clock | August 3, 2007This post from March 27, 2006 starts with some of my old research and poses a new hypothesis.
The question of animal models
There are some very good reasons why much of biology is performed in just a handful of model organisms. Techniques get refined and the knowledge can grow incrementally until we can know quite a lot of nitty-gritty details about a lot of bioloigcal processes. One need not start from Square One with every new experiment with every new species. One should, of course, occasionally test how generalizable such findings are to other organisms, but the value of models is hard…
clock | August 3, 2007
Statistical analysis of crew-members' deaths on Starship Enterprise, including various risk factors.
(Via)
clock | August 3, 2007A month has passed.
It was a steep learning curve, but I think I have climbed high enough on it to be confident that I'll be fine on my own back in Chapel Hill. Being a part of the PLoS team is such an exhillarating experience - there is so much energy and optimism around the office, everybody from CEO to the newest intern living, breathing and dreaming Open Access 24/7.
Not to bore you about the job any more - you will be hearing about PLoS over and over again here - let me, for now, just show you some pictures (under the fold) from the farewell party last night at Jupiter in downtown…
clock | August 3, 2007 This post is a modification from two papers written for two different classes in History of Science, back in 1995 and 1998. It is a part of a four-post series on Darwin and clocks. I first posted it here on December 02, 2004 and then again here on January 06, 2005:
II. Darwin on Time
There is a season for everything
And a time for every purpose under the heaven:
A time to be born, and a time to die:
A time to plant and a time to reap.... (Ecclesiastes)
In this section I will attempt to evaluate from Darwin's writings what he thought about the selective role of environmental periodicities…
clock | August 2, 2007This post about the origin, evolution and adaptive fucntion of biological clocks originated as a paper for a class, in 1999 I believe. I reprinted it here in December 2004, as a third part of a four-part post. Later, I reposted it here.
III. Whence Clocks?
Origin, Evolution, and Adaptive Function of Biological Clocks
The old saw about the early bird just goes to show that the worm should have stayed in bed. (Heinlein 1973)
Now darkness falls.
Quail chirps.
What use Hawk eyes?
(Basho)
Local/temporary and global/universal environments. In the study of adaptive functions, usually the question…
clock | August 1, 2007The memories of long love gather like drifting snow, poignant as the mandarin ducks who float side by side in sleep.
- Lady Murasaki
clock | August 1, 2007I started my stay in San Francisco with a dinner at Incanto and ended it tonight with a dinner at Incanto again. Last time, the duck fries were not on the menu, but this time I had better luck. Delicious!
clock | August 1, 2007Four Stone Hearth #20 is up on Afarensis.
Festival of the Trees #14 is up on Via Negativa
Circus of the Spineless #23 is up on Words And Pictures.
Tangled Bank 85 - The Reductionist's Tale is up on Migrations.
Carnival of the Liberals #44 is up on The Richmond Democrat.
130th edition of The Carnival Of Education is up on Dr. Homeslice.
clock | August 1, 2007On this day one year ago, PLoS ONE opened its doors to manuscript submissions. Chris Surridge, the Managing Editor, wrote a blog post recounting the past year:
The initial success of PLoS ONE is something unprecedented in scientific publishing. It has been achieved because of the commitment and faith of hundreds of people: PLoS staff, editorial and advisory board members, reviewers, authors and particularly readers. And yet this is only a very small step towards an open, interactive and efficient literature that will accelerate scientific progress. Over the coming months, we will take…
clock | August 1, 2007The textbook example of commensalism was always the interaction between trees and the birds who make nests in those trees - it was always assumed that the birds gain from this relationships, while the trees are not in any way affected by it.
Now, a new study came out, demonstrating (for the first time, as far as I know - is that correct?), that the relationship between at least some trees and some birds is actually mutualism, i.e., both partners profit from the relationship:
Chickadees, nuthatches and warblers foraging their way through forests have been shown to spur the growth of pine…
clock | August 1, 2007This post, originally published on January 16, 2005, was modified from one of my written prelims questions from early 2000.
EVOLUTIONARY PHYSIOLOGY OF BIOLOGICAL CLOCKS
"Circadian clocks allow organisms to predict, instead of merely react to, cyclic (predictable) changes in the environment". A sentence similar to this one is the opening phrase of many a paper in the field of chronobiology. Besides becoming a truth by virtue of frequent repetition, such a statement appeals to common sense. It is difficult to imagine a universe in which it was not true. Yet, the data supporting the above…
clock | July 31, 2007and so this tree
Oh, that such our death may be!
Died in sleep, and felt no pain,
To live in happier form again:
From which, beneath Heaven s fairest star,
The artist wrought this loved guitar;
- Percy Bysshe Shelley
clock | July 31, 2007There are 32 new papers that just went live on PLoS ONE and here are a couple of titles that got my immediate attention:
Changing Hydrozoan Bauplans by Silencing Hox-Like Genes by Wolfgang Jakob and Bernd Schierwater:
Regulatory genes of the Antp class have been a major factor for the invention and radiation of animal bauplans. One of the most diverse animal phyla are the Cnidaria, which are close to the root of metazoan life and which often appear in two distinct generations and a remarkable variety of body forms. Hox-like genes have been known to be involved in axial patterning in the…
clock | July 31, 2007Flip Of Genetic Switch Causes Cancers In Mice To Self-destruct:
Killing cancerous tumors isn't easy, as anyone who has suffered through chemotherapy can attest. But a new study in mice shows that switching off a single malfunctioning gene can halt the limitless division of tumor cells and turn them back to the path of their own planned obsolescence.
Zebrafish Research Provides Answers About Neurological Development:
Zebrafish cost about a dollar at the pet store. They grow from eggs to hunting their own food in three days. Adults can lay up to 500 eggs at once... and you have more in common…
clock | July 31, 2007There is a new study this week about an unusual reproductive strategy in a bird, the Penduline Tit, which, if anthropomorphized, would appear to be an example of some really bad, deceptive parenting. But, Anne-Marie and Kate demonstrate the proper way to think about this. Obligatory Readings of the Day.
clock | July 31, 2007Encephalon #28 is up on Bohemian Scientist.
Gene Genie #12 is up on My Biotech Life.
Triskaidekaphilia: the 13th Carnival of Mathematics is up on Polymathematics.
Carnival of the Green #88 is up on Nicomachus.
Grand Rounds, Vol.3, n.45 are up on Health Business Blog
Radiology Grand Rounds XIV are up on Sumer's Radiology Site.
Pediatric Grand Rounds 2.8 (Harry Potter theme) are up on Highlight HEALTH.
Carnival of Homeschooling #83 is up on Mom is Teaching.
clock | July 31, 2007The Demise of Old-Fashioned Scholarly Journals? (I love the photo on the top of the article!)
Thoughts about the sea of information
Open Science like the start of Apple?
Nonsense, and pernicious nonsense at that.
Reading Journals Can Seriously Damage Your Wallet
Hybrid journals and the transition to OA
Oxford open access experiments
Oxford: Traditional Publisher Illustrates Leadership in Transition to Open Access
Transitioning to open access series
Course check: A conversation with three open access publishers about the challenges of sustainability
clock | July 31, 2007
If you are one of the few of my readers who actually slogged through my Clock Tutorials, especially the difficult series on Entrainment and Phase Response Curves, you got to appreciate the usefulness of the oscillator theory from physics in its application to the study of biological clocks. Use of physics models in the study of biological rhythms, pioneered by Colin Pittendrigh, is an immensely useful tool in the understanding of the process of entrainment to environmental cycles.
Yet, as I warned several times, a Clock is a metaphor and, as such, has to be treated with thought and caution…