Tangled Skeptics

Tangled Bank #61 is up on Epigenetics News.
Skeptic’s Circle #42 is up on Immunoblogging.

Clock News

Melatonin improves mood in winter depression:

Alfred Lewy and his colleagues in the OHSU Sleep and Mood Disorders Lab set out to test the hypothesis that circadian physiological rhythms become misaligned with the sleep/wake cycle during the short days of winter, causing some people to become depressed.
Usually these rhythms track to the later dawn in winter, resulting in a circadian phase delay with respect to sleep similar to what happens flying westward. Some people appear to be tracking to the earlier dusk of winter, causing a similar amount of misalignment but in the phase-advance direction. Symptom severity in patients with seasonal affective disorder correlated with the misalignment in either direction.

Model of Internal Clocks Reveals How Jet Lag Disrupts the System:

Recent research suggests that every cell in the body actually has its own clock–liver cells prepare for digestion at particular times of day; patterns of hormone production and brain activity exhibit cyclic peaks and valleys, says Siegelmann.
“The circadian system is really fundamental, it affects our behavior, our physiology and emotions,” she says. “The clock organizes the whole body into a very nice dance, and it organizes people together into a larger social orchestra.”
The so-called “local clocks” have natural circadian cycles that range from 21 to 26 hours, says Siegelmann. They are synchronized by the SCN, but the pathways and mechanisms by which this coordination happens aren’t fully understood. Evidence has recently emerged that the SCN itself is compartmentalized. One clump of cells responds to and processes information about light, they then alert an intermediate group of cells that transmit the information to more peripheral components.
This hierarchy within the circadian system introduces a time-delay in getting the entire body adjusted to a new environment, suggests Siegelmann. The delay is based, in part, on the strength of the connections between the different parts of the SCN, between the SCN and the peripheral clocks, and on the differing rhythms of the local clocks, she says.
To explore the dynamics of the system and how it responds to disruption Siegelmann and Leise designed a model with parameters reflecting this hierarchical nature. The model accounts for the SCN’s light-responsive component, its intermediate component, and the various peripheral components. It incorporates behavioral data, physiological data and what’s known about differences in natural circadian rhythms in the peripheral tissues. In rats, for example, internal organs such as the liver and lungs take a relatively long time to become synchronized with the SCN.
Simulations of the model revealed certain properties about both the stability and adaptability of the system, Siegelmann says. The light sensitive compartment of the master clock responds quickly, providing flexibility, whereas the intermediate compartment of the SCN seems to act as a buffer against small perturbations in the cycle.
The simulations suggest that the system gets most out of whack when the master clock is shifted forward between five and eight hours. After such a large leap, it appears that the master clock actually overshoots the desired time. Then, following a slight delay, the intermediate component and some of the peripheral components overshoot as well, depending on their inherent circadian time and their connectivity with the master clock. For example, the peripheral components that already tend to lag actually try to catch up by backtracking, achieving a leap forward of six hours by delaying themselves 18 hours.

PIG at the altar

The fisking of Chapter 15 of Wells’ PIG is now up on Panda’s Thumb. It has something to do with church! Wonder, what has church to do with the “science” of Intelligent Design?!

War on Science coming near you!

My SciBling Chris Mooney, as part of his book-signing tour, is finally coming my way. So, if you are from these parts and are interested in the Republican War On Science, make sure to check October 28th and/or 29th on your calendar.

Millenium

I already told you that my daughter is crazy about cats as well as getting really good at photography. Occasionaly I break down and post pictures of cats (but never on Friday!) just because she took them. So, you have had the opportunity to meet Marbles and also Biscuit and even both of them together. And she managed to catch me on camera as well. Nobody else wants their pictures online, but we forgot the dog! So, here is the first ever online picture of Millie, our toy poodle. Her real name – Millennium – comes from the date of her birth: just a couple of weeks before Y2K when the civilization was supposed to evaporate. We all survived and here she is (and her age is easy to calculate and remember):
newest%20pics%20August%202006%20003.jpg

My picks from ScienceDaily

Ancient Raptors Likely Feasted On Early Man, Study Suggests:

A new study suggests that prehistoric birds of prey made meals out of some of our earliest human ancestors. Researchers drew this conclusion after studying more than 600 bones from modern-day monkeys. They had collected the bones from beneath the nests of African crowned eagles in the Ivory Coast’s Tai rainforest. A full-grown African crowned eagle is roughly the size of an American bald eagle, which typically weighs about 10 to 12 pounds.

Red Fish, Blue Fish: Distinctive Color Keeps Gene Pools Healthy:

Long-running evolutionary biology research on fish populations by UC Riverside scientist David Reznick has yielded new findings into how fish keep their gene pools healthy. Female fish tend to choose males with distinctive or rare coloration, thus ensuring that no one genetic line smothers out less common ones.

Dogs And Smog Don’t Mix: Pets In Homes May Lead To Increased Rates Of Bronchitis In Children:

A new study from USC researchers suggests that having a dog in the home may worsen the response to air pollution of a child with asthma.

Sunscreens Can Damage Skin, Researchers Find:

Are sunscreens always beneficial, or can they be detrimental to users? A research team led by UC Riverside chemists reports that unless people out in the sun apply sunscreen often, the sunscreen itself can become harmful to the skin.

How The Body’s T Cells React To Parasitic Diseases:

While scientists understood how T cells worked in certain kinds of diseases, one area has remained murky: disorders caused by protozoan parasites. Now, because of a study just published and led by scientists at the University of Georgia, researchers are closer than ever to understanding how T cells respond to parasitic diseases that kill millions each year.

Researchers Identify Antibiotic Protein That Defends The Intestine Against Microbial Invaders:

Researchers at University of Texas Southwestern Medical Center have identified a protein that is made in the intestinal lining and targets microbial invaders, offering novel insights into how the intestine fends off pathogens and maintains friendly relations with symbiotic microbes.

Pretty bird

American%20Goldfinch.jpgI have never seen these birds around here before, yet, over the last few days I saw tons of them all over the place. Where did they come from? Why do they seem to still be paired this late in the summer?
At first, I saw them flying, mostly from the car, and their flight is undulating, almost pulsating. Then, yesterday when I was walking the dog, I followed a pair around, from tree to tree, until I managed to get a good look at one of them for a good minute or so. I was surprised at how much larger they look in flight than when sitting still.
Anyway, after getting a good look, I went home and figured out that this is definitely American Goldfinch. I don’t have right kind of photo equipment to take a picture of such a small and flighty bird from a distance, so I am showing you a picture found on the Internet instead. A beautiful bird!

Bird Haiku

I And The Bird #31 is up on Migrateblog. Enjoy the poetry leading you to the best bird-writing on the Internet.

Happy birthday, Mother of Frankenstein

Mary%20Shelley.jpgMary Wollstonecraft Shelley was born on August 30th, 1797. She is very old now, but a team of mad scientists is working on resurrecting her with jolts of electricity.

It’s very much a sunrise!

Joe Lieberman’s communications director, Dan Gerstein, claims the sun rises in the West. Seriously. And will not back down. What more proof you need to know that Lieberman is a Republican, waging his own “independent” war on science in hope of appeasing Inhofe & Co. all in the spirit of moderaiton and bipartisanship?

Another nice thing about the beginning of the school year

Now that the school has started, we (meaning ‘ScienceBloggers’) are getting feedback messages from science teachers who were able to buy supplies for their classes because you, our readers, pitched in back in June and donated mountains of money through the DonorsChoose program.
I want to thank you all again for doing such a good deed. And, as far as I can see, none of us has removed the DonorsChoose button from our sidebars, so you can always add some more to the science teaching projects of your choice.
P.S. The first note I got very early and do not have it any more in my mailbox The last note I got is this:

Dear Coturnix,
Thank you very much for the DNA and genetic kits. Working in Los Angeles has brought some difficulty. There are not many tools that we can use in the middle school that keep projects hands-on and keep the students engaged and stay within the standards of the subject matter. My administrator could not justify this purchase. I think he had no idea what really came out of doing these labs. Again I want to thank you. I will enjoy teaching this subject area with these new materials.
Sincerely, Donna Taylor
Curtiss Middle School

The Clock Metaphor

Chad wrote a neat history of (or should we say ‘evolution of’) clocks, as in “timekeeping instruments”. He points out the biological clocks are “…sort of messy application, from the standpoint of physics…” and he is right – for us biologists, messier the better. We wallow in mess, cherish ambiguity and relish in complexity. Anyway, he is talking about real clocks – things made by people to keep time. And he starts with a simple definition of what a clock is:

In order to really discuss the physics of timekeeping, you need to strip the idea of a clock down to the absolute bare essentials. At its core, a clock really has only one defining characteristic: A clock is a thing that ticks.
OK, I’m using a fairly broad definition of “tick,” here, but if you’ll grant that leeway, “ticking” is the essential property of clocks. In this context, “ticking” just refers to some regular, repetitive behavior that takes place in a periodic fashion.

This reminds me that a “biological clock” is a metaphor. A useful metaphor, but a metaphor nonetheless (and just like metaphors of cellular machinery are taken literally by Creationists, they have been known on occasion to talk about circadian clocks as if they had real wheels and cogs and gears!).
I want to stress that the clock metaphor has been very useful for the study of biological rhythms. Without Pittendrigh’s insight that cycles in nature can be modeled with the math of physical oscillators, we would be probably decades behind (unless someone else of authority in the field at the time had the same insight back then) in our understanding of the underlying biology. Just check how useful it was in the entire conceptualization of entrainment and photoperiodism. The Phase-Response Curve, based on the math of physical oscillators, is the Number One tool in the chronobiological repertoire.
But, just as most people in the field take the clock metaphor for granted and without much thinking, there have been a few people who questioned its utility for some areas of research. For instance, for the study of biological rhythms in nature within an ecological and evolutionary context, Jim Enright proposed a metaphor of an audio-tape set on continuous play (Enright, J.T. (1975). The circadian tape recorder and its entrainment. In Physiological Adaptation to the Environment (ed. F.J.Vernberg), pp. 465-476. Intext Educational Publishers, Ney York.). Only a dozen or so publications since then took him seriously and tried to apply this concept. Today, in the age of CDs and iPods, who even remembers audio tapes?
While fully utilizing the utility of the clock metaphor and applying it myself in my own work, I was always cautious about it. Aware that it is a metaphor, I always wondered if it constrains the way we think about the biological process and if we may miss important insights by not thinking in terms of other possible metaphors.
While far from mature, my thinking is that different metaphors apply best to different areas of research and different questions. While the clock metaphor is great for understanding the entrainment of the circadian system (including whole organism, tissues and individual cells) and photoperiodism, and Enright’s endless tape (or some modern substitute) may be useful for ecological studies (including temporal learning and memory), other angles of study may require other concepts.
For instance, I think that the study of what goes inside the cell can benefit from a different metaphor. Studying the molecular basis of circadian rhythms may best be done by utilizing a Rube-Goldberg Machine metaphor: event A triggers event B which starts process C which results in event D….and so on until the event Z causes the event A to happen again. If that last step is missing, it is not a circadian rhythm – it is more akin to an hourglass clock in which something outside of the system needs to start the process all over again.
For studying the outputs, i.e., how the circadian system orchestrates timing of all the other processes in the body, the metaphor may have to fit the organism. An ON-OFF switch is the best metaphorical description of the clock system in (Cyano)bacteria, where there are only two states of the system: the day state and the night state. For something a little bit more eukaryotic, a relay may be a better metaphor (more than two, but not too many states). The metaphor of a rod in car engines (how are those called in English and do modern cars even have those any more?) that times the opening and closing of cylinders would be fine for fungi and plants and perhaps some invertebrates.
But I had a hard time coming up with a decent metaphor that could apply to complex animals, like us. So far, the best I could come up with is the barrel of a Player Piano. Many little knobs on its surface determine when each note will be played. If you make the barrel rotate slowly and the song lasts 24 hours, then outputs from circadian pacemakers are knobs and the target organs (and peripheral oscillators in them) are those long prongs that make music. Can you think of a better metaphor?

Animal Husbandry in Limbaugh-world

Rush thinks one needs to slaughter a cow in order to get butter. And he blames liberals and the UN for being a fat idiot.

Liberals at Home

Carnival of the Liberals #20 is up on The Greenbelt – the next one will be in two weeks on Archy.
The latest Carnival of Homeschooling is up on Category Five – the next one will be next week on Why Homeschool.

Parasite of my parasite is not my friend

Blogging on Peer-Reviewed Research

Parasite of my parasite is not my friend
Re-post from May 17, 2006, under the fold…

Continue reading

I like my son’s new science textbook

The school has started and I have not yet met my son’s teachers, but he brought home his science textbook yesterday. Of course I had to take a look….and I really liked it! It is North Carolina Edition of McDougal Littell “Science” for 8th grade.
While I am still stunned that all of science is bunched together this late in schooling (I had physics, chemistry, earth science and biology as separate subjects from 5th through 12th grade every year), but at least the way this is bunched looks good. It is divided into five units, each taking, I guess, about two months to cover. The first unit is earth science, second is biology, third is oceanography, fourth is chemistry and fifth is again biology.
The earth science unit covers structure of Earth and plate tectonics; the geological time scale, rocks and fossils (connection to biology); and natural resources, including energy sources from oil to wind power.
The water unit covers water cycle, fresh water, frozen water and underground water; fresh water as a resource; ocean systems, currents, waves and tides; and oceanic environments (connection to biology) and resources.
The chemistry unit covers atomic structure, elements and the periodic table; chemical bonds and compounds; chemical reactions and energy; and carbon-based molecules (connection to biology).
The second biology unit covers the cell structure and function; biochemistry, energy and membrane transport; cell division; growth, development and health; and bacteria, viruses and protists.
But it is the first biology unit that I was really interested in, as it covers evolution, classification and population ecology. I have to say that I was very impressed with the evolution chapter. It is long, it is clear and explains evolution very well. It explains the scientific method, defines the scientific (as opposed to colloquial) meaning of ‘theory’, tells the story of Charles Darwin, and explains natural selection in a nice, easy-to-grasp way. Nothing wishy-washy about it.
I am just as happy with the classification and ecology sections as well, except that I am not so sure about their continued use of the Six Kingdoms division of Life – is the Three Domains system still that new and controversial, or did the authors think that the old division is easier to teach?
I particularly like the long chapter on evidence for evolution. It is divided into three parts: fossil evidence, biological evidence (i.e., comparative embryology, anatomy, physiology and behavior) and molecular evidence. For the latter, they printed a sequence of a gene, placing the human and mouse versions of the same gene one below the other and highlighting nucleotides that differ. When I looked closely, I realized they chose to use the sequence of Clock gene! I felt right at home. That sequence has been known for only about ten years now. We certainly did not know anything about this back when I was in school.
I’ll have to get in touch with the science teacher to see how closely the curriculum follows the book – I’ll be very happy if it does. At least here in Chapel Hill there should be no fear of any parents complaining about evolution for dogmatic reasons.

Fido, get off the bed!

Do dogs get jealous? At just the most inopportune moments?

Periodic Table of SciBlings

If you are confused by the sheer number of ScienceBloggers and need to know who is who and what everyone writes about, you should check the periodic table of SciBlings. Then, check out more detailed descriptions of some of the blogs and keep checking in the following days for the descriptions of others. A graphic, looking just like a real periodic table may be in the making soon…

Slaughtering the PIG continues….

Mark Perakh debunks Chapter 16 of Jonathan Well’s poor excuse of a book. The chapter is on alleged new “Lysenkoism” in today’s American science, which has nothing to do with historical Lysenkoism.

Grand Green Education

Carnival of the Green #42 is up on The Disillusioned Kid.
Carnival of Education #82 is up on Thespis Journal.
Grand Rounds, V. 2, No. 49 is up on Protect the Airway.

Obligatory Reading of the Day – Postmodern Authoritarians

Mr.WD continues with his series on “Postmodern” Christianity – here is It’s still that old time religion, Part III.
Sara Robinson continues her series on authoritarians: Tunnels and Bridges, Part III: A Bigger World

Bloggers matter….

…..and smart politicians know this.

So, dolphins are dumb and manatees are smart?

Yesterday, we were putting down media reports on a study that purports that dolphins are not intelligent despite behavioral studies and big brains. Today, NYTimes has a much better article arguing that manatees, despite their small brains, are more intelligent than previously thought.
It is a longish article but well worth reading. The idea is that manatees don’t have too small brains, but overlarge bodies, and, since they are herbivores with no prey or predators, they do not need to reserve vast portions of their brains for tackling hunting and defense.

Brain size has been linked by some biologists with the elaborateness of the survival strategies an animal must develop to find food and avoid predators. Manatees have the lowest brain-to-body ratio of any mammal. But, as Dr. Reep noted, they are aquatic herbivores, subsisting on sea grass and other vegetation, with no need to catch prey. And with the exception of powerboats piloted by speed-happy Floridians, which kill about 80 manatees a year and maim dozens more, they have no predators:
“Manatees don’t eat anybody, and they’re not eaten by anybody,” Dr. Reep said.
But he also suspects that rather than the manatee’s brain being unusually small for its body, the situation may be the other way around: that its body, for sound evolutionary reasons, has grown unusually large in proportion to its brain.
A large body makes it easier to keep warm in the water — essential for a mammal, like the manatee, with a glacially slow metabolism. It also provides room for the large digestive system necessary to process giant quantities of low-protein, low-calorie food.
————————–snip——————————–
Manatees have a relatively thick cerebrum, with multiple layers that may, Dr. Reep suspects, indicate complexity despite a lack of folding.
In any case, he said, brain convolution “doesn’t seem to be correlated with the capacity to do things.”
More to the point, intelligence — in animals or in humans — is hard to define, much less compare between species, Dr. Reep said. Is the intelligence of a gifted concert pianist the same as that of a math whiz? Is a lion’s cunning the same as the cleverness of a Norwegian rat?
The manatee is good at what it needs to be good at.

The rest of the article focuses on manatees’ sensory capabilities, especially the somatosensory system. Manatees have vibrissae (long hairs, usually seen only around the faces of animals like cats and dogs), which are thought to be involved in the sense of touch, spread all over the body. The article incorrectly states that the only other mammal with vibrissae all over the body is rock hyrax. There is another one, though, which is much better studied in this regard – the naked mole-rat.
Also, the article states that manatee is unique among mammals in the ability to hear infrasound. That is also wrong – a lot of mammals, especially large mammals are capable of hearing infrasound. The best studied are elephants and whales, but it was also described in giraffes (von Muggenthaler, E., Baes, C., Hill, D., Fulk, R., Lee, A., (1999) Infrasound and low frequency vocalizations from the giraffe; Helmholtz resonance in biology, invited to the Sept. 2001 AZA conference, presented at the regional Acoust. Soc. Am. conference 2001.) and rhinos, while the infrasound vocalizations were made from okapis, tigers, horses and cows, as well as in some non-mammalian vertebrates, including crocodiles and perhaps some birds.
So, in light of our discussion yesterday, what do you think?

Call for action!

Previously unopposed, “…the most notorious creationist on the Ohio State Board of Education, Deborah Owens Fink, has a challenger in the Novemeber 7th election.” The election is non-partisan and the serious challenger is Tom Sawyer. You can get all of the details from Ed Brayton (as well as additional views by Chad, John and Kevin). Ed writes:

“Sawyer is the former mayor of Akron, a former state legislator and an 8 term US congressman from Ohio. Sawyer’s bonafides for a board of education seat are impressive. He is a former school teacher, and husband of a school teacher. He was the chairman of the House Education Committee during his time in the state legislature of Ohio, and was a member of the education committee in the US House of Representatives as well. So this is a guy who brings an enormous amount of experience to the job, which has Owens Fink scared.”

So, this is a good opportunity to replace the Queen of Darkness with a serious person, and thus ensure that kids in Ohio get served education instead of indoctrination.
What can you do to help?
Visit Tom Sawyer’s campaign website, where you can get informed, volunteer to help if you live in Ohio, or donate to the campaign if you live elsewhere. This is a fight worth fighting and let’s do everything we can to help Sawyer get elected.

Science Blogging – what it can be

Publishing hypotheses and data on a blogFrom quite early on in my blogging endeavor, I was interested in exploring science blogging, what it is, what it can do, and what it can become. So, check out some of my earliest thoughts on this here and here.
Then, over about a month (from April 17, 2006 to May 17, 2006) I wrote a gazillion posts on this topic, and many science bloggers chimed in in the comments or on their own blogs. The repost of all of them together is under the fold. Check the originals (and comments) here:
April 17, 2006: Publishing hypotheses and data on a blog – is it going to happen on science blogs?
April 20, 2006: Blogs as cited references in scientific papers
April 20, 2006: More on publishing data on blogs
April 23, 2006: Even more on science online publishing
April 25, 2006: And even more on science online publishing
April 30, 2006: Social networking for scientists
May 05, 2006: Science Blogging
May 11, 2006: Free online science publishing
May 17, 2006: Publish in Open Access Journals if you want to get cited!
And I have never fogotten it – check out this, this and this. So, let’s start this topic all over again!

Continue reading

The Republican War On Science

RWOS%20cover.jpgMy SciBling Chris Mooney, the first science blogger I ever discovered (and whose blogroll let me into the scienceblogging world) is the author of one of the most important books of last year, The Republican War On Science.
I have read the hardcover as soon as I got it (and my copy was shipped in the first batch) and intend to read the paperback as soon as it arrives in my mailbox – which should be today or tomorrow as the book started shipping yesterday. Until your own copy arrives in the mail (and it will be soon, of course, as you are about to order it), you should check out the book homepage where you can learn more about the book, read the new Introduction which explains how much difference there is between harcover and paperback versions, you can read an excerpt and see if there will be a book-signing event in your town this fall.
So much has already been said about the book and so many reviews have been published, I never managed to find my own angle to write a review myself. Perhaps reading the new edition will give me an inspiration for an outrageous rant in the near future!

Marbles

And here’s the kitten:
kitty%20pics%20August%202006%20021.jpg

Update on Life

Summer is officially over. Kids are back in school. I am pretty much a stay-at-home-Dad these days and this is even more obvious during breaks in the school calendar.
And we certainly had a great summer, starting even before school ended, with our trip to New York City. We went to the pool a lot and generally had a nice laid-back family time together.
Coturnietta spent a week in a science-technology summer camp, then ran off to the beach with her cousins and my mother-in-law for a week. She read a bunch of books (all with cats as main characters – she is a huge cat lover). She had such a good time this summer, she was not that excited about school starting again. She has the best teacher in the school this year, the same one my son had three years ago. We have great communication with the teacher so we are looking forward to a good school year for her.
She has also mastered the use our digital camera, taking pictures mostly of our cats (you can see two of those in other posts tonight). Her birthday is coming up in a couple of weeks and, if we can afford it, we want to buy her a digital camera of her own.
Coturnix Jr. started the summer with some math-advance algebra school and, unfortunately, spent his birthday in the ER (don’t ask) while at the beach. He did not get to see his friends over the summer as much so he is much more eager to go back to school. So far, I have not met his teachers, but he says he likes them all. The language arts teacher he was dreading suddenly decided to retire so he had a big sigh of relief.
Mrs. Coturnix quit smoking a couple of months ago and is doing great with it. Still, all those night shifts in the ICU are making her tired.
As for me, apart from having a great time with my kids all summer, managing to read a couple of books, and enjoying the community spirit here at Seed ScienceBlogs, the end of summer also gave me a renewed enthusiasm about finally finshing my Dissertation. Blogging helped – it brought me an offer to use space where I can write in peace in quiet. It is in a corner of a computer lab which is mostly devoid of people. The computer (according to my specifications) has been isntalled and, hopefully tomorrow, all my strange old software will be properly installed on it and working fine so I can get started on making hundreds of grapsh that are still missing from the thesis.
Taking such a long break from writing was not all bad. Now that I am thinking about my data again, with a fresh eye, I am seeing new things and coming up with new interpretations. I am looking forward to tackling the stuff again. I also have to fill a little gap in literature (2004-2005), so if I read something interesting, that may result in a cool blog post.
Due to renewed effort at thesis writing, I may blog a little less – perhaps 5 instead of 10 posts a day! But I’ll try to make those posts good. I have a couple of dozen ideas of topics I’d like to tackle soon, so those posts will keep coming. Also, November is coming closer, so there may be not just more chronobiology but also more politics here in the near future.
Unfortunately, this time of year always poses the same problem – summer is expensive! I get little or no teaching over the summer. Kids need to be fed, taken places and entertained. They both have their birthdays. And then there is the Back To School shopping for necessities, followed by our anniversary (no presents – just a night out).
So, we are in a big hole. I have squirreled away just enough to cover the next rent, and went to the grocery store and filled the fridge. I have already milked my mother and mother-in-law out of everything they had and there is nothing left for any other bills. I am afraid that power, water, telephone and internet may get cut off by the end of the month and there is nothing I can do about it. So, if you are in the Triangle area and know of a flex-time job, let me know. Or if you’d rather hit the PayPal or Amazon button down on the bottom of the sidebar, I’d appreciate it as well. I hate begging like this, but I see no other option. Thank you.

Biscuit

My daughter is getting really good at photography. Here is one from her recent set of pictures – our older cat, Biscuit:
P1010082.JPG

Happy blogiversary!

Mike’s wonderful blog 10,000 Birds is three years old. Go say Hello.

Who put “Judeo” in “Judeo-Christian”?

Certainly not Jews.

The Secret is Lies

In the ongoing series of fiskings of Jonathan Wells’ PIG book over on Panda’s Thumb, Andrea Bottaro has posted his verbal destruction of Chapter 9.

Brain in a Spin

Encephalon #5, the NeuroCarnival, is up on Developing Intelligence

Kevin in China #18 – a mandarin rat, another mystery frog that is NOT in the Atlas of Amphibians of China, and the Chinese-speaking Godzilla

Well, nobody in the comments here or here could help Kevin identify the mystery frog yet (if you are a herpetologist or fancy being one, take a look) and now Kevin caught yet another, even more mysterious frog. Can you help him identify it? Leave a comment here if you recognize what frogs are these.
Anyway, if you are fan of the series of adventures of Kevin in China (and if not, you should start the series from the beginning – you WILL get hooked), the new field report is under the fold.

Continue reading

Lithium, Circadian Clocks and Bipolar Disorder

Blogging on Peer-Reviewed Research

Lithium, Circadian Clocks and Bipolar DisorderYou probably realize by now that my expertise is in clocks and calendars of birds, but blogging audience forces me to occasionally look into human clocks from a medical perspective. Reprinted below the fold are three old Circadiana posts about the connection between circadian clocks and the bipolar disorder, the third one being the longest and most involved. Here are the links to the original posts if you want to check the comments (especially the first comment on the third post):
January 18, 2005: Clocks and Bipolar Disorder
August 16, 2005: Bipolar? Avoid night shift
February 19, 2006: Lithium, Circadian Clocks and Bipolar Disorder

Continue reading

Katrina blogswarm

If you write something related to Hurricane Katrina today (or have already done so recently), let Shakespeare’s Sister know so she can include your link in the Big Anniversary linkfest.

Dolphins Are Intelligent!

Where does one start with debunking fallacies in this little article? Oy vey!

Dolphins and whales are dumber than goldfish and don’t have the know-how to match a rat, new research from South Africa shows. For years, humans have assumed the large brains of dolphins meant the mammals were highly intelligent.

No, we knew dolphins were smart millenia before we ever looked at their brains. The ancient Chinese knew it. Aristotle knew it. And the idea that brain size has anything to do with intelligence is, like, sooo 19th century.

Paul Manger from Johannesburg’s University of the Witwatersrand, however, says it is not intelligence that created the dolphin super-brain — it’s the cold. To survive underwater, these warm-blooded animals developed brains that have a lot of insulating material — called glia — but not too many neurons, the gray stuff that counts for reasoned thinking.

Wow! Since when are glia “insulating material”? A few years ago, for my Neuroscience class, I had to remember at least 10 functions of glia – not one of them having anything to do with insulation, or even structural support. It’s all about function – neurons and glia work together to process information. Anyway, I will blame this on the stupidity of the reporter as I doubt that anyone with such archaic ideas would ever be allowed to dissect a dolphin and publish a study in a decent journal.

Yet while dolphins aren’t as smart as people tend to think, they are as happy as they seem. Manger said dolphins have a ”huge amount” of serotonin in their brains, which is what he described as ”the happy drug.”

Sure, if you get your science from Cosmo and Glamour. Do I really have to start listing all the functions of serotonin now? Or try to define “happiness” in such simplistic terms that it can be explained with a single chemical?
It is not quite clear, but it appears that Alon Levy agrees with the study. But Lindsay is having none of it. She cites the self-recognition paper as well as some personal testimony of the researcher who did that study. When that paper came out I was teaching a “Readings in Behavioral Biology” graduate seminar and all the neuro faculty showed up for class and tried valiantly to destroy the paper – with no avail. It is good.
Dolphins are darn smart. They play (check this pdf). They have complex communication and complex social interactions.
So, how does this kind of argument ever show up? Because of anthropocentrism. Two types of anthropocentrism, to be precise.
First, the concept of “intelligence” is often defined in human-like terms. If an animal can do stuff we do, it is deeemed smart. If it can be easily trained like our immature offspring can, it is smart. If it can talk, it is smart. If it builds structures, it is smart. BS. Intelligence has to be defined from the vantage point of that species: what makes ecological and evolutionary sense for that species to be able to do. Bees are smarter than ants because they have a more sophisticated ability to orient in space and time, not because they speak English, French and Chinese.
Now, don’t get me wrong now. Since we are intelligent, looking for intelligence in other animals may benefit from comparison to humans. The trouble is, people go for specifics of human capabilities, instead of a general idea what intelligence is.
Writing “Hamlet” is an ecologically relevant ability for humans. It kept old Will fed and clothed for a few months, after which he wrote the next play. Why would an insect need to write theater plays? It is not ecologically relevant to it. It does not aid survival and/or reproduction.
Intelligence is the ability to learn fast and learn a lot of pieces of information relevant to one’s ecology. It is the ability to hold many of those pieces in one’s mind simultaneously, to juggle them and analyse them and notice patterns. It is the ability to play with that information, to get new ideas and test them, to note and remember the results of those tests. It is the ability to use this novel informaiton to invent novel behaviors – doing different stuff at different places at different times. In short, intelligence is the ability to do science! Behavioral flexibility is the hallmark of intelligence – not the specific types of behaviors.
The second anthoropomorphism considers the underlying anatomy. Why should unrelated species of high intelligence have brains similar to us? They evolved their high intelligence at different times, in a different lineage, with different raw materials to work with, and under different ecological pressures, for different purposes.
Many birds are very intelligent – but in their own way. Clarke’s Nutcrackers, African Grey Parrots, pigeons, and most corvids (ravens, crows, jays) are highly intelligent creatures with huge capabilities for episodic memory (remembering spatial and temporal aspects of personal experiences), play, problem-solving, spatial orientation and perhaps even insight (planning for the future). And their brains look nothing like ours.
Octopus is a very smart animal. Its brain looks nothing like ours.
Macs and PCs can do all the same stuff (roughly), but look nothing like each other under the hood. Many kinds of harware can run the same kinds of software and do same kinds of things, so why should brains have to be all built the same way in order to make an animal “intelligent”?
So, leave the dolphins alone, at least until the Startide Rising.
Addendum: I forgot to note that glia are not white matter. Axons are white matter while neuronal bodies are grey matter. Glia surround both. It is the color of Schwann cells (a type of glia) that makes axons look whitish.
Thus, more grey matter means more neurons. More white matters means more connections. What is more important: gazillions of scattered cells, or the complexity of their connections? I’d say connections.
Addendum II: Dave Munger wrote a valid criticism of what I wrote here (and somehow I missed his earlier post on this subject):

I agree that intelligence is tremendously difficult to define, but I’d suggest that the perspective of an individual species is a poor place to start. Based on that notion, every organism can be said to be intelligent, because every organism is highly adapted to its environment. When we say an animal is “intelligent,” we’re defining intelligence from our own perspective: the point is to identify animals that are similar to ourselves.

I’m not sure that the point is to identify animals that are similar to ourselves, but even if it is, similar in what way? The general mental capabilities (that we still need to define) or specific capabilities (which I argued here against)?
As for looking at each species individually, I agree that it is impossible to do it in isolation, but eahc species can be compared with other species in its own group, e.g., birds with birds, insects with insect, and then broader, all with all. If we define, provisionally, intelligence as fast learning, high processing power and flexibility of behavior, then we can compare species without looking at specific items that are learned, specific informaiton that is processed and specific behaviors that are flexible. For some species, being inflexible is a great adaptive trait – doing everything by the pre-programed schedule can work wonderfully for a long period of time. Other species evolve flexibility which allows them to spread on a broader spatial range and perhaps allow them to survive a longer geological time.

Pluto in schools

Educators, i.e., science teachers, are not too unhappy about the change in taxonomy of planets. Some argue they can use it as a lesson in the way science always changes.

Obligatory Reading of the Day – Authoritarians II

Sara Robinson is on the roll: Tunnels and Bridges, Part II: Nothing to Fear But Fear Itself

Tar Heel Tavern

The Tarheel Tavern #79 is up on Kivi Leroux Miller’s blog on Freelance Writing.

New Orleans, one year later, is still a ghost town

Last year, there was so much blogging about Katrina, I thought that the best thing I could do was create a large linkfest of everyone else’s posts. That is what I did – check it out here, a nice one-stop-shopping for the analysis and opinion at the time. If you need to refresh your memory that is the place to go. You can also find most of the iconic images collected in one place here.
But I did not entirely abstain from commenting myself, though I was trying to look for angles nobody else covered and news nobody else had – which was hard to find at that time. So, I blogged about how animals fared in the hurricane, especially horses.
I wrote about the refusal to take an offer of aid from Cuba and how free market killed NoLa.
I think I was the very first to blog about Kanye West and what he said on TV (as I was watching as it happened). I was also one of the first to report when Brownie was fired (or resigned).
I found four separate timelines. The frame of a looting mob was recognized and attacked early. And there were touching (and telling!) survivor stories that needed a wider audience.
There was humor.There was inside-the-Beltline politics.
I looked for what other people said at the time, including Lakoff, Kerry, Edwards and some others (and recognized early that the events may favour Edwards for 2008).
And there was much, much more.
I wrote two less newsy and more opinionated posts – Stop Beating on Bush! and We The People and upon re-readng them a year later, I still agree with every word in them.
Finally, when I wrote this – Ghost Town – many people scolded me for being so pessimistic. It turns out, I was right. New Orleans has still not recovered its population.
A large chunk of that population is not back yet. Some plan to come back, a year later, but still do not have a place to live. Others have assimilated in other places. The magic of living in New Orleans is dwarfed by the reality of survival.
The place has not been fixed yet. The dams are not built to sustain another hurricane of that size. The wetlands have not been restored. The big river is still fighting to change its course.
And the locals are still fighting over the urban project for the city: some have a vision of Disneyfied, white, upper-middle-class New Orleans; others react by insisting on restoring the city exactly as it was, warts and all, good and bad, shacks and slums and everything else. Voices of moderation and smart urban planning are overpowered by emotionally-charged voices of the two extremes. It is unfortunate that I was right. I wish I wasn’t.

Carnivals this week

George has posted a last call for submissions for the next edition of the Teaching Carnival – all about Higher Ed, life in academia, etc. He is hosting it on WorkBook this Friday, September 1st, so send your entries on time to: georgehwilliams at gmail dot com
Next Tangled Bank (science, nature, medicine, environment and intersection between science and society) will be held on Epigenetics News this coming Wednesday. Send your entries to: admin AT epigeneticsnews DOTcom or host AT tangledbank DOT net.
Carnival of the Liberals will be on Wednesday on The Greenbelt. Send entries to: cotl DASH submissions AT carnivaloftheliberals DOT com
Next Carnival of the Green will be on August 28th on The Disillusioned Kid. E-mail your entries to: carnivalofgreen AT gmail DOT com
Next Mendel’s Garden will be on Evolgen on September 1st. E-mail: evolgen [at] yahoo [dot] com.
Next edition of The Synapse will be on The Mouse Trap on September 3rd. Send your entries to: the.synapse.carnival {AT} gmail
Next Encephalon will be on September 11th on Retrospectacle. E-mail: encephalon DOT host@gmail.com
Next Grand Rounds – this Tuesday on Protect the Airway. Entries go to: airwaycontrol AT protecttheairway DOT com
Next edition of the I And The Bird will be hosted by Migrateblog on Thursday. Send your links to: mariya DOT strauss AT gmail DOT com
Also on Thursday, new Skeptic’s Circle should get Immunoblogging out of a long hiatus. E-mail to: aeger AT hotmail DOT com
On Wednesday, Carnival of Education goes to Thespis Journal. Send your entries to: thespis148 AT gmail DOT com
Philosopher’s Carnival will next be on Philosopher’s Playground on September 4th. E-mail: sgimbel AT gettysburg DOT edu
Next History Carnival will be on September 1st on Frog in a Well – Japan. E-mail: sharon AT earlymodernweb.org.uk
Next carnival of Bad History will be on September 22nd on World History Blog. E-mail: miland[at]usa2014[dot]com
Next edition of the Circus of the Spineless will be held on Sunbeams From Cucumbers. Send your entries by August 29th to: sreuland AT gmail DOT com
Next edition of the Festival of the Trees will be held on Burning Silo, so send your entries to Bev by August 29th to: burning-silo AT magickcanoe DOT com
As there are so many carnivals worth paying attention to and some people come to me for information, I’d really like it if the managers and hosts of carnivals will put me on their e-mailing lists so I can get information about calls for submissions and shout-outs once they are posted in time to post a link here. Which carnivals did I miss today?

Bugs and Trees

Next edition of the Circus of the Spineless will be held on Sunbeams From Cucumbers. Send your entries by August 29th to: sreuland AT gmail DOT com
Next edition of the Festival of the Trees will be held on Burning Silo, so send your entries to Bev by August 29th to: burning-silo AT magickcanoe DOT com

Hot Peppers, again.

Amanda, a fellow hot-pepper-lover, reminds me that I have not finished my Hot Pepper series. It is supposed to be a THREE-part series, but I only wrote two parts so far, the introductory (personal) post and answering the question why are peppers hot (quite a popular post of mine, linked and e-mailed around a lot, I noticed) – an evolutionary account from peppers’ perspective.
I still owe you the third part trying to explain why people (at least some people, like Amanda and myself) like to eat hot food. It turned out to be a much more exhaustive area of research (and dispute) than I initially expected so I left it for later, once I have more time and the weather cools off a little bit…but I promise I will write it sooner or later. In the meantime, read what Amanda and her commenters have to say on the subject.
But, as an Intermission, here’s a little more on my personal relationship with hot food:
Indian Tandoori restaurants in the USA are fixing much milder food than their counterparts in the UK.
My initiation to the cuisine was in London (in 1980, I believe). My cousin who lives there and his family took me to a Tandoori restaurant. He told the waiter that I was a novice to which the waiter grinned broadly and brought me a foot-high stack of napkins and an extra glass of water.
Then, we ordered the “mild” stuff for me from the menu. The waiter was still grinning. The food arrived. Bread was hot. Salad was hot. Chicken was hot. Vegetables were hot. I LIKE hot food, but I was crying and quickly depleting my stash of napkins, my two glasses of water and a glass of yogurt.
In the end, my mouth was so numb, I tried the hottest spices they had and could not feel a thing.
Needless to say, I went back to Tandoori restaurants many times since and am quite disappointed that the US version is so mild.

Katrina blogswarm

Yup, the Katrina blogswarm is supposed to be tomorrow, but Publius and The Science Pundit could not wait.

Well, I am not an engineer…

…so I’d have my priorities straight. But checking my Sitemeter referrers list would come in at #2, LOL.

My picks from ScienceDaily

Childhood Sleep Apnea Linked To Brain Damage, Lower IQ:

In what is believed to be the first study showing neural changes in the brains of children with serious, untreated sleep apnea, Johns Hopkins researchers conclude that children with the disorder appear to suffer damage in two brain structures tied to learning ability.

Constant Lighting May Disrupt Development Of Preemies’ Biological Clocks:

Keeping the lights on around the clock in neonatal intensive care units may interfere with the development of premature babies’ biological clocks.
———-snip—————
he 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.

Pure Novelty Spurs The Brain:

Neurobiologists have known that a novel environment sparks exploration and learning, but very little is known about whether the brain really prefers novelty as such. Rather, the major “novelty center” of the brain–called the substantia nigra/ventral tegmental area (SN/VTA)–might be activated by the unexpectedness of a stimulus, the emotional arousal it causes, or the need to respond behaviorally. The SN/VTA exerts a major influence on learning because it is functionally linked to both the hippocampus, which is the brain’s learning center, and the amygdala, the center for processing emotional information.

A Wandering Eye: Single Cells Come Running To Form An Eye:

Eyes are among the earliest recognisable structures in an embryo; they start off as bulges on the sides of tube-shaped tissue that will eventually become the brain. Researchers from the European Molecular Biology Laboratory (EMBL) in Heidelberg have now discovered that cells are programmed to make eyes early in development and individually migrate to the right place to do so.
The study, published in the journal Science, overturns the textbook model of the process and suggests that also other organs might be formed by the movement of single cells rather than sheets of entire tissues.

On The Track Of Tiny Larvae, A New Model Elucidates Connections In Marine Ecology:

A computer model newly developed by researchers combines ocean current simulations and genetic forecasting to help scientists predict animal dispersion patterns and details of the ecology of coral reefs across the Caribbean Sea.
———————–snip———————
This test showed that combining the oceanographic and genetic models allowed the researchers to successfully predict genetic patterns on a regional scale. This breakthrough approach to integrating genetic and oceanographic models helps predict genetic links among several locations and is an important new tool for the management and ecological study of marine protected areas.

Evolving Defenses Rapidly Suppress Male Killers:

In the game of survival, anything goes–even the selective extermination of males. Male killing is the preferred strategy for a diverse group of bacteria that infect insects and other arthropods. Aside from its tabloid appeal, male killing offers biologists a platform for investigating genetic conflict–evolutionary battles between competing elements within the same genome. Male-killing bacteria are passed from mother to offspring, but only males die from infection, suggesting that males harbor genetic elements that allow them to succumb to infection.

Do You Know What You Eat?

Eric Schlosser, Marion Nestle, Michael Pollan, Wendell Berry, Troy Duster, Elizabeth Ransom, Winona LaDuke, Peter Singer, Dr. Vandana Shiva, Carlo Petrini, Eliot Coleman & Jim Hightower recently participated in a Nation forum: One Thing to Do About Food. Here are a few excerpts – go read the whole thing:

“Once you learn how our modern industrial food system has transformed what most Americans eat, you become highly motivated to eat something else.”
“….the American food system is a game played according to a precise set of rules that are written by the federal government with virtually no input from anyone beyond a handful of farm-state legislators. Nothing could do more to reform America’s food system–and by doing so improve the condition of America’s environment and public health–than if the rest of us were suddenly to weigh in.”
“There is one very simple thing that everyone can do to fix the food system. Don’t buy factory-farm products.”
“Corporate control thrives on monocultures. Citizens’ food freedom depends on biodiversity.”
“Industry and the production ethos have robbed people of the knowledge of food and reduced it to pure merchandise–a good to be consumed like any other.”
“An addiction to treating the symptoms of problems rather than correcting their causes is an unwise choice made by our society as a whole.”
“In the very short span of about fifty years, we’ve allowed our politicians to do something remarkably stupid: turn America’s food-policy decisions over to corporate lobbyists, lawyers and economists. These are people who could not run a watermelon stand if we gave them the melons and had the Highway Patrol flag down the customers for them–yet, they have taken charge of the decisions that direct everything from how and where food is grown to what our children eat in school.”

Triangle Bloggers Barbecue

So, you must know by now, that last night I went to the Triangle Bloggers BBQ, hosted by Anton and his wonderful wife Erin. Needless to say, it was great fun, though I had perhaps a beer too many….(but the food….don’t let me get started on food – it was great)
Who was there? Local activists Will and his wonderful family (thank you for driving to the party), Brian and Ruby (thank you for driving from the party), my SciBling Abel, another fellow science blogger Reed Cartwright, the link to blook-publishing Jackson Fox, fellow Edwards supporter Jim Buie, meetup regulars Steve Cory, Josh Steiger, Perry and Roy Kim and several others.
Anton has posted a few pictures on Flickr and you can see me on one or two. I hope others add their photos as well.

Blog about Katrina this Monday!

A year ago this Monday, Katrina hit the Gulf states. We all blogged like crazy.
Since Bush Administration is desparately trying to supress the memory of their debacle, King Cranky and Melissa suggest we do a blogswarm – everyone blogs about Katrina on Monday and Shakes will collect the posts in a huge linkfest.
Need a reminder and a collection of facts? Check this Katrina timeline (via Arse Poetica)