Wednesday, May 29, 2013

Bubonic plague, inbreeding Neanderthals and shipwrecked marble for a Roman-era temple

by Salman Hameed

[Updated below]

It is hard now to keep up with spectacular science news. Nevertheless, it is sometimes good to pause for a bit to appreciate the way scientists find clues about history. Here are three news items in the same issue of Science that I found riveting. This just reminded me of the crude nature of evolution-creation debates - and how those discussion take place in a parallel dumb universe ("where is the missing link?"; "Evolution is just a theory" etc.).

Here is the story of the bubonic plague. It was suspected that the Byzantine empire was hit by a bubonic plague that hastened its decline in the 6th century and later. This decline also facilitated the phenomenal expansion of Islam into the Byzantine territories. But do we know that this was a bubonic plague? Well now we do:
The Justinian Plague, which resurfaced regularly between the 6th and 8th centuries, is thought to have assisted the decline of the Roman Empire, but it has, until now, only been speculatively diagnosed as bubonic plague caused by the bacterium Yersinia pestis. Using stringent ancient DNA anticontamination protocols, Harbeck et al. have genotyped new material from the early medieval graveyard at Aschheim, Bavaria, dating from the 6th century. This graveyard contained 438 individuals, often in multiple burials—a sign of crisis. The amount of bacterial material available was scant, but Y. pestis was identified from one individual using five key single-nucleotide polymorphisms identified in recent phylogenies. Genotyping confirmed this isolate as basal to isolates from the 14th-century Black Death and the modern (19th-century) third pandemic and that, like the other pandemics, it originated in China or Mongolia.
Full article at: PLoS Pathogens 9, 10.1371/journal.ppat.1003349 (2013).

Then we have this phenomenal work of decoding of the Neanderthal DNA as well as another hominid group called the Denisovians. What is fascinating is that the researchers can tell not only that humans and Neanderthals interbred (yes - for those outside of Africa, about 2% of the DNA comes from Neanderthals), but that at least in some cases Neanderthal first cousins had offsprings:
Neandertals, the closest known relatives to modern humans, ranged across Europe to western Asia from perhaps 300,000 years ago until about 30,000 years ago. Their overlap in time and space with our ancestors had fueled debate about whether the two species had interbred. Then, in 2010, Pääbo's group published a low-coverage sequence (1.3 copies on average) of DNA from three Neandertal bones from Croatia, which showed interbreeding: About 2% of the DNA in living people from outside Africa originally comes from Neandertals (Science, 7 May 2010, pp. 680 and 710). 
That first Neandertal sequence was a huge accomplishment, as Neandertal DNA made up just a few percent of the DNA in the fossils, the rest being bacterial and other contaminants. Since then, the Leipzig group has found ways to zero in on human genetic material and to get more from degraded ancient DNA by using a sequencing method that starts with single, rather than double, strands of DNA. The approach provided a startlingly detailed view of the Denisovan pinkie bone (Science, 31 August 2012, p. 1028). 
But this powerful technique had yet to be applied to Neandertals. So Pääbo was thrilled when the DNA in the sample taken from the toe bone proved to be 60% Neandertal. The researchers were able to sequence each base 50 times over, on average—enough coverage to ensure the sequence is correct. This approach also provided low coverage of the genome from another fossil, a Neandertal baby's rib, more than 50,000 years old, from a cave in Russia's Caucasus region between the Caspian and Black seas. 
In a 10 p.m. talk to a full house, Pääbo offered some surprising results from the toe bone. For long stretches, the DNA from each parental chromosome is closely matched, strongly suggesting that this Neandertal was the offspring of two first cousins, he said. Comparing the data with those from the fossils from Croatia and the Caucasus showed that these populations were fairly separated from one another. The group also compared the chunks of Neandertal DNA found in living people with each of these three Neandertal samples. The closest match was with the Caucasus population, suggesting that interbreeding with our ancestors most likely occurred closer to that region.
Okay - so scientists, I think, are now invading the privacy of this inter-species relations. Do we really have to know what our ancestors were doing tens of thousands of years ago on those cold nights? ;) 

Actually we do.

Full story here (but you will need subscription). 

Okay - so moving on from our misbehaving ancestors to the shipwrecks carrying marble for temples. What is amazing here is that scientists can not only identify the dates of the shipwreck, but they can tell where the marble was quarried from and where it was headed. This is pretty cool (and Urdu speakers will know why Marble is called Sang-e-Marmar - the stone of the Marmara): 
Sometime between 100 B.C.E and 25 B.C.E., a wooden ship carrying almost 60 tonnes of
stone foundered in Aegean waters just off the coast of Turkey. It went down bearing its entire cargo, including eight massive drum-shaped blocks of white marble. Those blocks fit together to form part of a tapering column that likely stood more than 11 meters tall, plus a square uppermost piece: a Doric column. 
Two thousand years after the ship went down, archaeologists excavating what is now called the Kizilburun shipwreck have figured out exactly where the marble blocks came from and where they were heading, illuminating the marble trade in the Roman province of Asia Minor.
...
Carlson and classical archaeologist William Aylward of the University of Wisconsin, Madison. first set out to learn where the marble came from. As reported in a 2010 study in the American Journal of Archaeology, the team sent out samples of the marble for stable isotope analysis and other tests. The marble's values of the isotopes δ13C and δ18O and its spectroscopic details led them to Marmara Island, known as Proconnesos in Roman times, in the Sea of Marmara, the inland sea connecting the Aegean and Black seas. This island was the site of an important marble quarry when Asia Minor became a Roman province around 130 B.C.E. 
But where was the marble heading? The blocks' size and style suggest that the column was intended for a major public building, most likely a temple. Carlson and Aylward drew up a list of all the Doric-style monumental buildings under construction in the 1st century B.C.E. on coastlines south of the wreck site, the probable direction of travel away from the quarry. Then they searched for sites with a finished lower-column diameter of about 1.73 meters. They concluded that the marble was headed for the Temple of Apollo at Claros, where people in Roman times flocked to seek advice from oracles, just 50 kilometers from the wreck. That finding is "utterly convincing," says architectural historian Lothar Haselberger of the University of Pennsylvania. 
The data show that the quarry workers on Proconnesos were in close contact with the temple builders some 500 kilometers or more away, shaping the marble to the builders' exact specifications. The findings also show that the builders received columns in pieces in small shipments, hinting at a lengthy construction process. This information, says Carlson, "is the missing link that tells us a lot about this process."                   
Read the full story here (yes - subscription will be needed).                  

[Update - May 29th: So scientists can say quite a bit from DNA analyses about what humans and Neanderthals were doing tens of thousands of years ago, but according to the Council of Islamic Ideology in Pakistan, DNA analysis cannot be used as primary evidence in rape cases (it can be used as secondary evidence). Shame for that]. 

Monday, May 27, 2013

"Scientific Saudi" for science communication

by Salman Hameed

Over the years I have had numerous posts on Saudi Arabia - and a vast majority of them have been unflattering. Much of it justified as many of these posts have been critical of Saudi government's handing out of death penalties for petty things as well as for laws against women (yes - women still cannot drive in Saudi Arabia and need a male guardian's signature to obtain a passport).

But then there is some good news as well. About a year ago, a 25-year old medical student, Muath Alduhishy, started up Scientific Saudi and now its team has expanded to 6 members. Out of a population of 26 million, Saudi Arabia has 6 million Facebook users and has the second-highest ratio of internet users per population in the Middle East (after Iran). Therefore, there is enormous potential in Scientific Saudi.
Alduhishy, started a Facebook dedicated for science communication in Arabic. The page is titled

Here is an interview with Muath Alduhishy conducted by Mohammad Yahia of the excellent House of Wisdom blog:

1)      How did the idea for Scientific Saudi come about and how long have you been online?  
The idea of Scientific Saudi started over a year ago, when I noticed the high prevalence of English-speaking scientific groups in the social media, namely Facebook, while I couldn’t find any in the Arabic-speaking world of Facebook. 
However, there are plenty of pseudoscientific groups, which in lieu of providing updated, credible and verified scientific articles and news, they broadcast common factoids that have been circulating the internet since its establishment or, in other cases, they are religious-oriented groups that uses science as a means to support their spiritual believes. 
I couldn’t find any credible Arabic-speaking group that’s passionate to communicate science purely for the sake of educating and informing people about the astonishing and mind-blowing advances and breakthroughs that happen every day in the research centres and universities, as it was the case with the numerous English-speaking scientific groups that I’ve come across, albeit I did found a couple of amazing Arabic scientific groups later on, but they are extremely scarce and have negligible impact in terms of the quantity of fans. 
At this moment, I realised that it’s my duty to bridge the gap, or at least to attempt to do so, due to the fact that I have always been passionate about science and I’ve been nurturing my passion for years through listening to scientific shows and podcasts and subscribing to scientific publications, such as your sister science publication Scientific American, hence the name Scientific Saudi. 
I started the group by myself as a Facebook page at the end of July 2012. It was just an ad hoc step. I had no grand plan or long-term strategy at that time. I had this idea for a while so I wanted to do something about it. From the first day, I made a pledge to myself to distinguish my page by not publishing anything without a credible, and, where possible, peer-reviewed reference, and to preserve the intellectual rights of any materials or persons presented in the group. I know it seemed a bit extreme and overly ideal commitment, especially that I publish new posts every day, but I did strictly adhere to it and still do, with a few exceptions. Also, I request from every contributor to adhere to this golden rule of mine. 
Today, we have pages on Facebook, Twitter, Instagram and YouTube as well as an official website. We have over 30,000 followers in the aforementioned social networking websites, which is still a considerably scant number compared to the overwhelmingly ubiquitous religious, celebrities and trivia pages.

2)      What are your plans to expand on what you have right now?We are currently in the phase of expansion and development, which means focusing on increasing our impact and spreading further out. We are being gradually recognized in the world of social media as it’s evident in your reach to us. Also, we are interested in collaborating the efforts with other scientific groups and with individuals who share the same passion as us. You can read more about our goals as well as our mission and message here http://www.scientificsaudi.com/about-16051606-160615811606.html
And of course, a question on evolution also shows up:

5)      I see you have several articles on Darwin and evolution – topics that are often thorny in the Arab world, and might be especially so in Saudi Arabia. How do you handle these topics? And has there ever been a backlash against you for your coverage of these topics? 
This is a good question, I have to say. However, before I answer it, you should know that we are committed to not discuss religion or politics in our published work, which is really an unprecedented proposition in the Arabic-speaking world. Most of the Arabic scientific speakers and communicators, albeit they are few, have strong religious tendencies. 
I, myself, have no problem with that at all, but the problem is that many of them handle scientific theories that might contradict with their religious views with an unscientific mentality. I was listening the other day to a highly regarded scientific communicator in the Islamic world talking about Darwin’s evolution theory as if it was a ‘conspiracy’ to dehumanise people, and that it has no plausible scientific basis. He clearly has no clue how significant is the evidence that supports this theory, or at least he appears so. 
Now to answer your question, yes, we do care greatly about scientifically and objectively explaining such major theories that shaped our current knowledge of the world. Darwin’s theory of evolution, in particular, is supported by a significant amount of evidence from different fields of science, and that’s what we care about here as a scientific group. Of course this means we will deal with a backlash from some of our readers, and we did, but we are still willing to answer every inquiry they have about such theories without judgment or reject. In fact, we have witnessed people who strongly disbelieve that humans have ever passed the stratosphere, others think that the big bang theory is just an absurd lie, and some who think that stem cells technology is a myth. If we are afraid of any backlash in the group, then we should quit science. 
However, it should be noted that if an opponent of any theory of science brought a plausible scientific evidence against it, then we are willing to adopt the evidence without hesitation. In short, science is our language in this group.

Read the full interview here.

Saturday, May 25, 2013

Saturday Video: Glenn Greenwald at Hampshire College

by Salman Hameed

From this past March, here is Glenn Greenwald talking about 'endless war' and growing Presidential powers in the US. The first part of the talk is about 40 minutes, and then he sits down for a discussion with Hampshire College faculty member, Falguni Sheth. The whole session is fantastic - but his discussion of Wikileaks is particularly worthwhile. For our purposes, there is a discussion of how the narrative of endless war allows the government to expand its power and how such things become normalized (for example, for many young adults, they don't even know pre-9/11 US). In any case, here is the talk:

Wednesday, May 22, 2013

Boneheaded US sanctions on reviewing Iranian science manuscripts

by Salman Hameed

If you are a US citizen, you cannot review a manuscript even if only one of the co-authors works for the Iranian government. Oh - and these sanctions apply even if the journal is base in the Netherlands:

Scientific journals are being asked to help tighten U.S. trade sanctions on Iran. On 30
April, the Dutch publishing behemoth Elsevier of the Netherlands sent a note to its editorial network saying that all U.S. editors and U.S. reviewers must "avoid" handling manuscripts if they include an author employed by the government of Iran. Under a policy that went into effect in March -- reflecting changes in a law passed by the U.S. Congress in December -- even companies like Elsevier not based in the United States must prevent their U.S. personnel from interacting with the Iranian government. 
The sanctions, aimed at punishing Iran for its pursuit of nuclear technology, have been broadened somewhat from previous rules issued by the enforcement agency, the U.S. Office of Foreign Assets Control (OFAC), a division of the Treasury Department. 
According to a treasury official, OFAC has not changed its "general license" policy for journals; it still allows them to publish articles authored by nongovernmental scientists from Iran and other sanctioned countries. The new wrinkle is that OFAC insists that all U.S. citizens, no matter who employs them, comply with the sanctions against papers authored by governmental researchers. That apparently prompted Elsevier to issue a warning to its employees.
This is insane. What stops complete insanity is the small concession that these sanctions do not (yet) apply on academic and research institutes and on non-governmental hospital and clinical settings. But remember, that it takes only one co-author in a governmental institutions (such as oil and gas) to trigger the sanctions. So what should the journal editors do? 
In a note to editors (a copy of which was obtained by ScienceInsider), Elsevier gives advice on what a manager should do if he or she can't find a non-U.S. person to work on a paper that requires special handling: "Please reject the manuscript outright." According to the note, the rejection should apologize to the submitter and explain that because of U.S. sanctions, "we are unfortunately unable to handle your manuscript."

Shameful. Read the full story here.

And all of this is beside the point that the US led sanctions of Iran on nuclear issue are, of course, hypocritical. Obama won (or more accurately, "was awarded") the 2009 Nobel Peace Prize for, amongst other illusions, the promise of the reduction of nuclear weapons. Instead, he has decided to cut non-proliferation funding in favor of more nuclear warheads:

Under the 2014 proposal, the Energy Department’s nuclear weapons activities funding — which includes modernization efforts for bomber-based and missile-based warheads — would be increased roughly 7 percent, or around $500 million, above the current level of $7.227 billion for these activities. 
The department’s nonproliferation programs, aimed at diminishing the security threat posed by fissile materials in other countries that can be used for nuclear weapons, would be cut by roughly 20 percent, or $460 million, below the current level of $2.45 billion, the officials said.
In combination with the expansive use of drones under Obama's watch, it is not surprising that there is now a petition to revoke Obama's Nobel Peace Prize (you can sign it here). Also read this Salon article Celebrating Our "Warrior President" by Glenn Greenwald.

In the mean time, I hope that these sanctions on science publications ignored by other publishers. This has happened before:
OFAC tangled with scientific journals almost a decade ago when it proposed much harsher restrictions on communications from Iran. That led to an organized protest by the American Institute of Physics, the Association of American Publishers, and others, resulting in the current understanding: OFAC permits the exhange of scientific but not government-sponsored communications from Iran. 

Monday, May 20, 2013

A panel on Contemporary Fantasy and Science Fiction from the Muslim world at Wiscon' 37

by Salman Hameed


If you happen to be in Madison next Sunday, you can attend a panel on Contemporary Fantasy and Science Fiction from the Muslim World as part of Wiscon' 37. Here are the details from the Islam and Science Fiction website:

A lot has happened since One Thousand and One Nights. Come and hear panelists discuss contemporary fantasy and science fiction from the Muslim world! We’ll talk about works by Muslim authors from different countries, both those available in English and those still awaiting translation. We welcome audience participation, so come with questions; we’ll bring our reading experience and boundless enthusiasm. A dystopian Cairo, a water planet and a magic library await you!
Location:    Concourse  Hotel, Capitol A Room
Schedule:    May 26, 2013 Sun, 2:30-3:45 pm
Panelists:   Muhammad Aurangzeb Ahmad, Amal El-Mohtar, Anwesha Maity, Sofia Samatar
Hashtag:    #MuslimFSF

No need for "meaning" as a cloud plunges into the supermassive black hole of our Galaxy

by Salman Hameed

Hydrogen gas swirling around the black hole at the center of our Galaxy as seen in radio waves

There is often heated rhetoric around science and religion debates. Some focus on showing the incompatibility of science and religion while some others find evidence of science in scriptures. But often the beauty of nature - as nature - gets left out. In fact, in 99% of the cases, science and religion have nothing to say to each other. In that spirit, here is a fantastic news story of the discovery of a Magnetar - a highly magnetized neutron star - very close to the central black hole of our own galaxy, the Milky Way. We are quite far from the central black hole (about 30,000 light years away) and don't have to worry about it. However, what is really cool is the fact that there is a gas cloud, G2, heading straight (actually it will be spiraling in) into Sagittarius A* - the supermassive black hole at the center of our Galaxy. The cloud is about 3 times as massive as the Earth and it is expected to swallowed some time between September of this year and March 2014. Now this is so cool that we (as in astronomers) can pinpoint such events with this kind of accuracy!

What does it have anything to with science and religion? Nothing. And that is the way it ought to be. Of course, if we (as in humans) were in the cloud that will be swallowed by Sagittarius A*, then there would be have been a lot of discussion of science, religion, and the meaning of our drift into the central black hole. Otherwise, thirty-thousand light years away, it is just a cool event.

Here is the story from this week's Nature:
The magnetar’s accidental discovery is a by-product of astronomers’ excitement about the arrival of the gas cloud, dubbed G2. The cloud, which is about three times the mass of Earth, was first spotted near Sgr A* in 2012 (and was later found in 2002 data). Its arrival would deliver insight into how objects accrete into the swirling disk of material around a black hole, as well as offering the first chance for astronomers to measure the time that it takes for objects to be captured and swallowed up.
Every flicker of emissions from Sgr A* sparks a flurry of speculation, intensifying the usual cycle of observation and coordinated follow-up that characterizes high-energy astronomy. Many telescope directors are scheduling additional monitoring of the Galactic Centre. The VLA, for example, is already scanning radio frequencies around Sgr A* every two months, and will do so every month once G2 arrives.
Read the full story here (may need subscription to access it).

And here is a short video that includes a simulation of what will happen to the cloud when it encounters the black hole:

Saturday, May 18, 2013

Saturday Video: NOVA's Decoding Neanderthals

by Salman Hameed

Our long lost cousins. Here is a fantastic NOVA episode on new genetic and archaeological discoveries about the Neanderthals.

Enjoy!


Watch Decoding Neanderthals on PBS. See more from NOVA.

Thursday, May 16, 2013

French Muslims unite on astronomical calculations for Ramadan

by Salman Hameed

Posts should resume their regularity here. Lets start with the news that The French Muslim Council (CFCM) has decided to start using astronomical calculations to set the dates for Ramadan. Hallelujah - oh I mean, Alhamdulillah!. It's about time, but still good to hear some common sense trust (faith?) in science. From our friend Tom Heneghan:
Council President Mohammad Moussaoui said the old method played havoc with French Muslims' schedules for work, school and festivities. France's five million Muslims are the largest Islamic minority in Europe. 
"Now all this will be simplified," he said, and promptly announced the Ramadan fast would begin on July 9 this year. 
Turkey began using scientific calculations to set the start of Ramadan decades ago. Muslims in Germany, who are mostly of Turkish origin, and those in Bosnia also use this method. 
Muslim minorities elsewhere in Europe often start Ramadan according to its beginning in their countries of origin, or in Saudi Arabia. That can lead to different ethnic groups starting it on different days, even in the same country.
"This is historic. Now all Muslims in France can start Ramadan on the same day," said Lyon Muslim leader Azzedine Gaci.
Read the full article here.

In other news, Pakistan will most likely maintain the excitement of shunning science in favor of naked eye testimonies. For last year's adventures, see this earlier post: Strife amongst Maulvis give astronomers a rare opening in Pakistan.

Saturday, May 11, 2013

Saturday Video: David Foster Wallace's "This is Water"

by Salman Hameed

This is commencement time. If you have 10 minutes (and yes, you do), watch this video dramatizing the 2005 commencement speech by the late David Foster Wallace. This is an abridged version but you  can read the full speech here. It is really fantastic and I also love the imagery used in the video. But ultimately, it is about how you create - or ought to - create meaning.

Do check this out.

Enjoy! (tip from Open Culture)

Friday, May 10, 2013

Political fatwas, tigers and stage falls. But elections in Pakistan have started...


by Salman Hameed


Pakistan's elections have started (live updates here). Despite the bloodshed, assassinationstiger death (yes - it was too hot for this rare tiger used as an election prop), stage fallskidnappingtargeting of secular parties by the Taliban, there is a lot of enthusiasm for the elections. In case, you have been only hearing about the right and center-right parties in the elections, here is a reminder that socialist parties are also around. Here is the band Laal, which is known for singing political songs, imploring people to vote in the upcoming elections in this cool video:


Laal: Chapna (Habib Jalib) from Taimur Rahman on Vimeo.

Couple of other things entertaining things: To complete the mockery of fatwas, one of the politically religious parties, Jamiat Ulema-e-Islam-Fazl (JUI-F), declared that voting for Imran Khan's party is "haram":
Jamiat Ulema-e-Islam-Fazl (JUI-F) chief Maulana Fazlur Rehman on Saturday declared it ‘haram’ to vote in favour of Pakistan Tehreek-e-Insaf chief Imran Khan and his candidates.
Imran Khan, according to Fazl, is being sponsored by the West and the Jewish lobby. 
Fazlur Rehman used every word that would foment hatred against any person in the conservative masses of Pakistan. He called Imran an agent of “Americans, Jews, Ahmadis and a person of ill character”. 
“A person who could not make his own children Muslim nor Pakistani, is dreaming of becoming prime minister of Pakistan and making the country an Islamic welfare state,” Maulana said. 
“The Yahoodi (Jewish) lobby’s money is working (for Imran),” he said.
And he has sufficient evidence to back it up: His own word. Oh - he is so humble!
“I am asked, ‘what is the proof that he (Imran Khan) is an agent of the Jews,’ I say there is only one proof and it is my own responsible personality. I am so righteous that I would never talk ill against anyone. This is enough that Maulana Fazlur Rehman says that he is a Jewish agent.” 
He went on to give a joint declaration of the clerics belonging to the JUI-F. “We the Ulema have agreed that giving vote to PTI is haram. 
Anyone who casts his or her vote for Imran or to a person who is contesting election on the ticket on PTI is involved in haram and such a person is going against Sharia,” the chief of the JUI-F said.
Aha. And this is again a reminder that even when people say they want "sharia", it is unclear what sharia do they mean. But I also like another entertaining claim by the Jamaat Islami (JI) leader during the elections: the liberals in Pakistan should register themselves as a religious minority:

All those claiming to be liberals in a country made for the supremacy of Quran and Sunnah should register themselves as minorities, Jamaat-e-Islami Ameer Syed Munawar Hasan declared on Sunday. 
American intervention in the country had lead to anarchy and those siding with the US had no place in this country. If they were happy to call themselves as liberals, they should enter their names in the list of minorities, the JI chief suggested while addressing an election rally held at Bagh-e-Jinnah near the Quaid’s mausoleum.
No, no. This is not satire. But it is still funny.

On a more serious note, I will leave you with two more things. First, here is a fantastic music video by Beyghairat Brigade. It is brilliant, sarcastic, biting, and critical of the military and the colluding politicians. But it is also blocked in Pakistan - or at least in some parts of the country. Here it is:


Dhinak Dhinak by Beygairat Brigade | Official Video from Farhan Adeel on Vimeo.

Finally, check out this excellent article, The Tragedy of Pakistan, that provides an excellent context for the present election (tip 3quarksdaily):
Beyond simply outlasting a bloody election showdown against the TTP, the future leaders of the Islamic Republic of Pakistan will have to drastically reform an extractive and unaccountable state apparatus in order for the democratic project to have a chance of succeeding against the violent and ideological onslaught of anti-government militants. 
With 180 million people, 100 nuclear warheads and nearly 50 banned terrorist outfits, Pakistan has always been too strategic for the politics of the country to be swayed by what its people want. As the unwanted stepchild of the anti-colonial South Asian independence struggle, Pakistan came out of the partition of the subcontinent with an ignominious legacy as Britain’s military buffer zone against threats from the west. Though the British kept all of India under a firm paternalistic rule, the provinces that make up present-day Pakistan were deliberately denied political development because of their utility as a recruiting ground for soldiers and landowning elite collaborators. Though constitutional reforms came towards the tail end of British rule to give greater political representation to locals, they were little more than a cosmetic attempt to put an Indian face onto autocratic rule.
To this day, the country functions according to the structure developed over two centuries under the British Raj; the Civil Services of Pakistan, the backbone of government, traces its lineage to the colonial era Indian Civil Services — the elite English bastion of political power in India. The acknowledged expertise of bureaucrats, combined with their high-class social background, has vested them with veto power over the demands of ‘inept’ politicians in the formation of state policy. This has resulted in a modern Pakistani state that is not run by politicians but rather said to run in spite of them. 
The travails of a historically autocratic state have been intensified by the curse of geography. If it were located anywhere else, Pakistan would be dismissed as irrelevant — and might then enjoy greater control over its domestic policy. Instead, it is surrounded by Afghanistan, a hotbed of dysfunction where the War on Terror was inaugurated, Iran, a declared rogue state attempting to develop nuclear capabilities, and China and India, the two major emergent threats to American economic might. Before 1989, Pakistan was also neighbor to the Soviet Union. With such borders, Pakistan has traditionally served as a critical outpost of support to Western interests in a hostile region. 
In light of this, it is understandable why the governors of Pakistan, civilian and military, failed to establish accountable and responsive institutions of political economy. It also explains why the country is held hostage to the neoliberal economic program and security paradigm. Since 1948 when the Pakistani army leveraged the country’s location vis a vis Soviet Russia for a lucrative position as a US proxy in South Asia, global stakeholders have jumped at the chance to pay for the privilege of maintaining some form of control over Pakistan’s goings on. Presiding over a resource rich but economically weak nation, the country’s leaders have been unable to fight the impulse to accept. This has encouraged outward-looking politicians to mortgage Pakistan’s foreign policy and loot as much as they can from state coffers before they are inevitably and unceremoniously thrown out of power. The free flow of money has disincentivized military governments — for military governments are the disproportionate beneficiaries of Western aid — from doing the hard work of creating a sustainable tax infrastructure in the country, one that would push the people of Pakistan to invest in their own country, or financial regulatory bodies which would require the government to show returns on that investment. 
The most fundamental obstacle, however, to the implementation of democratic governance in Pakistan has been ideological. As control over people has become territorialized by the borders of an ever-shrinking state, ideologies particularly pan-Islamist ones have found themselves competing for limited territory and votes — and therefore power. In such an environment, the atmosphere of tolerance has been shattered by the arrival of an exclusivist religious ideology from the Persian Gulf. Seeking regional proxies in South Asia to counter Shiite Iran, the Gulf States and particularly Saudi Arabia have invested a large amount of capital in the Pakistani state while promoting the development of a strict and doctrinaire Wahhabi Islam. It has penetrated the country via new Saudi-funded madrassas, or religious schools, that are blossoming across the country, some of which have subsequently been implicated in training terrorists. These institutions have made a home in the absence of a state that long ago abdicated responsibility for responding to demands for public education and welfare.

And it concludes with this:
The autonomy and integrity of the nation has long been the plaything of others. Now the Taliban are providing the single greatest impetus in recent times for national soul-searching. Martyrdom for the sake of democracy in Pakistan will only be meaningful if state and society succeed in formulating a functional and responsive government. Otherwise, the ideological vacuum and lack of public support of the present Islamic republic will provide an easy path for a calculating and determined militant opposition to enforce its repulsive dogmas on the country.

Read the full article here.

In the mean time, lets hope the elections go smoothly and without violence.

Wednesday, May 08, 2013

How did feather's evolve? by Carl Zimmer

by Salman Hameed

Carl Zimmer has written some fantastic books on evolution, including this textbook intended for non-majors: The Tangled Bank: An Introduction to Evolution. Also check out his blog: The Loom. Here is a short video where he explains the evolution of feathers. Enjoy!

Tuesday, May 07, 2013

Pre-election views of Pakistanis on economy, political leaders, and internal and external threats

by Salman Hameed


Pakistan's elections are scheduled for May 11th. There have already been a tremendous number of casualties - mostly by the Taliban (of the Pakistani flavor) targeting the relatively more secular parties. Here is from the horse's mouth:
“Taliban shura had decided to target those secular political parties which were part of the previous coalition government and involved in the operation in Swat, Fata and other areas of Khyber Pakhtunkhwah,”adding that “the organisation followed the instructions of the Taliban shura and that it was the shura that decided which political parties to target, where and when.” 
To another query that the Taliban were making ground and paving way for some parties to win the elections and denying space to others, he said: “neither we are against nor in favour of the PTI, PML- N, JI and JUI-F,” adding  that “We are against the secular and democratic system which is against the ideology of Islam but we are not expecting any good from the other parties either, who are the supporters of the same system, but why they are not targeted is our own prerogative to decide.”
Shamefully, none of the parties not targeted by the Taliban have unequivocally condemned this Taliban assault on democracy. But to add to the uncertainty, just a few hours ago, Imran Khan of PTI also got injured when he fell off a lifter while getting on a stage for a political rally. This is big news as he is one of the leading contenders in the upcoming elections.

But what are the major concerns of Pakistanis? The Pew forum has a new survey out that focuses on Pakistan. Perhaps, not surprisingly, crime and terrorism is at the top at 95 and 93% respectively. But note that even Sunni-Shia tensions are labeled as a "very big problem" by over half of the respondents, and the conflict between the government with the judiciary and the military is not considered that much of a problem.


At the same time, most people also feel that the country is on the wrong path, with Zardari's approval ratings in the teens (and that is the least surprising result of the survey):


Here is a graphical representation of the opinion on the direction of the country. Note that 2007 was the start of major Taliban incursions into Pakistan (not completely unrelated to the US drone policy in the tribal regions - but that really picked up from 2009 onwards), an increase in suicide bombings in major cities and the assassination of Benazir Bhutto. The following years also saw its impact on the economy. 

But then check this out. The Taliban are seen as much of a threat as India. This is important as often people think that there is widespread for Taliban. But this poll suggests that there is broad recognition of the danger posed by the Taliban: 

Similarly, there is very little support for the various extremist groups, including those that are focusing on Afghanistan. Unfortunately, the question does include those groups that are primarily involved in targeting Ahmadi and Shia minorities. In any case, here are the views on extremist groups:

But there is still support for the military, religious leaders, the media, and even the courts (despite their utmost effort to destroy the trust gained in the Lawyers' movement). As per religious leaders, it would have been interesting to see individual names instead of a generic religious leader which people may idealize in a particular way.  Ah - but the poor police - it is only above Zardari...


You can find the full report here.

Sunday, May 05, 2013

Lessons from "The Gatekeepers" and "Incendies"

by Salman Hameed

The situation in Syria is has been awful for the past two years and there is an ever present danger of the conflict spreading into the neighboring countries. Israel attacked a shipment of missiles that it believed were meant for Hezbollah in Lebanon. Just a few hours ago, there were four large explosions near Damascus, and there is a possibility that it is the second strike by Israel inside Syria in two days. From the New York Times:
Four explosions just west of Damascus shook the ground across the Syrian capital early on Sunday, sending fiery mushroom-shaped clouds towering over the landmark Mount Qasioun and brightening the night sky in a demonstration of firepower more potent than anything the residents of the city, a government stronghold, have witnessed during more than two years of war.  
 The Syrian government immediately blamed Israel for the explosions, whose power appeared to far outstrip that of any weapons in the rebels’ arsenals. Israeli officials refused to confirm that Israeli forces had carried out the strikes, which the Syrian deputy foreign minister, speaking on CNN, called “an act of war.”

With much still unexplained about the effects and motivations of the attack, it rattled the region, which has lived in fear that the Syrian war will lead to a wider conflict. It was unclear whether Israel, if it carried out the strikes, sought to intervene in Syria’s civil war or was simply expanding its campaign to prevent the Syrian government from transferring weapons to Hezbollah, the militant Shiite organization in Lebanon that is Syria’s ally and one of Israel’s most dangerous enemies. 
The attacks could end up providing psychological and perhaps military assistance to the Syrian rebels, who over the last several weeks have faced losses in a series of government offensives around Damascus and the city of Homs to the north. For the rebels, any damage to crucial military structures from the attacks — said by opposition activists to have hit bases of elite troops as well as weapons stores — would be offset by political complications if the explosions are linked to Israel.        
In this context, I wanted to point to a new documentary out, The Gatekeepers, that interviews six surviving former heads of Israeli security agency, Shin Bet. Most of the focus there is on Israel-Palestinian conflict. Nevertheless, it is a sobering film on the nature of conflict. You will find plenty of things to agree and disagree in this film. Here is our Film Autopsy of The Gatekeepers (see here for other Film Autopsies):



While we are on the subject, I also wanted to highlight a fantastic movie about the Lebanese civil war as well. Incendies is set in a country that looks a lot like Lebanon in the 1970s and it exposes the absurdity and the futility of the factional war that engulfed Lebanon for several years. This is an intense film. If you haven't seen, you should definitely check it out. Here is our Film Autopsy of Incendies:

Thursday, May 02, 2013

Using Biblical stories to talk about science

by Salman Hameed

I have lamented in the past on the efforts to find science in the Qur'an and other religious books (see On the futility of finding science in the Qur'an and other scriptures). But here is a book by Steve Jones, The Serpent's Promise: The Bible Retold as Science, that uses Biblical stories to talk about science. I think this is an interesting exercise, and since he is not trying to bring religion into science, it can also work. I don't know how he treats religion, but the review in last week's Nature is quite positive:

The Serpent's Promise is a believer's book. It expresses belief in the power of language, imagination, scholarship, high art, enduring myth, tribal tradition, unforgettable poetry, irrational vision and inspired insight. If you wanted to find all of these things between just one set of covers, you might pick up the Authorized Version of the Bible; but this is a not a
book by somebody who believes in God. It is a book by the distinguished geneticist, broadcaster, lecturer, writer and Welshman Steve Jones, who has a sharp awareness of moral imperative and a warm feeling for those Joneses before him who invoked the bread of heaven and yearned to be safe on Canaan's side. It is the ambivalence at the heart of this book which makes it so hugely enjoyable and, perhaps, so important. 
Jones' story is not of the science of the Bible, but of the science invoked by the Bible. The Good Book (his words, his capitals), he says, was always more of a guide book, “a handbook to comprehend the world ... it sits firmly in the genealogy of ideas. Science is its direct descendant.” In each chapter he takes a text — from Genesis or the Gospel of John, from Ecclesiastes or Matthew, from Exodus, Leviticus, Job and so on — as the starting point for a rationalist sermon on a biblical theme. So Jones uses Genesis 6:4 (“There were giants in the earth in those days”) as a springboard less for talking about Goliath than for using “the power of science to illuminate myth” and for discussing the growth-hormone disorder acromegaly, linked to tumours of the pituitary gland. The long life described in Ecclesiastes 11:8 prompts reflections on insulin, the French paradox (high consumption of saturated fats coupled with low rates of coronary heart disease), the joys of red wine, the connections between sex and death and the enhanced lifespans of castrati.
And here is a bit on genetics:

He is, of course, terrific on genetics. Jewishness is historically defined by descent, and the Bible is big on begetting. The stories told in human DNA sometimes square with tradition, and sometimes do not. Yes, the human race was all but extinguished — but perhaps more than once. Yes, the mutations in the male Y chromosome point back to a single progenitor in Africa 100,000 years ago. But the mother of all humans — the only one whose daughters all had daughters — lived in Africa 200,000 years ago. Adam and Eve can never have met, “let alone have committed the first and perhaps least original of all sins”. 
About half of all the Ashkenazim, the biggest group of Jews, share descent from just four women (the number of women who survived on the Ark, Jones teasingly reminds us). Half of all Russian males have a Y chromosome linked to the historical Arya people of Iran. But this is not the case in Germany — Teutonic purists of the early twentieth century who claimed Aryan supremacy in fact shared their chromosomes with people in the Middle East. They had on average a closer tie with the Jewish men they despised than with the Arya. Almost all native Britons can trace descent from a single anonymous individual who lived around the thirteenth century. The most recent universal common ancestor for the entire planet dwelt about 100 generations ago in the Bronze Age, perhaps around the time of the destruction of Solomon's Temple in Jerusalem in 600 BC. As we count back through the generations, our ancestors multiply. But populations were smaller, so we begin to share forebears. We have roots in common, says Jones: “Ancestry is a forest not of pines but of mangroves.”
Read the full review here (you may need subscription to access it).