Saturday, December 21, 2013

The danger of infallible heroes: On Jefferson and Jinnah

Aside:  I have been thinking on and off about this particular blog post from the inestimable (personal opinion alert!) Ta Nehisi Coates, which examines the tension between the anti slavery/abolitionist writings of Thomas Jefferson and his status as a slave owner in 18th century post independence American society. Here is a completed version of my thoughts

In the context of the American narrative (see American exceptionalism, the American Dream, Manifest Destiny, and Empire of Liberty), the liberation of (some of) the United States from British rule in the late 18th century is the cornerstone upon which the modern American identity is constructed. Within this framework, the American founding fathers enjoy a divinity of sorts, characterized by unmatched strength, wisdom, courage and a lack of moral failings.

In his writings, Ta Nehisi Coates points out a mismatch (a rather mild term in the context of slavery) between the anti abolitionist writings of Jefferson, where he passionately argues the moral and practical problems of slavery:
The whole commerce between master and slave is a perpetual exercise of the most boisterous passions, the most unremitting despotism on the one part, and degrading submissions on the other. Our children see this, and learn to imitate it; for man is an imitative animal. 

This quality is the germ of all education in him. From his cradle to his grave he is learning to do what he sees others do. If a parent could find no motive either in his philanthropy or his self-love, for restraining the intemperance of passion towards his slave, it should always be a sufficient one that his child is present. But generally it is not sufficient. The parent storms, the child looks on, catches the lineaments of wrath, puts on the same airs in the circle of smaller slaves, gives a loose to his worst of passions, and thus nursed, educated, and daily exercised in tyranny, cannot but be stamped by it with odious peculiarities. The man must be a prodigy who can retain his manners and morals undepraved by such circumstances. 

And with what execration should the statesman be loaded, who permitting one half the citizens thus to trample on the rights of the other, transforms those into despots, and these into enemies, destroys the morals of the one part, and the amor patriae of the other. For if a slave can have a country in this world, it must be any other in preference to that in which he is born to live and labour for another: in which he must lock up the faculties of his nature, contribute as far as depends on his individual endeavours to the evanishment of the human race, or entail his own miserable condition on the endless generations proceeding from him. With the morals of the people, their industry also is destroyed. For in a warm climate, no man will labour for himself who can make another labour for him. 

and his role as a slave owner, who "punished slaves by selling them away from their families and friends, a retaliation that was incomprehensibly cruel even at the time".

This contradiction between Jefferson's "founding father" persona and his moral failings as an individual creates an unease within the American national narrative. Attempts to resolve this contradiction either utilize the "man of his times" trope to justify/contextualize his slave owning status (historically inaccurate since some slave owners at the time set their slaves free) or worse deliberately belittle it. Rejecting the individual moral failings of national leaders/icons rather than reworking the national narrative to embrace them is problematic.

Historical events, or rather public perception of them, play an important role in shaping national identity. This identity informs the social, political context from which politicians/policy makers arise, in turn influencing which domestic and foreign policies are instituted. This is especially relevant in the current social and political atmosphere in Pakistan. The creation narrative of Pakistan as a "Muslim" (an ever changing definition nowadays) state is the cornerstone of our national identity. It is central to current ad nauseum emphasis on Muslim religious devoutness within the public sphere and the exclusion of non-Muslim and non-believing Pakistanis from it.

I would like to argue that examining the founding fathers of Pakistan, especially Jinnah, through the lens of the national narrative rather than as historical individuals underpins the limited scope of our current domestic and foreign policy.  An example of this is the deliberate removal of Jinnah's affection for alcohol from state approved historical narratives. Akbar Ahmad suggests that notion of a Jinnah who enjoyed alcohol is seen as weakening his Islamic identity and by extension that of the state. As historian Ayesha Jalal has pointed out, examining Jinnah as a historical figure remains an exercise in hagiography rather than that of genuine scholarship. This emphasis on the Islamic identity of both Pakistan and it's creator(s) is largely responsible for the increasing religious fundamentalism in our society. Although, the forced inclusion of religion into the Pakistani public sphere is the result of General Zia ul-Haq's policies, the divine status afforded to Jinnah and his contemporaries in our national narrative provided the vertebrae upon which these policies could be clothed.

As Coates points out on Jefferson:

At some point we are going to have to develop something beyond an infantile desire to know whether Daddy was a "good guy" or a "bad guy." In fact, Daddy was an avowed white supremacist, whose words help inspire the black freedom movement. Daddy was an American slave-holder to the end, who brilliantly elucidated the moral and practical problem of American slavery. Daddy railed against miscegenation, while practicing it.
Let me contextualize this from a Pakistani perspective.

At some point we are going to have to develop something beyond an infantile desire to know whether Jinnah and the founders of our nations were "good Muslim men" or not. In fact, Jinnah was a secular individual who enjoyed his alcohol, while creating a state based on religion. Jinnah opined that Muslims were a separate people that neither inter-dined nor inter-wed with other religious communities while he married a Parsi woman. Jinnah dismantled the oppressive power of colonial rule, while imposing the Urdu language upon non Urdu speaking peoples. Jinnah adopted the language, dress and culture of his colonial oppressors while ensuring that Indian Muslims had a seat at the table in post-colonial India.

Lastly, I would like to point out that while both Jinnah and Jefferson were fallible, complex and contradictory individuals that are afforded a divine status in their respective societies, I am by no means implying that their actions are equivalent (secularism and language oppression ≠ slavery). I  do not view Jinnah's secular leanings as moral failings, but rather a representation of the complexity of his person and a refreshing contrast to his one dimensional persona within our Islamicized national narrative. However, I would also emphasize that Jinnah should not be afforded divine status within our society. A critical assessment of his politics is necessary for constructing a new national narrative, one that acknowledges the wrongs of our history and pushes to right them.

Thursday, December 19, 2013

Daily Discoveries: Real Time Wind Map of the Earth

The state of wind patterns on earth at 8:30pm (EST) today. Check out the wind patterns in your region via this "hypnotically beautiful" real time wind map (via

h/t Juan Cole and Tree Hugger

Saturday, August 3, 2013

Ten Lessons I have learned from doing field work

In case you haven't noticed, I have been AWOL from this blog for almost the entire summer now. Why? Because I have been doing field work for my PhD which involves sampling daphnia from lakes in the Muskoka region of Ontario (Canada). I still have a few weeks to go, more than thirty lakes to sample and a large number of experiments to run but I'm taking stock of my experience so far. Here are the ten most important lessons I have learned so far: 
1) There is no such thing as free time. 

2) There is no difference between weekdays and weekends.

3) Expect the unexpected...apparently Murphy's law came into existence when some dude named Murphy tried to set up an experimental mesocosm in a lake.

4) Crying doesn't solve your problems....but it does make you feel better...just don't do it when the undergrads are watching.

5) Become one with the swarm. You can't hide from mosquitoes, blackflies, deerflies or horseflies

6) Bruises are very sexy....especially when they match.

7) Rope is NOT just rope. Good rope makes field sampling enjoyable. Bad rope...the name says it all.
8) If/when PhD supervisor suggest adding more components to your field experiment, citing it will make your publication better...just say no...a potential "insert prestigious scientific journal of your choice here" publication doesn't feel as good a 8 hours of sleep. 
9) A good field assistant can make a difference between a manageable field season and an absolute disaster. A great field assistant can make field work seem enjoyable...most of the time. Thanks for all your help so far, Phil!
10) Enjoy the definitely makes up for all the hard work and the setbacks.

Tuesday, March 12, 2013

Daily Discoveries: So you want some fancy colours for your graph?

Just came across this awesome website for generating optimally distinct colours for plots. Not only does it provide the user with a palette of distinct, yet complementary colour choices, it also generates distinct variations of the same colour and allows for the user to manipulate the colour space for a light or dark background. Of course, it gives HEX numbers for all selections, which means that your colour palellte can be utilized when creating plots in R.

(h/t Steve Walker)

Wednesday, January 30, 2013

Some good news from Timbuktu

 Credit: Wikipedia

I have an update on the status of the damage to the Timbuktu manuscript collections, The New Yorker reports that a large number of manuscripts from these collections were transported out of the city, when it fell to Ansar-e-Dine. However, the status of the majority of manuscripts remains unknown.

More details available here

Tuesday, January 29, 2013

A destruction of our shared history

Credit: World Atlas

Credit: Lonely Planet

As many of you might be aware, France is leading a coalition of forces on a nation wide offensive in the west African nation of Mali. Almost six months ago, following a military coup overthrowing then president Amadou Armadi Toure,  Al-Qaeda linked Islamists rebels Ansar-e-Dine and the Tuareg rebel group MINA took control of Northern Mali. This alliance broke down when the Ansar-e-Dine called for the imposition of Sharia law in this region.

After months of back and forth negotiations and truce between the Ansar-e-Dine and the Malian Army, including a number of UN resolutions, the Islamist rebels launched an offensive in southern Mali capturing the city of Konna, on January 10th. On Jan 11th at the behest of the Malian military regime, Frace launched operation Serval, a air and ground military intervention in Norther and Central Mali, which has been successful in pushing back the rebels (for more details see this comprehensive timeline of the conflict by France 24).

As the Islamist rebels retreat from Northern Mali, which includes the famous city of Timbuktu, it has been reported that they set fire to a historic library, housing  thousands of important manuscript collections, a literary heritage that dates back to the 15th and 16th century.

Written in  Arabic, as well as the local languages of Songhai, Tamashek and Bambara, these collections contained accounts of history and laws of the region as well as poetry and stories of North Africa. At a time when Africa as a continent was considered by European colonists as devoid of civilization, lacking literature, history and art, the discovery of these collections were instrumental in creating an African narrative and obliterating the myth of African history consisting solely of oral tradition.

As Essop Pahad, former director of the Timbuktu Manuscripts project points out:

The manuscripts gave you such a fantastic feeling of the history of this continent. They made you proud to be African. Especially in a context where you're told that Africa has no history because of colonialism and all that....The writings are so forward-looking on marriage, on trade, on all sorts of things. If the libraries are destroyed then a very important part of African and world history are gone.

There have been no further details as to the extent of the damage, but many (myself included) hope that some, if not most of the collections are preserved. If the reports on the destruction of these collections are true, then we have lost an important portion of our shared history.

In a similar vein, it should be noted that as part of the invasion of Iraq, American and Polish military presence in the ancient city of Babylon resulted in major damage to one of the oldest archaeological sites in the world. More details here.

Guest Post on the EEB and flow

I have a guest post on the rather awesome EEB and flow discussing my experiences as a minority in ecology. Check it out and let me know what you think. Also relevant is this piece in Science Careers on the difficulties minority women scientists face in europe.

P.S. I owe you one, Caroline

Monday, January 21, 2013

Science edition: Does parsimony make sense in an inherently complicated world?

Parsimony (aka Ockham's Razor) is one of the major heuristic (general guiding rule or observation) frameworks in theoretical ecology when it comes to constructing models that attempt to describe the processes underlying ecological communities, broadly defined here as all species in a area. Of course, I'm glossing over the debate about what exactly is a "species" and what constitutes this mysterious "area". My interest in using theoretical methods in ecology, a logical consequence of my romantic pre-PhD student notions about the perceived coolness of community over population ecology combined with the fact that I (sometimes) happened to be in close proximity to Peter Abrams, has brought me face to face with the parsimony in all of it's forms.

Perhaps it's the pervasiveness of all of the ecological bandwagons in our midst (cough, IDH, cough, phylogenetic community ecology, cough, neutral theory) or the fact that it is becoming increasingly difficult to find an overarching theory that provides an explanation for all/most patterns of biodiversity, even though we all secretly want to be the person to theorize it, but the notion that Hypothesis A better explains Phenomenon A than Hypothesis B, simply because it holds fewer assumptions feels hollow from a logical/philosophical perspective. After all, why should the simplicity of a hypothesis be any indicator of how true it is?

From a theoretical modelling perspective, the ideal model involves the simplest number of variables, with a certain set of assumptions that may or may not be realistic for the system that the said model is hoping to explain. Simon Levin (1975) emphasizes:

    "Most models (...) are not meant as literal descriptions of particular situations, and thus generate predictions which are not to be tested against precise population patterns. On the other hand, such models, if handled skillfully, can lead to robust qualitative predictions which do not depend critically on parameter values and can stimulate new directions of investigation."

 There is an inherent trade-off between the number of variables utilized and the extent of the explanatory power of the model. Fewer variables means a simpler model, but less explanatory power for the entire system. More variables make a model complex allowing for greater explanatory power for the entire system. However, this leads  to difficulty in identifying which variables/processes are important within the system of interest. The optimal model is one which minimizes the number of variables while increasing the explanatory power of the model

While I agree that the balance between the number of variables included in the model and the explanatory power is important, I am not very convinced that when choosing between two models with similar explanatory power, the model with the fewer variables is the better model.

In her work, "Feminist epistemology as local epistemology",  philosopher of science, Helen Longino points out three criticisms against Ockham's razor:

i. This formulation begs the question what counts as an adequate explanation.  Is an adequate explanation an account sufficient to generate predictions or an account of underlying processes, and, if explanation is just retrospective prediction, then must it be successful at individual or population levels?  Either the meaning of simplicity will be relative to one’s account of explanation, thus undermining the capacity of simplicity to function as an independent epistemic value, or the insistence on simplicity will dictate what gets explained and how.
ii. We have no a priori reason to think the universe simple, i.e. composed of very few kinds of thing (as few as the kinds of elementary particles, for example) rather than of many different kinds of thing.  Nor is there or could there be empirical evidence for such a view.
iii. The degree of simplicity or variety in one’s theoretical ontology may be dependent on the degree of variety one admits into one’s description of the phenomena.  If one imposes uniformity on the data by rejecting anomalies, then one is making a choice for a certain kind of account. If the view that the boundaries of our descriptive categories are conventional is correct, then there is no epistemological fault in this, but neither is there virtue.
Orkses, Schradder-Frechette and Belitz (1994) contend that:
Ockham's razor is perhaps the most widely accepted example of an extra-evidential consideration. Many scientists accept and apply the principle in their work, even though it is an entirely metaphysical assumption. There is scant empirical evidence that the world is actually simple or that simple accounts are more likely than complex ones to be true. Our commitment to simplicity is largely an inheritance of 17th-century theology.
Despite a lack of evidence suggesting the inherent simple nature of the universe (in fact, we have evidence of the opposite), parsimony has been very useful tool for examining natural phenomena. Statistical methods such as Principal Component Analysis (PCA) describe complex phenomena in terms of simple components that account for the variation observed in data. In Bayesian inference, parsimony  is an underlying principle for model selection (see Jeffreys and Berger (1992) Ockham's Razor and Bayesian Analysis).

From the perspective of pragmatism, simplicity is ideal for a number of reasons. As Hoffmann, Minkin and Carpenter (1997) point out simple hypothesis are more vulnerable to falsification than complex hypothesis, as fewer components in model result in less flexibility. If we ascribe to a Popperian view where a good scientific hypothesis is one that can be falsified, then a model which is more falsifiable than another is the better model. Simpler models due to their simplicity tend to be more readily comprehensible than complex models, although this comprehensibility has nothing to do with accuracy. Simpler models are also more intuitive, as in the case of the example provided below by Hoffman et al. (1997)

There are a number of ways to describe the relationship between these data point.

The two relationships presented above are among the many possible relationships that can exist between the data presented. Most of us would agree that the linear relationship provide a better fit to the data than the complex functional form. Goodness of fit tests, would confirm this intuitive choice.

There seems to be dichotomy between the usefulness of parsimony as a tool for understanding complex phenomena and it's (potentially disturbing) philosophical implications about the nature of reality. Is it possible to utilize parsimony without buying into these problematic assumptions? Is it intellectually dishonest to ignore the philosophical failings of this technique, if it plays an important role in the scientific method? Or merely a pragmatic admission of the limits of our intellectualcapabilities as a species in understanding an infinitely complicated universe? 

Tuesday, January 1, 2013

Happy New YeaR!

I apologize to my (few) readers in advance. Be prepared to indulge in some serious statistical nerdiness.

Considering that I just spent New Year's eve making changes to a phylogeny (family tree of organisms based on shared evolutionary characteristics) of North American freshwater fishes using the rather brilliant statistical package "R", I thought that it would be very appropriate to ring in 2013 with a pResent.

Disclaimer: I did not write the code myself (I wish I had though). All credit goes to  Weicheng Zhu and Yihui Xie,  who are much cooler people (as demonstrated below) than I am.

Set Fireworks in R 2011

Here is the code for this animation:

fire <- function(centre = c(0, 0), r = 1:5, theta = seq(0,
    2 * pi, length = 100), l.col = rgb(1, 1, 0), lwd = 5,
    ...) {
    x <- centre[1] + outer(r, theta, function(r, theta) r *
    y <- centre[2] + outer(r, theta, function(r, theta) r *
    matplot(x, y, type = "l", lty = 1, col = l.col, add = T,
        lwd = lwd, ...)
f <- function(centre = rbind(c(-7, 7), c(7, 6)), n = c(7,
    5), N = 20, l.col = c("rainbow", "green"), p.col = "red",
    lwd = 5, ...) {
    ani.options(interval = 0.1)
    lwd = lwd
    if (is.vector(centre) && length(n) == 1) {
        r = 1:n
        l = seq(0.1, 0.6, length = n)
        matplot(centre[1], centre[2], col = p.col, ...)
        for (r in r) {
            fire(centre = centre, r = seq(r - l[r], r + l[r],
              length = 10), theta = seq(0, 2 * pi, length = 10 *
              r) + 1, l.col = rainbow(n)[r], lwd = lwd, ...)
    else {
        matplot(centre[, 1], centre[, 2], col = p.col, ...)
        l = list()
        for (i in 1:length(n)) l[i] = list(seq(0.1, 0.6,
            length = n[i]))
        if (length(l.col) == 1)
            l.col = rep(l.col, length(n))
        r = 1:N
        for (r in r) {
            for (j in 1:length(n)) {
              if (r%%(n[j] + 1) == 0) {
                r1 = 1:n[j]
                l1 = seq(0.1, 0.6, length = n[j])
                for (r1 in r1) {
                  fire(centre = centre[j, ], r = seq(r1 -
                    l1[r1], r1 + l1[r1], length = 10), theta = seq(0,
                    2 * pi, length = 10 * r1) + 1, l.col = par("bg"),
                    lwd = lwd + 2)
              else {
                if (l.col[j] == "red")
                  fire(centre = centre[j, ], r = seq(r%%(n[j] +
                    1) - l[[j]][r%%(n[j] + 1)], r%%(n[j] +
                    1) + l[[j]][r%%(n[j] + 1)], length = 10),
                    theta = seq(0, 2 * pi, length = 10 *
                      r%%(n[j] + 1)) + 1, l.col = rgb(1,
                      r%%(n[j] + 1)/n[j], 0), lwd = lwd,
                else if (l.col[j] == "green")
                  fire(centre = centre[j, ], r = seq(r%%(n[j] +
                    1) - l[[j]][r%%(n[j] + 1)], r%%(n[j] +
                    1) + l[[j]][r%%(n[j] + 1)], length = 10),
                    theta = seq(0, 2 * pi, length = 10 *
                      r%%(n[j] + 1)) + 1, l.col = rgb(1 -
                      r%%(n[j] + 1)/n[j], 1, 0), lwd = lwd,
                else if (l.col[j] == "blue")
                  fire(centre = centre[j, ], r = seq(r%%(n[j] +
                    1) - l[[j]][r%%(n[j] + 1)], r%%(n[j] +
                    1) + l[[j]][r%%(n[j] + 1)], length = 10),
                    theta = seq(0, 2 * pi, length = 10 *
                      r%%(n[j] + 1)) + 1, l.col = rgb(r%%(n[j] +
                      1)/n[j], 0, 1), lwd = lwd, ...)
                else fire(centre = centre[j, ], r = seq(r%%(n[j] +
                  1) - l[[j]][r%%(n[j] + 1)], r%%(n[j] +
                  1) + l[[j]][r%%(n[j] + 1)], length = 10),
                  theta = seq(0, 2 * pi, length = 10 * r%%(n[j] +
                    1)) + 1, l.col = rainbow(n[j])[r%%(n[j] +
                    1)], lwd = lwd, ...)
card <- function(N = 20, p.col = "green", bgcolour = "black",
    lwd = 5, ...) {
    ani.options(interval = 1)
    for (i in 1:N) {
        par(ann = F, bg = bgcolour, mar = rep(0, 4), pty = "s")
        f(N = i, lwd = lwd, ...)
        text(0, 0, "Happy New Year", srt = 360 * i/N, col = rainbow(N)[i],
            cex = 4.5 * i/N)
ani.options(interval = 0.2)
card(N = 30, centre = rbind(c(-8, 8), c(8, 10), c(5, 0)),
    n = c(9, 5, 6), pch = 8, p.col = "green", l.col = c("rainbow",
        "red", "green"), xlim = c(-12, 12), ylim = c(-12,