Well, I got another paper revised and out the door a couple of hours ago (it started life as a series of blog posts on microbial species here), so I am feeling almost lightheaded. But I have one other paper to revise and a grant application to write, and a conference on evidence based medicine to go to, all in the next fortnight, so all in all, I'm not exactly spare with time right now. So serious blogging (= defending agnosticism against the atheist hordes) will be a bit light for a while now. I was thinking of doing one on clades, to introduce folk to phylogenetics. Eventually.
The grant application might spin off a few posts on biodiversity measures. I use this blog sometimes as a way of taking notes, so excuse the scatty nature of these posts if they come your way.
This past year has been one of the more, errr, "interesting" ones of my otherwise mundane life. A major screwup in the university has meant that the people I came here to work with are gone or will be leaving soon. I failed to get an interview for four jobs. My species book has been knocked back or suffered reviewer roulette from 9 publishers. My marriage ended (amicably; we are still friends, but a 19 1/2 year trial period is enough), and I moved, selling a house we bought less than a year ago at a loss (what is it with me and real estate? I have lost money on every house I have bought. Think of it as expensive rent...). This next year can only be better.
But I am optimistic. I feel motivated to do some serious work, and I have an Idea, which I will be working on over the next couple of years. I also have to rewrite my book, of course, and try again. It'll be a killer if I finish it, believe me. I have a new paper half done on the essentialism myth in biology, and I'll be visiting some ecology departments around the country in the next month or two as well. So life is not dull, exactly. But there are times I wonder what it's like to have a social life. I had one once. I remember it well.
Oh, and I went back to the gym yesterday, and muscles that according to the textbooks don't exist are complaining...
Enough about me. The Idea: I think that the unifying concept of biology is not genetics, or systems, but thermodynamics. Organisms are dissipative structures - this hasn't been taken as far as it ought to be. Ecosystems are also dissipative structures, as are populations, and even species. This brings development, metabolism, ecology, evolution and even structural biology into a single domain. Of course, it also means that biology is wholly supervenient on physics, but I can live with that. I may expound on this further, but I'm waiting to see the draft of Alex Rosenberg's book on the topic (we had similar ideas, so since he's established, I have to give him priority. Another Great Idea of mine that someone else had first... the latest in a long line).
So check in from time to time and see if I have gone further into the void than usual.
John, best of luck with all your projects this year. I'm particularly interested in whatever you write about the essentialism myth in biology.
Thermodynamics is a lot like evolution. If you think you understand it, you probably don't. :-)
I'm reminded of this on a daily basis by people who write me about the thermodynamics in my book. On this topic it seems you can't please any of the people any of the time!
Good luck, John. A lot of folks, including me, share the general suspicion that life is part of a general, law-like tendency of nature to build up complex structures the better to dissipate energy. Unfortunately, attempts to nail the idea down have wrecked many a reputation--Brooks and Wiley come to mind. Evidentally some theoretical discovery is needed to come up with a case convincing to the physicists or, alternatively, to show us that we were barking up the wrong tree all along.
The most recent attempt to understand evolution thermodyanmically that I've seen appears in a book by R.J.P. Williams and J.J.R. Frausto de Silva: The Chemistry of Evolution, which understands the grand revolutions in the history of life as depending on the exploitation of a series of inorganic elements as indispensible catalysts and reaction centers that make possible everything from anerobic respiration to complicated nervous systems. The book appears to be a long riff on the potentialities of the periodic table, but the chemistry is deployed to explain energy flows.
I'll join the chorus of well-wishers -- I hope that this year works out better. I'm very interested in this thermodynamics thing  and your stuff on essentialism is always worth reading.
 If I recall correctly, if your idea pans out, biology will be supervenient on thermodynamics, but not necessarily mechanics, unless someone's fixed the Poincare recurrence problem while I wasn't looking! Well, it amuses me, anyway...
Count me in as another well-wisher. I'm surprised your book hasn't found a publisher: I hope there's some good, constructive criticism in amongst the rejections.
I'd be interested in seeing what your thoughts are on diversity measures, having done a bit on them myself (=putting the boot into species richness estimators).
Have you talked to Bill Sherwin in Sydney? He's got this idea that Shannon's entropy could be used to measure biodiversity across different scales. I'm not sure I'd try to connect it to your Big Idea, but it might at least be worth exploring.
There was a note up in the old lab here (when we were next to the museum) which said (roughly) that the Second Law of Thermodynamics, as it applies to life, states that organisms survive by making a bigger mess of their environment.
The new ID paradigm: Three
Larry is correct about the understanding of thermodynamics, but there's a lot of work being done in specialist cases lately, and I thought it might be time to bring them together rough and ready. [Side note: a philosopher I know well said at a recent conference "but organisms are closed systems, so the second law of thermodynamics doesn't apply" which I had to bite my tongue over.] In particular there's work done on thermodynamics and ecosystems.
Brooks and Wiley failed largely because they didn't separate the physical aspects of thermodynamics from the information similarities of information theory, a stumbling block a lot of philosophers and biologists don't surmount. They treated the mathematical equations as synonymous, when we know that while all information processing has to be thermodynamically active, not all thermodynamics is informational. Since I want to eliminate information talk except in those rare cases where the system is actually an information processor (like cell signalling, and nervous systems), I do not want to do that.
On Shannon diversity - this is an old metric used in biodiversity. It goes back to the time of Fisher, although Margalef is perhaps the first to use it explicitly. Since Shannon's metric is a measure of difference, it of course can be used, but the choice of "units" to measure is crucial, and that seems not to have been resolved yet. Genes? Species? Trophic nodes? It's up for grabs.
Scale invariant measures, eh? Sounds interesting. I'll go see him when I'm in Sydney.
Margalef, R. (1968), Perspectives in Ecological Theory. Chicago: Chicago University Press.
Ah, but did you stop smoking?
As to the atheist horde, I'll keep biting 'em on the knees until you can back to smiting them hip and thigh.
Ah, but did you stop smoking?
Yes. Twice. I'm gearing up to do it again too.
Good luck, John.
It's probably way behind your particular curve, but can I remind you of a couple of papers that I've mentioned in talk.origins discussions in the past:
"Life as a manifestation of the Second Law of Thermodynamics" (Schenider and Kay)(available in various formats from http://citeseer.ist.psu.edu/schneider94life.html)
"Ecosystems as Self-organizing Holarchic Open Systems: Narratives and the Second Law of Thermodynamics"
Kay has a page at http://www.jameskay.ca/about/thermo.html specifically on the general issue - unfortunately, when I checked this morning, the links to his papers don't work - that's entropy, man...
(Update - it seems that that page has been abandoned - try http://www.nesh.ca/jameskay/www.jameskay.ca/pubs/index.html for a page with up to date links to the above and a whole heap of other papers on the topic).
Schneider and Sagan have a book on this:
Schneider, Eric D., and Dorion Sagan (2005), Into the cool: energy flow, thermodynamics, and life. Chicago, Ill.: University of Chicago Press.
The blurb indicates they are going for a unification approach too.
"The Idea: I think that the unifying concept of biology is not genetics, or systems, but thermodynamics."
I'm sorry to hear that. Once evolution takes over, the physical substrate and its 'laws' are background idiosyncrasies to be taken advantage of, as the vulture said of gravity.
E-mail me. ASAP.
Just as I thought - you're way ahead...
Is the Schneider/Sagan book worth a look? I've read the Nature review (I like Doyne Farmer's comment - referencing the bookjacket comparison to Darwin - that "While it may be wise to stand on the shoulders of giants, it is not advisable to stand back to back with one and call for a tape measure"), which is happy about it while it sticks to thermo, but complains that the linkage to selection processes is never explained.
I'll let you know when I read it. Schneider is The Man on biothermo...