Clock Tutorials
clock | August 14, 2006
This post was originally written on February 11, 2005. Moving from relatively simple mammalian model to more complex systems.
I have previously described the basic properties of the circadian organization in mammals. Non-mammalian vertebrates (fish, amphibians, reptiles and birds) have more complex circadian systems than mammals. While the suprachiasmatic area remains a site of circadian pacemakers, it is, unlike in mammals, not the only such site.
The pineal organ, which in mammals is a purely secretory organ, is directly photosensitive in other vertebrates (with the exception of snakes)…
clock | August 14, 2006
This February 06, 2005 post describes the basic elements of the circadian system in mammals.
The principal mammalian circadian pacemaker is located in the suprachiasmatic nuclei (SCN) of the hypothalamus. The general area was first discovered in 1948 by Curt Richter who systematically lesioned a number of endocrine glands and brain areas in rats. The only time he saw an effect on circadian rhythms was when he lesioned a frontal part of hypothalamus (which is at the base of the brain) immediatelly above the optic chiasm (the spot where two optic nerves cross). Later studies in the 1970s…
clock | August 14, 2006
I wrote this post back on February 02, 2005 in order to drive home the point that the circadian clock is not a single organ, but an organ system comprised of all cells in the body linked in a hierarchical manner:
In the earliest days of chronobiology, the notion of circadian organization was quite simple. Somewhere inside the organism there was a clock. It was entrained by light via photoreceptors (e.g., the eye) and it drove the rhythms of various biochemical, physiological and behavioral events in the body:
Very soon this simple notion became difficult to sustain in light of new data.…
clock | August 14, 2006As I announced last week, this week will be All Clocks All The Time. Why?
First, I need to move some of the old posts from Circadiana over here, at a faster rate than I've been doing so far. Second, I'll be quite busy this week. Third, I need to hype myself up for the final effort at my Dissertation so blogging about any other topic would be counter-productive (not that it's not gonna happen...)
So, here is the deal. Over the next five days I will repost some old and write some new posts on three big topics in Chronobiology: circadian organization, entrainment and photoperiodism.…
clock | August 7, 2006A 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).
As I have mentioned before, there was quite an angst in the field of chronobiology around 1960s about the lack of undestanding of circadian and other rhythms at cellular and subcellular levels. Experiment involved manipulation of the environment (e.g,. light cycles) and observing outputs (e.g., wheel-running rhythms), while treating the clock, even if its anatomical location was known, as a "black box".…
clock | July 31, 2006 I wrote this post back on January 23, 2005. It explains how clock biologists think and how they design their experiments:
So, are you ready to do chronobiological research? If so, here are some of the tips - the thought process that goes into starting one's research in chronobiology.
First, you need to pick a question. Are you interested in doing science out of sheer curiosity to discover stuff that nobody knew before (a very noble, but hard-to-fund pursuit)? Or would you prefer your work to be applicable to human medicine or health policy, veterinary medicine, conservation biology, or…
clock | July 17, 2006This 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 | July 10, 2006This 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 3, 2006
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.
It appears that every scientific discipline has its own defining moment, an event that is touted later as the moment of "birth" of the field. This can be a publication of a paper (think of Watson and Crick) or a book ("Origin of Species" anyone?). In the case of Chronobiology, it was the 1960…
clock | June 26, 2006
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.
Here is a brief overview of the concepts and terms used in the field of chronobiology. I will write much more detailed accounts of various aspects of it in the future.
Seasons of the year, phases of the moon, high and low tides, and alternation between night and day are examples of cyclic changes in the environment. Each presents a different…
clock | June 19, 2006 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:
There are traditionally three approaches to research and teaching of physiology: biochemical, energetic, and homeostatic. The three are by no means exclusive and all good physiologists will include all three in their work and teaching, but each with a different emphasis.
Biochemical approach is typical of human/medical physiology. Physiological mechanisms are described at lower and lower levels, until the molecules…
clock | June 12, 2006
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.…