Friday, March 28, 2014

Climate Change: A Background Noise of Our Daily Lives

There doesn't seem to be any way to make climate change a fun topic to discuss.  I suppose it inhabits an obtuse region in our minds that is best ignored, least we start to worry about something that we won't be around to have to cope with.

I attended a conference in the last several days in which the state of many of the most beloved American national, state and city parks were discussed.  The conversation frequently returned to the reality that increasingly large portions of the limited funds for our parks are now being directed to try to mitigate the impacts of climate change.

In the East Bay Regional Park System, more than two million dollars per year now needs to be directed toward eucalyptus tree removal.  These trees are becoming an increasing fire hazard with the increased intensity droughts.  It was mentioned that many of the lakes, which also form part of the East Bay watershed, may be dry for part of the year in the not too distant future.

On the east coast, the directors of several parks on the eastern seaboard, including of one park on Long Island that is a popular weekend vacation spot for New Yorkers, mentioned that rising sea levels are driving the need for complete park redesigns and flood control.

In the same conversation, a planner of Central Park mentioned that a single extreme squall in 2009 had destroyed 500 trees at one end of the park in just a few minutes.

These are only the most obvious impacts.  The longer term more gradual impacts, the species extinctions and shifting ecosystems, are buried away in scientific papers.

One woman, a coordinator of a major park system in Boston, mentioned that her now adult children, who had experienced the coral reefs in the Caribbean while growing up, recently had told her that there's no point in teaching their children about coral reefs because they soon won't exist.  She and her children already had witnessed the disappearance of these reefs in many places.

Not discussed in the conference, but strangely experienced in the last year by people I personally know, were the related "hundred year" floods in Boulder, Colorado and Calgary, Alberta.

There doesn't seem to be much in the press.  All of this mounting evidence of climate change just becomes part of the background noise of our daily lives.

Tuesday, March 25, 2014

Social Evolution in Structured Populations, Again

First, let me say that I've long been interested in altruism.  What accounts for generosity?  It's a complex behavior that surely has many motivations.  A cynic would say that there are no true acts of generosity.  Perhaps, but I would reply that at least sometimes, altruism is motivated by the pleasure of being altruistic.  We must have evolved to derive pleasure from altruism, at least sometimes and under certain conditions.

Several years ago, I was perplexed when a series of articles were published in which E. O. Wilson expressed his thoughts on eusociality.  Take, for instance, the Slate article Altruism and the New Enlightment:

E. O. Wilson stated: "Eusociality, where some individuals reduce their own reproductive potential to raise others' offspring, is what underpins the most advanced form of social organization and the dominance of social insects and humans. One of the key ideas to explain this has been kin selection theory or inclusive fitness, which argues that individuals cooperate according to how they are related. I have had doubts about it for quite a while. Standard natural selection is simpler and superior. Humans originated by multilevel selection—individual selection interacting with group selection, or tribe competing against tribe."

To me, something seemed off about this.  Perhaps for insects, behavior was rigidly assigned.  However, at least for mammals, it seemed to me that social behavior was fluid.  Mammals, even the same individual mammals, seemed capable of both acts of spite and acts of altruism.  An example of altruism would be polar bears befriending sled dogs.

Yet, these very same polar bears probably also occasionally attack polar bear cubs.

A close observer of dogs and cats would know that they often become fast friends.  Yet, the very same cats would probably viciously claw the nose of a dog it didn't know.

It has always seemed to me that human behavior and human altruism is at least just as fluid and temporal.

With this in mind, I was delighted to see the recent paper Social Evolution in Structured Populations.  The full text of the paper is available for a modest price via Readcube.  (This is the first time I've accessed a paper by way of Readcube and I was quite impressed.)

One of the key points of the paper is that studies of altruism have mostly focused on fecundity.  Yet, the paper points out that survival must also have played a role in the development of altruism:

"In most previous models, the costs and benefits altruism or spite are assumed to affect the fecundity of individuals, and costs and benefits for survival have received much less attention, despite the fact that such effects are equally plausible and should hence be incorporated in general models of social evolution."

"The identities of the individuals who die and reproduce depend on the individuals’ fecundity and survival potential, both being affected by social interactions and by the rules according to which the population is updated."

Another key observation of the paper is that "altruism requires some form of assortment so that altruists interact more often with altruists than defectors."  In other words, altruism can only work when similarly functioning altruists find each other.

In order to account for both fecundity and survival, the paper employs two step updating rules: death-birth and birth-death.  Costs and benefits of social interactions in both steps are considered (both fecundity and survival).

The paper assumes weak selection such that the fitness effects of interactions are small.

The implication of the two step updating is nicely illustrated in Supplementary Figure 1.

"Competition in the first step is among all individuals that are one dispersal step away, while competition in the second step is among all individuals that are two dispersal steps away. These two different competition neighbourhoods are illustrated in Supplementary Fig. 1 in the case of a lattice-structured population. In other words, for both DB and BD updating rules, the first step, which involves choosing a first individual globally among all individuals of the population, results in a narrower competitive radius than the second step, in which another individual is chosen locally among the neighbours of the first individual. Thus, whether social interactions affect the first or the second step results in a difference in the spatial scale over which social interactions affect competition."

Step 1:

"The offspring of an individual are located one dispersal step away, which happens to correspond to the competitive radius during the first step of the Moran process. Individuals are therefore directly competing against their offspring, and the detrimental effects of kin competition exactly cancel the social benefits of living next to related individuals. As a result, population structure barely has any effect on the evolution of social behavior."

Step 2: 

"In contrast, population structure is of crucial importance for the evolution of social behavior whenever social interactions affect the second step of the process. This is because the radius of the competitive circle is wider at the second step (two dispersal steps away): individuals are therefore competing against less related individuals, on average, than at the first step."

The paper considers four classical games: Prisoner’s dilemma, Snowdrift, Stag hunt and Simple Spite. These are illustrated in Figure 3 of the paper (not shown here).  I didn't get around to understanding the rules in each of these games.  The paper points out that altruism (in the case of Prisonner’s dilemma, Snowdrift and Stag hunt) is most favoured if benefits are allocated to the second step of the process, which gives more weight to interactions of individuals of the same type.

In the discussion of the games, the paper described cases where social interactions are of the same type on both steps.  However, the paper then emphasizes that the theoretical framework allows for the consideration of mixed cases.  Evidently, this will be elaborated on in a subsequent publication.

I really like this paper as it moves us toward understanding how both fecundity and survival have driven the development of altruism.  Another strength of the paper is that it permits modeling of strategies where both spite and altruism come into play in the same individual.  I’m looking forward further publications from this group.

Thursday, March 20, 2014

The Newest Organized Labor Group: Startup Employees

The Newest Organized Labor Group:  Startup Employees
Tekla S. Perry
IEEE Spectrum
19 March, 2014
More than 300 employees of Silicon Valley companies gathered last Friday night in Palo Alto to share war stories and to start developing what organizers called a "Startup Employee Equity Bill of Rights".
Mary Russell, an attorney, and Chris Zaharias, who ran tech sales teams at a number of start-ups and recently founded SearchQuant, put together the event. They hope it represents the beginning of a movement, bringing more transparency and fairness to the process of equity compensation for start-up employees.
The launch was much bigger than the two had anticipated. They originally expected a couple of dozen attendees (start-up employees only, no founders or venture capitalists allowed), and had scheduled the meeting to be held in a downtown office. When RSVPs pushed 300, they scrambled to relocate it to the theater at a local high school. And the crowd of engineers, computer scientists, and business grads pretty much filled the joint.
They came because they had gotten raw deals from a start-up in the past, were in the process of negotiating employment contracts with start-ups right now, or are working for most established companies but hoping to join start-ups in the future. In any case, they came because they feel lost when they try to understand the way start-ups compensate employees.
Indeed, Zaharias said, according to a 2011 survey, two-thirds of start-up employees don’t know the number of shares their companies have outstanding—which means that even if they know the number of shares they are entitled to, they have no idea how to value those shares.

That may not sound like a big deal to someone working at a traditional company, who might think something along the lines of “they get the stock for free, so what are they complaining about?” But start-up equity doesn’t come free—it comes in place of traditional salary. Start-up employees sacrifice current income to make a bet on the future, but, as Zaharias and Russell pointed out, the dice are often loaded. Even if employees know how much equity they have when they sign on, that number changes as more stock is issued [known as stock dilution]. In addition, people can be fired just before they vest or right after a sale in order for companies to recapture equity, and companies can give themselves the right to repurchase shares at an “official” valuation that is actually much less than the company is worth.

Monday, March 17, 2014

Experimental Confirmation of the Inflationary Big Bang Theory of the Universe

The BICEP-2 Telescope at the South Pole

My daughter was off school today, so we decided to head to the California Academy of Sciences.  We had to catch the latest planetarium show on The Dark Universe.  What a strange coincidence.  The scientist introducing the show announces that a cornerstone of the Big Bang theory, the inflationary model, has been experimentally confirmed by scientists at the South Pole BICEP-2 telescope.  As a quick explanation of the significance of this discovery, the inflationary model seeks to explain the apparent uniformity in the cosmic microwave background radiation which was first discovered by Arno Allan Penzias and Robert Woodrow Wilson at Bell Labs in 1964.  Microwave background radiation has cosmological significance, but also practical significance for radio communication. 

One of the puzzles of this discovery was why the microwave background would be uniform.  Everywhere you look in the sky, you see the same level of background radiation.  To explain this, Alan Guth in 1979 proposed the inflationary model to try to explain it.  He argued that if the universe had expanded very quickly in its first instant, that would account for the uniformity.

It appears that scientists at the BICEP-2 Telescope today have found evidence of this very rapid expansion.  The announcement was made this morning.

Here are a few articles I think do a good job of presenting the discovery:

Key Signature of the Big Bang's Origin Discovered
Sky and Telescope
Alan MacRobert

Detection of Waves in Space Buttresses Landmark Theory of Big Bang
NY Times
Dennis Overbye

MEMO: POLARBEAR scientists available for comment on cosmic microwave background & inflation
UK Berkeley News Center
Robert Sanders

Telescope captures view of gravitational waves
Nature Breaking News
Ron Cowan

New evidence from space supports Stanford physicist's theory of how universe began
Stanford News Service
Bjorn Carey

Backing the Big Bang
Harvard Gazette
Alvin Powell

Evidence of young universe's growth spurt is discovered
Los Angeles Times
Amina Khan

Monday, March 10, 2014

Social Evolution in Structured Populations

     The paper: 
     Social Evolution in Structured Populations
     F. Débarre, C. Hauert, M. Doebeli
     Nature Communications Volume: 5, Article number: 3409
     DOI:doi:10.1038/ncomms4409 Received 09 October 2013
     Accepted 06 February 2014 Published 06 March 2014


ZENBU is a data integration, data analysis, and visualization system enhanced for RNAseq, ChipSeq, CAGE and other types of next-generation-sequence-tag (NGS) based data. ZENBU allows for novel data exploration through "on-demand" data processing and interactive linked-visualizations and is able to make many-views from the same primary sequence alignment data which users can uploaded from BAM, BED, GFF and tab-text files.


Wednesday, March 5, 2014

Growing up in Accra


[A Charity Event held at the Ghana National Science Museum, with Kwame Yeboah and the OBY Band (Ohia Behe Ya Band).  Reviving this essential and beloved part of Ghana's musical history.]
. . . Rains that the clouds spewed dropped on the soft edge of dignity
We enjoyed games in the market 'cause there was key soup
Elders greeted each other - you could feel the serenity
The football that we played didn't know stadiums like the Bundesliga
We were both players and referees - back then we didn't know FIFA . . .
Update (March 8, 2014):
From "The Atenteben and Odurugya Flutes" by J. H. Kwabena Nketia:
"The interpretation of the tunes should be guided by traditional practice.  Short pieces may be repeated as a whole or in appropriate contrasts e.g. solo/chorus alterations, alterations between atenteben and odurugya solos, alternations between flutes and voices (humming, singing to a nonsense syllable etc.)  A number of them could also be played in a cycle, or arranged in the form of a suite.  Pieces with similar modal structure or similar rhythmic foundation can be easily combined.  It is our hope, therefore, that creative performers will find this book useful as a source material for building up their repertoire of flute pieces."

The Atenteben and Odurugya Flutes
A Tradition of Innovation: An Exploration into the History, Cultural Role and Playing of the Atenteben and Odurugya flutes of Ghana
Shaun C. Laughlin

Dr. Yonatan Sahle's Talk: the African Origins of Human Intelligence

Dr. Yonatan Sahle now holds the Glenn Isaac Postdoctoral Seat in the Human Evolution Research Center at UC Berkeley.  In this talk, Dr. Sahle discusses his views on the development of human intelligence, along with his recent research on the earliest projectile points in the world.


Sahle Y, Hutchings WK, Braun DR, Sealy JC, Morgan LE, et al. (2013) Earliest Stone-Tipped Projectiles from the Ethiopian Rift Date to >279,000 Years Ago. PLoS ONE 8(11): e78092. doi:10.1371/journal.pone.0078092

Monday, March 3, 2014


David C. Baird
Physics at RMC:  The First 125 Years
ISBN 978-0-9919047-0-9
pages 82-85

As part of setting up the new Science and Engineering program at Royal Military College in 1957, we (Tom Hutchison and David Baird) embarked on preparing a Third Year physics laboratory course.  As with all the laboratory courses in the preceding junior year, the course was constructed to follow the traditional pattern in which the students, working in pairs, were provided with detailed instructions for every step of their experiment.  These instructions included all the relevant theory, the setting up of the apparatus (including if necessary, circuit diagrams), the schedule of the measurements, the drawing of graphs and the calculation of final answers.  Nothing was left to the skill or imagination of the student.  The purpose in these ritualized exercises was not clear.  Such was the unquestioned practice that was almost universally followed in those days.

At the end of the 1957-58 academic year, Tom and I decided to pay homage to our stern Scottish heritage of laboratory education and give the students, for the first time, a laboratory examination.  Without thinking, we apparently assumed that in the laboratory courses that were part of all their physics courses in the preceding three years, the students must have learned something of how to actually do experiments.  In addition, thinking to let the students down gently, we chose a simple experiment.  We gave the students a dish-shaped glass "watch glass", a steel ball bearing that could roll in the watch glass, and appropriate measuring equipment for dimensions and time.  A small piece of paper stated that the requirement for the examination was to derive an expression for the period of oscillation as the ball rolled back and forth and make the necessary measurements to derive a value for the acceleration of gravity.

At the time appointed for the examination, the students were admitted and Tom and I confidently strolled around the laboratory, innocently expecting to supervise the busy activity of the students.  Instead, there was complete stillness and profound silence.  After half and hour of total inactivity it finally dawned on us that after three whole years of traditional laboratory courses the students still did not have even the most remote idea of how to conduct an experiment.  Eventually, we wrote the necessary formulae on the blackboard and coaxed the students through their "exam."  It was an enlightening experience for Tom and me.  For the students, it was sufficiently traumatic that one senior retired officer (an ex-Commandant of the RMC) recently accusingly mentioned it to me.

Tom and I were forced to recognize that almost all time spent in our earlier highly structured laboratory classes had been wasted.  The students had no idea of the nature of measurements and their uncertainty, the nature of theoretical models, the significance of graphical analysis of the experimental results, or the nature of the final statement one could make about the experiment or the results.

For the 1958-59 school year, I attempted to construct a syllabus for the Third Year laboratory class to address this.  It was a dismal failure.  After two whole years of following recipes in the preceding labs, the students had no intension whatsoever of actually working to acquire something as esoteric as experimental independence.  It was clear that, like learning a foreign language, experimenting involved basic mental attitudes that would have to be acquired at the earliest possible stages.

I asked Tom if I could have the First Year lab.  This had traditionally contained nothing but experiments that consisted of a series of illustrations of the lecture course material in "recipe book" style.  This we now totally discarded.  The new program consisted of a mixture of lecture material and experimental procedures chosen specifically to illustrate the various aspects of measurement uncertainty, measurement statistics, graphical analysis and the analysis of experimental results.


Experimentation, An Introduction to Measurement Theory and Experiment Design (Link)

Sunday, March 2, 2014

Thomas Sherret Hutchison

Some of you, if you've been reading this blog recently, will know that I went to a military college.  Yes, well, how did a Vancouver granola kid end up at the Royal Military College of Canada (RMC)?

In fact, I had grown up in Vancouver (British Columbia) and even volunteered for a bit at the Greenpeace office in the 70s (before it became an international going concern.)  It had occurred to me that, like most of my other classmates at Magee Secondary School, I would probably end up going to the University of British Columbia.  There was only one problem.  I had a private pilot license and I really wanted to be a commercial pilot.  In Canada, at that time, there were pretty much only two ways that you could become a commercial pilot:  (a) become a bush pilot or (b) join the Air Force. 

As it happened, as I was considering my options, for the very first time, RMC, under pressure from Canada's Prime Minister Pierre Trudeau, had decided to accept women.

I was also quite interested in science and I heard that RMC had a pretty good science program.

Finally, I also wanted to escape the west coast, at least for a while.

And that is how I ended up standing there in first year physics lab, in my damn uniform, trying to remember what I should write under "Method" and whether or not I should have separate sections for "Discussion" and "Conclusion".  So here comes Professor Hutchison.  At this time, he was several years before retiring.  I'm sure he thought I was a complete novelty and I distinctly had the impression that he thought I should be taking English Literature or Anthropology at Queen's or U of T not Physics at RMC.  In spite of this, I think he took me on as a special case.   He would come to where I was rushing to throw my "Experiment" together and try to give me a few suggestions.  He had a Scottish drawl and a very dry wit which, at the time, I did not fully appreciate.  I somehow survived the first year Experimentation lab in part due to his patient attention.  Dr. Baird was also a professor in the Experimentation lab.

I took a class in solid state physics from him in second year which was very good.

He would often try to talk to me about golf.  Golf!  "We are not running a country club here, Professor Hutchison."  My chosen sports were cross country running and track and I was usually in no mood to discuss golf.  I did tell him one time that my Dad liked golf. I could tell that he made the point of writing that in his mental notebook.

In third year, I ran across him at a social function.  By this time, my class load was particularly heavy and my formerly very dedicated running schedule had been down graded a bit.  I had figured out that I could use the after class "training" to instead escape (jog) to Kingston in order to hang out with some of the students at Queens University.  Hutchinson was chiding me about not being a very dedicated athlete.  Misunderstanding him, I quietly vowed not to speak to him again.

And I never did.  I graduated a year later.  I never said goodbye.  He retired.  He died in the mid-nineties.

I found out quite recently that he had told David Baird that he knew what I was up to.  He knew that I had been escaping to Queens.  He apparently thought it was funny and was delighted for me.

So sad.

Thomas Sherret Hutchison

Ukraine Crisis

Susan Ormiston of the CBC on the news of the Ukraine Crisis
Latest developments reported at CBC News (Link)
Canada's Foreign Minister John Baird Condemns Russia's Military Action (CBC News) (noon, PST, 3/2/2014) (Link)

Ukraine:  what will happen now?  (UK Guardian) (7:43am, PST, 3/2/2014) (Link)

Ukraine mobilizes troops after Russia's 'declaration of war' (CNN) (12:17pm, PST, 3/2/2014) (Link)

Ukraine (UK Guardian), continually updated (Link)