Google Importer
Google Importer is a useful Spotlight plugin that includes Google searches in Spotlight searches. This helps integrate your search into one interface, which seems like an obvious progression of Apple’s Spotlight technology.
Google calendar
Google Calendar has been featured in the news recently, and for good reason. Many of us have wanted access to a good online calendar program. One of my favourite features of Google Calendar is its integration with Gmail. If Gmail detects an event in your email message, a link appears that sends the information to Google Calendar. This is incredibly convenient and, seems to me, is one of the great promises of computers: reducing the tedious work that occupies much of our day.
An Inconvenient Truth
This looks like an incredibly important film. I hope it breaks all of the box office records.
Analysis of Count Data
When response variables are composed of counts, the standard statistical methods that rely on the normal distribution are no longer applicable. Count data are comprised of positive integers and, often, many zeros. For such data, we need statistics based on Poisson or binomial distributions. I’ve spent the past few weeks analysing counts from hundreds of transects and, as is typical, a particular challenge was determining the appropriate packages to use for R.
Getting Evolution Up to Speed
There’s a common notion that our technology has slowed, or even stopped, human evolution. Evidently, this is not true as researchers have found many locations of strong positive selection in the human genome. New evidence suggests humans are evolving more rapidly – and more recently – than most people thought possible. But for some radical evolutionists, Homo sapiens isn’t morphing quickly enough. (Via Wired News.)
SSHRC and the theory of evolution
This is quite a surprise, McGill University’s Brian Alters had his proposal to study the effects of intelligent design on Canadian education rejected by the Canadian Social Sciences and Humanities Research Council. A stated reason for the rejection was that Alters did not provide “adequate justification for the assumption in the proposal that the theory of evolution, and not intelligent design theory, was correct.” Granted, funding proposals can be rejected for a variety of reasons and the opinions of the reviewers do not necessarily reflect those of the funding body.
Deschooling, Democratic Education, and Social Change
Matt Hern provides an interesting podcast available from Canadian Voices. He considers the 150 year history of compulsory state education and asks what benefits it has provided. The basic question is, Why do we send our kids to school? Although the answer seems obvious, he takes a different approach and argues for alternatives to public education. I’m always fascinated when someone argues against what I believe to be obvious. That’s when I learn the most about my biases.
Desktop Manager
I’m convinced that no computer display is large enough. What we need are strategies to better manage our computer workspace and application windows. Exposé and tabbed browsing are great features, but what I really want is the equivalent of a file folder. You put all of the relevant documents in a folder and then put it aside for when you need it. Once you’re ready, you open up the folder and are ready to go.
Managing project files
As I accumulate projects (both new and completed), the maintenance and storage of the project files becomes increasingly important. There are two important goals for a file structure: find things quickly and don’t lose anything. My current strategy is as follows: Every project has a consistent folder structure: |-- analysis |-- data |-- db |-- doc |-- fig `-- utils analysis holds the R source files of the analysis. These, typically, are experiments and snippets of code.
Sun grid
Sun’s new Grid Compute Utility could be a great resource. As I described in an earlier post, running simulations can be a challenge with limited computer resources. Rather than waiting hours for my computers to work through thousands of iterations, I could pay Sun $1, which would likely be sufficient for the scale of my work. This would be well worth the investment! I spend a single dollar and quickly get the results I need for my research or clients.
Automator, Transmit, and Backup
The Strongspace weblog has a useful post about using Transmit and Automator to make backups. One challenge with this approach is backing up files scattered throughout your home folder. The solution is the “Follow symbolic links” option when mirroring. I created a backup folder and populated it with aliases to the files I’m interested in backing up. Mirroring this folder to Strongspace copies the files to the server. The other option is to use the “Skip files with specified names” feature, but this rapidly filled up for me.
Remote data analysis
My six-year old laptop is incredibly slow, particularly when analysing data. Unfortunately, analysing data is my job, so this represents a problem. We have a new and fast desktop at home, but I can’t monopolise its use and it would negate the benefits of mobility. Fortunately, with the help of Emacs and ESS there is a solution. I write my R code on the laptop and evaluate the code on the desktop, which sends the responses and plots back to the laptop.
Rails, sqlite3, and id=0
I’ve spent the last few days struggling with a problem with Plantae’s rails code. I was certain that code like this should work: class ContentController 'show', :id = @plant.id else ... end end def show @plant = Plant.find(params[:id]) end ... end These statements should create a new plant and then redirect to the show method which sends the newly created plant to the view. The problem was that rails insisted on asking sqlite3 for the plant with id=0, which cannot exist.
The Globe and Mail-- Constitutional reform
How about a constitutional right to a healthy environment? The Constitution of Canada guarantees its people important rights, such as freedom of religion, freedom of expression, fair trials, free elections, and language rights. But the effective exercise of these rights is impossible without safe water to drink, wholesome food to eat, and clean air to breathe. The right to a clean and healthy environment – arguably the most fundamental right of all – is conspicuously absent from our Charter of Rights and Freedoms, despite being a feature of the constitutions of many other nations.
Taxonomy release
Plantae now supports the addition and updating of species names and families. A rather important first step. Now onto adding character data to make the site actually useful.
plantae foundations
I’ve made a variety of important changes to plantae’s foundations. For the curious they are: Converted the webserver from apache to LightTPD. LightTPD is fast and easy to configure. Plus it has built-in support for FastCGI which makes plantae run much faster. Set up a Subversion repository. This manages the code for plantae and allows me to track and reverse changes. This will also be very useful if someone else helps with the coding.
Sexual interference within flowers of Chamerion angustifolium
Hermaphroditism is prevalent in plants but may allow interference between male function (pollen removal and dispersal) and female function (pollen receipt and seed production) within a flower. Temporal or spatial segregation of gender within a hermaphroditic flower may evolve to reduce this interference and enhance male and female reproductive success. We tested this hypothesis using Chamerion angustifolium (Onagraceae), in which pollen removal (male) and pollen deposition (female) were measured directly on hermaphroditic and experimentally produced unisexual flowers.
Plant breeding systems and pollen dispersal
This book of about 600 pages is written to provide practitioners of pollination biology with a broadly based source of methodologies as well as the basic conceptual background to aid in understanding. Thus, the book reflects the expertise of the assembled a team of internationally acclaimed scientists. Pollination biology enjoys over 200 years of scientific tradition. In recent years, the interdisciplinarity of pollination biology has become a model for integrating physics, chemistry, and biology into natural history, evolutionary and applied ecology.
The effect of protandry on siring success in Chamerion angustifolium (Onagraceae) with different inflorescence sizes
Protandry, a form of temporal separation of gender within hermaphroditic flowers, may reduce the magnitude of pollen lost to selfing (pollen discounting) and also serve to enhance pollen export and outcross siring success. Because pollen discounting is strongest when selfing occurs between flowers on the same plant, the advantage of protandry may be greatest in plants with large floral displays. We tested this hypothesis with enclosed, artificial populations of Chamerion angustifolium (Onagraceae) by experimentally manipulating protandry (producing uniformly adichogamous or mixed protandrous and adichogamous populations) and inflorescence size (two-, six-, or 10-flowered inflorescences) and measuring pollinator visitation, seed set, female outcrossing rate, and outcross siring success.
Effect of population size on the mating system in a self-compatible, autogamous plant, Aquilegia canadensis (Ranunculaceae)
In self-compatible plants, small populations may experience reduced outcrossing owing to decreased pollinator visitation and mate availability. We examined the relation between outcrossing and population size in eastern Ontario populations of Aquilegia canadensis. Experimental pollinations showed that the species is highly self-compatible, and can achieve full seed-set in the absence of pollinators via automatic self-pollination. We estimated levels of outcrossing (t) and parental inbreeding coefficients (F) from allozyme variation in naturally pollinated seed families for 10 populations ranging in size from 32 to 750 reproductive individuals.