Nothing new under the Sun

Archy has a great summary of the history of planetary discovery, which puts the current question of Pluto and plutons in perspective. Did you know how Pluto got its name? Hint: it was not after Mickey Mouse’s dog.

What Is Lab Lit?

What Is Lab Lit?From January 30, 2006, a look at the “new” genre and the hype around it…

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Essential Science Fiction

Essential Science FictionWhat is your list of essential science-fiction books? I composed mine back on December 27, 2005 and I still agree with myself on it. Click on the spider-clock icon to see the comments on the original post.

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Kevin in China #17 – Drinking liquor with a snake heart makes your eyes clear

A broken taxi, a mouthy snake, and a question about snake embryology.

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How to appeal to the Multiple Intelligences of Voters

How to appeal to the Multiple Intelligences of VotersThis review of Howard Gardner’s “Changing Minds” I wrote on July 4, 2004 on www.jregrassroots.org and re-posted it on Science And Politics on August 25, 2004, so the political implications are quite outdated….

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Books: “The Postman” by David Brin – chillingly current…

Books: 'The Postman' by David Brin - chillingly current...This review was first written on April 14, 2005…

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The Book Meme

The Book MemeThis was the first of several book-related memes I did, back on April 05, 2005. Follow the responses of people I tagged as well. And if you have not done this version yet, and you like the questions, then feel tagged and post your answers on your blog…

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Previewing Books on Blogs, and “Institutionalized” by Fred Smith and Joe Schmoe

<a href="Previewing Books on Blogs OK, this is not a re-post of one old post, but three. The first one, from December 17, 2005, introduces Institutionalized. The second one, from January 20, 2006, adds some more info about the book. Finally, the third one, from May 17, 2006, gives a paragraph-long review of the book within a bigger question – what should a blogger do when faced with a stack of books sent kindly by authors and publishers for preview? What should one do if one does not like the book? Under the fold….

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The Grand Centennial Rounds

The 100th edition of Grand Rounds is up on The Examining Room of Dr.Charles.

Triangle Bloggers Barbecue

If you are a blogger and you are in the Triangle area of North Carolina this Friday, I hope to see you at the Triangle Bloggers Barbecue. Sign up on the Wiki there if you know you can show up for sure.
Let’s have fun kicking off the Fall ’06 Triangle Blogger Season!

Obligatory Readings of the Day

Archy on how politicians try to create conventional wisdom and on parallels between Balkans and Iraq.
Mr.WD on a new moevement within Christianity – Postmodern Christianity (part I).
Publius on the NSA ruling: Part I, Part II, Part III. Lindsay disagrees with some of his points.
Lance on ‘conservative’ movies and the Western ideal of beauty and what it says about the person holding it.
Jill is back from trekking around the Balkans and has a good one up – Tradition, Family and Property.
Melissa on The Oldest Profession.
Amanda on Nunberg’s Talking Left and Projection.
Pam has a personal experience with the stupidity of the recent airline (Cinnabon) security and encounters Minds that need to be washed out with soap.
The surgeon who worked to save Kentucky Derby winner Barbaro from a broken leg will try to save an Erie Zoo Polar bear, reports Russ.
Echidne on covert enemies, the new CNN poll and the IRS.

Books: “Coming To Life” by Christiane Nusslein-Volhard

Several ScienceBloggers are reviewing Coming To Life today (see reviews by Janet, Shelley, RPM, Nick and PZ Edit: Razib has also posted his take), each one of us from a different perspective and looking from a different angle, so go read them to get the full scoop.
PZ Myers reviewed the book a few weeks ago. Someting that struck me was that PZ said that the book :

“….assumes nothing more than that the reader is intelligent and curious. Seriously, you don’t need a biology degree to read it!”

…while a reviewer, Edward F. Strasser (a math PhD whose hobby is reviewing books from this angle – how readable they are for laypeople) on Amazon.com states the opposite:

“I don’t think that a person who has never seen this material before is ready for this book, but I think that many people who need it for review will be OK.”

So, when I started reading the book I decided to try to empty my mind of all the knowledge I have and to read it like a complete lay-person. I wanted to see who is right – PZ or Strasser – and try to determine who is the real audience for the book.
First, I have to tell you that I absolutely LOVED the book. And that may be its biggest problem. The book will be appreciated the best by people like me – biologists with expertise in another field who want to brush up on their evo-devo (and just devo) and have an easy reference on the bookshelf. The book does absolutely great for people like that.
But, will it do the same for others? Developmental biologists do not have a need for it because they already know everything in it and 100 times more. But how about complete laymen, people with minimal formal science education but a keen interest in science, people who read popular science magazines, watch Discovery channel and read ScienceBlogs?
I’d say Yes, but very cautiously. In a way, the book is deceptive. Its small size and pretty cover art suggest a breezy read. But it is not. It is a textbook disguised as a non-fiction bestseller. The tone is a matter-of-fact, unexcited monotone. Trying to speed though it will be a disaster. Why?
A textbook on developmental biology would be an expensive, 1000-page, lushly illustrated avalanche of nitty-gritty details. Making the book small by eliminating a lot of that detail means that what remains is highly concentrated. Every sentence matters. Every sentence is a summary of a thousand papers.
There is no “filler” material, e.g., anecdotes and personal stories or interesting examples of, for instance, exceptions to the the rules in a strange species, or philosophical musings, kind of stuff that will let your focus wane every now and then without serious consequences to understanding. Only occasionally she slides in a little bit of history which is always a welcome change of pace on top of being very informative and placing the material in a historical context.
You need to slow down and read every sentence with concentration. Perhaps stop and think what it means every now and then. Sometimes you wish she has NOT omitted some of the details which may serve as a useful illustration of a big principle she is describing in that sentence or paragraph.
Several times I caught her using a technical word without explaining (or at least defining) it first. If you did not have Intro Bio recently, or are not generally well informed on basic genetics and molecular biology, that would throw you off, and make you rush to the back of the book to check the Glossary – something that breaks the flow of reading any book.
So, the book is great for people who have some biology background (at any level) but not much knowledge of developmental biology – people like sophomore biology majors. But how do you get them to slow down and read the book carefully? Well, use it as a textbook! For an Introduction to Development course. I am serious! It’s that good.
The instructor could spend time in class explaining the principles described in the book – a process which slows down the reading of the book. Then, each instructor is free to add as much or as little detail in lectures as the level of the course requires, plus cool examples, flashy images and videos, etc, and add a couple of more readings, e.g., scientific papers and reviews.
Heck, it could be used even for a General Biology class for science majors (e.g., a summer speed class). Genetics, development and evolution are the core of biology, so adding a couple of lectures (with additional notes or a similar book) on physiology, behavior and ecology at the end (and those can be built upon the edifice of genetics, development and evolution covered before), would work just fine in some contexts, eliminating the need for students (like mine, the adults) to buy huge expensive textbooks that only intimidate them with the wealth of detail. It would give the instructor more freedom to design a course well.
Why do I think that this book is better as a potential textbook than the usual texts? Apart from size, price, friendliness and giving the instructor greater freedom, I really like the way the material is explained.
From the very first sentence, and reinforced throughout the book, the message is that the cell is the smallest unit of life. Not genes. Cells. While most textbooks fall into the philosophically untenable habit-of-mind that “genes use cells to make more genes” or “cells are places where genes perform the work of life”, Nusslein-Volhard constantly explains stuff within the proper way of thinking – “genes are tools that cells use to change, to do their job within the organism, and to make more cells”. The shift is subtle. She rarely states it this directly and openly, but if you are reading the book specifically looking for it (as I did), you notice that the word-choice and the way of explainig things is always within this mode of thought. She also, whenever that is appropriate, never forgets to mention important influences of the internal and/or external environment on cells and tfe developing organisms.
The book also makes a gradual progression over levels. After basic introductions to evolution, heredity and molecular biology, she starts with the cell and how it uses genes to change its own and neighboring cells’ properties. As the chapters move on, there is less and less talk of genes and more and more talk of cells, tissues organs and whole organisms, ending with the return to evolution in an excellent chapter on Body Plans.
Understanding that most of the readers will be anthropocentric, she then devotes a chapter to the development and reproduction in those lousy lab animal models – humans.
The final chapter on controversial aspects of developmental biology and its practice – covering stuff like cloning, stem-cell research etc., is as calm and even-tempered (almost dry) as the rest of the book. More importantly, the conclusions given there are derived directly from the science described in the rest of the book, with no Culture-Wars code-words that can trigger automatical resentment on the part of readers that are involved in Culture Wars on one side or the other. Again, it provides the neccessary background that can be useful for a class discussion. And its dry, science-y tone is exactly what is needed for such a discussion.
So, if you are a biologist and you want to refresh and update your knowledge of development really fast and easy – get this book, it is better than any other in this respect.
If you are not a biologist, but have a keen interest and some background, get the book but do not expect to breeze through it in two hours. Do not be deceived by the small size and pretty illustrations Dr.Volhart drew herself. Give yourself a week to read this book, then read it slowly and with full concentration. Read that way, it is worth its weight in gold.
And if you are more interested in the “evo” side of evo-devo and a more future-oriented book (Coming To Life summarizes current knowledge with no speculations about the future), read “Biased Embryos and Evolution” (see my review) – the two books nicely complement each other.
My question to Dr.Nusslein-Volhard: Is it possible to turn Developmental Systems Theory into a useful experimental program and, if so, will that provide discoveries and insights that are lacking within the current paradigm?

Godidiots in the news again

Church Fires Teacher for Being Female:

The minister of a church that dismissed a female Sunday School teacher after adopting what it called a literal interpretation of the Bible says a woman can perform any job – outside of the church.
The First Baptist Church dismissed Mary Lambert on Aug. 9 with a letter explaining that the church had adopted an interpretation that prohibits women from teaching men. She had taught there for 54 years.
The letter quoted the first epistle to Timothy: “I do not permit a woman to teach or to have authority over a man; she must be silent.”
The Rev. Timothy LaBouf, who also serves on the Watertown City Council, issued a statement saying his stance against women teaching men in Sunday school would not affect his decisions as a city leader in Watertown, where all five members of the council are men but the city manager who runs the city’s day-to-day operations is a woman.
“I believe that a woman can perform any job and fulfill any responsibility that she desires to” outside of the church, LaBouf wrote Saturday.
Mayor Jeffrey Graham, however, was bothered by the reasons given Lambert’s dismissal.
“If what’s said in that letter reflects the councilman’s views, those are disturbing remarks in this day and age,” Graham said. “Maybe they wouldn’t have been disturbing 500 years ago, but they are now.”
Lambert has publicly criticized the decision, but the church did not publicly address the matter until Saturday, a day after its board met.
In a statement, the board said other issues were behind Lambert’s dismissal, but it did not say what they were.

Do I really need to comment on this?

Clock News

Three interesting press releases/news-reports today. Click on links to read the whole articles:
Daytime light exposure dynamically enhances brain responses:

Exposure to light is known to enhance both alertness and performance in humans, but little is understood regarding the neurological basis for these effects, especially those associated with daytime light exposure. Now, by exposing subjects to light and imaging their brains while they subsequently perform a cognitive test, researchers have begun to identify brain regions involved in the effects on brain function of daytime light exposure. The findings are reported by Gilles Vandewalle and Pierre Maquet of the University of Li ge, Derk-Jan Dijk of the University of Surrey, and additional colleagues and appear in the August 22nd issue of the journal Current Biology, published by Cell Press.
Our brain does not use light only to form images of the world. Ambient light levels are detected by our nervous system and, without forming any image, profoundly influence our brain function and various aspects of our physiology, including circadian rhythms, hormone release, and heart rate. These responses are induced by a special non-image-forming (NIF) brain system, which researchers have begun to characterize in animal models. In human studies, much work has focused on the effects of nighttime light exposure, but little is known about daytime responses to light. Especially mysterious are the neural correlates of these responses, and their temporal dynamics. Such issues are of significant interest given that daytime sleepiness is a major source of complaint in modern society and has considerable socio-economic implications.
In the present study, the researchers showed that a brief (21-minute) morning exposure to a bright white light increases alertness and significantly boosts the brain’s responses to an experimental test that requires attention only to sound. In a parallel neuroimaging analysis, this boost in alertness was found to correlate with responses in various areas of the brain, including regions of the cortex known to support performance on the auditory test. The regional brain changes were found to be highly dynamic, dissipating within a few minutes. These new findings therefore show that light exposure, even during the day, can quickly modulate regional brain function in areas involved in alertness and non-visual cognitive processes.

UM scientist sheds light on workings of internal clock:

Meredith specifically studied gates known as BK channels that control large flows of potassium out of the cell. Prior research suggested that BK channels were controlled by the core clock, so it made sense to Meredith that the channels might play some role in the generation of circadian behaviors.
To make the connection, Meredith, a self-described scientific jack-of-all-trades, brought a mixed bag of new scientific tools and techniques to an old problem.
The first step required her to combine genetic engineering with behavioral science. She engineered mice that had no functioning BK channels in their clock neurons, then watched how they acted. When exposed to light, the engineered mice behaved just like those with BK channels: They ran on their wheels at night and slept during the day. But when the engineered mice were kept in the dark they went haywire.
“We saw a very dramatic difference,” Meredith said.
Their strict schedule loosened and they roamed their cages and ran on their wheels at erratic times. Their daily amount of activity stayed about the same, but it was spread out more evenly over the 24-hour period.
Their strict schedule loosened and they roamed their cages and ran on their wheels at erratic times. Their daily amount of activity stayed about the same, but it was spread out more evenly over the 24-hour period.
Meredith had, for the first time, established a link between specific circadian behaviors in the mice and an ion channel on clock neurons.
But the jump from cellular structure to behaviors was a large one. She still needed to find out how her engineering had affected the intermediate step in the process: the electrical signaling in the brain. This phase of the study required her to switch gears and study the electrical properties of nerve cells.
She found that the clock neurons in her engineered mice generated signals different from those in normal mice. Moreover, the odd patterns of signaling corresponded to the odd patterns of behavior in the mice.
Meredith and her colleagues at Stanford had connected the dots between the BK channel and mice behavior patterns. In the engineered mice, the core genetic clocks seemed to be working fine, but the clock appeared to be unable to communicate well with the parts of the brains where actions such as wheel running were generated.
“The signal for time is no longer being transmitted to the legs,” Meredith said. “It’s like you have an actual clock and you put a piece of tape over it so you can’t see the dial anymore.”
The results of her study were published in June in the journal Nature Neuroscience. Her work appears to be the first to link a specific cellular structure in the clock neurons to specific circadian behaviors patterns they generate, said Roberto Refinetti, a psychologist at the University of South Carolina and editor of the Journal of Circadian Rhythms.
“The clock itself has been much-studied,” Refinetti said. “The novelty of this is being on the output side.”

Constant Lighting May Disrupt Development of Preemie’s Biological Clocks:

Every year about 14 million low-weight babies are born worldwide and are exposed to artificial lighting in hospitals.
“Today, we realize that lighting is very important in nursing facilities, but our understanding of light’s effects on patients and staff is still very rudimentary,” said William F. Walsh, chief of nurseries at Vanderbilt’s Monroe Carrel Jr. Children’s Hospital. “We need to know more. That is why studies like this are very important.”
Although older facilities still use round-the-clock lighting, modern NICUs, like that at Vanderbilt, cycle their lighting in a day/night cycle and keep lighting levels as low as possible, Walsh said. Also, covers are kept over the isolets that hold the babies in an effort to duplicate the dark conditions of the womb.
The finding that exposure to constant light disrupts the developing biological clock in baby mice provides an underlying mechanism that helps explain the results of several previous clinical studies. One found that infants from neonatal units with cyclic lighting tend to begin sleeping through the night more quickly than those from units with constant lighting. Other studies have found that infants placed in units that maintain a day/night cycle gain weight faster than those in units with constant light.
The research is a follow-up from a study that the McMahon group published last year which found that long periods of constant light disrupt the synchronization of the biological clock in adult mice. In all mammals, including mice and humans, the master biological clock is located in an area of the brain called the suprachiasmatic nuclei (SCN). It influences the activity of a surprising number of organs, including the brain, heart, liver and lungs and regulates the daily activity cycles known as circadian rhythms.

Why All Lard Is White

Why Piglets Shudder To Keep Warm:

Brown fat helps newborn mammals maintain their body temperature by burning fat, which converts into heat. The protein UCP1 (Uncoupling Protein 1) has a key role in this energy conversion, which takes place in the cell mitochondria.
No brown fat or UCP1 protein has been found in domesticated pigs, however. In their study, Berg and colleagues show that the UCP1 gene was shut down about 20 million years ago in an ancestor of the wild boar. They identified four different mutations, each of which would be sufficient to knock out the function of the protein.
This ancestor of pigs thereby lost the ability to use brown fat to maintain body temperature after birth. A reasonable explanation for this is that brown fat was not essential during a period in the evolution of pigs, in which they lived in a warm climate, says Leif Andersson, who directs the research team.
The ancestor of the domesticated pig, the wild boar, is the only pig that lives in cold climates. All other species inhabit tropical or subtropical climates. The wild boar has compensated for the loss of brown fat by a series of adaptations for survival in a cold climate. It is the only hoofed animal that builds a den when it is time to give birth see, and its young shudder to maintain their body temperature. In modern pig production, heat lamps are used to help the newborn piglets retain their body temperature.
The findings show that an important biological function can be lost if it is not vital to life during a period in the evolutionary history of a species; and that if the living conditions once again change, compensatory mechanisms can be developed. The findings we present are fully consistent with the theory of evolution. An important trait can be lost if it is not absolutely necessary to life during the development of a species, says Leif Andersson.

Books: “Ira Foxglove” by Thomas McMahon

This is not a re-post. This is a brand new book review.

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Books: “The Wimp Factor: Gender Gaps, Holy Wars, and the Politics of Anxious Masculinity” by Stephen J. Ducat

 FemiphobiaThis is not a real review – I never got to writing it – but it is about a book I mention quite often in my blog posts and think is one of the most insightful about the conservative mindset. Written originally on October 21, 2004:

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Reading Recommendations: Books about Clocks and Sleep

Reading Recommendations: Books about Clocks and SleepThis list, written on December 17, 2005, is still quite up-to-date. There are also some more specialized books which are expensive, and many of those I’d like to have one day, but I cannot afford them (though I have placed a couple of them on my wish list, just in case I see a cheap copy come up for sale):

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Books: “The Cultural Origins of Human Cognition” by Michael Tomasello, part II

CogBlog - Tomasello: Chapter 2 The review of the second chapter was written on September 06, 2005:

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Books: “The Cultural Origins of Human Cognition” by Michael Tomasello, part I

CogBlog - Tomasello: Chapter 1 The Cultural Origins of Human Cognition by Michael Tomasello was the first book (and still the only one so far) we were reading in the newly minted CogBlogGroup, a group of bloggers reading stuff about cognitive science. You can download the whole book in PDF or the first chapter only in html. This was the first of two parts (I never finished the book nor rerview!), originally posted on August 20, 2005:

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Books Around The Clock

Continuing with the five-day plan method of blogging, leaving the All Clocks All the Time behind us, we are starting the third week with a theme – Books Around The Clock.
Over the next five days, you will see both reposts (mostly in AM) and new posts (mostly in PM) about books. There will be straightforward book reviews. There will be NYRB-style reviews in which the book is just an excuse for me to go off on a rant. There will be Book Memes. There will be lists of books on various topics I recommend. And anything else you may recommend in comments or by e-mail.
Before we start, you may want to check out some stuff I posted here earlier, e.g., my reviews of Biased Embryos and Evolution by Wallace Arthur, Evolution’s Rainbow by Joan Roughgarden, George Lakoff’s Moral Politics and E.J.Graff’s What Is Marriage For? and Five Fists of Science by Matt Fraction and Steven Sanders.
Perhaps you can also see my versions of the Oldest Book Meme and One Book Meme and my choices of Science Books from my Childhood. Just keep checking out the Books category all week (and perhaps take a peek at the Books category on my old blog).
And if any of my SciBlings write about books this week, I will link to them here as well. Let’s have fun!

Obligatory Reading of the Day – liberal suicidal tendencies

I know, I know, David Brin is one of those “high-moral-ground”, fervently ideological, vehemently frothing at the mouth centrists, but he sometimes writes really good stuff. And this post is pretty good:

Now try this. Imagine a person who holds all of the correct views except one.
Suppose – on just that one issue – a person strongly takes the opposite view. Not quietly, but openly, and vigorously.
Now picture how that person would be received in most liberal gatherings.
What name would they be called?

Read the post. He may put it a little too harsh, but he is not wrong.

Welcome to the new SciBling!

Josh Rosenau has moved from his old Blogger blog to my virtual neighborhood here on Seed. Go check out the brand new version of Thoughts From Kansas!

Oh, yes there are atheists in foxholes!

Oh yes there are atheists in Foxholes!
In the latest Newsweek:

There are no atheists in foxholes,” the old saw goes. The line, attributed to a WWII chaplain, has since been uttered countless times by grunts, chaplains and news anchors. But an increasingly vocal group of activists and soldiers–atheist soldiers–disagrees. “It’s a denial of our contributions,” says Master Sgt. Kathleen Johnson, who founded the Military Association of Atheists and Freethinkers and who will be deployed to Iraq this fall. “A lot of people manage to serve without having to call on a higher power.”
It’s an ongoing battle. Just last month Lt. Gen. H. Steven Blum, chief of the National Guard Bureau, said, “Agnostics, atheists and bigots suddenly lose all that when their life is on the line.” Atheist groups reacted swiftly, releasing a statement that “Nonbelievers are serving, and have served, in our nation’s military with distinction!” The National Guard said it received about 20 letters objecting to Blum’s statement, and said his comments were “intended to clearly illustrate the positive spirit of camaraderie, human understanding and inclusion of our fine men and women in the National Guard.”
In the past several years, atheists have organized letter-writing campaigns against Katie Couric, Tom Brokaw, Bob Schieffer (who issued a public apology) and other news anchors for repeating the “no atheists in foxholes” line on TV. And on Veterans Day 2005, several dozen atheist veterans paraded down the National Mall bearing American flags and signs reading ATHEIST VETERAN–WE SHARED YOUR FOXHOLES! Johnson says atheists in the military face prejudice. “Before I got to be the rank I am I had to keep my head down and my mouth shut. I had commanding officers who made it clear that they wouldn’t tolerate atheism in their ranks.” Military leaders deny any discrimination. “Service in the military is open to people of all creeds and religions,” says Michael Milord, a lieutenant colonel in the Air National Guard. Officially, the Department of Defense considers atheism a creed like other faiths. New recruits can choose ATHEIST, AGNOSTIC, or NO RELIGIOUS PREFERENCE for their dog-tag identifications. And an atheist symbol, which resembles an atom, is among the dozens of “approved emblems of belief” that can appear on the headstones of fallen soldiers in military cemeteries. Would a soldier really die without faith? Bowling Green State University’s Ken Pargament, a professor specializing in the psychology of religion and coping, says: “If someone is a committed atheist, they’re likely to stay a committed atheist.”

How is that last sentence the answer to the question asked in the previous sentence? Duh?
You can read my answer to the question if there are atheists in the foxholes here
Update: Archy takes time to dissect this more fully…and more damningly to the dumb Lt. Gen. Blum.

Hangover Sunday in North Carolina

Tar Heel Tavern #78: A Light, Tasty Way to Beat a Hangover is up on Scrutiny Hooligans.

Abusing History, one carnival at a time

Carnival of Bad History #8 is up on Liberty and Power

All Ye Heathens….

Carnival Of The Godless #47 is up on Revolvo Inritus.

Strengthen your synapses…

…by giving your brain a workout – read The Synapse #5 at Retrospectacle

A fantastic picture of a polar bear exhaling underwater

From the NorthCarolina Zoo in Asheboro:
polar%20bear%20exhales.jpg
(Hat-tip: Russlings)

Listen to the Song of the Orca

Every now and then, David Niewert takes a break from discussing Far-Right White-Supremacist groups and writes a beautiful post on orcas (after all, Orcinus blog has been named after these beautiful whales). Here’s the latest.

The Power of the Thousand Electrodes

Mapping The Neural Landscape Of Hunger

The compelling urge to satisfy one’s hunger enlists structures throughout the brain, as might be expected in a process so necessary for survival. But until now, studies of those structures and of the feeding cycle have been only fragmentary–measuring brain regions only at specific times in the feeding cycle.
————–snip——————
In their paper, Ivan de Araujo and colleagues implanted bundles of infinitesimal recording electrodes in areas of rat brain known to be involved in feeding, motivation, and behavior. Those areas include the lateral hypothalamus, orbitofrontal cortex, insular cortex, and amygdala. The researchers then recorded neuronal activity in those regions through a feeding cycle, in which the rats became hungry, fed on sugar water to satisfy that hunger, and then grew hungry again.
“This allowed us to measure both the ability of single neurons to encode for specific phases of a feeding cycle and how neuronal populations integrate information conveyed by these phase-specific neurons in order to reflect the animal’s motivational state,” wrote the researchers.
By isolating and comparing signals from particular neurons in the various regions at various times in the cycle, the researchers gained insight into the roles neurons in those regions played in feeding motivation and satisfaction, they wrote. The researchers found that they could, indeed, distinguish neurons that were sensitive to changes in satiety states as the animals satisfied their hunger. They could also measure how populations of neurons changed their activity over the different phases of a feeding cycle, reflecting the physiological state of the animals.
Importantly, they found that measuring the activity of populations of neurons was a much more effective way of measuring the satiety state of an animal than measuring activity of only individual neurons in an area. And the more neurons they included in such populations, the more accurate the measure of that satiety state, they found.
Araujo and colleagues concluded that their analysis showed that while single neurons were preferentially responsive to particular phases in the metabolic status of the animal as it went through a hunger-satiety-hunger cycle, “when combined as ensembles, however, these neurons gained the ability to provide a population code that allows for predictions on the current behavioral state (hunger/satiety) of the animal by integrating information conveyed by its constituent units.”
“Our results support the hypothesis that while single neurons are preferentially responsive to variations in metabolic status, neural ensembles appear to integrate the information provided by these neural sensors to maintain similar levels of activity across comparable behavioral states,” they concluded. “This distributed code acting across separate hunger phases might constitute a neural mechanism underlying meal initiation under different peripheral and metabolic environments,” they wrote.

I’ve seen Miguel Nicolelis (one of the authors – the guy in whose Duke lab this was done) talk about some of his other research on rats (and monkeys) using the power of multielectrode recordings – on somatosensory perception. I did not know he was interested in hunger.
Leptin is a hormone that is associated both with hunger and with circadian rhythms. It provides a link between timing and the feeling of hunger, e.g., why you crave carbs (cereal and cookies) in the morning and fats (steak) in the evening. I’d love to know if they saw any influences in the time-of-day on their data.

Blog Potterica

Harry Potter Carnival #29 is up on The Pensieve (Edit: you can dig through the archives of the carnival there). I remember linking to the first two editions but then forgot about this cool carnival. Go check it out.

A long stroll through the geneticist’s garden

Mendel’s Garden #4 is up on The Innoculated Mind

This is probably an ancient joke, but it is new to me…

A kangaroo bounds round the Australian outback. Every now and then she stops and a little penguin climbs out of the kangaroo’s pouch. It looks awfully sick and promptly vomits.
Thousands of miles away in Antarctica, a little kangaroo sits in the snow shivering, crying and mumbling to itself, “Damned #$%^&* student exchange program!”

The Lost Highway Expedition

Visit the Balkans, join the Lost Highway Expedition (already in progress):

A massive movement of individuals will pass through Ljubljana, Zagreb, Novi Sad, Belgrade, Skopje, Prishtina, Tirana, Podgorica and Sarajevo. The expedition will generate projects, art works, networks, architecture and politics based on the found knowledge. Projects developed from the expedition will lead to events in Europe and the US.

Should we rewrite the textbook chapters on voltage-gated potassium channels?

Correct me if I am wrong, but I think this is really ground-breaking:
Study Finds Brain Cell Regulator Is Volume Control, Not On/off Switch:

He and his colleagues studied an ion channel that controls neuronal activity called Kv2.1, a type of voltage-gated potassium channel that is found in every neuron of the nervous system.
“Our work showed that this channel can exist in millions of different functional states, giving the cell the ability to dial its activity up or down depending on the what’s going on in the external environment,” said Trimmer. This regulatory phenomenon is called ‘homeostatic plasticity’ and it refers, in this case, to the channel protein’s ability to change its function in order to maintain optimal electrical activity in the neuron in the face of large changes within the brain or the animal’s environment. “It’s an elegant feedback system,” he added.
——-snip——–
Using this technique, postdoctoral fellow Kang-Sik Park revealed 16 sites where the protein is modified by the cell by via addition of a phosphate group. Further study–in which each of the sites is removed to reveal its role in modulation– followed by careful biophysical analyses of channel function by postdoctoral fellow Durga Mohapatra, revealed that seven of these sites were involved in the regulation of neuronal activity. Since each site can be regulated independently on the four channel subunits, the neuron can generate a huge (>1018) number of possible forms of the channel.
Using this mechanism, Kv2.1 channels are quickly modified, even mimicking the activity of other potassium ion channels. “The beauty of doing it with a single protein is that it is already there and can change in a matter of minutes. It would take hours for the cell to produce an entirely different potassium channel,” Trimmer explained.
Based on these results, Trimmer and his colleagues hypothesize that parts of the Kv2.1 channel protein interact in ways that make it either easier or harder for it to change from closed to open. The protein, they believe, can exist in either loose states that require low amounts of energy, or voltage, to change from one state to another or a locked-down state that requires lots of energy (high voltage) to open or close. The number and position of phosphate molecules are what determine the amount of voltage required to open the channel.

It just makes intuitive sense. It appeals to my aesthetic sense as well. And it is a great example of the power of evolution.
Potassium-Channel-2-2004.JPG

So, elephants actually run (leave the ground with all four feet at the same time)

Have You Ever Seen An Elephant … Run?:

Dr John Hutchinson, a research leader at the UK’s Royal Veterinary College (RVC), has already shown that, contrary to previous studies and most popular opinion, elephants moving at speed appear to be running. Now with funding from the Biotechnology and Biological Sciences Research Council (BBSRC) his team is using Hollywood-style motion capture cameras combined with MRI and CT scans of elephants to build 3D computer models of elephant locomotion to show the forces and stresses at work on muscles, tendons and bones.
The research team has been working with elephants at UK wildlife and safari parks and will shortly travel to Africa and Thailand to study wild animals. Fifteen temporary markers are placed on the elephants’ joints and the animals then move past a motion capture camera, recording at 240 frames per second, at varying speeds. Back in the lab the researchers can then use the footage to reconstruct the rotations of the elephants’ joints on a computer, creating a 3D stick model of the animal.
The computer models are being used to establish how limb structure relates to elephant locomotion and to determine finally if elephants really can run – or in scientific terms, at some point do they have all their feet off the ground at the same time? Dr Hutchinson said: “We are particularly interested how elephants coordinate their limbs and working out which joints contribute most to the length and frequency of their steps. In examining whether elephants truly run or not we need to understand what limits their top speed. Is it the tendons and muscles having to withstand the impact of 7 tonnes of elephant or is it something else?”

Read the whole thing. I love this kind of stuff! I remember when, back in the late 1980s, I first saw a study (from Bulgaria, I believe) done like this – of a horse jumping over a fence. Way cool!
Next step – how do elephants fly! Certainly you’ve heard the old true-life anecdote:
Two elephants are sitting on a tree. A third elephant flies by. The first elephant turns to the second elephant and says: “Hmmm, I bet her nest is close by”
0610_elephant.jpg

Happy Birthday Ogden Nash

The American poet Frederick Ogden Nash was born at Rye, New York on this day in 1902. After family finances prevented him from finishing even a year at Harvard, he struggled as a school teacher (a class of 14-year-olds caused too much stress), bond broker (he sold but one bond in 18 months, and that to his godmother), advertising copywriter, children’s book author (The Cricket of Carador sold only 900 copies), but finally thrived as an editor at Doubleday. He dashed off some very silly poetry to relieve office boredom, his boss suggested he send a few to the New Yorker where he was first published in 1930. He never was able to sell his more serious poetry, which forced him to write over 1500 pieces that amused us, and a little prose to quote.

An occasional lucky guess as to what makes a wife tick is the best a man can hope for, Even then, no sooner has he learned how to cope with the tick than she tocks.
Family: A unit composed not only of children, but of men, women, an occasional animal, and the common cold.
Happiness is having a scratch for every itch.
Middle age is when you’ve met so many people that every new person you meet reminds you of someone else.
People who work sitting down get paid more than people who work standing up.
Progress might have been all right once, but it’s gone on too long.
– All from Ogden Nash, 1902 – 1971
From Quotes of the Day
So, here is my mostest favouritest Nash poem – I Will Arise And Go Now
In far Tibet
There live a lama,
He got no poppa,
Got no momma,
He got no wife,
He got no chillun,
Got no use
For penicillun,
He got no soap,
He got no opera,
He don’t know Irium
From copra,
He got no songs,
He got no banter,
He don’t know Hope,
He don’t know Cantor,
He got no teeth,
He got no gums,
Don’t eat no Spam,
Don’t need no Tums.
He love to nick him
When he shave;
He also got
No hair to save.
Got no distinction,
No clear head,
Don’t call for Calvert;
Drink milk instead.
He use no lotions
For allurance,
He got no car
And no insurance,
No Alsop warnings,
No Pearson rumor
For this self-centered
Nonconsumer.
Indeed, the
Ignorant Have-Not
Don’t even know
What he don’t got.
If you will mind
The box-tops, comma,
I think I’ll go
And join that lama.
And now for my Balkan readers, the absolutely amazing translation of the poem by Dragoslav Andric which is about a million times better, more rhythmic and funnier than the English original:
Ustajem sad i idem
Cak u Tibet
Zivi lama,
Nema tata,
Nema mama.
Nema zena,
Nema deca,
jok mu treba,
Streptomeca.
Nema sapun,
Nema plakar,
Ne zna najlon,
Ne zna bakar.
Nema slager,
Nema rok,
Ne zna Presli,
Bitls jok.
Nema desni,
Nema zubi,
Ne zna pasta
Pa u tubi.
Voli sece
Kad se brije,
Bas ga kosa
Briga nije.
Ne zna sljoka
Kao neko,
Nema bonton,
Pije mleko.
Ne zna sta je
Klozmetika,
Nema kola
Da se slika.
Nema stampa
i te stvari,
Nepotrosac
To je stari.
Taj sebicnjak
Samo drema,
Nema pojam
Ni sta nema.
Zato, zarez,
Kazem svim,
Idem nadjem
Druzim s njim.

Random Quotes Meme

Yeah, I know everyone is doing it, but when I first tried I never got quotes that were really satisfying. But when PZ set up a random 5 from his own vault, I got an embarrasment of riches. So here are the first 5 I liked from there:
Creeds made in Dark Ages are like drawings made in dark rooms
[Joseph McCabe, The Story of Religious Controversy, 1929]
So far as I can remember, there is not one word in the Gospels in praise of intelligence.
Bertrand Russell
The kindly God who lovingly fashioned each and every one of us and sprinkled the sky with shining stars for our delight — that God is, like Santa Claus, a myth of childhood, not anything a sane, undeluded adult could literally believe in. That God must either be turned into a symbol for something less concrete or abandoned altogether
[Daniel Dennett, “Darwin’s Dangerous Idea”, p. 18]
There is one notable thing about our Christianity: bad, bloody, merciless, money-grabbing and predatory as it is – in our country particularly, and in all other Christian countries in a somewhat modified degree – it is still a hundred times better than the Christianity of the Bible, with its prodigious crime- the invention of Hell. Measured by our Christianity of to-day, bad as it is, hypocritical as it is, empty and hollow as it is, neither the Deity nor His Son is a Christian, nor qualified for that moderately high place. Ours is a terrible religion. The fleets of the world could swim in spacious comfort in the innocent blood it has spilt.
[Mark Twain, “Reflections on Religion”]
It is fear that first brought gods into the world.
[Petronius Arbiter, Satyricon]

Friday Weird Sex Blogging – I’ve Been Defeated

I had several ideas for today’s edition that I thought were really great, until I saw this. There is nothing I can write today that can get any better. I know when I am outcompeted and I bow to His Tentacled Majesty. I’ll try something better next week….

So, do you like “Five-Day Plans”?

Well, the first five-day plan, all-politics blogging, kinda happened all on Echidne of the Snakes where one post got 120+ comments (mostly nasty) while the same post here got 5 nice comments. So, you pretty much missed out on all the fun if you just came here.
The second five-day plan, all about clocks is now officially over. I could not resist, of course, jumping in with short posts on other topics every now and then, which was probably refreshing for those not too heavily into nitty-gritty chronobiology.
So, tell me, do you like 5-day plans or not? And if so, what should be the next week’s theme?
I was thinking about doing a week of book reviews since I have read a bunch of good stuff recently (and not so recently). As you know, I like to do book reviews NYRB-style, using a book review as a pretext and excuse to grind my own axes. So far, I have posted (or re-posted) only my reviews of Biased Embryos and Evolution by Wallace Arthur, Evolution’s Rainbow by Joan Roughgarden, George Lakoff’s Moral Politics and E.J.Graff’s What Is Marriage For? and Five Fists of Science by Matt Fraction and Steven Sanders.
I could re-post the old reviews of “Changing Minds” by Howard Gardner, “Collapse” by Jared Diamond, “The Postman” by David Brin, Max Barry’s “Jennifer Government”, Greg Bear’s “Darwin’s Radio” and Darwin’s Children”, “The Sex Lives Of Teenagers” by Lynn Ponton and “The Cultural Origins of Human Cognition” by Michael Tomasello. I could also re-post (and update) my “favourite” lists on politics, science and clocks/sleep.
Then, I could sit down and write about “Intuition” by Allegra Goodman, “Ira Foxglove” by Thomas McMahon, “Omnivore’s Dillema” by Michael Pollan, “Institutionalized” by Fred Smith and Joe Schmoe and”Holy Cows & Hog Heaven” by Joel Salatin. If I still had time and energy, I could go back in time and review books I read earlier but never reviewed, e.g., “The Wimp Factor” by Stephen Ducat”, “Marriage – A History” by Stephanie Coontz, “Republican War on Science” by Chris Mooney (I may want to wait until the paperback arrives, though), “Superpatriotism” by Michael Parenti, etc.
What do you think?

Daddy is Blogging….

Under the fold….

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Why hibernating animals occasionally wake up?

One of the several hypotheses floating around over the past several years to explain the phenomenon of repeated wake-up events in hibernating animals although such events are very energy-draining, is the notion that the immune system needs to be rewarmed in order to fend off any potential bacterial invasions that may have occured while the animal was hibernating:

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Evolution and Design class

Allen McNeill’s Cornell course on Evolution and Design is now over and the student papers have been posted online.
Dan comments on some of them.

Philosophical Green Animals

Carnival of the Green #40 is up on Camden Kiwi.
Philosophy Carnival 34 is up on El Blog de Marcos.
Friday Ark #100 (congratulations!) is up on The Modulator.

All-Clocks-All-Week is now officially over

I know most visitors do not read longer posts, especially not posts on arcane topics likeentrainment of circadian rhythms which filled this blog all week long.
But I wrote them for myself and everything else is profit. I wrote them because I wanted to hype myself for my own Dissertation writing. Even if no one reads those posts, I feel better having written them.
This whole exercise was quite instructive to me. Re-reading my old papers again, after 4-5 years made me see them in a different light. Compare, if you are interested, the way I described the data in my papers to the way I described them in blog posts! With a 20-20 hindsight, I now emphasize some things that I barely mentioned in the papers, while not paying too much attention to the ideas described at length in the papers.
When you just start out on some work and design a series of experiments, you live in that naive, megalomaniacal world in which you believe that all the experiments will work perfectly and the results will turn out exactly as you expect, confirming your brilliant new hypothesis.
A couple of years later, when all is done, you are feeling more than a little down. Several experiments did not work at all. Some worked as expected but the stats are not as clear-cut as you hoped for. Others worked fine but the results do not agree with your pet hypothesis. But data need to ger published so you sit down and explain them, although your heart has not completely changed your mind yet at the time.
But a few years later, bad experiments forgotten, it is easy to look at the work more objectively. Now I know not only what was published before, but also what was published after (and what I did subsequently and did not publish yet). I now know how the other people responded to my papers, who cited them and what for, and how the work slowly changed my own thinking on the topic. Now I look back at them and think – hey, they are not Science/Nature material but they are good, certainly not as bad as I thought they were back then.
I guess that is one part of the learning experience of graduate school – learning to live with a mismatch between expectations and reality and learn to cherish what you got.
Also, in a blog post, I could also give you behind-the-scenes story of how the paper came about in the first place, the true motivations for doing the work, exactly who did what (instead of just a line-up of co-authors), if there was ant competition or colaboration involved, how the work influenced our thinking long-term, and wild speculations that do not directly flow from the data but are only inspired by them.
We’ll get back to normal programming next week…. and of course some Firday Weird Sex Blogging later tonight.

Kevin in China #16 – It’s not easy to catch a swimming frog

Kevin is back in the field, catching herps with abandon…

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Chossat’s Effect in humans and other animals

Chossat’s Effect in humans and other animalsChossat's Effect in humans and other animalsThis April 09, 2006 post places another paper of ours (Reference #17) within a broader context of physiology, behavior, ecology and evolution.
The paper was a result of a “communal” experiment in the lab, i.e., it was not included in anyone’s Thesis. My advisor designed it and started the experiment with the first couple of birds. When I joined the lab, I did the experiment in an additional number of animals. When Chris joined the lab, he took over the project and did the rest of the lab work, including bringin in the idea for an additional experiment that was included, and some of the analysis. We all talked about it in our lab meetings for a long time. In the end, the boss did most of the analysis and all of the writing, so the order of authors faithfully reflects the relative contributions to the work.
What is not mentioned in the post below is an additional observation – that return of the food after the fasting period induced a phase-shift of the circadian system, so we also generated a Phase-Response Curve, suggesting that food-entrainable pacemaker in quail is, unlike in mammals, not separate from the light-entrainable system.
Finally, at the end of the post, I show some unpublished data – a rare event in science blogging.

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Happy second blogiversary to me.

No, not here, but I wrote my first post on my first blog on Wednesday, August 18, 2004.
2144 posts on Science And Politics
220 posts on Circadiana
76 posts on The Magic School Bus
498 posts on A Blog Around The Clock

StoryBlogging, AIDSblogging and more….

StoryBlogging, AIDSblogging and more[Slightly edited post from May 04, 2006] Collecting stories has become a really exciting endeavor lately. While writing down people’s stories has been done since time immemorial, on stone tablets, clay tablets and papyrus scrolls, the modern technology allows more people to record oral and written histories than ever before.
Everyone can now write, make an audio or video recording, and publish their life stories. We can tap into the wisdom of the elders and preserve their memories for posterity. The history will not be written only by winners, and, gasp, by semi-automated textbook-writing committees, but by many, many eye-witnesses of the events, each bringing in something personal, a slightly different perspective, a new anecdote, a curious fact or a piece of trivia.
It is really exciting to see how many people are investing much of their time and energy on making modern technologies available for recording history.
For instance, Junior League of Durham and Orange Counties’s REACH OUT TO SENIORS campaign is collecting stories by and about local senior citizens.
Dick Gordon’s new NPR radio show, The Story lets people tell their stories on the air, and saves them as podcasts on their WUNC page.
StoryCorps makes it easy for everyone to record and publish audio interviews. Log on to their site and find out if a StoryBooth will be close to you soon.
The Remembering Site and Our Story make it easy to publish your writings and pictures and helps you write your stories and biographies.
Finally, many people have used standard blogging platforms (as well as services like Flickr) to write their stories, publish their podcasts, photographs and videos. As the number of blogs increases exponentially, it is hard to keep track of the break-down of blog types, but I suspect that most blogs are still of the ‘personal journal’ type, .i.e. storyblogging.
Here in NC, Anton Zuiker is spearheading the effort to get people to record their memories and stories on blogs. Most definitely check out his Storyblogging blog for news and updates and for information on how to get involved.
What I am really interested in are travelogues – stories of people who have been abroad and stayed there for a while, not as tourists, but integrated into the local communities, perhaps doing some work there. Scientists doing fieldwork. Soldiers stationed abroad. Doctors Without Borders surely have stories to tell. Anyone who has ever experienced jet-lag and culture-shock.
A friend of mine is about to leave for Honduras as a part of the World Camp for Kids program. I tried to warm her up to the idea that many people would be interested in reading the stories about her experiences there and that a blog is the easiest, chepaest, quickest and most reliable medium to do so. I did not have much time, but I hope that the idea lingers in her mind and perhaps, one day, becomes a reality.
Another friend went to Ghana over two summers. The first summer, she did the research on the local women’s knowledge and understanding of AIDS and attitudes towards sex. The second summer, she utilized the results of her research to work on HIV/AIDS and sex education for local women. After graduation, she went to Lesotho for a year to do the same thing – education of local women about AIDS.
While she was gone, it was diffult to stay in touch. I thought a million times how great it would be if she had a blog that she could update every now and then, whenever she could get online. I’d like to hear her stories about the first impressions of Africa, the biggest culture shocks, the most interesting people she got to know there, the most common (as well as most surprising or outlandish) misperceptions women have about AIDS and about sex, about difference between Ghana and Lesotho, about changed perceptions on America and her own life, and much, much more.
I wish she could have run something like The Nata village blog, or, more ambitiously, the Blogswana project, in which one healthy and one AIDS pateint – both Botswanans – will be paired up and blogging together and for each other about Africa, AIDS and blogging.
Perhaps it is not too late. She is now back in the USA, but already gone ot of NC. I’ll try to persuade her to write her stories now – it is never too late and it does not need to be “fresh”. Better late than never.
Good memories, well written, are what is important. I’ll try to get her to start a blog and if she does I will link to it to let you know. Or, alternatively, I could get her to write a guest-post here every now and then and tap into my ready-made pool of regular readers.
[Edit: Don’t you just love adventures of Kevin in China?]
So, do you have a cool story to tell?