The PhD Movie

Brought to you by Jorge Cham, creator and illustrator of Piled Higher and Deeper.


PHD Movie Trailer from PHD Comics on Vimeo.


Looking forward to seeing this ... something's got to vindicate my decision to continue the grad student life as a postdoc ....

What feels better?

I love my mom.  In part because I already show great promise of growing up to be like her.  Even though she has a Droid and not an iPhone, autocorrect has been as cruel to her as it has been to me, though she's less adept at correcting bad autocorrect mistakes before sending out the final text.  That moment before you figure out that autocorrect is to blame for the very disturbing feeling that your mom just gave you is quite funny, but only after the fact.  I give you, yesterday's autocorrect slip up of the day:

In case you can't figure it out, I'm pretty sure that she meant, "Good...makes me feel better."  Once she realized the mistake she informed me that she actually did not type "nakedness feel better" and then promptly admitted that it was still true though.

My Street!

I know that most places have a "Cook Street" somewhere ... my hometown has one too.  But it still excites me to see a Cook Street in San Francisco!

We like to move it, move it ... on MUNI

The month of May has whizzed right by me, but not without a lot of fun-filled days and nights.  My family actually came out to visit me (Mom, Dad, Sister and her boyfriend) for Dad's 60th birthday bash!  It was outrageously fun- we toured all over San Francisco and a little outside the city too.

In the city we went to the Golden Gate Bridge, Fort Point, the Exploratorium and Palace of Fine Arts, Tartine, Dolores Park, the Castro, Duboce Park, Alamo square, Golden Gate Park, the DeYoung Art Museum, Ocean Beach, Chinatown, Ferry Plaza, Fisherman's Wharf, Ghirardelli Square, the marina, Alcatraz, and much more.  Outside the city we made it to Berkeley, the Marin Headlands, Sausalito, Muir Woods, and Sonoma.  All of this in just under one week!  We were pretty busy.

While the family was visiting, they became acquainted with our public transit system here called MUNI.  Before their visit, I prepared by getting enough electronic commute cards, called Clipper cards:

Once the family arrived, they each received a card to get around in the city.  It essentially costs $2 for two hours of riding on MUNI in the city, a pretty good deal if you strategize your trip well.  I also didn't want them to lose track of *their* Clipper card, so I labelled the back of each one with a biology word that would stand out to them and that they could associate with their card in particular:

If someone ever stole it, there would be an easily identifiable marking too - handy especially considering that my credit card account is linked to those cards!

Do you know what each of those words means?

Episode 23

The atheism and science podcast that me and my friends work on together just released our 23rd episode!  Check it out - here's the summary from the Pascal's Bettors website:

• Matt starts us off with Spreading the Bad News regarding the misconceptions about the Crusades

• Joel reads off some news items about the ACLU defending Christians, rape being declared as "God's Will" and another attempt to teach the bible in a public school

• Liz inspires us with some Words of Lizdom via Richard Dawkins

• John discusses an uplifting Church In State segment where the UK prioritized secular morality over religious hatred.

• Liz discusses some Pope-pourri, specifically a lawsuit german lawyers are using to take on the Pope

• Nik discusses the ethics of the Supreme Court's ruling in the Snyder v. Phelps case for the latest Ethics Corner

• Finally, we wrap up with a religious trivia question about the Jewish Mezuzah from Matt

We love getting feedback to, so use the "contact us" form on the website to let us know what you think and if you have any question or subject you'd like us to cover.

Going out with a ... freeze

Discoblog over at DISCOVER learned me something new today:  "cremation, which uses the same amount of energy as driving almost 5,000 miles, releases mercury into the atmosphere."  


What a terrible thing to do to the environment!  I always thought that, aside from donating your body to science, cremation was the most cost-effective and ecologically friendly way to go (avoiding wood and metal coffins, large tracts of land, etc.).  Well apparently there's a more environmentally friendly way to depart this mortal coil.


In short, a company called Promessa will freeze your body with liquid nitrogen (using no nasty embalming fluids) to the point that your frozen self becomes incredibly brittle.  Then a sonicator is used to essentially vibrate the frozen stuff into a fine powder before evaporating the water in the dust and planting your remains back into the ground.  The biggest environmental benefits appear to be no embalming fluid contamination, no inorganic burying material, and less space taken up.  Here's a depiction from Promessa's website of the freezing process:

Let this be my living will: if I die and my body cannot be donated to science, I want to be frozen and shattered into billions of tiny dust particles just like in Terminator 2.  

It's Natural

In my limited experience, this is still the most effective argument to win people over and get them to understand that homosexual desires are as natural as fruit bat blow jobs during copulation or male Right Whales double penetrating a female under the midday sun.  Via wickedgayblog:

New Podcast Episode Up

My friends and I have put up the 20th episode of our atheism podcast for Pascals Bettors - go take a listen!  We're pleased to say that we over 10,000 downloads already - so if you're one of our listeners, thanks!

God Fucks Up: Science Saves the Day

For all of those out there who might still believe in a god, your god is a douchebag – unless, of course, you think that human life results from an embryo naturally developing from the fusion of a sperm and an egg (which is susceptible to teratogens, natural genetic aberrations, environmental influence, etc.).  Otherwise, some deity just gave a pre-born baby a giant deadly tumor that weighs more than the baby itself (pictures below).  Oh, and if you think there's a god behind the natural events leading to human life, I’m sure you also think a god is responsible for creating the universe.  If so, your god is also responsible for everything in it, including the natural phenomena that lead to deadly cancers.  Try as he/she/it might, even divine corruption did not stop doctors from blocking the evil masterwork of giving a baby in gestation a giant tumor.

The fascinating story was recently published in the Journal of Pediatric Surgery entitled: “Preoperative embolization of giant sacrococcygeal teratoma in a premature newborn”.  In other words, “We [doctors] cured a prematurely born baby of a deadly tumor that weighs more than the baby itself.”  This was no small feat – your god has had … well … an eternity to perfect the art of giving living things cancer – scientists and doctors have only had a hundred years or so to really fight back.  Great news: we’re getting better at beating god’s evil plans!  In fact, this particular method of foiling god’s cancer plans has only been used once before.

At about 20 weeks of pregnancy the large tumor was identified as a sacrococcygeal teratoma, or SCT.  Teratomas are special tumors that can also be very dangerous – they originate from your germ cells (the cells that make sperm or egg depending on if you’re a male or a female).  SCTs are one of the most common forms of teratomas because they arise in the pelvic region, right where germ cells can end up if they get off track from your gonads.  In this particular case, the mother was immediately give corticosteroid treatment to ease her immune system and protect the baby.  This particular tumor was immature meaning that it had very aggressive and potentially malignant cells inside it.  After close monitoring of the mother and unborn child, the mother suddenly entered labor at 30 weeks and the doctors had to perform a C-section.  This is what they found attached to the baby after delivering her:

The combined weight of baby and tumor was 3.43 kg.  The tumor itself weighed (1.86 kg) more than the baby (1.57 kg)!  Unfortunately these kinds of tumors are very dangerous to cut off (ressect) because of the huge risk of bleeding.  The bigger the tumor, the bigger the arteries carrying blood, the bigger the risk of the baby bleeding to death before the doctors can save her.  Fortunately, the doctors have science on their side.  After taking a picture called an arteriogram, the doctors were able to see the main artery that was sourcing the blood to the tumor (see the arrow):

 Normally doctors try to keep your blood stream clean of cholesterol – otherwise you might get a clot that will stop the blood flow and kill you.  In this case, the doctors reckoned that they could induce an artificial clot (called an embolism) right at the site of the artery branching off to the tumor to block the blood flow and attempt to choke it off from oxygen and food – this way, when they ressect the tumor there would be less risk of bleeding.  So, they used a commercial product called Gelitaspon (small gelatin sponges) and injected some in the artery leading into the tumor.  You can see here that this successfully reduced the blood flow to the teratoma:

At this point the doctors ressected the tumor and the bleeding was minimal.  Unfortunately there was a lot of cell death from the tumor that had still managed to circulate in the baby’s bloodstream (hemolysis) which caused major problems, culminating in a full on cardiac arrest (heart attack).  The baby’s heart stopped for a full 6 minutes.  SIX MINUTES!  I guess god really didn’t want this baby to be born.

Fortunately, doctors provided injections of gluconate, insulin, adrenalin, hydrocortisone, and other science-y drugs that saved the baby’s life.  After 6.5 weeks the baby was allowed to leave the hospital and has been receiving monthly checkups every since.  Despite a solid effort by your god, the baby survived.

If you’re someone who likes to give a god credit for things like the sunrise, the ocean’s tides, the formation of the grand canyon, and/or the “miracle” of human life, then it’s high time you also start giving your god credit for the viruses, bacteria, and cancers that are so good at destroying human beings.  Let’s face it – if you think a god is behind the scenes of nature, then to human beings, your god is a douchebag.

Schumann Piano Concertos

Tonight Joey and I are headed to the San Francisco Symphony to hear the Schumann piano concertos. It starts at 8 so I'm going to stop blogging and go find my seat!

I'M NUMBER ONE!

My latest paper got accepted for publication in the journal Development and I'm pretty stoked about it - a lot of time, energy, sweat, and even a few tears went into my most recent manuscript. After publishing, every scientist hopes that their work will be noticed and cited throughout the field. You can always go check online and see how many times your paper has been cited, or whether or not your paper has been deposited in the pubmed database.

Well, today I got a very nice surprise, however temporary it may be. One of the hottest topics in cell biology today is turning a terminally differentiated cell (like a skin cell) into a pluripotent stem cell (like an embryonic stem cell), which can then be used to make any other cell type you want. It's a pretty powerful phenomenon that promises to revolutionize regenerative medicine. The process by which a differentiated cell reverts back to a more pluripotent state is referred to as reprogramming.

Imagine my delight when, after going to the pubmed database and typing in "reprogramming" to see what the latest and greatest reports are saying, my very own paper showed up! Take a look at this screenshot:

Here are two zoom pics if you can't see it:

That's my name there - Cook MS! Now, as cool as this is, my excitement is a bit tempered for two reasons:

1) In a day or two, when the next paper with the keyword "reprogramming" comes into the database, my paper will be kicked out of the number one spot. It will stay in the list for "reprogramming", but everything is listed in chronological order of publishing date.

2) The subject of my paper was not directly about turning differentiated cells into stem cells, nor did we (the authors) list "reprogramming" as a key word. The work is on a very related topic, but we do not include any direct reprogramming experiments - it seems as if the paper is listed because it has implications for and we discuss reprogramming. Still cool, but it's not as if we're changing a paradigm or anything.

However, for today I will revel in the knowledge that despite all of the research going on in the entire world about one of the hottest topics in stem cell biology, my paper is temporarily listed as number one in the pubmed research database associated with the term "reprogramming".

Woohoo!

Pascal's Bettors #16

Hey Everyone!

A new podcast has been up since last week. Give it a listen!

The Perfect Gas Station

What is wrong with San Francisco? Besides all those other things you just thought of? I'll tell you - gas stations. I mean, the actual, physical setup of the structure and the odd amenities offered and not offered.

Ok, sure, there are plenty of wonderful attributes to this city I moved to almost two and a half months ago. But for all the fuss about reducing my carbon footprint and using public transit, sometimes I need to still drive my car to get to far away places or locations that public transit doesn't connect.

Besides, San Francisco is one of the most dense cities in the US - the streets are lined with cars that need to be taken care of and also need fuel.

Enter the confusing and inept world of SF gas stations.

Statement of disclosure: I have only been to four different stations in the city so far. I know an n=4 isn't great, but it's enough to get my complaints!

#1 why do you advertise the CASH price and not the credit? Because you want to trick me to your station, then laugh when I don't have cash. I never knew there was such a thing as gas CASH vs. gas CREDIT price. I had NEVER paid for gas with cash until I moved to this city. For those who don't know, the credit price is 30 cents more expensive PER GALLON!

#2 Why must you have payment "islands" instead of letting me pay at the fuel pump like every other gas station? Everyone must crowd around a central computing unit, and there are a surprising number of old ladies and foreign nationals that are confused by the endeavor.

#3 Why have a fee for using a debit card? Credit cards already charge me 30 cents extra PER GALLON! And if you don't have cash, you must pay a fee to use your debit card. Is this more incentive to pay with cash? Is there a big financial benefit for you to do this?

#4 Why do you have flat screen TVs at the pump but now towels or fluid so that I can wash my windshield? I thought that was one of the main staples at gas stations across the country - apparently not in San Francisco.

These are just a few of my frustrations in dealing with SF gas stations so far. If you have the answers to these, or any other quirky questions about gas stations on the left coast, please let me know. Otherwise, I will let you know when I find the first all-organic gas station. Oh, wait a minute...

Double the science, double the fun

Just inherited a nice PC monitor in my lab. Now I can do science TWICE as fast!

I AM

An agnostic because of science, an atheist because of probability, an anti-theist because of religion.

For your clarification.

Crossing the Continent to the Left Coast! (Part I)

Well, I got a job in San Francisco - godless, gay, liberal Mecca, BUT home to MUCH woo-woo that I'm sure you will hear about on my blog.

I'm currently crossing the country, driving the I-80 route with my dad towing many of my possessions in a 6'x12' U-Haul trailer. It's been a pretty smooth ride so far. We started in Nashville, NC and left around 8:30AM yesterday. After traveling down I-40 to Winston Salem we caught 52 North past Pilot Mountain into Virgina, then West Virginia (onto I-77 via I-74), hopping on to I-64 west at Charleston, entering Kentucky, and finally getting all the way to Ferdinand, Indiana. We're a few miles away from one of the largest water theme parks on the North American Continent called Holiday World - in fact, they have the longest water slide in the world (interestingly, after asking how long the slide must be to be the longest slide in the world, the hotel front desk worker responded that it is effectively "two minutes" long. I'm not an avid water slide lover, so I'm not exactly sure how long that is). The comfort Inn we're staying at is FULL of children age 2-12 and their parents who don't know how to make sure they behave.

I've been using the "check in" feature on Facebook mobile to let my friends know where I am throughout the day. I started checking in at local churches as we passed by, because I figured that you all might get a kick out of thinking that I'm stopping in to pay my "respects" or something.

We're on the edge of the time zone change and are up early to get on the road with some sunshine. We made it about 670 miles yesterday. I'll try to log on and let you know how we do today!

Talk to you again in another 700 miles or so :-)

One more day

Going to see Joey tomorrow

:-)

Going to start with this:

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.