Thursday, September 26, 2013

EvoDevo begins in Venice!

Maryna P. Lesoway | PhD Student | Abouheif Lab

I’m in Venice this week, participating in a week-long summer school at the Instituto Veneto di Scienze Lettere ed Arti. This is the third edition of the course, which brings together students and investigators interested in evolutionary developmental biology (EvoDevo). 

Instituto Veneto di Scenze Lettere ed Arti
We’ve already completed four days of the course, which the instructors have been asked to structure as a discussion of what we don’t know in EvoDevo. The idea is that science is really driven by asking questions about things we don’t fully know or understand, can be a much more useful approach than simply re-stating what is already understood, particularly from a teaching perspective. And if the goal of science is to increase our understanding of the world that we live in, we need to ask good questions!

It has proven to be a much more challenging approach than a more typical organization, particularly to learn that many of the foundations that we take for granted are not nearly as stable as we generally think. For example, we’ve spent a great deal of time talking about evolutionary family trees – phyolgenies. These are trees that tell us how species relate to one another and give us a better understanding of how characters have evolved through time (i.e. the direction of change). These are incredibly powerful tools for evolutionary developmental biology, but we often assume that published trees are set in stone. Or at least in wood, to stay with the tree metaphor. However, these are really just our very best guesses, and even with lots of data and good evolutionary models, we still can’t accept them at face value. Even when we build trees using genomic approaches, which means using even more data, is really difficult because we are often asking questions about what evolved hundreds of millions of years ago. And adding fossil data it is often insufficient for understanding evolution on these very long time scales. Maybe we’ll be able to resolve this, but maybe we can’t. 

I’m learning incredible amounts of information, but also about how little we really know about development’s role in evolution. This field have been an area of active research for at least the last twenty to thirty years, and although we have answered many questions, we have raised even more. But, we are also developing new techniques, using greater diversity of animals as models for development and evolution, and changing views about how development integrates into evolutionary theory. It may seem a bit discouraging at times, to think of all the work that has been done, and what a long way there is to go yet, but at the same time it is incredibly exciting. As was quoted one of today's lectures, we may be as confused as ever, but at least it is now on a higher level, and about more important things! 

Venice is also the home of the spandrels of San Marco, made famous in evolutionary biological circles by Gould and Lewontin’s criticism of the adaptationist paradigm – how structures don’t have to be “for” anything, much like the spandrels in St. Mark’s Bascilica here in Venice – the spandrels are a structural result of having a dome centered over an arch, and have not been produced with the express idea of being surfaces to decorate with angels. In biology as well, many features may simply be a result of developmental or structural constraints, rather than an adaptive outcome. And yes, the spandrels of San Marco are beautiful!

Monday, April 1, 2013

CAUT President on Basic Research

Time to question federal funding priorities

Back Print
By Wayne Peters

The Canada Excellence Research Chairs program will fund 11 new chairs at eight Canadian universities at a cost of about $55 million over five years. The November 2012 announcement comes on the heels of the program’s first competition in 2010 that saw 18 chairs at 13 institutions funded at a cost of about $190 million over seven years. The program is preparing to launch a third round of awards in 2015.

With almost $250 million now committed to 29 individuals at only 21 institutions across the country, this is a significant concentration of resources to a very small group of researchers, especially when their research is expected to align with just four areas of strate­gic importance to Canada, as defined by the federal government.

A rough calculation shows that more than a million dollars is committed annually to each chair. By comparison, the Natural Sciences and Engineering Research Council of Canada’s Discovery Grant funding for basic research currently supports about 10,000 ongoing projects across a broad range of interests. In the 2012 Discovery Grant competition, 2,161 researchers were funded at an average grant level of about $31,000.

The Canada Excellence Research Chairs program was instituted to attract leading-edge research and world-class researchers to Canada. It is part of a recent, bigger push by the federal government to bridge the so-called innovation gap in this country by investing in innovation and research capacity in certain priority areas: environmental sciences and technologies; natural resources and energy; health and related life sciences and technologies; and information and communication technologies.

The 2012 federal budget purportedly committed $1.6 billion through its Economic Action Plan to a more effective promotion of innovation, although it is unclear just how much of this represents new money. Much of the money is targeted at creating value-added jobs consistent with the government’s new approach to supporting innovation that focuses resources on private sector needs.

This approach is driven in part by statistics such as the Global Innovation Index — co-published by the World Intellectual Property Organization, a specialized agency of the United Nations, and business school INSEAD — which ranked Canada 74th out of 141 countries in innovation efficiency in 2012. Innovation efficiency is a country’s ability to convert its commitment to innovation inputs such as investments in education, people and infrastructure (Canada ranked 10th on this measure) into innovation outputs such as new products, employment and patents (Canada ranked 20th on this one).

Rankings such as these suggest Canada is just not very good at capitalizing on the outcomes of its existing research and development infrastructure. This is the view, at least, of the Independent Panel on Federal Support to Research and Development, appointed by the Minister of State for Science and Technology following the 2010 federal budget. It released its report, “Innovation Canada: A Call to Action,” in late 2011.

The panel’s key recommendation is the creation of a national Industrial Research and Innovation Council with a clear mandate for “business” innovation, not simply innovation. The distinction here is an important one as it implies much more prominence will be given to the private sector as the primary innovator. And, it seems clear, in this context, that innovation is really commercialization. Consistent with this, the panel advocates for a policy shift in supporting the private sector — away from indirect funding (usually as tax credits) to a more direct approach through grants, and easier access to venture capital and government procurement. Further, it recommends this be done in a more targeted way.

This is a significant shift away from basic research to more targeted research with anticipated commercial value. In this model, federal investments will support a narrow, short-term commercialization strategy that links research outcomes directly to business interests, while largely neglecting basic academic research at our institutions.

In the 2012 federal budget no additional funds were provided to the three granting councils that support the basic research of thousands of academics in Canada. In fact, over the last five funding years, base funding to the three granting councils dropped by almost $90 million at a time when significantly more money was being allocated to a select group of research “stars.”

Additionally, vital programs such as NSERC’s Major Resources Support grants and the Research Tools and Instruments grants have been eliminated. Dedicated research facilities have been closed as a result of underfunding, including the Experimental Lakes Area project — a unique and internationally-acclaimed freshwater laboratory in northwest Ontario — and the Polar Environment Atmospheric Research Laboratory, Canada’s northernmost research station that tracked ozone depletion, air quality and climate change.

The money allocated to just one Canada Excellence Research Chair could have maintained such research efforts and many others like them.

Two things are at issue here. First, the federal government’s focus on commercialization diverts support away from basic science research in this country and targets it for the private sector. This strategy overlooks the reality that research, development and innovation are intertwined enterprises that exist along a continuum of activity. Basic research provides the building blocks on which everything else depends. Shifting resources away from it undermines the whole scientific and innovation agenda.

Second, the funding that does remain for basic research in this country is increasingly being concentrated into support for fewer individuals and for research in specific areas of strategic relevance to the government, as demonstrated by the Canada Excellence Research Chairs program. This leaves thousands of Canadian researchers starving for support and struggling to build and maintain their research programs. Sadly, it also means that many great ideas will never see the light of day due to a lack of funding or simply because they fall outside the government’s targeted research areas.

Is this good policy for funding Canada’s research? I think not.

Saturday, March 23, 2013

On The Importance of Basic Research

Stay tuned!

The Abouheif lab will begin blogging on the importance of basic research as the key for innovation.

A fascinating 30 minute video on Sky Islands!

PhD student Marie-Julie Fave will be defending her thesis this Wednesday (March 27th, 2013) @ noon in room W4/12.

She did some spectacular work on the role that organismal  development plays in responding to climate change in the Arizona Sky Islands.

Check out this nice 30 minute video on climate change in Sky Islands starring Meryl Streep!:

Friday, February 15, 2013

DEBATE: Huffington Post article

Usaama al-Azami


Muslims and Evolution in the 21st Century: A Galileo Moment?

Posted: 02/14/2013 2:39 pm

Early last month, a conference was held in London, entitled "Have Muslims Misunderstood Evolution?" under the auspices of The Deen Institute, an organization which aims at promoting engagement between the Islamic tradition and modernity. The event sparked off a debate on social media and op-ed columns regarding the place of evolution in the Islamic worldview.
The conference, whose lectures were recently published online, brought together scientists like Prof. Ehab Abouheif and Prof. Fatimah Jackson with theologians like Dr Usama Hasan and the prominent Shaykh Yasir Qadhi. Also invited was Dr. Oktar Babuna, representing the hardcore creationist ideas of Harun Yahya, who is deemed by many Muslim scholars to be a charlatan. Sadly, by the end of the day, Babuna was reduced to such a laughing stock that even Qadhi distanced himself from him.
Abouheif and Jackson made their case for evolution in a style reminiscent of the bestselling and quite compelling book, "The Language of God," by devout Christian geneticist Francis Collins. Babuna's creationist ideas were roundly rejected by all the other panellists. What I found most interesting, however, was the theological discussion.
Although Qadhi, who is more of a specialist in theology than Hasan, soundly rebutted Hasan's apparent suggestion that Muslim scholars had discovered and believed in modern evolutionary theory centuries ago, his response that scientific evolution and Islamic theology are at loggerheads is considerably overstated. For one, Hasan pointed out that preeminent center for Sunni Islamic learning, al-Azhar University, holds that the theory of evolution does not fundamentally contradict Islamic belief. In addition, the influential, if controversial, Egyptian scholar, Yusuf al-Qaradawi, stated three years ago on a special Arabic Al Jazeerashow dedicated to this subject that even if evolution were true, there is no reason for it to conflict with Islamic theology. Some conservative Muslims have attacked (in Arabic) al-Qaradawi for his statements.
My own suggestion to Muslims grappling with such an issue is to recognize that when it comes to what we believe, science and religion address two kinds of truth: empirical and revealed. Empirical (observation-based) truth is the stuff of science. It's contingent on our sense perception, and humanity's current state of knowledge. It's truth with a lower-case t. It's relative to what the human senses can access at a given point in time, and makes no claims to being absolute. This is not to belittle it, as most empirical truths are what we consider facts, like the fact that the spherical earth goes around the sun.
Revealed truth, by contrast, is based upon revelation which, if you believe it, is Truth with a capital T. For the believer, it is absolute, not relative. Our knowledge of empirical truth can and has improved over time; just as the once held 'fact' that the sun goes around the earth has been corrected with the passage of time. No reasonable person believes this 'fact' today; though the ancients may have been justified in thinking it was genuinely scientific. Revealed truth, on the other hand, claims to be constant, absolute, and unchangeable.
Problems of this kind are nothing new for Muslim theologians. An example is the statement of the Prophet that: after the sun sets, it goes to the Throne of God and prostrates, before rising again from the East. This statement is recorded in multiple collections of Prophetic statements including the respected Sunni collections of Bukhari and Muslim. Muslims additionally believe that such statements from the Prophet constitute revealed truth. The reality is that virtually no Muslim theologian has ever taken such revealed truths to be statements of empirical truth. In such an instance, a Muslim will believe in the revealed truth, but not think this means that the empirical truth is wrong. Rather, the two kinds of truth address different domains, the moral and the empirical (what is observable through the senses). The first addresses what Muslims should believe as a matter of faith, and how they should behave; and the other is whatever a reasonable person believes about the observable world based on the current state of human knowledge.
How does this relate to the theory of evolution for Muslims?
I'm not arguing for the truth of evolution in this piece, for that I recommend Collins' book mentioned above. I'm only presenting how, if it were deemed empirically true, as it nearly unanimously is in the scientific community, it should cause Muslims no trouble with respect to their traditional Islamic beliefs. If the Qur'an appears to be making empirical statements about creation, like the Prophetic statement above, it doesn't need to be understood in an everyday literal sense, even if we hold it to be True in an metaphysical sense. Many Muslims will be familiar with the fact that same logic applies to the many seemingly anthropomorphic descriptions of God in the Qur'an.
Some commentators have described this conference as marking a Galileo moment for Muslims. I would argue that this isn't quite the case, as Islamic religious authority is decentralized, and there is no formal 'religious establishment' that has binding authority over Muslims. With even the historic center for Sunni learning, al-Azhar University, and influential scholars like al-Qaradawi accepting that Muslims could believe in evolution--though neither seems to--it doesn't seem like this is a serious issue in theology. Rather it seems to be so only in the popular Muslim consciousness. As Muslims continue in the path of learning, as encouraged by the Prophet, I hope that a more nuanced attitude to this issue will emerge at a popular level, and then we can focus on more important discussions like that of climate change or alleviating poverty. This conference was an important step in that direction.

Tuesday, January 29, 2013

DEBATE: Backstage Interviews


In the mean time, here are the backstage 
interviews with debate participants :

DEBATE: The Economist magazine

Islam and science

The road to renewal

After centuries of stagnation science is making a comeback in the Islamic world

THE sleep has been long and deep. In 2005 Harvard University produced more scientific papers than 17 Arabic-speaking countries combined. The world’s 1.6 billion Muslims have produced only two Nobel laureates in chemistry and physics. Both moved to the West: the only living one, the chemist Ahmed Hassan Zewail, is at the California Institute of Technology. By contrast Jews, outnumbered 100 to one by Muslims, have won 79. The 57 countries in the Organisation of the Islamic Conference spend a puny 0.81% of GDP on research and development, about a third of the world average. America, which has the world’s biggest science budget, spends 2.9%; Israel lavishes 4.4%.
Many blame Islam’s supposed innate hostility to science. Some universities seem keener on prayer than study. Quaid-i-Azam University in Islamabad, for example, has three mosques on campus, with a fourth planned, but no bookshop. Rote learning rather than critical thinking is the hallmark of higher education in many countries. The Saudi government supports books for Islamic schools such as “The Unchallengeable Miracles of the Qur’an: The Facts That Can’t Be Denied By Science” suggesting an inherent conflict between belief and reason.

Many universities are timid about courses that touch even tangentially on politics or look at religion from a non-devotional standpoint. Pervez Hoodbhoy, a renowned Pakistani nuclear scientist, introduced a course on science and world affairs, including Islam’s relationship with science, at the Lahore University of Management Sciences, one of the country’s most progressive universities. Students were keen, but Mr Hoodbhoy’s contract was not renewed when it ran out in December; for no proper reason, he says. (The university insists that the decision had nothing to do with the course content.)
But look more closely and two things are clear. A Muslim scientific awakening is under way. And the roots of scientific backwardness lie not with religious leaders, but with secular rulers, who are as stingy with cash as they are lavish with controls over independent thought.
The long view
The caricature of Islam’s endemic backwardness is easily dispelled. Between the eighth and the 13th centuries, while Europe stumbled through the dark ages, science thrived in Muslim lands. The Abbasid caliphs showered money on learning. The 11th century “Canon of Medicine” by Avicenna (pictured, with modern equipment he would have relished) was a standard medical text in Europe for hundreds of years. In the ninth century Muhammad al-Khwarizmi laid down the principles of algebra, a word derived from the name of his book, “Kitab al-Jabr”. Al-Hasan Ibn al-Haytham transformed the study of light and optics. Abu Raihan al-Biruni, a Persian, calculated the earth’s circumference to within 1%. And Muslim scholars did much to preserve the intellectual heritage of ancient Greece; centuries later it helped spark Europe’s scientific revolution.
Not only were science and Islam compatible, but religion could even spur scientific innovation. Accurately calculating the beginning of Ramadan (determined by the sighting of the new moon) motivated astronomers. The Hadith (the sayings of Muhammad) exhort believers to seek knowledge, “even as far as China”.
These scholars’ achievements are increasingly celebrated. Tens of thousands flocked to “1001 Inventions”, a touring exhibition about the golden age of Islamic science, in the Qatari capital, Doha, in the autumn. More importantly, however, rulers are realising the economic value of scientific research and have started to splurge accordingly. Saudi Arabia’s King Abdullah University of Science and Technology, which opened in 2009, has a $20 billion endowment that even rich American universities would envy.
Foreigners are already on their way there. Jean Fr├ęchet, who heads research, is a French chemist tipped to win a Nobel prize. The Saudi newcomer boasts research collaborations with the universities of Oxford and Cambridge, and with Imperial College, London. The rulers of neighbouring Qatar are bumping up research spending from 0.8% to a planned 2.8% of GDP: depending on growth, that could reach $5 billion a year. Research spending in Turkey increased by over 10% each year between 2005 and 2010, by which year its cash outlays were twice Norway’s.
The tide of money is bearing a fleet of results. In the 2000 to 2009 period Turkey’s output of scientific papers rose from barely 5,000 to 22,000; with less cash, Iran’s went up 1,300, to nearly 15,000. Quantity does not imply quality, but the papers are getting better, too. Scientific journals, and not just the few based in the Islamic world, are citing these papers more frequently. A study in 2011 by Thomson Reuters, an information firm, shows that in the early 1990s other publishers cited scientific papers from Egypt, Iran, Jordan, Saudi Arabia and Turkey (the most prolific Muslim countries) four times less often than the global average. By 2009 it was only half as often. In the category of best-regarded mathematics papers, Iran now performs well above average, with 1.7% of its papers among the most-cited 1%, with Egypt and Saudi Arabia also doing well. Turkey scores highly on engineering.
Science and technology-related subjects, with their clear practical benefits, do best. Engineering dominates, with agricultural sciences not far behind. Medicine and chemistry are also popular. Value for money matters. Fazeel Mehmood Khan, who recently returned to Pakistan after doing a PhD in Germany on astrophysics and now works at the Government College University in Lahore, was told by his university’s vice-chancellor to stop chasing wild ideas (black holes, in his case) and do something useful.
Science is even crossing the region’s deepest divide. In 2000 SESAME, an international physics laboratory with the Middle East’s first particle accelerator, was set up in Jordan. It is modelled on CERN, Europe’s particle-physics laboratory, which was created to bring together scientists from wartime foes. At SESAME Israeli boffins work with colleagues from places such as Iran and the Palestinian territories.
By the book
Science of the kind practised at SESAME throws up few challenges to Muslim doctrine (and in many cases is so abstruse that religious censors would struggle to understand it). But biology—especially with an evolutionary angle—is different. Many Muslims are troubled by the notion that humans share a common ancestor with apes. Research published in 2008 by Salman Hameed of Hampshire College in Massachusetts, a Pakistani astronomer who now studies Muslim attitudes to science, found that fewer than 20% in Indonesia, Malaysia or Pakistan believed in Darwin’s theories. In Egypt it was just 8%.
Yasir Qadhi, an American chemical engineer turned cleric (who has studied in both the United States and Saudi Arabia), wrestled with this issue at a London conference on Islam and evolution this month. He had no objection to applying evolutionary theory to other lifeforms. But he insisted that Adam and Eve did not have parents and did not evolve from other species. Any alternative argument is “scripturally indefensible,” he said. Some, especially in the diaspora, conflate human evolution with atheism: rejecting it becomes a defining part of being a Muslim. (Some Christians take a similar approach to the Bible.)
Though such disbelief may be couched in religious terms, culture and politics play a bigger role, says Mr Hameed. Poor school education in many countries leaves minds open to misapprehension. A growing Islamic creationist movement is at work too. A controversial Turkish preacher who goes by the name of Harun Yahya is in the forefront. His website spews pamphlets and books decrying Darwin. Unlike his American counterparts, however, he concedes that the universe is billions of years old (not 6,000 years).
But the barrier is not insuperable. Plenty of Muslim biologists have managed to reconcile their faith and their work. Fatimah Jackson, a biological anthropologist who converted to Islam, quotes Theodosius Dobzhansky, one of the founders of genetics, saying that “nothing in biology makes sense except in the light of evolution”. Science describes how things change; Islam, in a larger sense, explains why, she says.
Others take a similar line. “The Koran is not a science textbook,” says Rana Dajani, a Jordanian molecular biologist. “It provides people with guidelines as to how they should live their lives.” Interpretations of it, she argues, can evolve with new scientific discoveries. Koranic verses about the creation of man, for example, can now be read as providing support for evolution.
Other parts of the life sciences, often tricky for Christians, have proved unproblematic for Muslims. In America researchers wanting to use embryonic stem cells (which, as their name suggests, must be taken from human embryos, usually spares left over from fertility treatments) have had to battle pro-life Christian conservatives and a federal ban on funding for their field. But according to Islam, the soul does not enter the fetus until between 40 and 120 days after conception—so scientists at the Royan Institute in Iran are able to carry out stem-cell research without attracting censure.
But the kind of freedom that science demands is still rare in the Muslim world. With the rise of political Islam, including dogmatic Salafists who espouse a radical version of Islam, in such important countries as Egypt, some fear that it could be eroded further still. Others, however, remain hopeful. Muhammad Morsi, Egypt’s president, is a former professor of engineering at Zagazig University, near Cairo. He has a PhD in materials science from the University of Southern California (his dissertation was entitled “High-Temperature Electrical Conductivity and Defect Structure of Donor-Doped Al2O{-3}”). He has promised that his government will spend more on research.
Released from the restrictive control of the former regimes, scientists in Arab countries see a chance for progress. Scientists in Tunisia say they are already seeing promising reforms in the way university posts are filled. People are being elected, rather than appointed by the regime. The political storms shaking the Middle East could promote not only democracy, but revive scientific freethinking, too.

DEBATE: The London Times article

NEWS: Muslim leaders urge Islamic community to rethink evolution theory

My news story published in the Times
Muslim leaders from around the world have urged the Islamic community to rethink their stance on the theory of evolution. 
In the first debate of its kind in the UK, prominent Muslim scientists and theologians tried to reconcile Islam with evolution, at the Institute of Education, London, to an audience of around 850 people.  Saturday’s event, which had to be moved from its original location at Imperial College, London, following protests by Muslim students, was titled ‘Have Muslims misunderstood evolution’ and was organised by the Deen Institute, which aims to promote Islam and intellectuality.
“We must accept the truth [of evolution] to progress and move forward into the 21st century,” said Professor Ehab Abouheif, a Muslim Evolutionary Biologist at McGill University, Montreal, Canada. “Have Muslims misunderstood evolution? My answer is a resounding yes. Biological evolution is a fact,” he added.
evo1The message was echoed by Professor Fatimah Jackson, Professor of Biological Anthropology at the University of North Carolina who converted to Islam in the 1970s. “I’m a scientist, biologist and I believe in Allah. Evolution was no hindrance for me to become Muslim,” she said.
Professor Jackson emphasised that “the theory of evolution has been hijacked by atheists” and faith and evolution “complement” each other.
Many modern-day Islamic scholars believe evolution to be incompatible with Islam, unlike Christianity, which has largely embraced it.
Dr Usama Hasan, a scientist and former Imam at Masjid al-Tawhid in East London, received death threats in 2011 when he advocated Islam was compatible with evolution. Despite retracting his statements soon after, for fear of his life, he used the stage to clarify his position.
“Evolution is a Muslim theory. John William Draper, the 19th century scientist and contemporary of Darwin, called it the Mohammedan theory. I even once preached against evolution until I looked into it,” he said.
However, the pro-evolutionists clashed with Dr Oktar Babuna, a Turkish scientist and representative of Harun Yahya, a world-leading creationist.
“Darwinism is nonsense, evolution is not a fact and there is nothing in the Quran about it,” he said. “I will pay anyone £5m if you find me a transitional fossil,” he added.
Dr Babuna found little support from his fellow panelists, was accused of misunderstanding evolution and taking Muslims back to the 19th century.
Yasir Qadhi, an American Muslim scholar and theologian, the last of the five panelists, refused to ally himself with Dr Babuna but refused to budge on the evolution of Adam. “Islamically, it’s not problematic whatsoever to accept a universal common ancestor for all life on earth with one exception: and that is humans.”
Qadhi, a renowned rhetorician, accused Hasan of performing “fanciful, hermeneutical gymnastics” by trying to reinterpret the “vivid” creation story.
However, Hasan believes it’s important not to remain entrenched with Islamic orthodoxy, as it has been proven wrong in the past.  He also made a case for reinterpretation of scripture partly because “there are hundreds if not millions of young Muslims who have lost their faith because of science”.
Ishaq, a Muslim optometrist who attended the debate said: “There was a need for it. It was entertaining and intellectually stimulating. It was a good platform for Muslim thinkers to come together to deal with these issues.”