Who needs God when you have biologists?

Yes, I’m being very sensationalist – but this still freaking awesome. Craig Venter’s research team has officially created the first artificial organism. The complexity of this endeavour is mind boggling – a genome isn’t a simple thing – which makes this very technically impressive. But in addition to being able to say “Look what we can do!”, this also has a number of large implications for future projects. Now that we can make our own genomes, we can create artificial organisms specialized for fuel production, insulin production, etc… How neat is that?!

PZ has a more scientific summary, and Jerry Coyne has a very good “quick guide” for the not so biologically inclined readers.

I do like Coyne’s response to those that are wondering if biologists are “playing God”:

But what creationists cannot get around is the increasing demonstration that life is merely an immensely complicated chemical reaction. Venter’s team made a genome able to direct and support life using off-the-shelf nucleotides and some other reagents. Eventually, in a few decades, they’ll be able to make a fully living bacterium in the same way. And then we will have played God, at least the way religious people mean it. …Life is just complex chemicals—nothing more, nothing less.

Biology is awesome*!

*Obviously not a biased statement.

Why people won't watch CSI with me

From here:
Because finding a contaminated sample of cells, extracting the DNA, successfully amplifying a clean PCR, genotyping or sequencing it, and editing your perfectly clear and uncontaminated results always takes about ten minutes. And nothing ever fails. Ever. They must pray to the PCR Gods more than I do. Oh, and not to mention they have a genetic database of every human on earth to compare their DNA to. Even if BLAST ever did grow that large, it would take hours, if not days of computational time to find the correct match.

Yeah, now whenever I watch CSI with my dad, he’ll just turn to me and ask, “That’s nothing like how it actually works, is it?” Nope.

And as a side note, you know you’ve been working on your honors thesis too long when a graph jam graph annoys you. The Y axis is horrible, and there are no error bars! I can definitely go from tissue sample to sequence data in 3 days if everything works perfectly, and I’ve also had it take up to two months (stupid low sodium clean up procedure!). …I’m a nerd.

Why people won’t watch CSI with me

From here:
Because finding a contaminated sample of cells, extracting the DNA, successfully amplifying a clean PCR, genotyping or sequencing it, and editing your perfectly clear and uncontaminated results always takes about ten minutes. And nothing ever fails. Ever. They must pray to the PCR Gods more than I do. Oh, and not to mention they have a genetic database of every human on earth to compare their DNA to. Even if BLAST ever did grow that large, it would take hours, if not days of computational time to find the correct match.

Yeah, now whenever I watch CSI with my dad, he’ll just turn to me and ask, “That’s nothing like how it actually works, is it?” Nope.

And as a side note, you know you’ve been working on your honors thesis too long when a graph jam graph annoys you. The Y axis is horrible, and there are no error bars! I can definitely go from tissue sample to sequence data in 3 days if everything works perfectly, and I’ve also had it take up to two months (stupid low sodium clean up procedure!). …I’m a nerd.

My professor’s Holocaust story

Today is Holocaust Remembrance Day. On Friday our newspaper ran a piece about the upcoming Greater Lafayette Holocaust Remembrance Conference, which featured the story of one of my former professors here at Purdue. As a former student, her story was especially touching to me, but I thought all of you would enjoy it. I’ve added some more information in sparse parts, taken from here.

Anna Berkovitz had a normal childhood until 1944. Now, years later, she still has nightmares of her family being taken from their home by the Nazis.

“I was 13 years old at the time when I was taken with my family to Auschwitz, just before D-Day,” said Berkovitz, Purdue Professor Emerita of biology.

At the concentration camp, Berkovitz and her family faced grim odds of survival. Six hundred thousand Hungarian Jews entered the camp between May and September of 1944. In just three months, 500,000 were killed.

“The killing machine was so effective that names were not even taken when we arrived.”

Berkovitz’s grandparents, aunts, uncle, cousin and probably her father were among the victims of the genocide conducted by the Nazis.

Her survival, as Berkovitz says, can only be accounted for by a series of miracles. …

Anna and Elizabeth were taken to Camp-C in Birkenau. To this day Anna ponders how she survived six months of brutal treatment, harsh conditions, starvation and disease there.

In November 1944, Anna and Elizabeth were transferred to a slave labor camp near Magdeburg, Germany, where they were put to work in an underground ammunition factory. Ten days prior to the end of World War II, they were liberated by the Swedish Red Cross and taken to Sweden, where they spent three months in a sanatorium recovering from malnutrition and physical and emotional traumas. …

This year, Berkovitz will be attending the conference, but participating in these events brings personal pain.

“It’s very difficult for me … to me it’s just like it happened yesterday, so I don’t need a conference to remember.”

Still, Berkovitz recognizes and even asserts the necessity of the conference and sees participating as a duty.

“I think I owe it to the people who died to be remembered.”

Berkovitz’s story does not end in Sweden; rather, her rescue from tyranny marks the start of a new journey that defies the unthinkable trauma of the Holocaust.

In Sweden, Berkovitz maintains that she suffered from no depression or bitterness and looked forward to the future.

“I could have lived my life as a victim, but I did not,” she said. …

In April 1946, Anna and Elizabeth emigrated to the United States. They arrived in Los Angeles pennyless and not speaking English. In order to resume her schooling, Anna worked as an au-pair for several years. During this time she completed four years of high school and four years of college, graduating from U.C.L.A. in January 1952 with a B.S. degree in bacteriology and with Phi Beta Kappa and magna cum laude honors. While working as a laboratory technician, Anna met Leonard Berkovitz, who was then a post-doctoral fellow at Caltech. They were married in June 1953, and their sons Dan and Kenneth were born in 1956 and 1960, respectively. During this period Anna worked part time in various cancer research laboratories.

In 1962 Leonard accepted a position at Purdue University, and the family moved to West Lafayette, Indiana. When Kenneth was in kindergarten, Anna decided to continue her formal education. She was accepted as a graduate student in the biology department at Purdue University. She was working on her Ph.D. thesis when, in 1967, she was asked to take a temporary teaching position to fill an unexpected vacancy in the department. This temporary position turned into a lifetime career of teaching, and while Anna never obtained her Ph.D., she earned a tenured position from which she retired in 2003 as Professor Emerita in Biology.

Anna’s efforts as a teacher, her dedication to her students and to the discipline were amply recognized by her students, colleagues and the administration. She was selected by the students as one of the Top Ten Outstanding Teachers in the School of Science 14 times, she received the Murphy Award, the top recognition of teaching excellence by the University, and was given the Chiscon Award for outstanding teaching performance by the Biology department. Anna was elected to the Teaching Academy at Purdue and her name is in the Purdue Book of Great Teachers.

In her retirement Anna has more time to travel, attend theater, to be active in her Temple, and to winter in California. But, what she most enjoys is still interacting with young people, be it her own five grandchildren or students at the University. She currently participates in the University Honors Program, where she developed a new course, “The New Genetics – New Perspectives, New Dilemmas,” which she teaches in the Fall semesters. …

Marveling at her accomplishments for the time – raising a family while entering a competitive career field as woman when it was rare – Berkovitz attributes much of her drive to a belief that humanity was good. Only a small group of evil was responsible for her painful experiences.

“Unfortunately, now I see that there are still evil groups of people in the world killing or wanting to kill innocent people just because they are different from what they are,” she said. …

Though Berkovitz’s story is one of inspiration, she still bears emotional scars.

“I have recurring nightmares that I’m told that I have to pack up and leave home … that’s part of me; that’s part of my existence.”

Preventing scars such as these in others is a duty for Berkovitz; an obligation driving her to participate in programs such as the Holocaust Remembrance Conference.

“It’s very relevant to what’s going on in the world today.”

I had Dr. Berkovitz for the Honors Genetics course (mentioned in the article) and for Human Genetics, and she was one of my favorite professors here at Purdue. You could tell she was passionate about the subject, and she did a great job of explaining genetics. In class she would encourage stimulating discussions on eugenics, genetic testing, gene patenting, and abortion.

When she overheard me telling another student about the Society of Non-Theists, she asked to be put on the mailing list and has attended all of our pro-evolution events (including my talk about the Creation Museum). From our class discussions, I could tell she shared my liberal views. She even once showed us a clip of Stephen Colbert talking about DNA, and we were the only two to giggle when he talked about Jesus burying the dinosaurs.

But in addition to being a great professor and skeptic, she was a wonderful person. She would always take time to talk to me about random articles in the news she thought I would be interested in. She encouraged me to shoot for the stars when it came to genetics. When I was still considering becoming a genetic counselor, she encouraged me to get a PhD, saying someone with my skills in genetics should be doing research or running the clinic. And when I had asked her to write me a letter of recommendation for grad school, I discovered that her husband had passed away just a week before. Seeing someone I looked up to so much distraught and crying was horrible. I quickly told her I could easily find someone else to do it, but she insisted – even when overwhelmed with grief, she wanted to help her students.

I always said that this is exactly how I want to be when I was 80 – compassionate, skeptical, witty, and still excited
about science. That was before I knew her history as a Holocaust survivor. To think that she became such a strong woman and wonderful scientist even through that tragedy is amazing. She’s a role model to everyone, but especially to female scientists. I can only hope to be half the woman she is when I’m 80.

My professor's Holocaust story

Today is Holocaust Remembrance Day. On Friday our newspaper ran a piece about the upcoming Greater Lafayette Holocaust Remembrance Conference, which featured the story of one of my former professors here at Purdue. As a former student, her story was especially touching to me, but I thought all of you would enjoy it. I’ve added some more information in sparse parts, taken from here.

Anna Berkovitz had a normal childhood until 1944. Now, years later, she still has nightmares of her family being taken from their home by the Nazis.

“I was 13 years old at the time when I was taken with my family to Auschwitz, just before D-Day,” said Berkovitz, Purdue Professor Emerita of biology.

At the concentration camp, Berkovitz and her family faced grim odds of survival. Six hundred thousand Hungarian Jews entered the camp between May and September of 1944. In just three months, 500,000 were killed.

“The killing machine was so effective that names were not even taken when we arrived.”

Berkovitz’s grandparents, aunts, uncle, cousin and probably her father were among the victims of the genocide conducted by the Nazis.

Her survival, as Berkovitz says, can only be accounted for by a series of miracles. …

Anna and Elizabeth were taken to Camp-C in Birkenau. To this day Anna ponders how she survived six months of brutal treatment, harsh conditions, starvation and disease there.

In November 1944, Anna and Elizabeth were transferred to a slave labor camp near Magdeburg, Germany, where they were put to work in an underground ammunition factory. Ten days prior to the end of World War II, they were liberated by the Swedish Red Cross and taken to Sweden, where they spent three months in a sanatorium recovering from malnutrition and physical and emotional traumas. …

This year, Berkovitz will be attending the conference, but participating in these events brings personal pain.

“It’s very difficult for me … to me it’s just like it happened yesterday, so I don’t need a conference to remember.”

Still, Berkovitz recognizes and even asserts the necessity of the conference and sees participating as a duty.

“I think I owe it to the people who died to be remembered.”

Berkovitz’s story does not end in Sweden; rather, her rescue from tyranny marks the start of a new journey that defies the unthinkable trauma of the Holocaust.

In Sweden, Berkovitz maintains that she suffered from no depression or bitterness and looked forward to the future.

“I could have lived my life as a victim, but I did not,” she said. …

In April 1946, Anna and Elizabeth emigrated to the United States. They arrived in Los Angeles pennyless and not speaking English. In order to resume her schooling, Anna worked as an au-pair for several years. During this time she completed four years of high school and four years of college, graduating from U.C.L.A. in January 1952 with a B.S. degree in bacteriology and with Phi Beta Kappa and magna cum laude honors. While working as a laboratory technician, Anna met Leonard Berkovitz, who was then a post-doctoral fellow at Caltech. They were married in June 1953, and their sons Dan and Kenneth were born in 1956 and 1960, respectively. During this period Anna worked part time in various cancer research laboratories.

In 1962 Leonard accepted a position at Purdue University, and the family moved to West Lafayette, Indiana. When Kenneth was in kindergarten, Anna decided to continue her formal education. She was accepted as a graduate student in the biology department at Purdue University. She was working on her Ph.D. thesis when, in 1967, she was asked to take a temporary teaching position to fill an unexpected vacancy in the department. This temporary position turned into a lifetime career of teaching, and while Anna never obtained her Ph.D., she earned a tenured position from which she retired in 2003 as Professor Emerita in Biology.

Anna’s efforts as a teacher, her dedication to her students and to the discipline were amply recognized by her students, colleagues and the administration. She was selected by the students as one of the Top Ten Outstanding Teachers in the School of Science 14 times, she received the Murphy Award, the top recognition of teaching excellence by the University, and was given the Chiscon Award for outstanding teaching performance by the Biology department. Anna was elected to the Teaching Academy at Purdue and her name is in the Purdue Book of Great Teachers.

In her retirement Anna has more time to travel, attend theater, to be active in her Temple, and to winter in California. But, what she most enjoys is still interacting with young people, be it her own five grandchildren or students at the University. She currently participates in the University Honors Program, where she developed a new course, “The New Genetics – New Perspectives, New Dilemmas,” which she teaches in the Fall semesters. …

Marveling at her accomplishments for the time – raising a family while entering a competitive career field as woman when it was rare – Berkovitz attributes much of her drive to a belief that humanity was good. Only a small group of evil was responsible for her painful experiences.

“Unfortunately, now I see that there are still evil groups of people in the world killing or wanting to kill innocent people just because they are different from what they are,” she said. …

Though Berkovitz’s story is one of inspiration, she still bears emotional scars.

“I have recurring nightmares that I’m told that I have to pack up and leave home … that’s part of me; that’s part of my existence.”

Preventing scars such as these in others is a duty for Berkovitz; an obligation driving her to participate in programs such as the Holocaust Remembrance Conference.

“It’s very relevant to what’s going on in the world today.”

I had Dr. Berkovitz for the Honors Genetics course (mentioned in the article) and for Human Genetics, and she was one of my favorite professors here at Purdue. You could tell she was passionate about the subject, and she did a great job of explaining genetics. In class she would encourage stimulating discussions on eugenics, genetic testing, gene patenting, and abortion.

When she overheard me telling another student about the Society of Non-Theists, she asked to be put on the mailing list and has attended all of our pro-evolution events (including my talk about the Creation Museum). From our class discussions, I could tell she shared my liberal views. She even once showed us a clip of Stephen Colbert talking about DNA, and we were the only two to giggle when he talked about Jesus burying the dinosaurs.

But in addition to being a great professor and skeptic, she was a wonderful person. She would always take time to talk to me about random articles in the news she thought I would be interested in. She encouraged me to shoot for the stars when it came to genetics. When I was still considering becoming a genetic counselor, she encouraged me to get a PhD, saying someone with my skills in genetics should be doing research or running the clinic. And when I had asked her to write me a letter of recommendation for grad school, I discovered that her husband had passed away just a week before. Seeing someone I looked up to so much distraught and crying was horrible. I quickly told her I could easily find someone else to do it, but she insisted – even when overwhelmed with grief, she wanted to help her students.

I always said that this is exactly how I want to be when I was 80 – compassionate, skeptica
l, witty, and still excited
about science. That was before I knew her history as a Holocaust survivor. To think that she became such a strong woman and wonderful scientist even through that tragedy is amazing. She’s a role model to everyone, but especially to female scientists. I can only hope to be half the woman she is when I’m 80.

Seattle, here I come!

While I alluded to it in a previous post, I still wasn’t 100% sure. But now it’s official – I’ll be going to the University of Washington to get my PhD in the Department of Genome Sciences in the fall!

That still sounds crazy when I say it. I’m going to go get a freaking PhD. Who knew that would happen ten years ago, when I was still amazed by the simple puzzle of a Punnett square, or when I still didn’t quite grasp the whole evolution thing. I’ve come a long way.

So come September, I will have officially escaped the Midwest. Wooooo! Though I admit, I’m nervous. I’ve lived in Indiana for the past 21 years (lived 5 minutes across the border in Illinois when I was an infant), and I’ve never lived in a big city. Purdue is only an hour and a half from my home town, so I was still close to family and retained some of my old high school friends. It’s kind of terrifying knowing I’ll finally be completely on my own. It’s like I’m an adult or something!

If you have any tips about grad school in general, the University of Washington, or Seattle, now’s a good time to let me in on all of the secrets. Or you can just use this post to celebrate along with me. Hurray!

Interdisciplinary research (comic)

I love PHD Comics. Because even though I say I read it to prepare me for grad school, it’s already so much like my life. For example:Let’s see…

I work in the Ecological Genetics Laboratory but get paid by Genetics (and previously Howard Hughes). My Advisor is in Forestry and Natural Resources but my other Advisor is in Ecology. Officially, I’m part of Biology in Lilly Hall…even though my office* is in Pfendler Hall. Most of my classes are on molecular & cell biology, yet technically my degree is in Genetics and Ecology, Evolution, & Environmental Biology. So basically, I belong in the Biology Borg Collective.

Okay, I guess that’s not too insane. But seriously, I’ve taken two advanced genetics classes and a tiny seminar class, and that’s good enough for a degree in Genetics. That’s kind of terrifying. Less microbiology, more genetics!

*Office = lab bench space that I have guarded dearly for three years and damnit who keeps moving my pipettemen and tiny tubes and tube opener?! *hoard hoard hoard*

Flip a switch; become a dude!

Okay, so it’s not exactly that simple; but researchers have found a gene that keeps females being…well, female. FOXL2, which was known to be involved with ovary growth, apparently keeps a woman’s body from turning into a man. Switch off FOXL2, and ovaries will start turning into testes and testosterone-producing cells will develop. Just think what this says about the human gender binary, or future less invasive methods for people undergoing gender reassignment.

*obligatory SCIENCE IS COOL flailing*

Sorry, that’s all the commentary you get, since my tonsils currently feel like they’re turning into…uh…inflamed…spikey…polka-dotted sadness*. Which I guess is better than testicles? Check out the article for a more detailed explanation, or for the genetically-inclined, read the original paper here.

*My wit fails me when I don’t feel well. I apologize.

Two mommies are better than one

Japanese researchers have found that female mice made from the DNA of two egg cells (bi-maternal or BM) have significantly longer lifespans than female mice made the “normal” way – from the DNA of an egg and a sperm. They think this is due to Rasgrf1, a imprinted gene on chromosome 9 of the father. BM females were also significantly smaller and lighter, which makes sense when you think of sex-specific selection. Males have increased fitness if they spend more energy growing bigger quickly because that will increase their number of mates. Females, however, get no benefit in growing bigger, since they’ll probably have the same number of mates no matter what. Losing paternally inherited genes dealing with this growth means they conserve energy and can live longer.

… *ahem*

SCIENCE IS SO FREAKING COOL!

Seriously, can you believe that we’re doing research like this? I actually remember asking a biology teacher in high school why we can’t just combine DNA from two eggs or two sperm and get a viable organism. They said it was impossible because of genetic imprinting – you need a set genes imprinted from mom, and a set imprinted from dad. But now we have the power to manipulate imprinted genes and do what we thought to be impossible just a few years ago. How cool is that?

And on top of that, I have to wonder what this means for gay couples. Obviously there’s a huge step between animal research and human research, but wouldn’t this be awesome for lesbian couples who could afford it? Not only do you actually get a daughter who is a genetic blend of both of her parents, just like any other child, but they may even have an extended lifetime? Awesome! I guess that would take away one of the ridiculous arguments fundies like to use – that you shouldn’t allow gay marriage because they can’t produce children. Ha, TAKE THAT FUNDIES! SCIENCE!

Video of my Creation Museum presentation

At long last, here’s the video of my presentation about my trip to the Creation Museum – yes, the one that Ken Ham is already blogging about. I do warn you, it’s long. My talk is about an hour and then there’s about 25 minutes of Q&A. The first couple minutes are a little rocky because I was kind of nervous, but then I get in my groove and I think it’s pretty good, if I do say so myself.

Overall I received very positive feedback, even from some of the theists in the room. As you’ll see if you watch the Q&A, Pastor Brent Aucoin of the Faith Baptist Church in Lafayette attended. He was nice enough to email me and ask if he could come to the event (of course he could!) and disclosed that he helped with the construction of the Creation Museum (and I can only assume he is the supporter that Ken Ham mentions in the post about my talk). He was very civil, and I thank him for that, but he did repeat the same creationist arguments that we hear over and over again. My favorite part is at the 1:09:00 mark. At the very least, watch it for my friend doing a literal *facepalm* twenty seconds later.

Though, the thing that made my talk totally worth it? My former Human Genetics professor (you can see her behind the Pastor) who’s 80-something, super liberal, intelligent, hilariously witty, a fan of Stephen Colbert, a non-theist, and a Holocaust survivor came up and shook my hand for about five minutes straight, saying how we needed more people like me who were brave enough to speak out against this stuff. Coming from someone I respect so much, that meant a lot.

Oh, and the tiny little blip about 50 minutes in isn’t us hiding something, it’s us changing the tape, haha.