Wednesday, December 7, 2005
In my investigations of ovule fates, I’ve needed to estimate regression parameters from discontinuous functions. A general term for such estimates is breakpoint regression. OFStatisticalEstimates.pdf demonstrates an approach using R for such estimates in the context of seed-ovule ratios. The code includes a mechanism for generating seed-ovule data that illustrate the types of functions that need to be considered.Wednesday, December 7, 2005
Sean Rice’s Evolutionary Theory is an excellent journey through the mathematical foundations of evolutionary biology. The book covers a wide array of theory, including single locus models, drift, Price’s Theorem, game theory, and multilevel selection. Despite the often intense content, the book is written with a great, economical style that is easy to read. More importantly, the consistent presentation of such a broad collection of theory highlights the unifying principles of evolution.Friday, December 2, 2005
I recently lost control of my email. The combination of mailing lists, alerts, table of content notifications, and actual email from friends and colleagues was reaching a few hundred emails a day. The insanity had to stop! Here’s how I regained control. Goals Before describing my solution, let’s consider what a good email system should provide? Notifications of relevant new messages. A process for keeping track of important and unanswered messages.Friday, October 28, 2005
The current setup at home is that I’ve added all of our music (several thousand songs) to our Mac Mini and then send it through AirTunes to the home stereo. The complication is that the stereo and computer are at opposite ends of the house. Ideally, I can use my iBook to control the Mac Mini without needing to walk down the hall, but how? One solution is to use VNC, which allows complete control of the Mac Mini.Sunday, October 23, 2005
Recently, I needed to combine several pdf files into one. The The Tao of Mac has a discussion of how to do this and I’m posting the code I used here so that I can find it again later. gs -dNOPAUSE -dBATCH -sDEVICE=pdfwrite -sOutputFile=out.pdf -c save pop -f *.pdf Running this from a directory containing only the pdfs to be combined produces out.pdf.Thursday, October 13, 2005
I have used this diagram of evolutionary ecology in a wide variety of contexts. In the hope that it may be useful to others, I have made it available to anyone interested. The OmniGraffle source file is available as EvolEcol.graffle.Monday, October 10, 2005
In collaboration with Jana and Steve Vamosi, I have started a new project called Plantae. The goal of this project is to create a community website for the collection of evolutionary and ecological data for plant species. An early prototype of the project is available and we welcome feedback on all aspects of the project. Although the current implementation is rather rough. I hope to make some rapid progress on the design and function of the site in the new year.Wednesday, September 28, 2005
Now that intelligent design is back in the Canadian news, we should consider (again!) the consequences of teaching intelligent design in the classroom. Intelligent design makes two postulates: Complexity cannot be explained by science. Given 1, complexity comes from an intelligent designer. Now, consider a science exam in any subject and the danger of intelligent design being taught in school becomes apparent. Physics question: Why does the earth orbit the sun?Friday, August 19, 2005
The Onion on Intelligent Falling theory: “David Pescovitz: The Onion brilliantly parodies Intelligent Design believers: KANSAS CITY, KS—As the debate over the teaching of evolution in public schools continues, a new controversy over the science curriculum arose Monday in this embattled Midwestern state. Scientists from the Evangelical Center For Faith-Based Reasoning are now asserting that the long-held ‘theory of gravity’ is flawed, and they have responded to it with a new theory of Intelligent Falling.Saturday, August 13, 2005
Mating by outcrossing plants depends on the frequency and quality of interaction between pollen vectors and individual flowers. However, the historical focus of pollination biology on individual flowers (floricentrism) cannot produce a complete understanding of the role of pollination in plant mating, because mating is an aggregate process, which depends on the reproductive outcomes of all of a plant’s flowers. Simultaneous display of multiple flowers in an inflorescence increases a plant’s attractiveness to pollinators, which should generally enhance mating opportunities.Saturday, August 13, 2005
Clonality is very common in flowering plants, but its consequences for sexual reproduction have rarely been explored. While clonal growth can increase the number of flowers a plant produces it may also limit reproductive success through pollen discounting (reduction in pollen exported to adjacent clones) and pollen limitation (failure of outside pollen to reach the centre of a clone). Using clones of domestic apple (Malus x domestica) that ranged from 1 to 5 orchard rows wide, we found that the patterns of siring success were consistent with the presence of pollen discounting, but we failed to detect evidence for pollen limitation.Saturday, August 13, 2005
Dichogamy, the temporal separation of gender within a flower, is widespread throughout the angiosperms, occurring in over 250 families. There are two forms of dichogamy: protandry, in which male function precedes female function, and protogyny, the converse. Dichogamy has traditionally been interpreted as a mechanism to avoid inbreeding. However, recent evidence indicates that this inbreeding-avoidance hypothesis cannot completely explain the evolution of dichogamy. An alternate hypothesis is that dichogamy acts to reduce interference between gender functions.Saturday, August 13, 2005
The outcrossing rate is a fundamental attribute of plant populations that determines population genetic structure, individual plant fitness, and ultimately speciation rates. The outcrossing rate can be influenced by population size through reductions in both mate availability and pollinator service. We investigated the effect of population size on the outcrossing rate in 10 populations of Aquilegia canadensis in Southern Ontario, Canada. Across a range of sizes from 32 to 750 reproductive individuals, we found that small populations (n 90, blue line).Monday, June 13, 2005
As I use R for data analysis and simulations, I become more comfortable and proficient with the R/S syntax and style of programming. One important insight is the use of vector assignments in simulations. I have often read that using such assignments is the preferred method, but until recently I had not realised the importance of this statement. To illustrate the use of vector assignments and their advantages, consider two models of the style illustrated below:Thursday, April 14, 2005
A particular challenge with maintaining a weblog is the uploading and resizing of images. The process involves choosing the correct images, creating large & thumbnail sized versions, uploading these images to the webserver, and posting the appropriate code into the weblog post. In the spirit of my last few posts, image2web is an applescript I use to automate this process: --user-specific variables property theAlbum : "Marked" --contains the images to be uploaded property theBasePath : "Monday, March 14, 2005
The CBC has begun an experiment with podcasting. I’m impressed with the progressive approach to technology that the CBC has adopted and hope they expand the experiment to more of their programs. This has the added effect of making my Quirks & Quarks download script obsolete.Saturday, January 29, 2005
Quirks & Quarks is the CBC’s excellent science program. I usually download the mp3 archives of the show on the weekends and listen while I walk Ceiligh. Of course, loading up the Quirks & Quarks webpage, finding the archives, downloading the mp3s, and adding them to iTunes takes at least a few minutes. Computers are much better and handling such tedium. Inspired by the success (for me) of the apod script, quirks.Sunday, January 23, 2005
The “Astronomy Picture of the Day” is a source of fantastic images. To take advantage of this resource, I went looking for a way to automatically set the current image as my Desktop background. A quick Google search turned up a perl script at www.haroldbakker.com. Although this was a great start, I wasn’t completely happy with the implementation of this script and decided to write my own. The apod.pl script is written in perl and both sets the Desktop background and copies a description of the image to the Desktop as an html file.Saturday, January 1, 2005
These data measured the genetic architecture of male-phase duration in Chamerion angustifolium. There are three files in the archive used to estimate genetic variances & covariances with VCE. Format: protandryHeritabilityData.dat: Contains the measured data for male- & female-phase duration, flower size, & display size protandryHeritabilityPedigree.ped: Contains the pedigree information for the selection experiment protandryHeritabilityVCE: Is the VCE file that configures the analysis Citation: Routley, M.B. & B.C. Husband. 2004. Responses to selection on male-phase duration in Chamerion angustifolium.Saturday, December 11, 2004
A recent column in the Globe & Mail reminded me of our Federal Government’s plan for reducing greenhouse gas emissions: the One Tonne Challenge. This campaign challenges each Canadian to reduce their contribution to greenhouse gas emissions by one tonne. The first step is to calculate your emissions and then implement recommendations for reductions. According to the online calculator, Kelly & I combined emit 4.23 tonnes annually. Fortunately, this is below the national average of 5.Thursday, November 18, 2004
Yet another useful site from Google: Google Scholar. The site provides an interface for searching the scientific literature with typical Google ease. Some preliminary tests suggest that it is quite effective at finding relevant literature.Sunday, November 7, 2004
I’ve written a script that imports a JSTOR citation page into BibDesk. To use the script, I suggest adding it to your script menu. Then, with the JSTOR citation page as the active web page in Safari, run the script and the citation will be added to the active BibDesk file. I use the first author’s last name and last two digits of the year as a cite key (e.g. Darwin59), you may want to change this to suit your style.Wednesday, October 20, 2004
Routley, M.B. Measuring the male gain curve. Ecology Retreat, University of Calgary DownloadWednesday, September 29, 2004
An interesting read from Wired News – The Crusade Against Evolution. In addition, the Panda’s thumb has been following and carefully dissecting the recent controversy over an intelligent design paper being published in a peer-reviewed journal. The evolution-creation debate seems to be resurfacing after a short time off. The debate is important and the intelligent design supporters have to be countered, but their arguments have become hackneyed.Sunday, September 12, 2004
Plants are sessile and, consequently, many species rely on pollinators for mating opportunities. However, pollinators do not necessarily visit every individual in a population with equal frequency. Plant attributes, such as floral display and reward provisioning, can influence the frequency of pollinator visitation. Furthermore, aspects of population density and structure may also influence visitation patterns. One effect of this unequal distribution of pollinator activity is that pollinators create networks of connections between plants in which a few plant receive many visits and many plants receive few visits.Thursday, June 3, 2004
Routley, M.B., L.D. Harder, & S.A. Richards. Ovule fates. Colorado State University Download SSE2004.pdfWednesday, April 14, 2004
There’s a powerful approach to modelling called dynamic state variable programming, covered in Dynamic State Variable Models In Ecology by Clark & Mangel. I’ll post more about the approach sometime, but for now I wanted to make an example from the book available. The first chapter of the book includes a guide through the creation of a patch foraging model. A fully implemented version is available in True BASIC, but I’ve decided to use R for all of my modelling and analyses.Tuesday, April 6, 2004
Until recently, I was able to use journal abbreviations in all of my manuscripts. Consequently, my .bib file contains only abbreviations in the journal field. Now I need to produce some bibliographies with full journal names. With a .bib file you can use macros to handle changing abbreviated names to full names. However, BibDesk cannot use macros. Instead I wrote a perl script that searches through a .bib file and creates a new file with journal abbreviations changed to full names.Sunday, April 4, 2004
I have been investigating issues of ovule and seed development recently. One question that has come up is: How much variation is there in seed size? I had analysed some seed set data for some earlier work with some image analysis software. Consequently I have a large data set of seed area and perimeter for Chamerion angustifolium. A rough look at the data is: The data set is available as seedSizeData.Thursday, April 1, 2004
The Ecological Detective by Ray Hilborn and Marc Mangel is an excellent source for learning how to analyse ecological data with sophistication. Traditionally, ecological data is analysed from the binary perspective of hypothesis testing. The goal of such testing is to either accept or reject a null hypothesis. Although it is well entrenched in ecological training and publication, this hypothesis testing has repeatedly been attacked by statisticians and many ecologists.