Yearly Archives: 2007

Bloggers in Spaaaaaace!

Carnival of Space #11 is up on Space For Commerce, by Brian Dunbar.

Lithium, Circadian Clocks and Bipolar Disorder

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

VIP synchronizes mammalian circadian pacemaker neurons

VIP synchronizes mammalian circadian pacemaker neuronsNo other aspect of behavioral biology is as well understood at the molecular level as the mechanism that generates and sustains circadian rhythms. If you are following science in general, or this blog in particular, you are probably familiar with the names of circadian clock genes like per, tim, clk, frq, wc, cry, Bmal, kai, toc, doubletime, rev-erb etc.
The deep and detailed knowledge of the genes involved in circadian clock function has one unintended side-effect, especially for people outside the field. If one does not stop and think for a second, it is easy to fall under the impression that various aspects of the circadian oscillations, e.g., period, phase and amplitude, are determined by the clock genes. After all, most of these genes were discovered by the study of serendipitously occuring mutations, usually period-mutations.
If the circadian properties are really deteremined by clock genes, then the predictions from this hypothesis are that: 1) every cell in the body shows the same period (phase, amplitude, etc.), 2) every cell in the body has the same period throughout its life, 3) every cell removed from the body and placed in the dish continues to oscillate with the same period as it had inside the body, and 4) the properties of the circadian rhythms are not alterable by environmental influences.
Stated this bluntly, one has to recoil in horror: of course it is not determined by genes! But without such an exercise in thinking, much work and writing (especially by the press) tacitly assumes the strict genetic determination. However, the experimental data show this not to be true. Period (and other properties) of the whole organism’s rhythms are readily modified by environmental influences, e.g., light intensity (Aschoff Rule), heavy water, lithium, sex steroids and melatonin. They change with age and reproductive state. There is individual variation even in clonal species (or highly-inbred laboratory strains). The period of the rhythms measured in cells or cell-types in a dish is not always the same as exhibited by the same cells inside the organism. Finally, the occurrence of splitting (of one unified circadian output into two semi-independent components differing in period)suggests that two or more groups of circadian pacemakers simultaneously exhibit quite different periods within the same animal.
Several years ago, Dr. Eric Herzog (disclosure – a good friend) has shown that even the individual pacemaker cells within the same SCN (suprachiasmatic nucleus – the site of the main mammalian circadian clock in the brain) exhibit different periods. When dispersed in culture, pacemaker neurons (originally taken from a single animal) tend to show a broad variation in periods (amplitudes, etc…).
As they grow cellular processes, two neurons in a dish may touch and form connections. As soon as they do, their periods change and from then on the two cells show the SAME period, i.e., they are synchronized. As more and more cells connect, they build an entire network of neurons, all cycling in sync with each other – same period, same phase, same amplitude. This is assumed to happen inside the whole animal as well – the unconnected SCN neurons of the fetus start making connections just before (or immediately after, depending on the species) birth and as a result, an overt, whole-organism rhythm emerges out of arrhytmic background.
But, what molecules are involved in cell-cell communication that allows the pacemaker cells to synchronize their rhythms? For several years, the most likely candidate was thought to be GABA, an inhibitory neurotransmitter produced by all SCN cells. Sara Aton, a graduate student in Eric Herzog’s lab (now postdoc at UPenn), set out to test this hypothesis. Over a few years and several papers, a different story emerged, culminating in this months paper in PNAS:

Continue reading

ClockQuotes

Life is something that happens when you can’t get to sleep.
– Fran Lebowitz

Help Save Serbia’s #1 Science Blog

Remember the threat of closing the KOBSON blog?
Well, Danica was a brave warrior for Open Science and published an article about this at a much more prominent place: on Global Voices Online.
While this may not be an immediate positive move for Danica’s own career, it is a good move towards persuading the powers-that-be in Serbia that the way forward is towards more openness, not the opposite.

Blogrolling for Today

Paralepsis


Fresno, Evolving


DSHR’s Blog


Open Left


Issues in Scholarly Communication


Tessa’s Braces


Professor Olsen @ Large


Occam’s Trowel


Enro, scientifique et citoyen

Is That Your Jet-Lag Treatment Showing or are you just Happy To See Me?

Is That Your Jet-Lag Treatment Showing or are you just Happy To See Me?If this gets more widely known (and, with this post, I am trying to help it become so), you can just imagine the jokes about the new challenges to the aviation industry and the renewed popularity of the Mile High Club, or the cartoons utilizing the phallic shape of airplanes!
Hamsters on Viagra Have Less Jet Lag, Research Shows (also Viagra helps jet-lagged hamsters, maybe humans, too: study and Viagra ‘improves jet lag’):

Hamsters given Pfizer Inc.’s Viagra adapted more quickly to changes in their internal clocks, scientists said.
Hamsters given sildenafil, the chemical name of the drug sold as Viagra, adapted more easily to altered patterns of light exposure to simulate changes caused by air travel across time zones. Long-haul travel desynchronizes the body’s alignment to the day-night cycle, leading to the disorientation of jet lag.
————snip—————-
The researchers synchronized the hamsters to a 24-hour day by simulating light-dark cycles. Once the hamsters adjusted to a cycle, they shifted the light-dark phases forward six hours. One group of hamsters was given saline; the other was given Viagra. The hamsters given Viagra got used to the change 4 days faster, on average, than their counterparts given a placebo. Viagra eased the transition that mimicked crossing the international dateline from west to east, known as phase advancing, and had no effect on a transition that mimicked westward travel.

There should be a rule in journalism making sure that no article about Viagra ever contains the words “harder” and “screw”, especially close to each other. Oooops!

“All animals, including humans, have a harder time with phase advancing,” said Colwell in a telephone interview today. “Humans are unique in our ability to screw up our timing system — you know, jet lag, shift work, staying up too late playing video games, or whatever.”

OK, now seriously…what does the study say?

Continue reading

San Francisco – a running commentary #2

Wow – this was (and still is) a very busy week. On most days, I just crashed early, without having the energy to blog very much (at least very much for me).
In the last dispatch, I forgot to mention I met Jimmy Wales who came to visit PLoS and we talked about Wikipedia and building online communities.
Under the fold are a bunch of new pictures…

Continue reading

Make your data freely available if you want to get cited more

This paper (by Heather Piwowar) is not that new, but it is only now starting to get some traction and I’d like to see more people be aware of it:

Background
Sharing research data provides benefit to the general scientific community, but the benefit is less obvious for the investigator who makes his or her data available.
Principal Findings
We examined the citation history of 85 cancer microarray clinical trial publications with respect to the availability of their data. The 48% of trials with publicly available microarray data received 85% of the aggregate citations. Publicly available data was significantly (p = 0.006) associated with a 69% increase in citations, independently of journal impact factor, date of publication, and author country of origin using linear regression.
Significance
This correlation between publicly available data and increased literature impact may further motivate investigators to share their detailed research data.

65% increase in citation is nothing to scoff about, dont’ you think?

Call for Action: guaranteed public access to publicly-funded research results

In the USA:

Effective this week, both the House and Senate Appropriations Committees have proposed FY08 spending bills that direct the National Institutes of Health (NIH) to change its Public Access Policy so that NIH-funded researchers are required to deposit copies of NIH-funded research into the online archive of the National Library of Medicine.
This is big step toward making the policy a success — we need your help now more than ever.
The bills now go to the full House and the Senate for approval. To help ensure success there, we ask that all supporters contact their Representatives AND Senators with support of the proposed bills by phone or fax as soon as possible. The House is expected to convene on Tuesday, July 17, so we ask that Representatives be contacted no later than MONDAY afternoon.
Contacting your Representatives and Senators:
ALA Legislative Action Center
Find your Representative
Find your Senator

And in Europe:

The German parliament just passed a new copyright law that will hinder the free exchange of scientific information. Thus, European copyright politics become more important to override this German decission in the future.
As in the US we have a movement in Europe for open access to publicly funded research results. The Petition for guaranteed public access to publicly-funded research results has been signed by nearly 26000 individuals and many institutions but of course it needs as many signatures as possible.

Clock Genetics – A Short History

Clock Genetics - A Short HistoryA short post from April 17, 2005 that is a good starting reference for more detailed posts covering recent research in clock genetics (click on spider-clock icon to see the original).

Continue reading

ClockQuotes

No one ever died from sleeping in an unmade bed. I have known mothers who remake the bed after their children do it because there’s a wrinkle in the spread or the blanket is on crooked. This is sick.
– Erma Louise Bombeck

Dawkins in San Francisco

Richard Dawkins is doing a reading/signing at Kepler’s bookstore this Saturday. Any Bay Area bloggers wanna go?

Bird Blogging of the Year!

I And The Bird carnival is two years old! The anniversary edition is appropriately hosted by its founder, Mike at 10000 Birds.

Cortisol necessary for circadian rhythm of cell division

Cortisol necessary for circadian rhythm of cell divisionA new paper just came out today on PLoS-Biology: Glucocorticoids Play a Key Role in Circadian Cell Cycle Rhythms. The paper is long and complicated, with many control experiments, etc, so I will just give you a very brief summary of the main finding.

Continue reading

Now You Can (and Should) rate papers on PLoS ONE!

I buried this information between numerous pretty pictures in a yesterday’s post, so let me now tell you a little bit more.
A couple of days ago, a new feature was introduced on all published papers on PLoS ONE. Along with commenting on and annotating each paper, you can now also rate it.
The rating system is familiar to all of you from other sites, I’m sure – it is a simple five-star system. You can rate papers on three criteria: Insight, Reliability and Style and let the software average your three ratings to produce a single number, as well as average your ratings with other readers’ ratings to produce a single number for each of the three criteria.
Read the Rating Guidelines first, then dig into the site and rate every paper that you read, while leaving a very brief explanation of why you rated the way you did – no need to get wordy, the Discussions comments and Annotations are designed for that.
For a more technical account, read what Richard Cave wrote about the new application, and then check Pedro’s post for a quick pictorial tutorial. If you have the Javascript turned off, you will need to turn it on in order to be able to rate the papers.
As Chris Surridge says (after explaining what this all really means): “Never read a paper on PLoS ONE without leaving a rating!” I strongly second Chris on this: go look around PLoS ONE, read the papers (or find those you have already read in the past) and rate them. Now.

How NOT to think about human behavior

Echidne, Amanda Marcotte, Laelaps and Larry Moran beautifully destroy the “Ten Politically Incorrect Truths About Human Nature” article from the recent issue of ‘Psychology Today’, the latest garbage from the Evolutionary Psychology crowd. Much fun was had by all….

Clock Tutorial #4: On Methodology

Clock Tutorial #4: On Methodology I wrote this post back on January 23, 2005. It explains how clock biologists think and how they design their experiments:

Continue reading

Obligatory Readings of the Day – competition vs cooperation in science

Four excellent, thought-provoking articles all in some way related to the idea of Open Science. One by Bill Hooker:
Competition in science: too much of a good thing
and three by Janet Stemwedel:
Clarity and obfuscation in scientific papers
Does thinking like a scientist lead to bad science writing?
OpenWetWare

Update on Tripoli Six

Revere, Orac and PZ have an update on the fate of the Tripoli 6. Revere explains:

The final act in the drama of five Bulgarian nurses and one Palestinian doctor imprisoned for seven years and sentenced to death by firing squad in Libya after being accused of deliberately infecting over 400 chidren with HIV in a children’s hospital in Bengazi … is now being played out in the Libyan capital of Tripoli.
Affirming the death sentence is a (regrettably) necessary first step in resolving the issue and, paradoxically, saving the lives and obtaining the freedom of the accused, whose confessions they say were coerced by torture. A precondition for a positive outcome for the accused was an agreement between the EU and Libya’s Gaddafi Foundation charity on funding lifetime care for the children, an agreement said to be in the tens of millions of dollars.
The announcement today that the deal has been affirmed along with news that the High Judicial Council will meet on Monday is believed to be a signal to the international community the sentences will be commuted. Until the Tripoli 6 have been repatriated and are free we can only update you on developments.

I’ll also post as soon as I hear how the events unfold.

Science Blogging Conference update

Science Blogging ConferenceAs you are probably aware, behind the scenes we are busily working on the organization of the 2nd Science Blogging Conference. The wiki is almost all set up – all that is missing are maps and information about travel, directions, etc. (and the dinner wiki) which will be there by the end of August. We will open the registration on September 1st, but you can always e-mail me with questions or to tell me about your intentions to register.
The program is slowly taking shape (go look – we have already lined up some phenomenal people to lead discussions), though I guess there will still be many changes and updates until the timetable and the content are firmly set in stone. The conference promises to be much bigger and better than the last one!
At this point, we are primarily working on securing funding. You (or your organization/company) can sponsor the conference (we’ll need cash, food, t-shirts, swag and other items), or donate, or sign up to volunteer.
If you click on this link you should be able to download a PDF file of a promotional flyer. Spread the word about the conference by printing out a few and pinning them to bulletin boards in places where you work or live.
Finally, let me use this post for my monthly reminder to nominate posts, your own or other bloggers’, for the 2nd science blogging anthology. Multiple submissions from the same blog are welcome. Use this online form. And go here to pick up the code that can help you spread the word about it.

New and Exciting on PLoS ONE

There are 19 new papers on ONE that were published this week (thus breaking the 600 papers number). Here are a couple that caught my eye (apart from those I already blogged about or will soon):
Imitation as Faithful Copying of a Novel Technique in Marmoset Monkeys:

This evidence of imitation in non-human primates questions the dominant opinion that imitation is a human-specific ability. Furthermore, the high matching degree suggests that marmosets possess the neuronal mechanism to code the actions of others and to map them onto their own motor repertoire, rather than priming existing motor-templates.

Natural Selection on Female Life-History Traits in Relation to Socio-Economic Class in Pre-Industrial Human Populations:

We found the highest opportunity for total selection and the strongest selection on earlier age at first reproduction in women of the poorest wealth class, whereas selection favoured older age at reproductive cessation in mothers of the wealthier classes. We also found clear differences in female life-history traits across wealth classes: the poorest women had the lowest age-specific survival throughout their lives, they started reproduction later, delivered fewer offspring during their lifetime, ceased reproduction younger, had poorer offspring survival to adulthood and, hence, had lower fitness compared to the wealthier women. Our results show that the amount of wealth affected the selection pressure on female life-history in a pre-industrial human population.

Genetic Variation for Cardiac Dysfunction in Drosophila:

A screen of fifty inbred wild-type lines revealed a continuous spectrum of pacing-induced heart failure that generally increases in frequency with age. High-speed video analysis of the inbred lines with high rates of inducible heart failure indicates specific defects in cardiac function, including arrhythmias and contractile disorders (‘cardiomyopathies’). A combination of bulked segregant analysis and single feature polymorphism (SFP) detection localizes one of the cardiac susceptibility loci to the 97C interval on the fly genome.

Locating Pleistocene Refugia: Comparing Phylogeographic and Ecological Niche Model Predictions:

Ecological niche models (ENMs) provide a means of characterizing the spatial distribution of suitable conditions for species, and have recently been applied to the challenge of locating potential distributional areas at the Last Glacial Maximum (LGM) when unfavorable climate conditions led to range contractions and fragmentation. Here, we compare and contrast ENM-based reconstructions of LGM refugial locations with those resulting from the more traditional molecular genetic and phylogeographic predictions. We examined 20 North American terrestrial vertebrate species from different regions and with different range sizes for which refugia have been identified based on phylogeographic analyses, using ENM tools to make parallel predictions. We then assessed the correspondence between the two approaches based on spatial overlap and areal extent of the predicted refugia. In 14 of the 20 species, the predictions from ENM and predictions based on phylogeographic studies were significantly spatially correlated, suggesting that the two approaches to development of refugial maps are converging on a similar result. Our results confirm that ENM scenario exploration can provide a useful complement to molecular studies, offering a less subjective, spatially explicit hypothesis of past geographic patterns of distribution.

The Importance of Poisoning vs. Road Traffic Injuries as a Cause of Death in Rural Sri Lanka:

Road traffic crashes are considered by the WHO to be the most important global cause of death from injury. However, this may not be true for large areas of rural Asia where road vehicles are uncommon. The issue is important, since emphasising the importance of road traffic crashes risks switching resources to urban areas, away from already underfunded rural regions. In this study, we compared the importance of road traffic crashes with other forms of injury in a poor rural region of South Asia.
——————
In poor rural regions of South Asia, fatal self-harm and pesticide self-poisoning in particular are significantly more important than road traffic injuries as a cause of death. It is possible that the data used by the WHO to calculate global injury estimates are biased towards urban areas with better data collection but little pesticide poisoning. More studies are required to inform a debate about the importance of different forms of injury and how avoidable deaths from any cause can be prevented. In the meantime, marked improvements in the effectiveness of therapy for pesticide poisoning, safer storage, reduced pesticide use, or reductions in pesticide toxicity are required urgently to reduce the number of deaths from self-poisoning in rural Asia.

Now, you know what to do: make annotations, post comments and rate the papers.

ClockQuotes

A quiet conscience sleeps in thunder.
– English Proverb

My picks from ScienceDaily

Songbirds Prefer The Latest Music: Golden Oldies Just Don’t Cut It With The Chicks:

When it’s time to mate, female white-crowned sparrows are looking for a male who sings the latest version of the love song, not some 1979 relic. And territorial males simply find the golden oldie much less threatening. Duke University graduate student Elizabeth Derryberry played two versions of the white-crowned sparrow song to the birds as part of her thesis research and found that a 1979 recording didn’t inspire them nearly as well as a 2003 recording of the very same song.

Birds Take Cues From Their Competitors:

The idea that animals other than humans can learn from one another and pass on local traditions has long been a matter of debate. Now, a new study reveals that some birds learn not only from each other, but also from their competitors. Through a novel field experiment, the researchers showed that female members of two migrant flycatcher species can acquire a novel preference for nesting sites on the basis of the apparent attraction of competing resident tits for nest boxes bearing an otherwise meaningless symbol.

Mimicry: Research Ends Debate Over Benefits Of Butterfly Defenses:

Scientists have furthered understanding of the relationship between predator and prey in an experiment designed to understand butterfly defence mechanisms. Researchers observed the behaviour of Great-tits foraging for artificial prey to understand more clearly how a species evolves to protect themselves from predators.

Continue reading

Old, Hot and Pretty!

New Habanero Blasts Taste Buds — And Pepper Pests:

The super-hot, bright orange TigerPaw-NR habanero pepper offers extreme pungency for pepper aficionados, plus nematode resistance that will make it a hit with growers and home gardeners. Plant geneticist Richard L. Fery and plant pathologist Judy A. Thies at the Agricultural Research Service (ARS) U.S. Vegetable Laboratory, Charleston, S.C., put the pepper through three years of greenhouse and field tests before determining, in 2006, that it was ready for commercial fields and backyard gardens.

Exhibiting A Pepper For Every Pot:

Peppers don’t have to be just green and bell shaped and relegated to the supermarket shelf or home garden plot. This genus of plants has the genetic potential to provide a wide array of possibilities for the kitchen and the ornamental garden and sometimes both at once. Research on peppers from the Agricultural Research Service (ARS) is being featured from June to November in an exhibit called “A Pepper for Every Pot” at the U.S. Botanic Gardens in Washington, D.C. This exhibit explores the diversity of peppers, including recently introduced varieties, and celebrates peppers’ beauty, flavors and nutritional benefits.

Ancient Americans Liked It Hot: Mexican Cuisine Traced To 1,500 Years Ago:

One of the world’s tastiest and most popular cuisines, Mexican food also may be one of the oldest. Plant remains from two caves in southern Mexico analyzed by a Smithsonian ethnobotanist/archaeologist and a colleague indicate that as early as 1,500 years ago, Pre-Columbian inhabitants of the region enjoyed a spicy fare similar to Mexican cuisine today. The two caves yielded 10 different cultivars (cultivated varieties) of chili peppers.

Related: Hot Peppers – Why Are They Hot?

Aphids and Enemies

You really don’t want to be an enemy of the aphids – two papers today! The first is quite straightforward:
Aphids Make ‘Chemical Weapons’ To Fight Off Killer Ladybirds:

Cabbage aphids have developed an internal chemical defence system which enables them to disable attacking predators by setting off a mustard oil ‘bomb’, says new research. The study shows for the first time how aphids use a chemical found in the plants they eat to emit a deadly burst of mustard oil when they’re attacked by a predator, for example a ladybird. This mustard oil kills, injures or repels the ladybird, which then saves the colony of aphids from attack, although the individual aphid involved usually dies in the process.

So, these aphids directly defend themselves against their own enemies by using the chemicals they derives from the plants they eat. But the next study introduces more complexity – several levels of the food web (i.e., tri-trophic relationship);
High Susceptibility of Bt Maize to Aphids Enhances the Performance of Parasitoids of Lepidopteran Pests:

Concerns about possible undesired environmental effects of transgenic crops have prompted numerous evaluations of such crops. So-called Bt crops receive particular attention because they carry bacteria-derived genes coding for insecticidal proteins that might negatively affect non-target arthropods. Here we show a remarkable positive effect of Bt maize on the performance of the corn leaf aphid Rhopalosiphum maidis, which in turn enhanced the performance of parasitic wasps that feed on aphid honeydew. Within five out of six pairs that were evaluated, transgenic maize lines were significantly more susceptible to aphids than their near-isogenic equivalents, with the remaining pair being equally susceptible. The aphids feed from the phloem sieve element content and analyses of this sap in selected maize lines revealed marginally, but significantly higher amino acid levels in Bt maize, which might partially explain the observed increased aphid performance. Larger colony densities of aphids on Bt plants resulted in an increased production of honeydew that can be used as food by beneficial insects. Indeed, Cotesia marginiventris, a parasitoid of lepidopteran pests, lived longer and parasitized more pest caterpillars in the presence of aphid-infested Bt maize than in the presence of aphid-infested isogenic maize. Hence, depending on aphid pest thresholds, the observed increased susceptibility of Bt maize to aphids may be either a welcome or an undesirable side effect.

Translation: transgenic corn has somewhat more nutritional value for the aphids. Thus, there are more aphids (per plant) on such corn. Thus, there is more “honeydew” (per acre) that they produce. Thus, there is more food (per acre) for the wasp. Thus, there are more wasps in the field. Thus, they are better able to control the population of moth caterpillars. Thus, there are fewer caterpillars to eat the corn. Final result: the farmer is happy. Now go to the paper itself and add comments, annotations and ratings to it.

Birds of Chernobyl

There is a new piece of information regarding the mammal vs. bird controversy in Chernobyl:
Brightly Colored Birds Most Affected By Chernobyl Radiation:

Brightly coloured birds are among the species most adversely affected by the high levels of radiation around the Chernobyl nuclear plant, ecologists have discovered. The findings — published online in the British Ecological Society’s Journal of Applied Ecology — help explain why some species are harder hit by ionising radiation than others.
Dr Anders Møller of the Université Pierre et Marie Curie and Professor Timothy Mousseau of the University of South Carolina examined 1,570 birds from 57 different species in the forests around Chernobyl at varying distances from the reactor. They found that populations of four groups of birds — those whose red, yellow and orange plumage is based on carotenoids, those that laid the biggest eggs, and those that migrated or dispersed the furthest — declined more than other species.

Perhaps, Sarah Wallace will take a break sometimes from looking at humans and take a peak at birds.

Brain and Mind articles

Our former scibling David Dobbs has posted/published two interesting articles about recent findings in neuroscience and behavior:
The Gregarious Brain in New York Times Magazine, about the Williams Syndrome:

If a person suffers the small genetic accident that creates Williams syndrome, he’ll live with not only some fairly conventional cognitive deficits, like trouble with space and numbers, but also a strange set of traits that researchers call the Williams social phenotype or, less formally, the “Williams personality”: a love of company and conversation combined, often awkwardly, with a poor understanding of social dynamics and a lack of social inhibition. The combination creates some memorable encounters.

It’s just your imagination — Or is it your memory? on the SciAm blog:

As we explored in the very first Mind Matters post, neuroscientists everywhere agree that the hippocampus is crucial to memory — but have rich and interesting disagreements about how this brain area creates and manages memory and what roles it might play in cognition. This debate was freshly enlivened in early 2007 when an innovative paper by Demis Hassabis (a former chess prodigy and games designer) and colleagues at the renowned University College London lab of Eleanor Maguire proposed that the hippocampus is vital not just for memory but also for imagination. As hippocampal researcher Andre Fenton notes in his review below, this discovery suggests both a vital new role for the hippocampus and a narrative-building mechanism common to memory, imagination, and thought. Interesting new ground, Fenton finds, but not without its hazards.

San Francisco – a running commentary

OK, so I’ve been here for about a week now. It’s been so far an exciting and overwhelming experience – there is so much to learn! And I am impatient with myself and want to get in the groove right now. I need to learn to slow down a little…
Anyway, I did manage to drop in here at the blog a couple of times and report on meetups with some local bloggers, but here is a little bit more about the week so far…

Continue reading

The Clock Metaphor

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:

Continue reading

Blogging for a job?

Seen on a forum:

I just heard something interesting on the news and I’d like to toss it out to the community for your thoughts….
Forget resumes, job boards, cold calling and even going to the company. The “BIG THING” is Blogging for a Job.
It seems that many recrutiers find YOU by reading your blog.
If this is the way to go, how do you get one started? What do you put into it??

Ha!!!!

Today’s carnivals

Grand Rounds 3.42 are up on Aetiology.
Carnival of the Green #85 is up on The Ester Republic.
International Carnival of Pozitivities #13 is up on ScribeSpirit eZine.
Four Stone Hearth #18 is up on Clioaudio.
Change of Shift n.2.v.2 is up on Nursing Jobs.
The Carnival Of Education: Week 127 is up on The Education Wonks.
Carnival of the Godless #70 is up on Friendly Atheist.
Carnival of Homeschooling: Week 80 is up on Why Homeschool.

ClockTutorial #2a: Forty-Five Years of Pittendrigh’s Empirical Generalizations

From the Archives
This is the third in the series of posts designed to provide the basics of the field of Chronobiology. This post is interesting due to its analysis of history and sociology of the discipline, as well as a look at the changing nature of science. You can check out the rest of Clock Tutorials here.

Continue reading

ClockQuotes

There is only one thing people like that is good for them; a good night’s sleep.
– Edgar Watson Howe

Everything You Always Wanted To Know About Sleep (But Were Too Afraid To Ask)

ClockWeb%20logo2.JPG
This post is perhaps not my best post, but is, by far, my most popular ever. Sick and tired of politics after the 2004 election I decided to start a science-only blog – Circadiana. After a couple of days of fiddling with the templae, on January 8, 2005, I posted the very first post, this one, at 2:53 AM and went to bed. When I woke up I was astonished as the Sitemeter was going wild! This post was linked by BoingBoing and later that day, by Andrew Sullivan. It has been linked by people ever since, as recently as a couple of days ago, although the post is a year and a half old. Interestingly, it is not linked so much by science or medical bloggers, but much more by people who write about gizmos and gadgets or popular culture on LiveJournal, Xanga and MySpace, as well as people putting the link on their del.icio.us and stumbleupon lists. In order to redirect traffic away from Circadiana and to here, I am reposting it today, under the fold.
[This is also the post included in ‘The Open Laboratory 2006’, the anthology of best science blogging]

Continue reading

Professor Steve Steve at PLoS

Professor Steve Steve (see more of his pictures) is now over his jet lag and decided to go to work with me today. Here he is meeting with Liz Allen, the PLoS Director of Marketing and Business Development:
Liz%20Allen%20and%20Prof.Steve%20Steve.jpg

Happy birthday, Nikola Tesla

This day, Tesla’s birthday, is proposed to become the Global Energy Independence Day. Let’s make it happen!
If you don’t know much about Tesla, my last years’ post about him may be of some help….

Clock News

menaker%26friend.gif
Menaker Awarded Farrell Prize in Sleep Medicine:

Michael Menaker, professor of biology and an international leader in the field of circadian rhythm research, received the Peter C. Farrell Prize in Sleep Medicine from the Harvard Medical School Division of Sleep Medicine during an event there on June 6.
The prize was awarded “in celebration of the life and work of Michael Menaker, trailblazer in circadian biology and prescient illuminator of how Light and Dark, the alternating ancient heritages of our planet, come to govern and synchronize living clocks.”
Menaker was cited as a “ground-breaking investigator of the first circadian genetic mutation in mammals as well as the architect of landmark experiments that elucidate how central and peripheral circadian oscillators are coordinated to each other and with the environment.
Previously Menaker was honored with Virginia’s Outstanding Scientists and Industrialists 2003 Lifetime Achievement Award.

Mike is my academic grandfather, which makes me a very common beast, really! Yes, he has published amazing stuff over the decades and did some really pioneering and revolutionary science. But, his probably greatest contribution to science is the enormous number of students he has advised over the years. He finishes every talk by showing slides (two slides? three these days?) with many, many names of all of his graduate students (typed in a freerunning actograph style) which reads like a who-is-who of Chronobiology. And that is just first generation of his academic offspring – the academic grandkids and great-grandkids are all over the world as well, doing top-notch and exciting science.

Horseshoe crabs

Such fascinating creatures! If you have missed it so far, don’t miss it now – the two-part series by Mark H on DailyKos:
Marine Life Series: Horseshoe Crab Basics
Marine Life Series: Horseshoe Crab Anatomy
One day when I find some time, I’ll have to write a long detailed post about the fascinating aspects of the circadian system and vision in the horseshoe crab (oh, some of which was done by Erik Herzog, so you know I like the stuff!).

Sean Digs It

I am sometimes not aware that my blogospheric friends know each other well. So, for instance, I had no idea that Sean Carroll of Cosmic Variance blog and the crew at Project Exploration (see the brown square on my left side-bar) are friends. But apparently they are. So, Sean went dinosaur digging and dug out a bunch of bones of a new genus (and took pictures of the process).

ClockTutorial #2: Basic Concepts and Terms

From the Archives
This is the second in the series of posts designed to provide the basics of the field of Chronobiology. See the first part: ClockTutorial #1 – What Is Chronobiology and check out the rest of them here – they will all, over time, get moved to this blog.

Continue reading

ClockQuotes

The best bridge between despair and hope is a good night’s sleep.
– E. Joseph Cossman

Basics: Biological Clock

Basics: Biological ClockConsidering I’ve been writing textbook-like tutorials on chronobiology for quite a while now, trying always to write as simply and clearly as possible, and even wrote a Basic Concepts And Terms post, I am surprised that I never actually defined the term “biological clock” itself before, despite using it all the time.
Since the science bloggers started writing the ‘basic concepts and terms’ posts recently, I’ve been thinking about the best way to define ‘biological clock’ and it is not easy! Let me try, under the fold:

Continue reading

Exclusive: Interview with Senator John Edwards on Science-Related Topics

I had a great pleasure recently to be able to interview Senator – and now Democratic Presidential candidate – John Edwards for my blog. The interview was conducted by e-mail last week.
As I am at work and unable to moderate comments, the comment section is closed on this post, but will be open on the previous post (here) where I hope you will remain civil and stay on topic. You are also welcome to comment on this interview at several other places (e.g,. DailyKos, MyDD, TPMCafe, Science And Politics, Liberal Coalition, the Edwards campaign blog as well as, hopefully, your own blogs).
I cannot answer any additional questions for Senator Edwards, of course, but there are likely to be other opportunities in the future where your questions can be answered so feel free to post them in the comments thread on the other post and I’ll make sure he gets them. The interview is under the fold:

Continue reading

Comments on the Edwards interview go here…

In a few minutes, I will post the interview with Sen. John Edwards on this blog. All the questions are related to science (and yes, it was not easy to cut down the number of questions and the length of each question – there is so much to ask) so they should be of interest to the readers of this blog.
As I am not a journalist or an analyst who needs to preserve an appearance of ‘balance’, I have always been unabashedly open about my support for John Edwards, first in 1998 when he ran for the Senate (that was the first election I could vote in after becoming a US citizen), then in 2003/04 when he ran for President (and subsequently Vice-President), and finally now, as he is running for President again.
Feel free to search this blog (or my old blog) for his name and see what I have written in his support before.
I have not been in the past, nor am I now, officially connected to the campaign (though I walk my dog in front of the Headquarters every day and say Hi to staffers I recognize), but I am a big fan. And hey, we are neighbors – a few months after I moved from Raleigh to Chapel Hill, John and Elizabeth did the same.
As I’ll be running to work (my brand new job) in a few minutes, I will not be able to hang around and moderate comments. I hope you all stay civil and on topic – I know it is politics and trolls will come out of the woodwork, but ignore them and I will clean up the thread when I come back online tonight.
Also in a few minutes, I will post links to the interview on DailyKos, MyDD, TPM Cafe, Science And Politics, Liberal Coalition and, of course, the Edwards campaign blog. I’ll add the specific links here once I have them, so you can see what others are saying and perhaps want to comment on those places as well.
If you are interested in more details of Edwards’ policy proposals related to science, technology, medicine and environment, check them out directly on the John Edwards campaign website and search the Issues and Press Releases.
You may also want to read and write comments on my diary on DailyKos, mydiary on MyDD, my diary on the Edwards blog, my diary on TPM Cafe, my post on Science And Politics and my post on The Liberal Coalition.
Also, read the commentary by other people (to be updated as links come in): Kevin Beck, Argo, Anterior Commissure, Omni Brain, Unscrewing the Inscrutable, Ed Cone, Griftdrift, Pharyngula, The Greenbelt, Backreaction, Mark Adams, Dispassionate Liberal, As Ohio Goes…, Blog For Edwards, Billy the Blogging Poet, Philgoblue, Corpus Callosum, Thus Spake Zuska, Pithing Contest, The Voltage Gate, Laelaps, Shakesville, .Benny’s Blog, Democratic Underground, Space Politics, Thoughts From Kansas, Hope for Pandora, Dispatches From The Culture Wars, Yesh, Gene Expression, Metachat, Accidental Blogger, Neurophilosophy, TPM Election Central, Seed Zeitgeist, Pam’s House Blend, The Scientific Activist, Mythusmage Opines, Wired Science, EENR at DailyKos, NCDemAmy on MyDD, Dragyn’s Breath, Boston for Edwards, All These Worlds, Treehugger, Election Geek, America on Mars, Mass Eyes & Ears, Lance Mannion, …

ClockTutorial #1 – What Is Chronobiology

ClockWeb%20logo2.JPG This is the first in a series of posts from Circadiana designed as ClockTutorials, covering the basics of the field of Chronobiology. It was first written on January 12, 2005:

Continue reading

Fighting for Open Access in Serbia

Vedran Vucic is a Linux afficionado in Serbia. He and his organization have gone all around Serbia, wired up the schools, taught the teachers and students how to use Linux, taught the teachers and students how to use various online educational resources ranging from blogs to ATutor, etc.
Vedran also gives technical support to about 40 Serbian bloggers whose work he also aggregates.
He is now putting a lot of energy into persuading scientists, especially the young, not-yet-entrenched ones, to go online and to promote Open Access. It is an uphill battle, but he is persistent!
You’ll see that he has PLoS as his top link on both of his websites.
Scientists in the developing world are going to be among the biggest beneficiaries of Open Access in the future and I am looking forward to working with Open Access promoters in various countries around the world. With Vedran and Danica, I already have a head-start with Serbia. Where are the others? E-mail me!

ClockQuotes

If it was an overnight success, it was one long, hard, sleepless night.
– Dicky Barrett

My picks from ScienceDaily

Many Insomniacs Turn To Valerian And Melatonin To Help Them Sleep:

A study published in the July 1st issue of the journal SLEEP finds that large segments of the U.S. population use valerian or melatonin to treat their insomnia.
The study, authored by Donald L. Bliwise, PhD, of Emory University in Atlanta, Georgia, focused on the data collected from 31,044 individuals from the 2002 Alternative Health/Complementary and Alternative Medicine Supplement to the National Health Interview Survey (NHIS).
Dr. Bliwise discovered that, of the survey sample, 5.9 percent used valerian and 5.2 percent used melatonin. Relatively greater use occurred in individuals under the age of 60. The decision to use such substances was made in consultation with a health care provider less than half of the time.

Continue reading

Professor Steve Steve is helping me work

Steve%20Steve%20at%20home.jpg
Steve Steve is traveling again. He is a big fan of PLoS…