Monday, March 14, 2005

Quarterly Summary

This blog is now three months old and, as it is Spring Break, this may be a good time to take a little break, take stock of what was accomplished so far and indicate the plans for the future.

Who am I trying to attract to this blog?

First, I'd like to see laypeople - non-scientists who are interested in clocks and sleep. Most of my readers are in this category, arriving here through the links on Boing Boing, Andrew Sullivan, Blogdex and Delicious. While you may come in through a link to a "fun" post, perhaps something in the categories of ClockNews, ClockQuotes or ScienceBlogging, I hope you look around and read the more serious stuff, too. Hopefully you will get "hooked". I will continue to write posts on various topic and at various level of detail, so hang around - there is something for everybody here.

Second, I want to see here biologists who want to keep up with chronobiology although it is not their area of expertise. Many such bloggers are already familiar with this blog through The Tangled Bank, the blog carnival of biology blogging, and Grand Rounds, the carnival of medical blogging.

Third, I hope to see more chronobiologists who want to find each other, chat, gossip, exchange information, etc. Only a couple are aware of this blog to date. In a couple of more months, when I think that the quantity and quality of content warrants it, I will inform the chronobiological community and actively recruit guest-bloggers.

Finally, I would like to see here students taking classes in chronobiology. The category Clock Tutorials is specially designed for you, as no good textbook is available at the moment. In fact, I am aware of four such students who have used my ClockTutorials as an aid in studying and they did remarkably well - at the top of their class - on the last mid-term exam. But watch out! When you check the ClockTutorials category, those posts marked as "CT" are likely to be basic non-controversial stuff. The other posts are, in the good blog tradition, strongly opinionated and have more of my voice in them, so you need to think carefully while reading those as your instructor may not neccessarily agree with all of my opinions.

What is the purpose and goal of this blog?

I wish to develop this blog in three phases. I think that this blog is currently in the middle of the first phase: building content and building readership, particularly non-scientific readers. The second phase will involve expanding the blog into a website of which the blog is going to be just one part. This will entail some technical learning on my part, some tweaking of design, and further expansion of content, i.e., not just my posts, but also links to other websites and blogs, to homepages of researchers in the field, etc.

I will try to make data-analysis software available, links to online versions of scientific papers, archives of historical documents (e.g., scans of Aschoff's doodles), job ads, links to related books on Amazon (or other bookseller), etc. Once I finish building the site, it will enter the third phase, where it will serve as the online hub for the chronobiological community: the starting place in a search for all information related to clocks and sleep, with the blog serving as a meeting-place where information is exchanged, meetings announced, job searches and student positions posted, collaborations started, etc.

An important part of this endeavor is the ClockTutorials series. I intend to finish this series of posts containing very basic information on various topics by May. After that, I will go back and add a couple of more posts on each topic containing much more detailed information, more references, and more figures (for some of which I will have to ask for permission). Thus I will build a layered inter-linked "textbook" containing, for each topic, a starting post that is very basic that further links to more advanced posts. Instructors can then use this as a teaching resource. Perhaps I can even edit the final product and form a PDF file that can be downloaded here for free (perhaps with a tip-jar if someone feels I deserve a donation). The best thing about an online "textbook" is that it is not a dead object - it can be and will be updated in real time, as the new findings get published.

Clock Tutorials

So far, in the ClockTutorials series I have written an introduction to chronobiology and a post explaining the basic terms and concepts one needs in order to be able to read the rest of the series. I have written a big, four-part post situating chronobiology within its philosophical and historical context, the first part describing Darwinian methodology, the second part covering early history of the field, the third part looking at evolution of clocks through Darwinian prizm, and the fourth part coming back to philosophical and methodological issues. Later, I have expanded on the historical part by also covering more recent history of the field, and expanded on clock evolution from a slightly different perspective. If you are interested in history, I have also written two posts describing how early chronobiology was lumped together with some bad science and some pseudo-science.

All of those early posts were ABOUT chronobiology. I made the transition from theory to practice through a post on methodology. Then, I got into the meat of the field, discussing circadian organization, first from a theoretical perspective, then giving examples of mammals and non-mammalian vertebrates, and finally adding what is known about three individual species: the Japanese quail, the ant-lion, and the human (understandably my most popular post, especially as it is heavily focused on sleep patterns). Since humans are not my "forte", I have also directed you to a website that does a better job on this topic, another one on bipolar disorders, as well as to a blog that covers a specialized topic of time perception in humans. I have also covered some recent research on melanopsin, melatonin, fruitflies, and mammalian clocks, and introduced you to the premier journal in the field.

What comes next is the hardest part of chronobiology - formal analysis of entrainment. This is not covered very clearly in old books and sometimes is not presented well in class either (though I was very fortunate when I took the class to have an exceptionally clear instructor). This is usually the part that pushes students' grades down as it is conceptually difficult. I have started very briefly on the topic earlier on, but within next couple of weeks I will try to present it in a series of short, bite-sized, and hopefully clearly written posts. If you bear with me, and end up understanding how Phase-Response Curves (PRC) are constructed, interpreted, modified and used, you will be able to understand the nitty-gritty physiological research that flows out of it. I may add a post on limit cycles as well, just for fun, but will, for now, avoid topological analysis and more complex mathematical modelling (perhaps I can get a guest-blogger later on to cover those topics).

If you grasp the PRC, you will be able to understand the subsequent topics regarding seasonality: both circannual rhythms and photoperiodism. After that, I will briefly cover the genetics and biochemistry of circadian clocks (including a historical perspective). The next topic involves development, including the embryonic development of the clock, the transfer of circadian (and photoperiodic) information from mother to fetus, and evidence for involvement of the circadian clock in timing of developmental events. The rest of the course is comparatively easy: Continuously Consulted Clocks (as used in spatial orientation), circatidal and circalunar rhythms. So buckle-up, we are ready to take off.


Blogger Sara said...

I have some responses for you in my blog. Thanks for visiting.

8:55 PM  
Blogger Sir Oolius said...

I'm still here!

8:36 PM  

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