what is on or off the printed page. QImage also performs its own interpolation to match the printer’s native resolution, eliminating the interpolation normally applied by printer drivers. QImage is also the package I use when I want to upsample a digital photo, again on the strength of its interpolation algorithms. QImage also performs image adjustments like “Exposure” (a normalization process), unsharp mask (sharpening), tone curves, blemish and red eye removal, and high-iso noise reduction. So QImage is pretty much the program to use when printing on-site to streamline a workflow.

To get from a large digital photo to web-sized photos and thumbnails, I am now using the ImageMagick package of command-line image manipulation tools, the “jpegoptim” command line tool, and several Perl scripts to automate things. “jpegoptim” permits the removal of EXIF information and comments, and the optimal recompression of JPEG photos. This typically reduces the size of a JPEG for web distribution to 1/5 to 1/2 of its original size. That helps a lot with both storage requirements for photos and bandwidth in serving them.

Because “jpegoptim” doesn’t take wildcards, at least in its Win32 version, I have written a Perl script to apply it to all JPEG files in a directory ( I have also written a Perl script to resize a file as a thumbnail, a somewhat larger version for web pages, and a version for use in PowerPoint presentations (, and another that automatically does this for all the JPEGs in a directory ( The resize operation does a “normalize” operation as well. The “jpegoptim” parameters are set to remove EXIF information and comments, then set the quality level at 60.

Rusty’s End of Season

Sunday the 19th was the last day in the 2005-2006 hunting season for rabbits. So Nick Matzke and I went with Rusty to check out a spot that Diane and I had visited before.

I was aiming to arrive about an hour before sunset. Rabbits tend to get active as night approaches, so I figured that we would spend some time just hanging out with Rusty until things — that is, rabbits — got hopping.

Nick arrived at my house late in the afternoon. I had my car packed and set to go. Rusty’s travel crate is a modified dog crate, and while it fit into the back seat of the Buick Century, it was a pretty tight fit. I had the telemetry receiver in, and Rusty’s transmitter was turned on. I had hunting pockets for Nick and I, and tidbits for Rusty, and a couple of pieces of rabbit. The meat went into a small cooler, along with a few soft drinks. So Nick parked his truck, got into my car, and we were off.

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A Rare Predator Bounces Back (Now Get It Out of Here) – New York Times

A Rare Predator Bounces Back (Now Get It Out of Here) – New York Times

A new federal report in January announced the obvious: that the Florida panther population must grow to survive — ideally, to three separate populations of at least 240 each — but that it is ever more desperate for space. The report, by the United States Fish and Wildlife Service, rehashed the thorny old idea of moving some of the cats to Central Florida and eventually to other states where they once roamed, like Georgia and Arkansas.

But there are no firm plans, and with the panther population still endangered but healthier than it has been in decades, South Florida is facing an equally thorny new question: what to do when panthers get too comfortable on human turf?

The article discusses one panther whose taste for chicken and even domestic cats took him out of the wild and into Busch Gardens at Tampa. The panther problem throws an uncomfortable light on one of the most contentious — and pervasive — of factors in the decline of wild populations of many species, habitat loss. Specifically, habitat lost to another species, Homo sapiens. It is a well-known principle of ecology that small, fragmented populations are more susceptible to extinction. But that is exactly the situation that obtains as human structures like interstate highways effectively subdivide territories and disrupt movement and migration pathways of non-flying species. Land put into cultivation does not support the previous biodiversity of a region. And suburbs are hostile to all but a few domesticated species, some wild species tolerant of proximity to humans (e.g., raccoons and opossums), and the usual pest species that profilerate in association with humans (e.g., rats).

The brass tacks are that if wildlife biodiversity is to be maintained at some modest fraction of its former amount, humans have to plan for it and stick to the plan. And that will mean that there will be significant amounts of land set aside as refugia, with easy access connecting separate refugia to encourage gene flow between populations. This is not a comfortable lesson, as it stands in contrast to the notion that development for human uses may continue until every last acre that can be exploited has been exploited. Habitat loss is unlike issues of pollution or global warming, where dealing with the latter two have undeniable direct benefits for humans, too. Stopping habitat loss, by contrast, has direct costs for humans and indirect benefits in the form of maintaining biodiversity. It requires analysis that takes into account the long term, not just short-term economics.

ScienceDaily: Scientists Discover Reason Behind Ear Canal In Chinese Frog: Ultrasonic Communication

ScienceDaily: Scientists Discover Reason Behind Ear Canal In Chinese Frog: Ultrasonic Communication

Amolops tormotus, also referred to as the concave-eared torrent frog, is the first non-mammalian species found to be capable of producing and detecting ultrasounds for communication, much like dolphins, bats, and some rodents. It does so, the researchers report, to make itself heard above the din of low-frequency sounds produced in its surroundings so that it can communicate territorial information to other males of its species. In addition to helping researchers puzzle out how the ear evolved, the research may one day enable scientists to develop new strategies or technologies that help people to hear in environments in which there is a lot of background noise.

Note the conjunction in the description above: capable of producing AND detecting ultrasounds. There are rather more non-mammalian species known to be capable of perceiving ultrasound, including a number of fish species and noctuid moths. Snapping shrimp are noted producers of ultrasound, and I am suspicious that many insect species that communicate using stridulation may actually be producing some frequencies above 20kHz. In other words, I think that the torrent frog’s capability in this regard may not be all that unique, but may simply indicate that there is a lot of work left to be done in characterizing the acoustic properties of both sound production and reception in various species.

ScienceDaily: UCSD Project Takes Fish Collection Into The Digital Age

ScienceDaily: UCSD Project Takes Fish Collection Into The Digital Age

Project coordinators will create a resource that allows scientists to remotely study a range of the world’s fish species, from the exotic to the mundane. In collaboration with the Birch Aquarium at Scripps, the scientists will also develop the “Digital Dissection Tool,” an educational program for high school students that capitalizes on the interactive scientific research aspects of the project.

“By creating the Digital Fish Library, we hope to develop a tool that stimulates students to think independently and naturally leads them into questions that they might want to investigate,” Frank said. “We hope to design an educational model that spurs students’ interests and teaches them how to conduct research. It’s not just teaching them about fish anatomy or physiology, it’s teaching them about magnetic resonance imaging, computation and visualization.”

Education modules within the Digital Dissection Tool will cover the basics of MRI, digital image processing of 3-D MRI data as well as aspects of marine biology. Under the guidance of co-investigator Cheryl Peach, Ph.D., of the Birch Aquarium–an expert in science education–elements of the project also will be incorporated into UCSD’s Academic Connections Program, an intensive, three-week summer learning experience for college-bound high school students.

This is a project with $2.5M in funding from NSF for 5 years. From the article, there seems to be at least one biologist in the fish collection at Scripps, one MRI imaging specialist, one MRI engineer, then one or more people at the Birch Aquarium. These folks live in the La Jolla area of southern California, a region with a completely ridiculous high cost of living. And they are producing custom MRI hardware, not an inexpensive thing to do. And producing software tools for education. This looks to be a tremendous bargain for $500K/year of funding. I’d be surprised if the NSF funding actually covered half of the actual costs involved in this project. You know, William Proxmire made a name for himself by heaping ridicule on things he thought were unworthy of spending taxpayer money on. I’d like to note here that we, the taxpayers, are getting way more than our money’s worth on this one.

Willard R. Elsberry, FTBA Hall of Fame

From the Lake City Journal, Feb. 25th, 2006:

The [Florida Transportation Builders Association] Hall of Fame has been established to honor, preserve and perpetuate the outstanding accomplishments and contributions of individuals who have brought and continue to bring significant recognition to the state of Florida in the field of transportation construction.


Willard R. Elsberry

A native Floridian, Mr. Elsberry was born and grew up in the rural community of Wimauma, in southeast Hillsborough County. He is a graduate of the University of Florida. Mr. Elsberry and his wife, Margaret, reside in Lakeland where he is president and treasurer of Superior Paving, Inc., a position he has held since 1965. Mr. Elsberry, a Certified Public Accountant, has worked tirelessly to promote the transportation industry. He has served as Chairman and board member of the FTBA, American Road and Transportation Board board member and as a director and treasurer of the Asphalt Contractors Association of Florida. He has been an active member of his community by volunteering his services to many organizations including the Heart of Florida Girl Scout Council, United Way of Greater Lakeland and as chairman of the Board of Trustees, Florida Annual Conference, The United Methodist Church.

Way to go, Dad!

Ark or Arc?

Porcher Taylor practices what he calls “satellite archaeology”. In the news over at CNN is Taylor’s highest-profile work, an analysis of what is billed as an anomaly on Mt. Ararat in Turkey.

Nevertheless, the anomaly may not be a ridge line of ice, snow and possibly rock, but an artificial ridge line, Taylor said. “I maintain that if it is the remains of something manmade and potentially nautical, then it’s potentially something of biblical proportions.”

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News in Science

A study finds that humans differ from chimps mostly in regulatory genes, confirming a thrity-year-old hypothesis. They looked at some 1,056 genes in this study across humans and several other primates, and found 60 percent of these had consistent expression levels across all the species. Some 19 genes were found to have significantly different expression levels in humans, and of those, the ones that were themselves transcription factors (that is, they regulate the expression of other genes) were all expressed at a higher rate than in other primates. The researchers say that this is consistent with what we expect in directional selection.

Another study confirms that chronic moderate tinnitus has a negative impact on performance on complex cognitive tasks. “Tinnitus is the perception of sound in the absence of auditory stimulation. Described as a “ringing in the ears” or “buzzing” or “whooshing” sound, it can be temporary, intermittent, or permanent.” What they do not say here is that tinnitus is often not merely something going haywire inside the brain, but is actually correlated with otoacoustic emission of sound. Many people don’t know that ears not only receive sound, but can produce it as well. This has been used to measure hearing in young children, and especially in people who cannot be instructed to respond to tones in a hearing test. The auditory system responds with an otoacoustic emission of similar frequency to a test tone, and tiny microphones in the ear canal can detect these otoacoustic emissions. In people with tinnitus, this process sometimes occurs inappropriately and continues long beyond any triggering stimulus.

A researcher at Purdue University claims to have achieved nuclear fusion in a tabletop apparatus. No, it isn’t “cold fusion”, the phenomenon claimed in work with electrically charged paladium grids in water. Instead, Prof. Rusi P. Taleyarkhan says that he observed fusion in “a small tabletop device by blasting a jar of solvent with strong ultrasound vibrations.

In their 2002 report, Dr. Taleyarkhan and his colleagues said fusion had been created when the ultrasonic vibrations caused small gas bubbles in the solvent to collapse quickly, generating superhot temperatures where fusion could occur.

So this is “cavitation fusion”, not “cold fusion”. Everybody got that? This should be interesting to see play out. There’s a lot of skepticism, and Purdue is investigating the research, especially since at the moment it appears to be irreproducible. Cavitation is itself a pretty widespread phenomenon. Snapping shrimp famously use cavitation in stunning prey, with a highly modified pincer providing the means of generating cavitation. Those studying cavitation have long noted its high-energy results, as free radicals are produced in suitable solutions. As such, cavitation is pretty corrosive to living tissue, which goes some way to explaining why snapping shrimp generate it externally.

Update: I used the phrase “cavitation fusion” as an apt descriptor of what was in Kenneth Chang’s report linked above, though the phrase does not occur in the article. However, a quick Google search shows that this is, indeed, the appropriate term, and that there are a number of published papers using the phrase.

“Evolution Rocks”

Sam Blackwood sent me this link. It goes to a page giving the lyrics to a song, “Evolution Rocks”, by “Overman”. A media player in my browser also automatically downloaded and played the song. Check it out.

Learning by Test

I’m gifted on test-taking. It’s one of the things that made me stand out in my academic studies. I scored high on the standardized tests. I think the valedictorian at my high school ended up with a higher score, but then he also took the SAT three times to get there. I was satisified with my first SAT score. I did end up taking the GRE twice, but that’s because I ended up applying to grad school some ten years after I first took it, and they won’t distribute a score that old. My advisor in grad school said that it was the GRE scores that Diane and I had that first brought attention to our applications out of the mass received at Texas A&M.

The falconry test for the joint state-federal permit system is a multiple-choice exam, too. In 1982, Diane was studying for that and staying with my family in Lakeland, FL, where the Fish and Game regional office is located. I asked her whether they might be able to seat me for the exam, too, and she said maybe. I asked about what was likely to be covered on the exam, and Diane started going over the various sources she had been reading since junior high school. The main reference was Beebe and Webster’s North American Falconry & Hunting Hawks, which does a great job of introducing the topic. Between Diane’s tutoring and my own aptitude at analyzing multiple-choice exams, I made a passing score.

Enough boasting, though. A new psychology study shows a link between test-taking and long-term retention of studied material. In particular, they found that repeated test-taking aids retention in the long term better than does repeated studying.

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Cough, Cough, Ouch, Ouch

The cold may be resolving itself, but various other issues are popping up. I started having abdominal pain yesterday. I was thinking about whether to trundle myself off to the emergency room, but I called an advice nurse at Kaiser, described my symptoms, and she said that they’d arrange a doctor’s appointment.

So I went to see the doctor today (escorted by Nick Matzke, who shepherded me around health care today — thanks, Nick!). Another thing that showed up today was a slight loss of feeling in my left hand. So I let my doctor know what’s been up (cold, abdominal pain, loss of feeling) and she looked me over. She did a palpation of my abdomen, confirming the region and extent of tenderness. She also listened to my lungs, and expressed concern that I might have an early case of pneumonia on the right side. So it was off to another building for a couple of chest X-rays. In the meantime, she contacted the gastroentorology folks at the hospital about my case. When we met again, she showed me the scanned X-rays on the computer in the exam room, a cool thing. No pneumonia, they showed, but I may have a small amount of atelectasis, which she assured me was not uncommon following a severe cold.

The gastroenterologists will want to see me soon, but not immediately. In the meantime, my doctor has set me up for a bunch of lab tests to follow a 12 hour fast. I figure to fast Sunday evening to Monday morning and get the labs taken then. Hopefully, I will get some news on the appointment with the gastroenterology people early next week, too. In the meantime, I should not stress my system too much, and head for the emergency room on the appearance of certain symptoms (I have the list). Oh, about the hand… could be compression of the ulnar nerve, carpal tunnel syndrome, or a couple other things. I may get a nerve conduction test by and by. What fun.

Nick and I grabbed sandwiches on the way back to my house, then watched some episodes of Firefly to take up time until the rush hour traffic was over.