The Return

It's been far too long. I'm breaking the silence with an update about a new course I'm working on through Udacity. It's called Tales from the Genome and it's going to be an awesome adventure into the biology of DNA, identity, and health. Below is a reprint of a post about the course that I wrote for the Udacity blog earlier today.

(DNA, the genetic code of life)

DNA is the organic software of almost all living things, and each individual cell is the hardware on which this genetic software is run. This amazing code, DNA, is the subject of one of Udacity’s newest courses launching this fall, Tales from the Genome: Adventures in DNA, Identity, and Health. This is an introductory course that will teach you basic genetic principles, regardless of your academic background. Together with the personal genetics service 23andMe, we will explore the biology of the most important code in your life: the human genome.

Most Udacity fans already appreciate the beauty of code, and most of you are likely to be far more expert at understanding and manipulating computer code than I am! (Although I am pleased with my progress so far in CS101). Still, I am continually surprised by how unfamiliar people are with their own personal genetic code wrapped up inside every cell of their body. Long before transistors, binary code, or the Internet, mother nature built her own coding system for all life on our planet. This code of life, billions of years in the making (Carl Sagan would be proud), is far messier, more dynamic, exceedingly more robust, amazingly more efficient, and absolutely more imperfect than man-made code.

Tales from the Genome will give you a taste of this complexity and begin to reveal exactly how much code is necessary to run a whole human body:

• Just as there are two possible values in binary code (0 and 1), DNA (the code of our genomes) has four possible values (A, T, G, or C).
• A single line of DNA code is always paired with another that can be inferred from the first: you may have heard of this before, DNA is almost always two strands that pair together in a regular way (the double helix).
• One copy of the human genome is 3 billion pairs of code letters, so 6 billion actual code letters total; and each cell has two copies of the genome, so that’s 12 billion letters per cell.
• Approximately 50 trillion cells in the human body means that you have approximately 1 yotta of DNA code letters. That’s 1,000,000,000,000,000,000,000,000 letters of code! If we think of one letter of DNA code representing one bit of information in computer code, then that’s equivalent to about 100 zettabytes of hard disk space. That’s more than 10 billion times more information available on today’s 2 Terabyte hard drives!

Somehow all of the DNA you have is wrapped up and organized inside your cells (and it doesn’t just sit there)! It is actively read all the time, even while you eat, sleep, and poop; every cell is reading different parts of the code, which makes that cell unique and allows it to do its job as a skin, stomach, blood, or brain cell. There are thousands of different cell types working together to make up who you are: one conscious being with specific traits and desires, a singular intelligence and personality.

But at the root of it all, you are a giant conglomeration of cells all meticulously reading the genetic code to keep you alive and functioning, forming the basis of all of your traits. Tales from the Genome will show you how to connect your genome to your traits and reveal what it really means to be human. We will explore the personal stories of people living with a variety of traits, from lactose intolerance to dwarfism to breast cancer to bipolar disorder. We will learn about how the genetic code controls these traits and what impact these traits have on individuals, their personal relationships, and society at large.

When you sign up for Tales from the Genome you will acquire a basic understanding of how this organic code of your genome is turned into flesh and blood. To hear more about the course and get updates on its launch in the fall, visit the overview page and click “Take the Class” to enroll. I hope you will join us on the adventure, and maybe you will find out the secrets your genome holds.

The Look of a Heathen

Let me set the stage:

Bojangles. 1:30PM.

ENTER: Me, the hungry atheist.

I order my favorite 4-piece supreme dinner, mashed potatoes with gravy, delicious honey mustard, and sweet tea. As I sit at the table eating this feast of kings, a suspicious looking middle-aged woman, placing what I assume to be jesus-tracts on cars outside, enters the restaurant, approaches me, and asks, "Do you know if you're going to heaven?"

Wondering at first if I was being recorded from some clandestine location for television, then realizing 'hey, this is north carolina, so probably not' I responded with, "What do you mean by heaven?" She looked confused, started to say something, but I just cut her off and said, "no, I'm not going to heaven." She proceeded to tell me that I could get to heaven through Jesus (if I wanted). I simply replied, "But I do not want to go to heaven."

Not to be de-railed with her witnessing, she sounded very parental and said, "You realize that you're talking about where you will spend eternity." I replied, "I intend to spend eternity where everyone else does - in the ground." With a glazed look in her eye and a forced smile on her face she blurted, "god bless you" and walked away.

I'm so proud to say that after four years of trying, I finally *look* enough like an atheist to get preached at like one by strangers. Thank you, Bojangles. Thank you, Durham.

God doesn't have a sense of humor apparently.

They say emulation is the highest form of flattery, but apparently impersonation is in bad taste ... especially if it´s of imaginary characters. In an article reported by The Seattle Times three days ago, a DJ named Revin John was fired from his job for a sketch released over Virgin Radio Dubai in Dubai of the United Arab Emirates. According to the article:

The Arabian Radio Network said in a statement Revin John had been "let go" over a sketch Monday on Virgin Radio Dubai in which he quoted an article about a U.S. court throwing out a lawsuit against God.

John then pretended to act out a telephone conversation with God, prompting complaints from listeners of "diverse faiths and nationalities," said a statement written in reponse to questions from The Associated Press.

"He intended to be funny, not to offend anybody," said Arabian Radio Network Chief Operating Officer Steve Smith. "However, what he did was highly offensive to the Muslim and Christian community in the UAE."

Apparently impersonating fictitious characters is only allowed if you're doing a sketch on Santa Claus, the Easter Bunny, the Tooth Fairy, pink unicorns, etc. In fact, I don't believe equal opportunity is shown to all deities here - I wonder: if he impersonated Zeus, Ra, or Quetzalcoatl would he have been fired? I reckon all gods are not created equal.

Mariam Zarouni, a 20-year-old chemical engineering student at the American University of Sharjah, said she was so offended by John's comments that she formed a group to protest the incident on the social networking Web site Facebook. It had 569 members by Wednesday evening.

"When somebody crosses the line, then you have to defend your religion," Zarouni said. "Honestly ... how can he do this? We're in a Muslim county. But even Christians would take offense to that. You can't insult God."

First off, when you create a facebook group, if you have less than 1,000 members you can hardly call yourself 'protest' group. A group on facebook called "Gay Marriage Killed the Dinosaurs" has almost 40,000 members. Secondly, if a 20-year-old chemical engineering student has time to be offended, she's not studying hard enough.

My favorite comment is "You can't insult God." Really? REALLY? To begin with, I was not aware that impersonation was in fact necessarily an insult. I figured that if we really wanted to insult god, it would take the form of, "Hey, god, your mom is so ugly, when she goes to the beach, cats try to bury her." No? Not appropriate? How about, "Hey god, while you were out last night killing all the first born, smiting the gentiles, and cutting the foreskin off of other babes, I was banging your wife." You're right. That's over the top. I'm gay, so I would probably bang god's husband, not his wife ... only if he was hot ... who I'm kidding, he's married to god, of course he's gonna be hot ... and probably a catcher, not a pitcher. After all, god is supposed to be omnipotent, that's got to come in handy sometimes.

I'm lucky enough to live in a country that truly believes in free speech. And I intend to practice that right until the day I die. There is no such thing as blasphemy. No topic should be off limits. When we decide that some things can't be said, that some things should never be discussed, we lose our freedom of speech and begin sliding down a slippery slope to fascism. When we make topics off-limits and cut ourselves off from free scientific inquiry, we end up with periods of history called the dark ages ... just ask the victims of the medieval inquisition or the salem witch trials.

And for any of you who may think that my views as an atheist are offensive, just remember what the people can do to a man or woman with a dissenting opinion. I'm sure you've learned about the holocaust at some point in your life ... the holocaust was a horrible, horrible stain on human history and I hope that it is not repeated, especially on that scale. Unfortunately there are people in this world who deny that the holocaust ever happened ... sick bastards. I bet you don't like their views either, just like me. But what should we do about it? Should we educate others about the truth? Should we oppose them in open public debate? Should we arrest and put in jail those people who claim the holocaust never happened? Right now, on October 25th, 2008, holocaust denial is explicitly or implicitly illegal in 13 countries: Austria, Belgium, Czech Republic, France, Germany, Israel, Liechtenstein, Lithuania, Luxembourg, Poland, Portugal, Romania, and Switzerland.

Does that scare you? I mean, I whole-heartedly disagree with flat-earthists and creationists but I would never promote legislation that would INCARCERATE them. Being free means you have the freedom to be smart AND stupid.

Don't forget that.

On a final note, Dubai is supposed to be the most liberal of the seven UAE states. The age of enlightenment began almost 400 years ago. Will it be another 400 hundred before the rest of the world catches up? 1000? The answer is up to us.

Not a moment too soon ...

It's been such wonderful weather lately - I was wearing shorts and t-shirts just last week before the temperature took a turn for the colder. Halloween is almost upon us, then the election (don't forget to vote!), then I'll teach a Saturday for Duke TIP, then the Graduate Student Symposium when Dr. Robert M. Hazen comes to talk about his origins of life research, then Thanksgiving, then our big choir concert, then finals, then some gift shopping, and finally a little christmas time with family. And right on time (about 2 weeks before Halloween) Rev. Donald Wildmon is starting his 'fight' to take back christmas!

That's right, we can't even get to "trick or treat" before we have to hear conservative wingnuts complain about the infamous and imaginary 'attack-on-christmas' propaganda. Rob Boston said it best in his blog entry:

Some stores, aware that not all of their customers celebrate Christmas, use a generic greeting. No one is trying to offend you or ruin your holiday. In fact, if you are really bothered by the type of holiday greeting you receive from a drug-store clerk in December, I'd like to suggest that you need to ask Santa to bring you a life.

Does anyone seriously think Christmas is under assault in the United States? Retailers certainly don't. In fact, they are starting to panic. Worried that the economic downturn might reduce spending this year, retailers are looking for ways to boost Christmas spirit - and sales. I imagine big corporations will instruct their employees to use any greeting possible if it will encourage more buying.

And therein lies the problem. Wildmon and his obsessive Religious Right pals continue to fixate on the use of the phrase "Merry Christmas," as if store workers' by-rote repetition of it will somehow cause Americans to infuse the holiday with more religious meaning. (It reminds me of how the Religious Right persists in believing that 30 seconds of watered-down, generic prayer in public school every day will make kids more devout.) Wildmon is looking at the business community to make Christmas more religious - the business community!

The 'Rev.' Wildmon is from the American Family Association. To fight back against the war on christmas they employed the use of ... buttons! Indeed, there are buttons and glossy stickers of all different sizes (and different prices for that matter) that you can buy to push back against the evil-doers who might be inclined to say 'happy holidays' instead of 'merry christmas' to be more inclusive of strangers they might meet.

In the words of the 'Rev.':

It's hard to believe that there are companies and individuals who want to ban "Merry Christmas" and replace it with "Holiday Greetings" because, they say, they don't want to offend anyone.

It gets better:

Christians can take a stand and proclaim to our communities that Christmas is not just a winter holiday focused on materialism, but a "holy day" when we celebrate the birth of our Savior. We can do it in a gentle and effective way by wearing the “It’s OK to say Merry Christmas” button.

But fighting back isn't free:

Purchase enough buttons for each member of your church and enough Glossy Stickers for each family to have one to go on their automobile. Urge your fellow members to wear their buttons and display the Glossy Stickers during the entire Christmas season.

If you are unable to sponsor your church yourself, ask your Sunday School class to make it a class project. You can even order buttons and Glossy Stickers to share with co-workers, children in Christian schools, customers, etc.

And for any of you nay-sayers who think that asking big-business to stop being so inclusive of everyone by wearing buttons won't work:

Some might think simply wearing a button or displaying a Glossy Sticker is a small thing, but God can use small things to make a big point, and to create opportunities to share the Good News. And what a great time to do that at Christmas!

That's right, is there anything god, zeus, athena, thor, apollo, ra, purple spaghetti monster, etc. can't do?

In response to their button, I'd like to offer my own:

The God Hypothesis ...

I'm totally exhausted from a weekend trip to DC and currently doped up on pain meds from the slipped disc in my back. Fortunately sleep will come shortly and a short operation on my back is scheduled for wednesday ... Halloween!

Contributing to my mental and physical exhaustion was today's return trip by bus, where there was quite an invigorating debate between myself and another fellow choral member on the subject of war, religion, and morality. Whereas science is my area of expertise, his skill is with history and politics. Several other people joined in from time to time to voice their opinion, but the argument stemmed heavily from the two of us. I was shocked to see his unwillingness to accept a gray world. There are many points I could describe for the sake of making my case, but I'll only select one at the moment - dealing with divorce.

Let's say, for example, that a woman and a man decide to get married. They go to the church to get marriage counseling before tying the knot, at which point their wedding is blessed in the eyes of God. Life is good for quite sometime, until the children come along, jobs don't work out well, and the husband begins to cope by drinking. In his inebriated state he begins to become physically abusive with his wife. Over time, this leads to more verbal, physical and mental abuse even during sober moments. The wife is terribly unhappy and sometimes fears for the well-being of herself as well as her children when her husband reacts during a particular rage. She finally decides that she wants to be separate from him as he shows no signs of change and lacks the willingness to hear her wishes. However it turns out that divorce is illegal, thus preventing the woman from escaping the tyranny of her husband and trying to start a new life as a single mother or with a second chance with another marriage. This doesn't sound much different than the political and legal issues abounding in southern Ireland in the mid- to late-1980s. Despite the woman being persecuted, she has no legal right to start anew, because divorce is seen by the Catholic faith as immoral and the Vatican does not endorse such practices.

As I was relaying this story to my friend, as a hypothetical, I wanted to know if he thought that the woman should be allowed to divorce her husband. His simple answer was "no" although to his credit (however little that may be) he seemed hesitant to say that. In his mind, since divorce and remarriage meant that the woman would end up with another man, that was clearly adultery as defined in the Bible and that is a sin in the eyes of God. As a result he felt it appropriate that she obey God's commands and stay married, even if she was being abused by her husband.

As if this isn't bad enough, the conversation moved to HIV in Africa. The Vatican does not approve of the use of condoms. It is a popular Catholic belief that condoms are (1) evil, (2) interrupt a holy process, and (3) actually promote sexual immorality. As for the first point, I can only say that tools in and of themselves are neutral. They can only be used by humans for good or evil. As for the second point, I hardly see how the production of gametes and their fusion to conceive another organism is hardly so precious - I'm positive that my friend has killed many flies before, which subsequently destroyed the sperm and eggs that would give rise to many future generations. The process isn't holy ... it's just natural. And finally for the third point, it's just simply not true. I've read from many credible sources that condom use does not increase or decrease sexual promiscuity among young people. My friend believes that the Pope is well within his right to denounce the use of condoms, despite the fact that should the Pope actually endorse the use of condoms, lay people who obey the word of the Vatican as law (which include many people in Africa) could be saved from the HIV epidemic. The case has been made that the Vatican has the opportunity to prevent these infections from occurring, but chooses not to endorse the method because the method is itself immoral - why is it immoral? ... because God said so.

Well, I guess that just says it all, doesn't it?

Life, Death, and Se(cts) in Between

I finally did it ... I created a blog. And it's about damn time.

It's a crazy world here, and trying to make sense of it is often times more than difficult. Perhaps documenting the crazy times will help me remember what I've learned and clarify things that still seem quite ambiguous.

It's only appropriate to mention that one of the driving factors in me starting this blog is the podcast 'The Skeptics Guide to the Universe.' I highly recommend it to open-minded people who want to be challenged and remain grounded when they seem to be surrounded by crazy people. I credit Leo DiNapoli for directing my fingers to the download on iTunes; I've finally managed to catch up on all 114 episodes, and I can't wait for each week's show to come!

I'm a grad student in the Cell Biology Department at Duke University. Tomorrow I'm supposed to present a paper on the molecular 'twisting' of the protein Dynamin that actually facilitates membrane pinching and subsequent endocytosis - I'm supposed to be working on it at this very moment, as I haven't even begun the presentation aspect yet. Instead, I've been sitting at my lab bench distracted by a friend's email concerning homeopathy.

Yes, that's right - you read correctly. Someone decided to email me the merits of homeopathy, as a legitimate cure for modern ailments - the FDA's official stance on it to be precise. He sent me this link: http://www.fda.gov/fdac/features/096_home.html

He actually sent it as an endorsement for homeopathy when, in fact, it is an indictment! The only reason the FDA doesn't call it quackery is because it would offend the many people of the world that practice it, and it wouldn't be very PC to do that, now would it?

Homeopathy functions on the founding 'law of infinitesimals' - it is just as counter-intuitive as it sounds. Diluting something down to mathematically NOTHING, claiming that the water retains an imprint of the substance, and then administering it to an ailing patient in hopes of 'stimulating' the body to respond. It involves a lot of what I like to call, 'woo woo magic.' Last night during a conversation (he's originally from India) my friend informed me that my close-minded nature was preventative to understanding the true merits of this sort of treatment - after all, back home in India there are numerous medical schools of homeopathy, millions of people who take homeopathic drugs, and his grandmother's arthritis got better after practicing homeopathy - clearly this is undeniable evidence that homeopathy works ... right?

There's a crucial logical fallacy that so many people commit because it can be very subtle - generally speaking it's a good rule of thumb, but you can never rely on it to tell the truth. The concept is so old, that there's a Latin phrase epitomizing the thought: 'post hoc, ergo propter hoc.' This essentially means that because something happened after an event took place, then that event must have caused what happened. When made explicit like this, it seems obvious that it's a mistake to think in such a way. But we commit this fallacy all the time. Especially when drugs are concerned - take aspirin for example: when you take 2 aspirin for a headache, and then your headache goes away, you initially think, "Hey! My headache is gone - the aspirin must have stopped it!" Not a bad thought, but by itself, this doesn't prove anything. Fortunately we've done many, MANY clinical studies, as well as medical research showing different receptors that aspirin can bind, and the physiological effects that taking aspirin can elicit. Not to mention that in double blind control tests, patients receiving aspirin fare much better than those taking a placebo. It's clear that aspirin works in very specific ways to manipulate your body and relieve pain, as well as perform a whole host of other reactions.

When it comes to homeopathy, we initially hear the same story - someone took a homeopathic drug and their headache stopped - they thought "Hey! There's something to this - it must have stopped my headache!" Unfortunately, the clinical trials have been done, and the medical research is in - there's no effect more than the placebo effect. People think that they're doing something to treat their problem, and the subjective symptoms begin to subside. But this NEVER holds up in group studies. Let's face it, based on the principle of dilutions, there's nothing in the potion to even cause harm. But based on the belief of a molecular 'imprint' in the water, by that definition alone, there should be imprints in the bottled water that you buy at the store that should cure you of all sorts of ailments - and cause lots of harm. This belief doesn't stand up to even a cursory glance - yet somehow hundreds of millions of dollars are made every year on drugs labelled 'homeopathic' ..... ohhhhhh - now I get it; the practice may not work, but if it doesn't cause harm, no one's going to stop you from making money.

Hooray for capitalism ... I think.