Now the wife has gone out for the evening;
The kid's fast asleep in his bed;
I head for the back room and turn out the lights,
New ideas racing into my head.
And I know that I ought to be stronger,
And I know that it just ain't right,
But my guilty pleasures are calling
And it's gonna be a long dark night!
I have guilty pleasures and
back-room treasures
To keep me happy all night long
The devil take wine,
loose women and crime
Give me coffee, science and song!
inst. break
Now some men fancy loose women
that they pick up in sleazy old bars;
Some find escape in the juice of the grape,
Some go racing in stolen fast cars.
But just give me a tape of old folksongs,
Black coffee as strong as it gets,
A beautiful (mathematical) model and a manuscript or two
And a terminal window onto the local cluster.
There's a two-meg stack of fresh data,
Some math that I ought to wrap my head around
The last revisions came in this evening
Of a manuscript I've been meaning to send off
Then maybe a round of debugging
There's always something else wrong,
If I don't fall asleep at the keyboard,
I might just write a new song.
Well the wife went to bed around midnight;
The kid'll be up before dawn.
I might crash at my desk about lunch-time,
But for now I'll just keep hackin' on.
Now some men fall for fast women,
for others the bottle's a curse;
For me it's black coffee and science,
And I can't tell you which one is worse.
Modified from Stephen Savitzky’s Guilty Pleasures
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: Coffe · Music · humour · science
So finally it has happened! Yesterday British PM Gordon Brown issued an posthumous apology to WW2 mathematician and computer scientist Alan Turing. It took the British government 57 years to get here! But I presume it’s better than never.
Here the email that came from from the PM…
Thank you for signing this petition. The Prime Minister has written a response. Please read below.
Prime Minister: 2009 has been a year of deep reflection – a chance for Britain, as a nation, to commemorate the profound debts we owe to those who came before. A unique combination of anniversaries and events have stirred in us that sense of pride and gratitude which characterise the British experience. Earlier this year I stood with Presidents Sarkozy and Obama to honour the service and the sacrifice of the heroes who stormed the beaches of Normandy 65 years ago. And just last week, we marked the 70 years which have passed since the British government declared its willingness to take up arms against Fascism and declared the outbreak of World War Two. So I am both pleased and proud that, thanks to a coalition of computer scientists, historians and LGBT activists, we have this year a chance to mark and celebrate another contribution to Britain’s fight against the darkness of dictatorship; that of code-breaker Alan Turing.
Turing was a quite brilliant mathematician, most famous for his work on breaking the German Enigma codes. It is no exaggeration to say that, without his outstanding contribution, the history of World War Two could well have been very different. He truly was one of those individuals we can point to whose unique contribution helped to turn the tide of war. The debt of gratitude he is owed makes it all the more horrifying, therefore, that he was treated so inhumanely. In 1952, he was convicted of ‘gross indecency’ – in effect, tried for being gay. His sentence – and he was faced with the miserable choice of this or prison – was chemical castration by a series of injections of female hormones. He took his own life just two years later.
Thousands of people have come together to demand justice for Alan Turing and recognition of the appalling way he was treated. While Turing was dealt with under the law of the time and we can’t put the clock back, his treatment was of course utterly unfair and I am pleased to have the chance to say how deeply sorry I and we all are for what happened to him. Alan and the many thousands of other gay men who were convicted as he was convicted under homophobic laws were treated terribly. Over the years millions more lived in fear of conviction.
I am proud that those days are gone and that in the last 12 years this government has done so much to make life fairer and more equal for our LGBT community. This recognition of Alan’s status as one of Britain’s most famous victims of homophobia is another step towards equality and long overdue.
But even more than that, Alan deserves recognition for his contribution to humankind. For those of us born after 1945, into a Europe which is united, democratic and at peace, it is hard to imagine that our continent was once the theatre of mankind’s darkest hour. It is difficult to believe that in living memory, people could become so consumed by hate – by anti-Semitism, by homophobia, by xenophobia and other murderous prejudices – that the gas chambers and crematoria became a piece of the European landscape as surely as the galleries and universities and concert halls which had marked out the European civilisation for hundreds of years. It is thanks to men and women who were totally committed to fighting fascism, people like Alan Turing, that the horrors of the Holocaust and of total war are part of Europe’s history and not Europe’s present.
So on behalf of the British government, and all those who live freely thanks to Alan’s work I am very proud to say: we’re sorry, you deserved so much better.
Gordon Brown
If you would like to help preserve Alan Turing’s memory for future generations, please donate here: http://www.bletchleypark.org.uk/
Petition information – http://petitions.number10.gov.uk/turing/
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
Tagged: Alan Turing, Gordon Brown, mathematics
Chuckie ‘D’ says:
I cannot persuade myself that a beneficent and omnipotent God would have designedly created parasitic wasps with the express intention of their feeding within the living bodies of Caterpillars.
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
Over the last week I have been migrating most of my public presentations and posters to Nature Precedings (NP). Until now I have always been hosting these on my own servers, but it gets tedious when one (or the server) moves or, even worse, the hosting server dies (which they all do sooner or later). Posting it all on NP gives these documents a permanent, safe resting place. As an added bonus they also get their own DOI (Digital Object Identifier) so (theoretically at least) they are indexed and findable in perpetuity and a snazzy Flash preview pane.
Here is the current list of my loot at NP. It pretty much covers the spectrum of stuff I have been working on since about 2003, from genetics/genomics of recombinational hotspots, evolutionary dynamics, population cycles, forest insect population dynamics, and more. As I am writing this, two submissions are still under curatorial review, but if they pass muster they should be up shortly.
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: Nature Precedings · manuscript · poster · presentation
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
