This just came out in the American Naturalist…
Fluctuating Population Dynamics Promotes the Evolution of Phenotypic Plasticity
Richard Svanbäck, Mario Pineda‐Krch and Michael Doebeli
Abstract:
Theoretical and empirical studies are showing evidence in support of evolutionary branching and sympatric speciation due to frequency‐dependent competition. However, phenotypic diversification due to underlying genetic diversification is only one possible evolutionary response to disruptive selection. Another potentially general response is phenotypic diversification in the form of phenotypic plasticity. It has been suggested that genetic variation is favored in stable environments, whereas phenotypic plasticity is favored in unstable and fluctuating environments. We investigate the “competition” between the processes of evolutionary branching and the evolution of phenotypic plasticity in a predator‐prey model that allows both processes to occur. In this model, environmental fluctuations can be caused by complicated population dynamics. We found that the evolution of phenotypic plasticity was generally more likely than evolutionary branching when the ecological dynamics exhibited pronounced predator‐prey cycles, whereas the opposite was true when the ecological dynamics was more stable. At intermediate levels of density cycling, trimorphisms with two specialist branches and a phenotypically plastic generalist branch sometimes occurred. Our theoretical results suggest that ecological dynamics and evolutionary dynamics can often be tightly linked and that an explicit consideration of population dynamics may be essential to explain the evolutionary dynamics of diversification in natural populations.
This is from the “Mario’s Entangled Bank” blog ( http://pineda-krch.com ) of Mario Pineda-Krch, a theoretical biologist at the University of Alberta.
Categories: Michael Doebeli · Richard Svanbäck · manuscript
Happy birthday Charles!
In the eyes of my four year old you invented the Tree of Life, you drive an Evolvo, and have a really really big beard. The real question is, however, what would you put in the loot bags.
A four year old's interpretation of Darwin's Tree of Life
This is from the “Mario’s Entangled Bank” blog ( http://pineda-krch.com ) of Mario Pineda-Krch, a theoretical biologist at the University of Alberta.
Categories: Charles Darwin · evolution · fatherhood
Chuckie ‘D’ says:
Nature is prodigal of time. She scrutinises every muscle, vessel, nerve. Every habit, instinct, shade of constitution. There will be no caprice, no favouring.
This is from the “Mario’s Entangled Bank” blog ( http://pineda-krch.com ) of Mario Pineda-Krch, a theoretical biologist at the University of Alberta.
Categories: Charles Darwin
January 29, 2009 · 1 Comment
The Canadian federal budget for 2009 has been released and it is hardly a surprise that science and research took a backseat. For example, the budget for Canada’s three research councils is slated to be cut by close to $150 million and peak in 2011-2012 at $87.2 million. It could be worse though, Genome Canada (a not-for-profit agency responsible for funding large-scale science and genetics), was not even mentioned in the budget. According to the Minister of State for Science and Technology,
Genome Canada was still receiving funds from the two previous budget announcements, and that these funds amounted to $106 million this year and $108 million next year.
For a government-run funding agency like the Natural Sciences and Engineering Research Council, no mention in a budget would mean a continuation of existing annual budgets
Although this hopefully will be the case, the lack of commitment is worrisome. Genome Canada, and the Canadian research councils provide critical funding to some of the brightest minds in Canada. With the recent promise of an increase in research funding south of the border this may be the beginning of a brain drain exodus. Obama is scheduled to visit Canada on February 19. Perhaps Harper should take this opportunity to learn a few things about the importance of allocating adequate funding to basic research.
Sandwalk has a more thorough analysis of what the budget says (not) about research.
This is from the “Mario’s Entangled Bank” blog ( http://pineda-krch.com ) of Mario Pineda-Krch, a theoretical biologist at the University of Alberta.
Categories: Barack Obama · Canada · Stephen Harper · science
In the year of evolution and its Darwin-mania let’s not forget Theodosius Dobzhansky, who made the first significant synthesis of Charles Darwin’s theory of evolution with Gregor Mendel’s theory of genetics in his book Genetics and the Origin of Species (1937) and was nominated for a Nobel Prize in 1975 (unfortunately he passed away the same year, if he would have lived a few more years he might just have got it).
Today is Theodosius’ 108th birthday, so Happy Birthday Theo.
Hat tip: Evolving Complexity
This is from the “Mario’s Entangled Bank” blog ( http://pineda-krch.com ) of Mario Pineda-Krch, a theoretical biologist at the University of Alberta.
Categories: Theodosius Dobzhansky · evolution
Notwithstanding a previous post, I love doing academic research. Until now, my main argument for why my job is so great is that I get paid to do what I love. A recent study has, however, added some unexpected icing on the cake. The study evaluated 200 professions to determine the best and worst according to five criteria inherent to every job: environment, income, employment outlook, physical demands and stress. As it turns out, being a mathematician is the best job one can have! Go figure – how does that add up? Well,…
According to the study, mathematicians fared best in part because they typically work in favorable conditions — indoors and in places free of toxic fumes or noise — unlike those toward the bottom of the list like sewage-plant operator, painter and bricklayer. They also aren’t expected to do any heavy lifting, crawling or crouching — attributes associated with occupations such as firefighter, auto mechanic and plumber.
Strictly speaking, of course, I am not a mathematician in the traditional sense, but rather more of mathematical biologist working at the interface of biology, math, and statistics. As it turns out, however, according to the study, being a biologist is ranked 4 and statistician is ranked 3. The average rank of these three professions is 2.7, but considering that my current gig is in a math and stats department I feel my job probably ranks a tad higher.
I wondering how the surfer-physicist profession fared?
This is from the “Mario’s Entangled Bank” blog ( http://pineda-krch.com ) of Mario Pineda-Krch, a theoretical biologist at the University of Alberta.
Categories: Mathematical biology · academia · jobs · math · science · statistics · theory
At last the plans for the Darwin Day celebrations at the University of Alberta (my current location) has been unveiled. The Department of Biology is organizing a seminar series on February 12 to honor Darwin and his contribution to biology and science.
Other activities include a Darwin food competition:
“Darwin studied or collected organisms in just about every phylum from mammals, birds, fish, reptiles, insectivorous plants, fungi to orchids, beetles and cactus. How many families can you get into one dish?” (I’d love to see this one as an entry)
a Darwin look-alike contest:
“Contestants will be judged based on their similarity in appearance, clothing, and mannerisms. Given that this contest appears inherently limited to males (but don’t let that stop you) we will have the judging done by women in the audience. Start combing your beards and contacting your tailors.”
a Darwin game show, Dance like a Victorian contest, What would you like to ask Darwin contest, etc.
The full schedule can be found here.
This is from the “Mario’s Entangled Bank” blog ( http://pineda-krch.com ) of Mario Pineda-Krch, a theoretical biologist at the University of Alberta.
Categories: Charles Darwin · University of Alberta · evolution
Tagged: Darwin Day
It’s barely three weeks left before February 12 and it’s time to order your Darwin Day gear (if you want it to arrive in time). Darwin Day t-shirt designs and other gear abound (e.g. here, here, here, here, here, here, here, and here), my personal favorite, however, (aside from Ray Troll’s designs of course) are the recent creations by Genomicron showcased here and here). Seriously, check out this, this, this. I know my tot will definitely be wearing this one.
All of this sweet loot can be found here.
BTW - 50% of the proceeds go directly to charity, and the rest will be spent on developing evolution web resources.
This is from the “Mario’s Entangled Bank” blog ( http://pineda-krch.com ) of Mario Pineda-Krch, a theoretical biologist at the University of Alberta.
Categories: Charles Darwin
Tagged: Darwin Day
January 20, 2009 · 1 Comment
A glimmer of hope for science and higher education in Barack Obama’s inauguration address:
We will build the roads and bridges, the electric grids and digital lines that feed our commerce and bind us together. We will restore science to its rightful place, and wield technology’s wonders to raise health care’s quality and lower its cost. We will harness the sun and the winds and the soil to fuel our cars and run our factories. And we will transform our schools and colleges and universities to meet the demands of a new age. All this we can do. And all this we will do.
This is from the “Mario’s Entangled Bank” blog ( http://pineda-krch.com ) of Mario Pineda-Krch, a theoretical biologist at the University of Alberta.
Categories: science
Tagged: Barack Obama, Politics
This alarming development was circulated today by the President of the European Society for Evolutionary Biology, Isabelle Olivieri:
I would like you bring to your attention the following situation. Because of reorganization in some Dutch Universities and money cutting in research, several colleagues from Leiden University will be fired by the end of the year if we do not react. They might be fired anyway, but I think that we should at least do our best for this not to happen.
The following evolutionary biologists will be fired or will not be able to continue their research: Jacques van Alphen (Marie Curie professor of Excellence), Tom Van Dooren, Frietson Galis (president of the European Society for Evolutionary Developmental Biology), Sacha Gultyaev, Patsy Haccou (Executive vice-president of the European Society of Evolutionary Biology), Ken Kraaijeveld, Femmie Kraaijeveld, Hans Metz (retired, but still very active), Rino Zandee.
People in Leiden have just set up a petition, which you will find here: http://evodevo.eu/petition/
I strongly encourage you to sign this petition, which will be sent to every person in the Netherland government who might be able to do something.
I think it is quite incredible that Darwins’year will see an entire and excellent department of evolutionary ecology close down and leave people without a job (even those with a “permanent” job!) because of budget restrictions. As written in the petition, although evolutionary biology will be heavily cut, molecular biology will be spared. This is part of an alarming national trend. Unfortunately, with growing creationism in Europe, and budget cuttings elsewhere (including, alas! France) I am afraid the Dutch trend will soon become international.
Please react ASAP !
Isabelle Olivieri
President of the European Society for Evolutionary Biology 2007-2009
This is from the “Mario’s Entangled Bank” blog ( http://pineda-krch.com ) of Mario Pineda-Krch, a theoretical biologist at the University of Alberta.
Categories: academia · evolution
Categories: PZ Meyers · atheism
Tagged: atheism
January 16, 2009 · 1 Comment
10. Not being able to get past the “To read this story in full you will need to make a payment” page
9. Lack of funding
8. Bad papers published in top journals
7. Getting scooped
6. Bad science happening to good scientist
5. Rejection letters
4. Dependence on expensive proprietary software
3. Adult colleagues requiring a spouse/parent to cook for them, wash their laundry, and wipe their…, face
2. Coauthors/collaborators that are doing…, well, nothing
1. Papers published in top journals that have your name all over them
This is from the “Mario’s Entangled Bank” blog ( http://pineda-krch.com ) of Mario Pineda-Krch, a theoretical biologist at the University of Alberta.
Categories: academia
Chuckie ‘D’ says:
One day, on tearing off some old bark, I saw two rare beetles, and seized one in each hand. Then I saw a third and new kind, which I could not bear to lose, so I popped the one which I held in my right hand into my mouth. Alas! it ejected some intensely acrid fluid, which burnt my tongue so that I was forced to spit the beetle out, which was lost, as was the third one.
This is from the “Mario’s Entangled Bank” blog ( http://pineda-krch.com ) of Mario Pineda-Krch, a theoretical biologist at the University of Alberta.
Categories: Charles Darwin
Traditionally the day-to-day activities of academic research has been a closed endeavor where research note books are usually only available to people in the lab. Open Notebook Science (ONS), in contrast, represents a revolutionary concept going against the grain of these traditions where research notebook are available online as they are written. Although it might take a while to turn the tide and make ONS an accepted and established practice there are many advantages to it. The ONS lab of Rosania Research Group summarizes it nicely,
Open Notebook Science is ideally suited for community-wide collaborative research projects involving mathematical modeling and computer simulation work, as it allows researchers to document model development in a step-by-step fashion, then link model prediction to experiments that test the model, and in turn, use feeback from experiments to evolve the model. By making our laboratory notebooks public, the evolutionary process of a model can be followed in its totality by the interested reader. Researchers from laboratories around the world can now follow the progress of our research day-to-day, borrow models at various stages of development, comment or advice on model developments, discuss experiments, ask questions, provide feedback, or otherwise contribute to the progress of science in any manner possible.
Ever since seeing Jean-Claude Bradley and Garrett Lisi’s Open Notebook Science endeavors at SciFoo a few months back I have been toying with the idea of starting a similar enterprise. Although Jean-Claude and Garrett practice ONS, their individual approaches to research could not be more different, as a result their online research notebooks are very different animals. Jean-Claude is running a rather typical academic lab (i.e. a PI + a band of postdocs and students) in experimental chemistry and utilizes a combination of a wiki and blog hosted by Wikispace and Blogger for his UsefulChem project. In contrast, Garrett Lisi runs a one-man band as an independent researcher in theoretical physics and uses TiddlyWiki for his Deferential Geometry research notebook.
Largely due to the inspirational efforts of Jean-Claude and Garrett’s I have been pondering of starting my own little ONS research projects. Initially it would consist only of the notebook from one of my solo projects. Trying an ONS approach on a project involving collaborators (particularly when one is not the PI) is tricky and beyond my means currently.
As a spin off from the GillepieSSA package that I developed I have embarked on a more ambitious project for developing stochastic simulation algorithms aimed specifically at ecological and evolutionary models (see the last project on my research page, i.e. computational algorithms for statistical simulations of ecological and evolutionary processes). As I am thinking of how to set this up I realized that there are specific requirement that I need the online notebook to have, e.g. 
support, an interface to an source control management system (e.g. Subversion or Git), a client side tool would be preferable, and it needs to be easy to back it up. So far the candidates are,
- TiddlyWiki, pros: supports
, nice non-linear approach where arbitrary posts (aka tiddlers) can be viewed and edited simultaneously, client side (doers not require web access), simple “installation” since the TiddlyWiki code and the contents reside in a single text file, simple hosting (no CGI required) cons: it is not clear how well the performance of the application scales for large projects, there does not appear to be an interface (in the form of a plug-in) to a source control management system, need to host it on a server.
- OpenWetware, pros: acts as a sort of glue for the Open Science community with the potential benefit of getting more exposure, aimed at academic research labs, the web hosting is taken care of, cons: servers side service (i.e. web access required), no interface to a source control management system, no obvious
capabilities (?).
- Trac, pros: interfaces with Subversion, cons: limited capabilities, server side application with complex set up requiring CGI capabilities.
Currently I am leaning towards Trac, although it complex to set it up (relative to the other options) I have used it for many years and are comfortable with it and really like the integration between the wiki and Subversion. Neil Saunders has a post on his blog What You’re Doing Is Rather Desperate about using Trac for managing research projects and using it as an open notebook system. With the proper plugin Trac might even be able to render .
This is from the “Mario’s Entangled Bank” blog ( http://pineda-krch.com ) of Mario Pineda-Krch, a theoretical biologist at the University of Alberta.
Categories: LaTeX · Open Notebook science · Science Foo · Subversion · open science
In 1996 Douglas Osheroff received the Nobel Prize in Physics together with David Lee and Robert C. Richardson for their discovery of the superfluid phase of helium-3, as a matter of fact, they actually discovered three superfluid phases. Superfluidity is a remarkable and unusual property that had previously been observed only in helium-4 and manifests itself by, for example, a lack of viscosity. As a result a superfluid liquid cannot be stored in an unglazed ceramic vessel, because it seeps out through the microscopic pores in the ceramic.Furthermore, if an empty beaker is lowered part way into the liquid, the liquid flows upward along the outside wall, creeping along the surface, , over the edge and down into the beaker until if finds its own level.
Last week Osheroff visited the University of Alberta and gave a presentation entitled “How advances in science are made”. In his talk Osheroff gives a brief history of low-temperature physics recapitulating his own discovery that led to the Nobel Prize. Out of his historical overview emerged a tale of five key strategies for making groundbreaking advances in science. According to Osheroff, the key research strategies that led to his prize winning discovery were,
- Use the best technology available.
- Do not reinvent the wheel, borrow technologies if possible.
- Look into unexplored regions of the landscape, or parameter space.
- Failure might be an invitation to try something new.
- Be aware of subtle unexplained behavior. Don’t dismiss it!
Ofcourse, making a ground breaking discovery might not be enough to get acknowledged. In Osheroff’s own words “If you want to win a Nobel Prize, you also have to live long enough”.
This was one of those talks where you loose track of time. It was not until it was over that I realized that it had gone on for over 90 minutes. The slides for the talk are available at Osheroff’s home page at Stanford University.
This is from the “Mario’s Entangled Bank” blog ( http://pineda-krch.com ) of Mario Pineda-Krch, a theoretical biologist at the University of Alberta.
Categories: Nobel Prize · physics
I recently moved to Canada to start a research position at the University of Alberta (hence my absence from the blogosphere). I am now spending my time at the Centre for Mathematical Biology in the Department of Mathematical & Statistical Sciences at UoA. My contact information is updated, my email stays the same, and my blog posts may end up having a more Canadian flavor to them I suspect.
I’ll miss UCD, the bike enlightened spirit of Davis, hanging out at Farmers Market, the smell of fresh manure in the morning, and going on late night roach hunts in the office…, but the show must go on. It’s time to embrace F150s, oily sand, Alberta beef, Mountain Pine Beetles, long cold winters, and wild roses.
This is from the “Mario’s Entangled Bank” blog ( http://pineda-krch.com ) of Mario Pineda-Krch, a theoretical biologist at the University of Alberta.
Categories: Uncategorized
September 16, 2008 · 1 Comment
In his TED talk Michael Shermer, an American science writer, historian of science, founder of The Skeptics Society, and editor of its magazine Skeptic, eloquently and rapaciously debunks claims of the paranormal, fringe groups, cults, claims, pseudoscience, non-science, junk science, voodoo science, pathological science, bad science, and plain old nonsense. Well worth watching if Intelligent Design, Creationism and other nonsense humbug gets to you.
He finishes of with a great anecdote about the British singer Katie Melua and her 2005 track “Nine Million Bicycles” (which made it to the UK 10 ten list) whose lyrics were disputed by science writer (and former physicist) Simon Singh. According to the story, when Simon heard the lyrics,
We are 12 billion light-years from the edge, That’s a guess — no-one can ever say it’s true, But I know that I will always be with you
he interpreted this as an assault on the accuracy of the work of cosmologists. He said,
Katie Melua has no right to call the age of the universe a ‘guess’ or quote it as 12bn years old when we now know it to be 13.7bn years old.
Simon graciously amended the lyrics and Katie, even more graciously, re-recorded the song with the revised and scientific correct lyrics,
We are 13.7 billion light-years from the edge of the observable universe, that’s a good estimate with well-defined error bars, Scientists say it’s true, but acknowledge that it may be refined, and with the available information, I predict that I will always be with you
Perhaps it does not “roll of” the tongue the way the original does, but it’s the intention that counts. The original (erroneous) version is here. The scientifically correct version is played in Michael Shermer’s TED talk. An interview with Katie Melua and Simon Singh retelling the story is available here.
This is from the “Mario’s Entangled Bank” blog ( http://pineda-krch.com ) of Mario Pineda-Krch, a theoretical biologist at the University of California, Davis.
Categories: Katie Melua · Michael Shermer · Simon Singh · TED · humour · physics · science
In case you just can’t wait until the Large Hadron Collider (aka LHC) unravels the Higgs Boson for the world to see (is that an oxymoron?) you can now get your very own Higgs. For only $9.75 (+S&H) you can get yourself your personal Higgs with a a “maximum of mass” from the Particle Zoo [blog]. It’s a bargain compared to the $6+ billion price tag of the LHC…, let’s see…, that’s a price difference of 9 orders of magnitude (give or take a few orders). Order your’s today and be the first one in your neighborhood to have a complete Standard Model. Caveat, a 9 orders of magnitude price difference might, in some people minds, appear as a deal too good to be true. Rest assure folks, this is not a lemon (albeit you need a few Higgs in order to have tangible lemons with a mass).
This is from the “Mario’s Entangled Bank” blog ( http://pineda-krch.com ) of Mario Pineda-Krch, a theoretical biologist at the University of California, Davis.
Categories: Higgs · LHC · humour · physics
