A true teacher doesn’t teach you to think like him, but to think without him.


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August 17, 2017 · 10:16 pm

Let me tell you why Al Jarreau’s passing saddend me more than any recent legend passing away. Goes way back to how I developed this “money wasting” habit of going to concerts.

It started early and it ran in the family. My Dad did it! I don’t know how much my brothers remember, but now that I think about it, from the freebie concerts on campus to LCLR, Swara Mahardhikka to Stevie Wonder in Ancol in the 80s, and some I missed when I went to school in the USA (yes I remember you guys regalling me with Phil Collins in Ancol stories), my Dad was kinda a softie when it came to live concerts. Or theater. I discovered not many Dads did that back then. And Mom? Oh you bet she enjoyed concerts. We all did.

So fast forward a bit to Al Jarreau. I remember it well. 1987. I was still a 3rd or 4th semester undergrad with no income (because living with parents standard back then) and everyone is excited about Al Jarreau coming to Jakarta for the first time. Al Jarreau. Spain. Take Five. After All. Morning… and the list goes on.  My track record of Jazz concerts up to that point was limited to routine standing under the trees in Jazz Goes to Campus trying to catch Candra Darusman playing.(I was total geek back then, ok? Well, still am). Anyway, as you can imagine the tickets were not cheap. I started giving subtle and not so subtle hints about begging for tickets. What made Dad give in? I think because it was after Idul Fitri or something. I remember mas Candra Darusman dropping by for a Idul Fitri visit and I started babbling about Al Jarreau and Dad with usual enigmatic style with the full intent of embarrasing me in front of my jazz hero (who just happened to be his student) said “Yeah, she’s begging for tickets to see Al Jarreau” Way to go DAD. Embarass me more will you?

But hey, as I learned later in life, Dad apparently preferred his children to have these experiences rather than buying expensive stuff. What stuff back then? I honestly don’t remember, but I do remember going to see Al Jarreau live, in Jakarta for the first time in my life. Later on, Chick Corea also in Jakarta. And the rest is history. So for those who wonder why I like to splurge on going from concert to concert, or waiting for Java Jazz every year for a decade, some for the Top 40 feeling: Chicago, David Foster, Bon Jovi, Bryan Adams, STING , some for the Been There experience: Billy Joel-Elton John (94), Jon Secada at the World Cup(94) and why I thought I was strong enough to do a stadium concert with Coldplay 2017 (apparently not) the life lession from my father, now dutifully passed on to the grand kids (got those Ed Sheeran tickets yet Aliya?) was that being a  fangirl/fanboy is welcome in the Ismangil household, because they give you memories of a life time. Of course, T&C apply.

Another one for childhood memories, so thank you Al, thank you for the music, thank you for signing my albums with your friends George Duke and George Benson, thank you for being you.

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February 13, 2017 · 5:37 pm

Religion is a culture of faith; science is a culture of doubt.

Richard Feynman

So be careful about being absolutely sure of something.

(via currentsinbiology)

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February 6, 2017 · 11:03 am


New bacteria groups, and stunning diversity, discovered underground

One of the most detailed genomic studies of
any ecosystem to date has revealed an underground world of stunning
microbial diversity, and added dozens of new branches to the tree of

The bacterial bonanza comes from scientists who reconstructed the
genomes of more than 2,500 microbes from sediment and groundwater
samples collected at an aquifer in Colorado. The effort was led by
researchers from the Department of Energy’s Lawrence Berkeley National
Laboratory (Berkeley Lab) and UC Berkeley. DNA sequencing was performed
at the Joint Genome Institute, a DOE Office of Science User Facility.

As reported online October 24 in the journal Nature Communications,
the scientists netted genomes from 80 percent of all known bacterial
phyla, a remarkable degree of biological diversity at one location. They
also discovered 47 new phylum-level bacterial groups, naming many of
them after influential microbiologists and other scientists. And they
learned new insights about how microbial communities work together to
drive processes that are critical to the planet’s climate and life
everywhere, such as the carbon and nitrogen cycles.

Karthik Anantharaman, Christopher T. Brown, Laura A. Hug, Itai Sharon,
Cindy J. Castelle, Alexander J. Probst, Brian C. Thomas, Andrea Singh,
Michael J. Wilkins, Ulas Karaoz, Eoin L. Brodie, Kenneth H. Williams,
Susan S. Hubbard, Jillian F. Banfield. Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nature Communications, 2016; 7: 13219 DOI: 10.1038/ncomms13219

Stunning diversity, visualized. All the known
major bacterial groups are represented by wedges in this circular “tree
of life.” The bigger wedges are more diverse groups. Green wedges are
groups that have not been genomically sampled at the Rifle
site–everything else has. Black wedges are previously identified
bacteria groups that have also been found at Rifle. Purple wedges are
groups discovered at Rifle and announced last year. Red wedges are new
groups discovered in this study. Colored dots represent important
metabolic processes the new groups help mediate.
Credit: Banfield Group

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October 25, 2016 · 11:03 pm


“I’m not Barack Obama. I’m not Bill Clinton. Both of them carry themselves with a naturalness that is very appealing to audiences. But I’m married to one and I’ve worked for the other, so I know how hard they work at being natural. It’s not something they just dial in. They work and they practice what they’re going to say. It’s not that they’re trying to be somebody else. But it’s hard work to present yourself in the best possible way. You have to communicate in a way that people say: ‘OK, I get her.’ And that can be more difficult for a woman. Because who are your models? If you want to run for the Senate, or run for the Presidency, most of your role models are going to be men. And what works for them won’t work for you. Women are seen through a different lens. It’s not bad. It’s just a fact. It’s really quite funny. I’ll go to these events and there will be men speaking before me, and they’ll be pounding the message, and screaming about how we need to win the election. And people will love it. And I want to do the same thing. Because I care about this stuff. But I’ve learned that I can’t be quite so passionate in my presentation. I love to wave my arms, but apparently that’s a little bit scary to people. And I can’t yell too much. It comes across as ‘too loud’ or ‘too shrill’ or ‘too this’ or ‘too that.’ Which is funny, because I’m always convinced that the people in the front row are loving it.”

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September 8, 2016 · 10:43 pm

Eid Mubarak!



Today, President Obama and First Lady Michelle Obama sent their warmest greetings to Muslims in the United States and abroad who are celebrating Eid al-Fitr, the holiday marking the end of Ramadan:

Muslim Americans are as diverse as our nation itself—black, white, Latino, Asian, and Arab. Eid celebrations around the country remind us of our proud history as a nation built by people of all backgrounds; our history of religious freedom and civil liberties, and our history of innovation and strength. These legacies would not be possible without the contributions of Muslim Americans that make our country even stronger.

Eid Mubarak! Here are a few of the letters that the President has recently received from Muslim Americans:

Noor Abdelfattah

Dear President Barack Obama,

I am Noor Abdelfattah. Born in Chicago in November of 97’, I was blessed enough to grow up on Chicago’s North Shore. Growing up as child of a Muslim immigrant, I truly realize how privileged I am to live in the greatest country in the world. My grandfather left his homeland in 1951, the year my father was born, in search of his American dream. My father would not meet his own father until he was sixteen years old. Coming to this country with very little, my father was unable to attend college. However, he would spend long hours working low-paid jobs in order to provide for his family. Both my parents and five older brothers faced many difficulties before I was born.

At age seven, my oldest brother was caught in a Chicago gang fight where he took a bullet in the face. Today, that same brother is thirty-three years old and a graduate of University of Michigan Law School. The sacrifices my parents endured for their kids allowed us to prosper within our educational careers. Together, the educational institutions we have attended include University of Illinois-Urbana Champaign, Northwestern University, University of Michigan, and Loyola University Chicago.

Growing up, my parents have always taught us to treat everyone with respect. Although I grew up Muslim, my parents sent my siblings and I to Catholic high schools that placed us in an environment different than our own. Being the only Muslim in my class, I was allowed to interact with people who were raised different than myself. The opportunities my parents have given me allowed me to enter college open minded. I have met people I consider friends from all over the world.

However, with the hostile attitude some people carry towards Muslims, I believe that it is important that we remain together as a nation. I believe that the tradition of hosting an Iftar Dinner at the White House during the month of Ramadan is one tradition that shows the diversity our country holds. We, as Americans, are accepted for what we practice and how we look. On behalf of the Muslims living in the land of the free and home of the brave, I want to thank you for standing firmly with us in rejection of those who are hoping to limit our rights. Additionally, as your term comes to an end, I want to thank you for all the hard work you have done for all Americans and the rest of the world these past eight years as the President of the United States.

All the best,
Noor Abdelfattah


Dua Yang

Assalamu Alaikum Mr. President,

I am a 28 year old Muslim American woman. I am proud of my faith and I make an effort everyday to show the goodness of Islam. Islam teaches about sincerity, kindness, compassion, perseverance, fairness, and so many beautiful qualities that I try to exhibit each and everyday I serve my students, my school, and community.

Yet, despite my efforts to be a model of the peace and beauty of Islam, I am labeled and treated as a terrorist. As someone dangerous, unwelcomed, and insignificant…. And while having American citizens to public figures degrade my value may come to be dispairing at times. What I have witness from the effect of islamophobia onto the young Muslim American population is even more atrocious. Fourth graders who insecurely share with me the opinions they’ve heard from the media that I can see has psychologically damaged their confidence in themselves. Children who are just starting to find confidence in themselves are having to question their worth in America.

This environment of hate is causing a new generation of young Muslims who are weary and scared. They want nothing but to have the freedom to pursue life with dignity.

Please remain strong on your grounds. Continue to speak out against those who seek to use Islam as a political tool to oppress. You don’t know it, but you are a hero to many Muslim American children who hear your words that ‘it’s not their fault’.

Ms. Yang


Aleena K.

Dear Mr. President,

As-Salaam-Alaikum. My name is Aleena K., and I currently go to Northwest High School in Germantown, Maryland. Per the requirements of an honors research program I participate in, I completed a senior research project on a topic of my choosing. I wanted to make my project something that I could use as a learning experience, something that would correctly embody the passion I have for helping people. That was when I settled on my topic: Muslim-Americans. As a practicing Muslim-American, I am all too familiar with the difficulties of being a Muslim in a non-Muslim majority country. Thus, my project, titled Split in the Middle: Why Muslim-American Teenage Girls Struggle with their Identity, was born.

Completing this project was difficult. I had to face not only my insecurities, but the harsh rhetoric of other Americans. Because one of the potential causes of an identity crisis is the media, I had browse through the comments section of various articles that pertained to Muslim-Americans. I spent a couple of hours, sitting on the floor of my bedroom, reading thousands of comments from other people throughout America. The multitude of people who expressed their desire for deporting Muslims shocked me the most. I am an American, I grew up here. I say the Pledge of Allegiance every day. And yet, I am a Muslim. I fast during the month of Ramadan and celebrate Eid. I read the Quran, go to religion class, and pray. Which one was I allowed to be? It is a question that plagues me to this day.

Today, I watched you give a speech at a mosque in Baltimore. You talked about how society needs to stop its rhetoric, because it is not fair to profile a group of people as a result of the actions of one person. You mentioned how we are not just Muslims, or just Americans, but we are both. We are Muslim-Americans. Amongst the negative comments and the rising hatred of Muslims in this country, your speech was like an oxygen tank. It allowed me to breathe a sigh of relief and give me hope that maybe, just maybe, there was an influential figure who believed in us.

As I am writing this letter, I am listening to Adele’s song “All I Ask” on her new album. And all I ask is for acceptance and tolerance from others. I know that this can eventually be achieved, not from the work of just one individual, but from Muslims and non-Muslims alike. From the bottom of my heart, I thank you for your faith in us.

Aleena K.

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The bright future for “epigenetics”


If you’re fascinated by epigenetics, as I have been my entire academic career, you may be dismayed to see the recent stream of negativity about our field, to which I have been a prolific contributor. There was our cautionary review in Nature Methods in 2013, a @PLOSblogs perspective in 2015, and a recent review in @PLOSGenetics co-authored with Ewan Birney and George Davey-Smith. In addition, there was the backlash this year to Sid Mukherjee’s piece in the New Yorker, which was featured in Nature News and involved a blog post from Jerry Coyne that aggregated a lot of scientists’ negative responses, including my own. Jerry has another post today which criticises a TED-Ed talk with over 146,000 views that propagates current but inaccurate concepts about epigenetics. Myself and Steve Henikoff are about to release a further review questioning some basic assumptions in epigenetics in Current Biology, getting away from the human phenotypic associations quagmire and raising some simple questions about the basic biology in this field.

When someone like Carl Zimmer writes a piece for the New York Times on epigenetics, the newsworthy aspect to the current discussions is the negative angle – witness how these scientists are revealing a controversy in what looked like a really attractive field externally. It’s like a family squabble in a soap opera on a trivial level, or a real-time witnessing of a momentous occasion as a field changes direction, on a more profound level. Either way, the story is the negativity.

The responses I have been getting to these recent publications are actually overall very positive. The negative responses focus on impracticality (the epigenetics ship has sailed, too late to do anything about it) (Peripheral blood is the only sample possible at scale from human subjects) (Testing more than just DNA methylation will make human studies too expensive) and some degree of dismissiveness (We can fix cell subtype effects analytically, stop banging on about it). 

What’s being missed is the positive component in each of these publications –  we describe how there is massive potential for the field of epigenetics, now that we recognise our problems with study interpretability. For example, a problem is DNA sequence variability influencing DNA methylation outcomes. If we identify the DNA sequence polymorphisms associated with the phenotype and confounding our DNA methylation interpretation, that’s not just a GWAS-like positive outcome, it comes with a possible genomic regulatory mechanism for free. A cell subtype effect confounding interpretation of the DNA methylation result is another insight into disease pathogenesis that would be embraced enthusiastically by a cell biologist. If we start to regard DNA methylation as a multi-purpose tool that reads out a number of properties of cell populations and the individuals studied, and cling less tightly to the cellular reprogramming hypothesis that is usually being studied, we open up our potential for discovery to a much greater extent.

I have also become much more Ptashnean in my viewpoint, not because I adhere unquestioningly to Mark Ptashne’s transcriptionfactor-or-nothing worldview, but because we need to rebalance the field to incorporate the undoubtedly important role of TFs in cell and genomic physiology. If you look at the illustration used for Carl Zimmer’s New York Times piece, typical of every introductory slide in a lecture about epigenetics, the obvious omission is the transcription factor – how do those pretty coloured blobs on histones and DNA know where to go in the genome without them? 

If we find what look like genuine cellular reprogramming events, not attributable to confounding influences, and we incorporate the idea that these are due to TFs changing their regulatory functions, we can start to use motif analyses and other studies to ascend the regulatory hierarchy and figure out what might have mediated these DNA methylation or other transcriptional regulatory changes, an extraordinary mechanistic insight. Without considering the role of TFs we’re attributing innate intelligence to DNA methylation or chromatin state modifiers, which almost certainly do not know where they need to go in the genome, or how this pattern should change as a response to a perturbation. 

We have so much potential for new discovery, for real insights into the mechanisms underlying phenotypic changes. Yes, we need to work harder to get to these insights, and expand our skill set beyond genomic assays or analyses, but these kinds of challenges are what we signed up for when we chose to be scientists.

I’m not negative about the future of epigenetics at all. I can’t wait for us to perform these new study designs, it really feels like the start of a extraordinarily exciting new era. Yes, the epigenetics ship has sailed, but we still have time to steer it away from the rocks that we see straight ahead and out to sea on a proper voyage of discovery.

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