New year and new paper! This just came out in the American Journal of Veterinary Research…
Potential impact of introduction of foot-and-mouth disease from wild pigs into commercial livestock premises in California
Mario Pineda-Krch, Joshua M. O’Brien, Clair Thunes, and Tim E. Carpenter
Abstract
Objective—To estimate potential spread of foot-and-mouth disease (FMD) if introduced from wild pigs in California and to evaluate efficacies of various control strategies.
Sample Population—Data for California livestock and from hunter surveys on wild pigs in California.
Procedures—A spatial, stochastic simulation model was used to simulate FMD epidemics that might occur if a dairy or beef herd were infected from contact with a wild pig. Index herd location and type were examined, in addition to different statewide movement ban (SWMB) durations, to determine their effect on extent of the epidemic.
Results—Duration, number of infected premises, size of simulated outbreak, number of culled animals, and spatial distribution of infected herds resulting from the simulated outbreaks varied considerably among geographic regions, depending on index case type and location. Outbreaks beginning in the southern region of California were consistently longest, whereas those beginning in the northern region were shortest. The largest outbreaks resulted from index cases located in the southern and valley regions, whereas outbreaks were smallest when originating in the Sonoma or northern regions. For all regions, when the index herd was a dairy herd, size and duration of the outbreak were consistently reduced with implementation of an SWMB ≥ 3 days.
Conclusions and Clinical Relevance—Introduction of FMDV from wild pigs into a dairy or beef herd could result in a large and rapidly spreading outbreak, potentially affecting large numbers of herds. Size and duration of the outbreak might be reduced with an SWMB; however, the impact is highly dependent on the index herd type and location.
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.
53.526326
-113.524765
Categories: manuscript
Came across my first letter of rejection for a submitted manuscript.
Dr Mario Pineda-Krch
Department of Theoretical Ecology
Ecology Building
S-223 62 Lund
Sweden
Dear Dr. Pineda-Krch
Your manuscript “On the potential for evolutionary change through meristematic cell-lineages” has been favourably reviewed by our editorial staff. In fact, we consider it to be the most brilliant paper ever submitted to this Editorial Office.
It is an honour and a privilege for our journal to publish this path-breaking work; however, due to the recent public discontent at clonal organisms – albeit sheep – we are going to postpone publication until a more feasible and favourable review of your work in the press can be anticipated. Meanwhile we suggest that you piss off to some remote Pacific island in order to avoid being lynched by ecological fundamentalists
Sincerely Yours.
<name removed>
Editor-in-chief
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.
53.526326
-113.524765
Categories: Torbjörn Fagerström · academia · humour · manuscript
Tomorrow, the Globe and Mail will publish a full-page advertisement by the World Wildlife Fund (WWF-Canada) outlining an open letter signed by over 500 Canadian scientists to Prime Minister Harper calling for strong Canadian action to address climate change, leading up to the global negotiations in Copenhagen in December.
To view the open letter, see http://wwf.ca/pmletter .Canadian scientists with a Ph.D. who wish to sign may still do so and the same link. Here’s the call out from WWF:
Dear Colleagues,
Please lend your scientific voice to the call for strong, global action to address climate change, leading up to the global negotiations in Copenhagen in December. Consider signing the open letter to the Prime Minister of Canada and all Parliamentarians that WWF-Canada will publish in a national newspaper before the global meeting starts Dec. 7th.
The current list of signatures can be found here. I have signed the open letter and hope you will do so, too.
Hat tip to Sally Otto.
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: Sally Otto · Stephen Harper · global climate change
Can you wish a book a happy birthday – sure you can! Happy birthday The Origin of Species, and many more to come. You were the one that enlightened us and showed us where we come from. You showed us our place in the web of life. You showed us that the human race is not the pinnacle of life. We are nothing more than a tiny twig in the evolutionary tree; a minute thread in the evolutionary tapestry. You showed us how all living beings share a common ancestry. You showed us that Nature has now special regard for humankind. You showed us that there is not plan.
150 years ago today, Darwin published On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. This is undoubtedly one of the, if not The, most important book in the history of humanity. Why? Because it was the first time a scientifically sound and coherent explanation for the origin and rise of the diversity of life was presented. It explains where we (and the rest of the living world) comes from and how we got here. The message it carries touches us all, no matter where we are, who we are, or what we believe in. If you haven’t read it yet in all that time…, what are you waiting for?
In the sixteenth century Nicholas Copernicus
told us the earth was a ball and, what was worse,
was not the center of the universe.
“Well and so,” we wanted to know,
“where does that leave us in the scheme of things?”
Wherever it left us,
we were just about learning to live with it
when three centuries later Charles Darwin
grabbed our attention with the news
that we were cousins to the kangaroos.
“And so,” we wanted to know,
“where does that leave us in the scheme of things?”
(Miller Williams – How Step by Step We Have Come to Understanding)
True aficionados read a facsimile of the First Edition of the Origin of Species
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 · Nature · Origin of Species · evolution
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
