Mario’s Entangled Bank

Here’s is a priceless quote from one of the great classical papers in theoretical ecology. It’s from Michael Rosenzweig’s 1971 paper Paradox of Enrichment: Destabilization of Exploitation Ecosystems in Ecological Time (Science 171: 385-387). This was written 37 years ago and it’s still holds true…, and we still have not learned our lesson.

Schemes for increasing primary productivity by enriching and ecosystem’s energy or nutrient flow are much in evidence today and are probably a reflection of the increasing demands of the world’s population. Such schemes may end in catastrophe.

Chuckie ‘D’ on the amazing duck feet:

When a duck suddenly emerges from a pond covered with duck-weed, I have twice seen these little plants adhering to its back; and it has happened to me, in removing a little duck-weed from one aquarium to another, that I have quite unintentionally stocked the one with fresh-water shells from the other. But another agency is perhaps more effectual: I suspended a duck’s feet, which might represent those of a bird sleeping in a natural pond, in an aquarium, where many ova of fresh-water shells were hatching; and I found that numbers of the extremely minute and just hatched shells crawled on the feet, and clung to them so firmly that when taken out of the water they could not be jarred off, though at a somewhat more advanced age they would voluntarily drop off.

This begs the question - did duck feet evolve for the dispersal of duck-weed or fresh-water shells? Perhaps this study will shed some light on this nagging question.

There is a letter in yesterday’s The Times by John Sulston and Joseph Stiglitz (both Nobel laureates)  about the ownership of science and how it is held back by outdated laws (think about that NPG). I’ll rest my case and let it speak for itself.

The ideal shared by almost all scientists is that science should be open and transparent, not just in its practices and procedures, but so that the results and the knowledge generated through research should be freely accessible to all. There is a broad consensus in the scientific community that such openness and transparency promotes the advancement of science and enhances the likelihood that the benefits of science are enjoyed by all. For more than a hundred years, these principles have been the bedrock of academia and the scientific community.

Hat tip: Open Access News

Here’s a clip from a documentary film by Frances Pinter and David Percy about business models in the publishing world that use Creative Commons licenses where Timo Hannay of Nature is talking about open content (not sure how open content differs from open access when it comes to peer-reviewed journal articles, but for the purposes of this post I’ll treat them as equivalent).

It’s nice to hear Timo Hannay’s view of open content (actually rather refreshing after reading Declan Butler’s tantrum piece). I am a bit puzzled, however. Does Hannay’s views represent the view of the Nature Publishing Group as a whole or do they represent only his own views? And, how does all of this  fits in with the Nature vs. PLoS runaway train of Declan Butler that has been whipping up a storm in the blogosphere over the last few days (see Bora’s post for a succinct summary). The pieces by Declan Butler (he actually has two stories, the second and the first) unequivocally give a impression that Nature is (as Timo puts it in the clip) one of those “hostile” and “reactionary” publishers that are in a “defensive mode” towards the Open Access publishing model that “give the whole industry a disservice”.

Hat tip: Open Access News

Good news for all of us that are interested in ecological modeling using R - Ben Bolker’s book Ecological Models and Data in R has been published by Princeton University Press.  Over the last year or so I have been reading drafts and blogging about the book (it was available at Bolker’s web site). I liked what I saw and have eagerly anticipated it’s publication. According to the book’s web site it will be published in September but can already be pre-ordered. I’ll report back once I get my hands on a copy of it.

To wet your appetite, here’s the table of contents and a snippet from the release statement by PUP:

Ecological Models and Data in R is the first truly practical introduction to modern statistical methods for ecology. In step-by-step detail, the book teaches ecology graduate students and researchers everything they need to know in order to use maximum likelihood, information-theoretic, and Bayesian techniques to analyze their own data using the programming language R. Drawing on extensive experience teaching these techniques to graduate students in ecology, Benjamin Bolker shows how to choose among and construct statistical models for data, estimate their parameters and confidence limits, and interpret the results. The book also covers statistical frameworks, the philosophy of statistical modeling, and critical mathematical functions and probability distributions. It requires no programming background­only basic calculus and statistics.

Wordle is a nifty little web application for generating word clouds of any text. Of course, I could not resist cloudifying The Origins of Species - all of its 154138 words. Makes a great desktop background.

Next year, 2009, is the 200th anniversary of Darwin’s birth (February 12, 1809), as well as being the 150th anniversary of the publication of his masterpiece, “On the Origin of Species” (November 24, 1859). Although much of the upcoming celebrations are centered on Darwin, the day when the world actually changed was 150 years ago on today’s date (July 1, 1858). This was the day when Charles Darwin and Alfred Russel Wallace’s joint discovery of natural selection, the main driving force of evolution, was announced for the first time by the Linnean Society of London. Two papers were read at the meeting and where jointly entitled On the Tendency of Species to form Varieties; and on the Perpetuation of Varieties and Species by Natural Means of Selection (the papers are available at the web site of the Linnean Society of London). Although the two contributions ultimately became one of the the greatest scientific milestones in history, at the time, few in the audience were able to take in the full importance of the announcement and it passed rather unnoticed. In his annual presidential report presented in May 1859 Thomas Bell wrote that

“The year which has passed has not, indeed, been marked by any of those striking discoveries which at once revolutionize, so to speak, the department of science on which they bear.”

Charles Darwin’s own recollections of the meeting and its aftermath were more prosaic. In his autobiography, written in 1876 for his children, he recalled,

“Nevertheless, our joint productions excited very little attention, and the only published notice of them which I can remember was by Professor Haughton of Dublin, whose verdict was that all that was new in them was false, and what was true was old.”

It is perhaps fitting that as we are about to start the celebrations of one of the greatest achievements in the history of science another scientific revolution is in the making. Science is currently undergoing a transformation from being a closed door enterprise where research was only accessible to the selected few having access to payed journal subscriptions, to an Open Access (OA) model where research is available freely online to anyone under limited copyright and licensing restrictions. The effect that OA will have on the way scientific research is accessed and disseminated cannot be underestimated and, in this respect, it has much in common with the way the evolutionary theory profoundly changed our world. That anyone can access high-profile ground breaking research instantaneously and free is a powerful idea. Research can now instantaneously and with no restrictions reach the small nonprofit research institute, the private citizen sitting at his desktop at home, journalists, artists, students and researchers in developing countries. Who knows, given the right opportunities, which includes unrestricted access to high-profile research, the next Darwin or Einstein may very well be from Africa.

There is perhaps no more compelling argument for OA and against closed-access than Jonathan Eisen’s inaugural editorial as the Academic Editor-in-Chief at PLoS Biology.

An amazing project is in the making at the University of British Columbia. The Biodiversity Research Centre is being erected at the very spot where the legendary Huts used to be located. The building will be home to the Biodiversity Research Centre and will contain offices for students and staff, instructional space, research labs, the and the Beaty Biodiversity Museum. The Beaty Biodiversity Museum will be a new public museum dedicated to enhancing the public’s understanding and appreciation of biodiversity, and making the research conducted by the scientists of Biodiversity Research Centre accessible to the public. As part of the exhibits the museum will display a complete blue whale skeleton in a glass atrium. The 26 m long skeleton of a blue whale that beached on the coast of PEI in 1987 and was excavated last winter will be making the 6000 km journey across Canada and will be the the first blue whale skeleton on display in Canada

The fascinating story and the amazing journey of this skeleton is described at the Beaty Biodiversity Museum Blue Whale Project pages.

Ok - I know I promised to report back from the meeting of the Canadian Society for Ecology and Evolution (CSEE) held at the University of British Columbia (UBC) in Vancouver. The two recent big wig meetings (both of which I could not attend) - Evolution 2008 and the meeting on Sex and Recombination - reminded me of my promise. So here we go.

This years meeting was only the third annual meeting of the Canadian Society for Ecology and Evolution (CSEE) which was formed only in 2006. 450 delegates attended this year’s meeting showcasing the world-class level of Canadian research in ecology, evolutionary biology, and biodiversity. The topics covered in the various sessions covered a much broader range than just ecology and evolution, e.g. invasive species, plant ecology, aquatic communities, evolutionary applications, conservation biology, host-pathogen, salmonid genetics, polyploidy, biodiversity, nutrients, reproductive biology, speciation, genetics, climate change, etc. (the full schedule is here)

There were 216 contributed talks (including yours truly), 80 contributed posters, 3 symposium with 23 additional presentations, 1 public seminar (by Dr. Ian Stirling), 3 receptions (opening reception, poster reception, and an amazing evening reception at the Vancouver Aquarium), 3 workshops (Symposium for Women entering Ecology and Evolution Today, Mesquite Workshop, How to Land a Job in Academia), 2 NSERC presentations, there were representatives from 10 publishing companies were present (incl. PLoS), and 52.7 tonnes of CO2 emissions were offset by donations to the Offsetters.

I particularly enjoyed Graham Bell’s presidential address Adapt , or Die (which is adapted from his recent paper in Evolutionary Applications freely available online in the inaugural issue of the journal) which was a powerful discourse on the evolutionary effects of global climate change. The lunch-workshop on Searching for and landing a job: How to get prepared for academia by Daniel Promislow (based on his book with the same name) attracted over 130 young graduate students and postdocs. The highlight of the meeting was, however, the evening reception at the stunning Vancouver Aquarium providing a sobering reminder of why we are doing research in ecology and evolutionary biology and what we may loose as the earths environment is changing.

There are some pictures from the meeting posted here.

Kudos to the organizing committee and all the volunteers who did an amazing job organizing and hosting this event.

I am looking forward to next year’s meeting at Dalhousie University in Halifax (May 14-16, 2009).

Chuckie ‘D’ says:

On the ordinary view of each species having been independently created, we gain no scientific explanation.

Due to the massive flooding in Iowa the meeting on Sex and Recombination was canceled. So for all of you sex-refugees out there here’s a bit of makeup sex advice from Dr. Tatiana herself. Apparently she gave a public lecture at the Evolution 2008 meeting.

Hat tip to Science Buzz

The Evolution 2008 meeting is in progress as I write (and I am cursing the noodly appendages of the FSM that I cannot be there). The next best thing to actually being there, of course, is to blogroll the meeting…, assuming that some evolutionists in attendance actually practice live blogging. I have not been able to find much so far, my current blog loot is:

• Fascinating Bugs (which does not say much)
• Greg Laden’s blog (a thorough post on the pre-conference teachers day)
• The Austringer (daily meeting tidbits)
• Pharyngula (is “physically present” and encounters a mathematical word salad)

Bring it on fellow evolutionists.

Perhaps unsurprising, the Lenski-Conservapedia affair continues. If you are not familiar with this saga The Pandas Thumb provides a rather extensive summary, or to keep it short (also from The Pandas Thumb):

… basically, Andy Schlafly has been demanding every bit of data from Richard Lenski’s work on the evolution of E. coli, despite the fact that Schlafly doesn’t have the background to understand it and doesn’t have any plan for what he would do with it if he got it. Lenski has been polite and helpful in his replies; his first response is a model for how to explain difficult science to a bullying ideologue. Now his second response is available, and while he has clearly lost some patience and is unequivocal in denouncing their bad faith efforts to discredit good science, he still gives an awfully good and instructional discussion.

So who are the two protagnosist? According to Pharyngula

Schlafly is a creationist and ideologue of the worst sort; he has no qualifications in biology,…

and according to Wikipedia Richard Lenski is:

an American evolutionary biologist. He holds the office Hannah Distinguished Professor of Microbial ecology at Michigan State University. In 1996 Lenski won a MacArthur Fellowship (a so-called “genius award”). In 2006, he was elected to the United States National Academy of Sciences. Lenski is best known for his long-term E. coli evolution experiment, and his work with digital organisms, using Avida.

Lenski’s response to the first letter from Schlafly is reprinted by Pharyngula and the response to the second letter is reprinted by The Pandas Thumb. Both posts has spawned a storm of comments (currently 143 at Pharyngula and 59 at The Panda’s Thumb).

My favorite is comment #11 in the Pharyngula post (the response to the first letter) which is priceless:

Schafly demanding data from Dr Lenski is like a 7 year old demanding his mother drive him to NASA headquarters to ask the chief commander there what kind of cheese the Moon is made of.

Apparently the Google Street View truck made a pass through Davis the other day and it seems that they did pretty thorough job. Here is a view of the little backwater street we used to live at.

It looks like they were not, however, able to get past the security gates around campus. I guess Google is not omnipotent after all.

Hat tip to Jonathan Eisen’s Davis blog.

For all of those of you living under a rock - Chuckie ‘D’ is coming to town! To make a long story short, check out Olivia Judson’s Darwinmania!

So apparently Chuckie ‘D’ is a blogger. Go figure - and I though I was being progressive.

Surely there will now be many new insightful quotes one will be able to ponder over, such as…

All the candidates who today aspire to lead that great nation [USA] will be convinced of the benefits of science and the truth of evolution I am sure.

Being a big Rokia Traore fan I was happy to find this post from TEDBlog in my blog roll this morning.

A perfect way of starting a day in the lab.

A while back I took the leap and changed my source control management system from Subversion to Git. This was not an easy or quick decision. Although I used Subversion for many years I had also grown increasingly unhappy with it’s quirks (it’s slowness, inflation of repository size, difficulty in merging, and its propensity for corrupting working copies).

It took a long time, however, to find a worthy replacement and then equally long to get around to the non-enviable task of migrating my repository (which consists of my entire home directory). A few months ago, however, I took the leap and migrated my entire repository to Git (which actually was surprisingly simple to do and without any hitches at all). After using Git for a while now I can only conclude that all the features that initially attracted me to Git work flawlessly. It’s distributed revision control system, where a working directory is a full-fledged repository with complete history and full revision tracking capabilities, not dependent on network access or a central server (in contrast to Subversion where you only checkout the revision you are asking for sans history), is incredibly useful particularly when working without network access (which I tend to do a lot). It’s is fast (even large commits are a matter of fraction of a second), the repository is small (the size of my repository went from 16GB under Subversion to less than 7Gb in Git - go figure), and merges are a breeze.

Yet another priceless piece of software from the wetware of Torvalds.

I am on my way to the 2008 annual meeting of the Canadian Society for Ecology and Evolution (CSEE). This year it is held at the University of British Columbia in Vancouver, my previous home base. It will be nice to catch up with friends and colleagues, hang out at UBC and in Vancouver for a few days.

Although one might perhaps not expect it, this is actually a rather sizable gathering with several concurrent session and probably a few hundred speakers coming from all over Canada (and beyond). Sessions cover all aspects of ecology and evolutionary biology, e.g. evolutionary applications, host pathogen dynamics, predation, salmon and stickleback genetics and evolution, conservation biology, biodiversity, population genetics, species interactions, and (of course) theoretical and statistical ecology. The line up for the meeting is awesome and I am really looking forward to it. I will be giving two talks during my stay here - one at the meeting and then an informal lab meeting style presentation in the Otto, Whitlock, and Doebeli labs.

Further report(s) will follow. Gotta go run and catch my flight now.