The Thoughts of a Frumpy Professor

............................................ ............................................ A blog devoted to the ramblings of a small town, middle aged college professor as he experiences life and all its strange variances.

Saturday, February 25, 2012

Words Fail Me at the Moment

I have not had much to say as of late. Part of the issue is that I have been quite busy with work, but another aspect is that I simply have felt quiet, not really having much to say.

I am still working on making my life more serene. It is not usual for me to not have much to say, but that is where I am right now. I think it may be cabin fever or some such thing. Late Feburary is often a difficult time for me. However, I do not feel "down". I simply feel.... nothing.


Wednesday, February 08, 2012


My mother's birthday was yesterday. I was not feeling in a mood to write about it then. I do feel a lot of sadness that she is not here physically with us. She would be 84 years old if she were alive. I miss her horribly. It is harsh to think about her passing, so most of the time, I do not think about her passing.

Yet, that is not wholly true. I would be more accurate in saying I *try* to not think of her passing, the rushing to the hospital in the middle of the night after being awoken by the horrid phone call from the nurse saying I needed to get there right "away". The seeing of her lifeless body, but feeling the warmth still in her hands and in her face. Feeling her face gently with my hands, sobbing uncontrollably, but knowing I would never get the chance to feel her warmth again, nor her face. Staying in her presence until the hospital staff forced me out of the room a few hours later, saying they needed to clean the room.

But I want to try to think of her in all the other ways I knew my mother... instead of seeing only the harsh last moments. Yet, it is difficult for me to do so. The intensity of the harsh emotions seems to overpower the gentle happiness and friendship I so much love and miss from my beautiful mother. I would so much prefer to recall the wonderfully rich conversations and general small talk we would have with each other. Yet, those beautiful memories are hard to bring up, where as the fear, sadness and horror pop up easily and unexpectedly.

I miss you, Mom. I love you, Mom. I wish you would speak to me in my dreams so that I may feel your presence again at least in that way.


Tuesday, February 07, 2012

Loopy Fish

This is a very interesting study looking at issues relevant to global climate change and species survival. It is interesting to ME because it combines those issues with a neurobehavioral slant. The increase in carbon dioxide is shown to alter the behavior of these fish.

Rising Carbon Dioxide Confuses Brain Signaling in Fish: Nerve Cells Respond to Acidifying Waters

By Janet Raloff in Science News
Web edition : Sunday, January 15th, 2012

Reef-dwellers such as this Australian damselfish may find their brain chemistry confused by dropping pH levels in the ocean.G. Nilsson

A new study may explain how rising carbon dioxide concentrations — and the ocean acidification they induce — can cause topsy-turvy changes in the behavior of fish. Like a flipped switch, the normal response of nerve cells can reverse as acidifying seawater perturbs how a fish regulates acids and bases in its body, including the brain.

“This could be a big deal,” says neurobiologist Andrew Dittman of the National Oceanic and Atmospheric Administration’s Northwest Fisheries Science Center in Seattle. Dittman, who was not affiliated with the study, says the new findings could go a long way toward explaining curious sensory changes observed in fish exposed to acidifying waters. The scary scent of predators, for example, can suddenly become alluring.

For the new study, published online January 15 in Nature Climate Change, Göran Nilsson of the University of Oslo and his colleagues homed in on brain chemistry.

The idea emerged after Philip Munday of James Cook University in Townsville, Australia, told Nilsson of behavioral quirks his laboratory fish were exhibiting in a high–carbon dioxide environment — conditions exemplifying ocean waters a half-century or more from now. Nilsson, a neurophysiologist, speculated that a connection between nerves and chemistry might be involved. “It was very much an ‘Aha’ moment,” Munday says.

Once excited, nerve cells need a chemical to calm them down. A compound known as GABA does this by unlocking a gate on the cells’ outer membrane, allowing ions of chloride and bicarbonate to enter and quiet the cell. Nilsson speculated that when a fish’s body attempts to maintain chemical balance in the face of rising ocean acidification, chloride and bicarbonate concentrations could become higher inside nerve cells than outside them.

Later, when GABA gates opened, chloride and bicarbonate would then rush out of the cell instead of into it. That would excite the cell instead of calming it, essentially reversing the nerve’s response to a stimulus.

To test the idea, Nilsson’s group briefly bathed some hatchling reef fish in a chemical that deactivates the GABA gateway. Among clownfish raised in a high–carbon dioxide environment, a predator’s scent in the water — normally repellent — proved an attractant. Until, that is, the researchers immersed these fish for 30 minutes in water heavily spiked with gabazine, which locks the GABA gate closed. When the fish then reentered carbon dioxide–enriched water, a predator’s scent proved repellent, the scientists found.

Fish normally show a preference for turning one direction versus another, the piscine equivalent of a human’s left- or right-handedness. In a second experiment, this time using Australian damselfish, Nilsson’s group showed that fish in a high–carbon dioxide environment exhibited no turning preference. After a brief bout in gabazine-laced water, however, the fish suddenly demonstrated a marked preference for turning in one direction or the other.

“These are really fascinating results,” says Dittman. But scientists need to confirm the idea by looking for actual changes in the cells, he says, not just reversals of sensory-based behavioral changes.

That’s hard to do with teensy, baby fish, Nilsson says, which is why he and Munday are now extending their new studies into adults.

So very interesting.


Monday, February 06, 2012


I have not spoken of it in a while, but I am still walking/jogging each and every day. Today is another "pretty" milestone of sorts for me... it is day 1234. I have walked each and EVERY single day for 5 miles.... come rain, or snow, or ice, or illness, or holiday.

That is an accomplishment I can feel some satisfaction in for myself. It is more consistency than I have EVER displayed in my life at being physically active.


Sunday, February 05, 2012

Thoughts on Faith

The first reading at Mass this week was the following from Job (7:1-7):

Job spoke, saying:
Is not man's life on earth a drudgery?
Are not his days those of hirelings?
He is a slave who longs for the shade,
a hireling who waits for his wages.
So I have been assigned months of misery,
and troubled nights have been allotted to me.
If in bed I say, "When shall I arise?"
then the night drags on;
I am filled with restlessness until the dawn.
My days are swifter than a weaver's shuttle;
they come to an end without hope.
Remember that my life is like the wind;
I shall not see happiness again.

I unfortunately feel like Job at times. I suspect we all do. But, perhaps my natural leanings in my personality are to feel this way a bit more than average. I do not like that about myself and wish to change. I need to keep working at making myself a better person. I do NOT and should NOT act like Job.


Saturday, February 04, 2012

Saturday Writings

In my effort to write more consistently, I always stumble at what to write on Saturdays. Today is no exception. I think I need a plan of sorts for Saturday's writings because that is the day of the week that is the biggest challenge to consistently post an essay. Suggestions would be greatly appreciated.


Friday, February 03, 2012

Damn, They Have All The Luck

I have never had the pleasure of trying marijuana, but as you all know, I greatly relish pipe tobacco. Below is a new study showing that indulgers in the green leaf may (at low doses) experience IMPROVED lung function. I wish a study would show that to be the case for my beloved brown leaf (pipe tobacco). I guess, maybe I should switch? Just kidding, but what does it actually feel like when a person indulges in the greener leaf?

Light Pot Smoking Easy on Lungs: For Those Who Did Inhale Infrequently, 20-year Study Shows Minor Pulmonary Improvement

By Nathan Seppa in Science News
Web edition : Tuesday, January 10th, 2012
Text Size

People who smoke marijuana for recreational or medical purposes might now breathe easier. Scientists report in the Jan. 11 Journal of the American Medical Association that occasional cannabis users don’t experience any loss of lung function.

In a 20-year study that included lung tests and a specific accounting of marijuana use, scientists also found that people who smoke more than 20 times a month and accumulate many years of use might have a slight drop in lung capacity over time. But the researchers are unsure of that finding since it was based on scant data.

The study is the longest ever conducted that measures cannabis smoking and lung function, uses standard lung measurements and includes thousands of volunteers, says Donald Tashkin, a pulmonologist at UCLA who wasn’t involved in the study. “That makes it important,” he says.

The data, he says, also suggest that marijuana is not a significant risk factor for chronic obstructive pulmonary disease, which includes emphysema. COPD is marked by loss of lung function and is typically caused by tobacco smoking.

The researchers tapped into a health study of 5,115 young adults recruited in 1985 and given lung tests periodically until 2006. The volunteers revealed whether and how often they smoked tobacco, marijuana or both. Most marijuana users in the study reported light use — a few times a month on average during the two decades.

After accounting for tobacco use, sex, race, body size and even pollution and secondhand smoke exposure, the researchers found that these light marijuana users had above-average scores for their age on lung function tests where they blew air into a gauge. People averaging somewhat higher use fared no better or worse than peers their age, while those who used cannabis at least 20 times a month for years showed hints of slightly reduced lung capacity, says study coauthor Stefan Kertesz, an internist at the University of Alabama at Birmingham and the Birmingham Veterans Affairs Medical Center.

Jeanette Tetrault, an internist and addiction specialist at Yale University School of Medicine, says the study is methodologically sound and the results are believable. But the potential for lung damage from frequent use makes a cautionary point, she says. “My concern is that giving the green light on light smoking might lead to heavy smoking.”

Besides, Tetrault says, a lung function test “doesn’t describe the entire picture.” Cannabis smoking causes increased coughing, phlegm production and wheezing, she says.

Kertesz agrees but notes that the large airways, the ones primarily irritated by marijuana smoke, seem to bounce back well. “Our bodies have evolved to recover from such short-term insults,” he says.

Marijuana has been approved for medical purposes in 16 states. Pharmacologist Karen Wright of Lancaster University in England says that while the new findings are reassuring for low-dose users, people who use medical marijuana regularly might be better off if they don’t have to inhale combustion fumes to do so. Researchers have made some progress on that front, having developed a spray containing two active cannabis components (SN: 6/19/2010, p. 16). “We should find better ways to administer cannabis compounds that are proven clinically to have a therapeutic benefit,” Wright says.

Very interesting.


Thursday, February 02, 2012


To be frank, politics as a topic on my blog has started to approach the zero point in terms of a graph of my interests. I have been becoming more and more jaded about ALL politicians over the last 10 years or so. My tendency to view each and every side of the political superstructure with a highly jaundiced eye feels wholly appropriate.

If I were to suggest the actual turning point, where I went from a person who *WAS* highly interested and motivated to learn political viewpoints *AND* thought the process of and participation *IN* politics was a valuable pursuit..... that turning point occurred far earlier than 10 years ago. It really started with two concurrent media changes that began in the mid-80s:

1. The blossoming of CNN as a media source really took hold in the mid-80s. Started in 1980, the original CNN was a rather grand channel that took pride in being a deeper, almost academic purveyor of news 24 hours a day. And, for a few years, it was a true delight. However its focus began to change by about 1987. The change was (in my opinion) brought about by the dollar (of course) and the way CNN thought it could continue to grow and expand in influence (and profit).... was in starting to have bombastic political pundits on programs who spouted nothing but harsh, unhelpful rhetoric. These assinine pundits ruined and destroyed the political landscape and wrecked havoc on daytime television as well.

2. The daytime television transition was similarly sinister as what transpired on CNN. In the mid-late 1960s a young fellow came on television and made a remarkable name for himself with a program that had insightful interviews and even reporting during the weekday. Now, I really did not watch this fellow, as I was too busy doing my own things at that time, but my beautiful mother and one of my sisters were utterly enchanted by this fellow and talked of him so often that I *felt* I did watch the shows. The fellows name was Phil Donahue. His "talk-show" was very exotic and different for daytime television of the day because it was not a soap opera, nor was it a gameshow. It was a blend of news reporting with deeper analysis and interviews. Granted some of the shows were a bit "fluffy" for my tastes even though I only heard about them second hand, but even with my only second-hand knowledge, I could sense a rather good, scholarly depth to the program.

Phil had the market all sewn up for a lot of years. But then came along a hellion on wheels (and not in a good way) named Sally Jesse Raphael. She (along with a few others like Oprah) started to make programming that was modeled after Phil Donahue. None of them could make a mark with a show that was as academic as Donahue, so in the Darwinian struggle to survive, they began to modify their shows to attract enough of an audience to garner more of the almighty dollar. Well, Oprah, of course, did a wonderful job appealing to the touchy-feely, emotional groups and as we all know has done very well with her programming. Raphael started out as a rather prissy, meek, mousy sort, and it looked like her days were numbered because she was definitely not getting as much in the way of "buzz" as others. However, she started a trip down the road to hell.... being a pundit sort herself, and creating the start of what has become known as tabloid television. She took the daytime talk show format, and turned it on its head to make it sordid, and nasty and all about looking at the tackiest, sleaziest, underbelly aspects of our society. AND THE DAMN THING ABOUT IT, was that it SOARED in popularity. We have been in that mentality ever since, and it is to a large extent (with the pundit issue above) the reason politics has grown so obnoxious and nasty.

So, I struggled for a lot of years to stay focused and interested in politics. But it is just too much. Everyone, no matter which party or side, lies, and does nothing but look out for themselves. There is not a single politician that represents me. And in my study of history, the last REAL president of merit in my opinion, was Theodore Roosevelt.


Wednesday, February 01, 2012

Just What I Need

The following article is long, but if you read the first part, you will see what interested me about this non-biology article. In this piece, it describes a camera that allows you to change the FOCUS of an image AFTER you have taken the picture. It is amazing, and is just what I need.... no more having the background be in focus and not the part of the image I want!

The Digital Camera Revolution: Instead of Imitating Film Counterparts, New Technologies Work with Light in Creative Ways

By Rachel Ehrenberg

January 28th, 2012 in Science News

Take a grainy, blurred image of a formless face or an illegible license plate, and with a few keystrokes the picture sharpens and the killer is caught — if you’re a crime-scene tech on TV. From Harrison Ford in Blade Runner to CSI, Criminal Minds and NCIS, the zoom-and-enhance maneuver has become such a staple of Hollywood dramas that it’s mocked with video montages on YouTube.

In real life, of course, no amount of high-techery can disclose data not captured by a camera in the first place. But scientific advances are now gaining ground on fictional forensics. The field known as computational photography has exploded in the last decade, yielding powerful new cameras capable of tricks once seen only in the labs of make-believe.

For a long time camera makers and operators focused mostly on getting more pixels. But the “pixel war” is over, says Marc Levoy, a pioneer in computational photography at Stanford University. Today’s manufacturers are looking beyond good resolution.

Low-cost computing and new algorithms, combined with fancy optics and sensors, are drastically changing how cameras re-create the world. Scientists have recently devised a camera that could spot a culprit by peeking around corners; another might divulge the identity of an attacker by collecting information reflected in a victim’s eyes. Other developments, some of which are making their way into commercially available cameras and smartphones, won’t necessarily help snag a bad guy but can turn anyone with a camera into a photo-grapher extraordinaire.

Researchers are, for example, finding ways to clean up pictures so that smudges or window screens disappear. The addition of unconventional lenses means pictures can be refocused long after a shot is taken. And the “Frankencamera,” recently developed at Stanford, is designed to be programmable, so that users can play around with the hardware and the computer code behind it. Such work may lead to previously impossible photos, researchers say — images that have yet to be imagined.
ECHO GIVEAWAYResearchers have recently designed a camera that can see around corners. Laser light leaving the camera (red) bounces off a door (blue) before hitting hidden objects. Echoes from the hidden objects (green) make their way back to the camera for analysis.Adapted by Janel Kiley

“The possibilities are not readily apparent at first,” write MIT’s Ramesh Raskar and Jack Tumblin of Northwestern University in Evanston, Ill., in a comprehensive textbook on computational photography set to be published this year. “Like a long-caged animal in a zoo destroyed by a hurricane, those of us who grew up with film photography are still standing here in shocked astonishment at the changes.”

Caught on camera

Until a few years ago, most digital cameras were basically film cameras, just with an electronic sensor doing the job of the film. These “filmlike” cameras use a lens to capture light from a 3-D scene, faithfully re-creating it as a 2-D image.

But in a digital camera, there’s no need for that re-creation to be faithful. Digital cameras have a tiny computer that processes incoming optical information before it is stored on the memory card. That computer can transform the scene, measuring, manipulating and combining visual signals in fundamentally new ways. With the help of tricked-out optics — such as multiple lenses in different arrangements — photographers can not only perfect the traditional recording of their lives, but they can also manipulate those keepsake shots to get something strange and different.

Advances in math and optics are now developing hand in hand, says Shree Nayar, head of the Computer Vision Laboratory at Columbia University. “When you worry about both of them at the same time, you can do new and interesting things.”
From an image of the eye, researchers at Columbia University can re-create exactly what a person is looking at.Computer Vision Laboratory/Columbia Univ.

One new and interesting thing is the ability to look around corners, beyond the line of sight. Developed in 2009 by Raskar, MIT graduate student Ahmed Kirmani and colleagues at MIT and the University of California, Santa Cruz, a new camera with a titanium-sapphire laser for a flash shoots brilliant light in pulses lasting less than a trillionth of a second. After the light ricochets off objects, including those not visible to the photographer, the camera collects the returning “echoes.” The camera then analyzes the photons that return and can estimate shapes blocked by a wall or other obstruction.

The technology might lead to devices that allow drivers to see around blind corners or surgeons to get a better view in tight places. It could also help first responders plan rescues in dangerous situations and crime fighters spot hidden foes.

Another technology that might aid real-world sleuths is the “world in an eye” imaging system, which can re-create a person’s surroundings from information reflected in a single eye. Using a geometric model of the eye’s cornea, Nayar and colleague Ko Nishino, now at Drexel University in Philadelphia, created a camera that detects where the cornea and the white of the eye meet. Computations then turn the cornea’s reflection of a fish bowl–like image into a map of the environmental surroundings projected on the person’s retina.

Using information on the tilt of the camera and the person’s eye positioning, whatever the person is looking at can be pinpointed, making the technology useful for eye-tracking studies where researchers want to know what a participant is paying attention to. The technology (which is available as a software package from the Computer Vision Laboratory) is also helping people look into the past. One photographer has been assessing reflections in the eyes of old photographs, exposing a blurred scene reflected in the eye of an old man in an 1840 portrait.

Picture perfect
With the Lytro, a photo can be refocused after it is taken. A bit of adjusting shifts the focus of a shot from background leaves (left) to a spider and its web (right).Eric Cheng/

If just capturing precious moments is more your style, many researchers, Nayar included, are exploring ways to enhance pictures taken for the more traditional purpose of archiving one’s life. There are methods for getting around that annoying shutter delay that makes you miss your shot, for deblurring moving objects and even for erasing raindrops that obscure what a picture was meant to capture.

Such tricks are gradually making their way into commercial cameras, or being made available as downloadable apps for use with smartphones. One new camera dubbed Lytro, developed by Ren Ng for his dissertation at Stanford, can readjust the focus post-shoot, so a picture can clearly render what’s nearby or far away.

Lytro’s trick is it that it employs “radically different optics,” says Stanford’s Levoy, who worked on those optics with Ng.

In between the main lens and the sensor, Lytro has an array of tiny lenses called lenslets that capture an entire light field — the intensity, color and direction of every ray of incoming light (in this case, that’s 11 million rays). Whereas a traditional camera captures some of the light leaving any one point in a scene and focuses it back together on a single pixel on a sensor, the lenslets distribute the light so it is recorded in separate pixels. This spread of information across pixels is encoded in the image, making refocusing later possible.

Lytro became commercially available last year, and another light-field camera may soon be available in smartphones. Last February Pelican Imaging announced a prototype for mobile devices that has an array of 25 lenslets. Like Lytro, Pelican promises images that can be refocused. But unlike Lytro’s boxy shape, this version would fit in the slender confines of a cell phone.
An app called SynthCam can make shots of buildings (Stanford quadrangle shown) look like miniature models.M. Levoy/Stanford Univ. Computer Graphics Lab

Arrays of full cameras (not just the lenses) also allow for interesting manipulations. When packed close together, the cameras approximate a giant lens, which means much more light is available for manipulating. Photos can thus be created with a shallow depth of field so that the photo’s subject is nice and crisp and the background is blurred, freeing the image from distracting clutter. A giant lens also means that a photographer can capture enough light from different angles to blur out foreground objects like foliage or venetian blinds, in effect looking around them. One of Stanford’s large-camera arrays has 128 video cameras set up 2 inches apart. The arrangement is like having a camera with a 3-foot-wide aperture.

Tweaks to a camera’s back end are also improving documentary potential. Image sensors have become much better at capturing light, so cameras can take many more pictures per second. A high frame rate combined with complex math means the camera can snap many versions of the same picture at different exposures and then merge them for the best results or select the best of the single images, a trick known as high dynamic range imaging.

New cameras can also deal with shutter lag. When set in a particular mode, the camera begins taking a burst of photos and temporarily saves them. The photographer gets the typical shot (the one taken when the shutter is clicked) as well as a series of shots from before and after.

“It’s something I’ve always wanted in a camera — for it to start taking pictures before something interesting happens,” says Tumblin. “So when your daughter is blowing out her birthday candles, you have a sequence of shots, one right after the other.”

Made to order

It’s all well and good that camera manufacturers are getting around to incorporating such advances, Levoy says. But he has higher hopes — that consumer cameras will one day be programmable, giving users the power to get exactly what they want out of the device.

“I came out of computer graphics where anyone can play around,” Levoy says. “The camera industry is not like that. It’s very secretive.”

While every digital camera has a computer inside, it’s usually locked in a black box. You can’t get in there and program it. Several hacking tools exist for liberating the code of particular cameras, but Levoy and his colleagues wanted to play around with settings without resorting to such measures. So Levoy and colleagues built the programmable Frankencamera.

Dealing with commercially available cameras “was just a painful experience,” says Andrew Adams, who worked with Levoy and is now at MIT. “So after getting sufficiently frustrated at the programming that exists, we decided to make our own camera.”

The Frankencamera started out as a clunky black thing built with off-the-shelf components (hence the “Franken”). But in the spirit of computer science, the camera is easy to program, running on Linux-based software. With a little effort, the camera can be made to, say, use gyroscope data to determine if it is moving when a picture is taken. If so, it can select the sharpest photo from a bunch that are taken, an application Adams calls “lucky imaging.”

Nokia was interested enough in the Frankencamera to help researchers make their computer code compatible with the Nokia N900. The researchers began using the N900 in the classroom and have been shipping it around the world to other academics in the field of computational photography.

“The first assignment was to replace the autofocus algorithm,” says Adams. “It was so cool; we gave them a week and they came up with better things than Nokia.”

One student took several pictures over circular objects from above and programmed the camera to average the pictures together, yielding an image that normally could be captured only with a much larger lens, says Adams. Several other manipulations have been explored, such as panoramic stitching, high dynamic range imaging and flash/no-flash imaging, which combines shots taken with and without a flash to create a photograph that displays the best of both. The Frankencamera team released its code in 2010, so anyone can add these capabilities to the Nokia N900.

The camera has also been set up for “rephotography,” the retaking of a previously taken photo, historic or otherwise. The camera looks for distinguishing features in a scene, such as corners, and directs the photographer with arrows to align the camera precisely, creating a second version of the original picture but in a new season or new time in history.

With all the new souped-up cameras rolling out, the dangers of shaky hands or poor lighting are rapidly becoming concerns of the past. And the ability to make a picture bizarre, or shocking, is now available to anyone with the right smartphone and app. But once Frankencameras and similar build-your-own devices are in the hands of enough people, the creative possibilities balloon. You name it, programmers will find a way to do it.

“There’s a catchphrase,” Adams says: “Computation is the new optics.”