Saturday, April 19, 2014

DeepDyve and ReadCube

With the advent of DeepDyve and ReadCube, for a modest cost, it is now possible for the public to easily get access to journal articles as they are published.  For instance, a number of important articles and discussions have recently been published in the Journal of Human Evolution (DeepDyve link) which I have not posted on this blog (and have not seen posted on other blogs).  For those curious about the latest developments, I'd highly recommend DeepDyve and ReadCube.

Wednesday, April 16, 2014

Is the STEM Crisis a Myth?

Published on Oct 17, 2013 
The September 2013 article "The STEM Crisis Is a Myth," by IEEE Spectrum contributing editor Robert N. Charette, triggered a hearty response from readers. Many commenters shared his view—that there is no shortage of scientists and engineers—and quite a few were against it. It seemed clear that a discussion of the issue should continue.

Read more:
IEEE Spectrum's Special Report:

Friday, April 4, 2014

Isapo-muxika (Crowfoot/Pied de Corbeau)

“What is life?  It is the flash of a firefly in the night. It is the breath of a buffalo in the wintertime. It is the little shadow which runs across the grass and loses itself in the Sunset.”

Isapo-muxika (Crowfoot/Pied de Corbeau),
Chief of the Siksika People (Blackfoot People)

Crowfoot biography by Hugh Dempsey
collected works of Hugh Dempsey

Siksika Nation wiki
Siksika Nation website

Wednesday, April 2, 2014

Let's Throw a Stanford-Oxford Money Party and Invite Only Our Male Friends"

Stanford is throwing a Big Data in Biomedicine conference.  (Link)

I generally try to ignore the pervasive gender imbalance all around me in technology, but in this case, it is so blatant and close to home, that I think I'll say something.

Apparently, the topic of the conference is "driving innovation for a healthier world."

I note that there are only six women speakers to this conference (out of 45, a ratio of less than 15%). [I originally thought it was only two, but recounting, there are six women, out of forty five.]

Given that many of the chosen speakers at the conference are not directly in the field of bioinformatics or statistics, but are in related fields such as public policy, traditional medicine, or radiology, it is inexcusable that the number of women researchers at this conference is not approaching half.  This is conference about health, after all, which impacts women at least as much as men.

Vinod Khosla is an invited speaker, as is John Hennessy, the President of Stanford, and Robert Gentleman, Senior Director of Bioinformatics at Genentech, and David Glazer, Director of Engineering at Google.

The conference is being held in Silicon Valley, where I live and work, as a woman engineer.  The same place where women technology workers struggle to get even three months of maternity leave and struggle mightily to re-start their careers, should they decide to take some time out in order to take longer than three months of maternity leave.  The same place where, as a result of not being able to take maternity leave, most children are not breast fed for more than a few months and therefore do not benefit from the known life long health benefits of breast feeding.

And how about that pay differential between women and men in Silicon Valley?  According to the Silicon Valley Business Journal, "as of 2012, men working full time in Santa Clara made a median $91,471 annually, compared to $56,996 for women." 

It is not as if there are not more women qualified to speak at this conference.  True, many of them may not be researchers at Stanford or Oxford, but some are researchers at companies such as Genentech.  I happen to know several who would definitely be more qualified than some of the speakers I see on the list.

It's really shameful.  Oxford and Stanford, Google, Khosla Ventures and Genentech should be ashamed to throw a boys' club money party and call it a "conference" on bioinformatics and "health". Health?  I'll believe it when I see these guys lobbying for at least six months of paid maternity leave across the board, career re-entry paths for women in technology, and gender parity at conferences.


Daniel and Lior, thanks for your comments.  Personally, I think it would be a shame for anyone to withdraw from the conference. 
I don't believe in tokenism, but I think the conference is really missing out by not having more women and more diversity in the mix.  I'm not in bioinformatics, but obviously, writing this blog, I've run across so many great papers this year from a very broad mix of researchers.  Many are not at Stanford or Oxford, but more women and a broader mix of people from different cultural backgrounds would richen and strengthen the conversation about future directions in bioinformatics, health and innovation. 
OK, Good.  Thanks Daniel and Lior.

Tuesday, April 1, 2014

EDGAR - Emission Database for Global Atmospheric Research

GHG (CO2, CH4, N2O, F-gases) emission time series 1990-2010 per region/country

The GHG total, expressed in metric ton CO2 equivalent is calculated using the GWP100 metric of UNFCCC (IPCC, 1996). The GHG are composed of CO2 totals excluding short-cycle biomass burning (such as agricultural waste burning and Savannah burning) but including other biomass burning (such as forest fires, post-burn decay, peat fires and decay of drained peatlands), all anthropogenic CH4 sources, N2O sources and F-gases (HFCs, PFCs and SF6).

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.