Stuck in the Middle

A girl in my program defended her thesis today. She did a great job and I was really kinda amazed at how well she did - how composed, etc. She had a nice story and backed it up with some nice data and I thought it all came together well. She started grad school a year after me, which kinda sucks. Science takes a really long time to do careful experimentation. And, of course, I pick the kind of science to do that takes even longer because I am working with living animals who have to produce embryos that have to be a certain quality in order to do the experiments. I also have a boss who is the worlds worst procrastinator. For example, he asked me to write a review article for an online journal which solicited this review from us. A review article is exactly what is sounds like - a survey of current and past literature on a particular subject framed in the context of general scientific scrutiny and skepticism. We were solicited in Dec 2007. I completed the manuscript in Feb 2008, after taking some time (likely about a month) to do the research and to bring together a comprehensive review article on what we know about a particular class of transcriptional repressors. This manuscript has been on the desk of my boss since then. He has not read it, he has not asked for any more input from me. Obviously the literature has advanced (meaning, it would take a major re-write on my part to bring it up to date). Absolutely nothing has been done in over 2 years. How frustrating is that? And to think, I have to get out, not one, not two, but likely three different papers this year, hopefully within the next few months. He has no concept of time, no idea how frustrating this whole thing is to me, even though I've told him over and over again. I have a feeling I would have graduated by now if I had chosen another lab to do my work in. Instead, I fester, and infuriate myself. And hope this is all preparing me for my future career. Whenever I get there.

Anxiety

My labmate is graduating. She's a year ahead of me and has been working on her thesis for a while. She's not really sure what to do with herself after she graduates, so she's been exploring lots of different career options. She's limited to a certain area because her husband has a job at a somewhat local school, and the economy's been shitty (as if you hadn't noticed). Having worked in industry, I keep encouraging her to stay patient and on top of things and that, eventually, she'll get the job she wants. Sometimes it's hard to take your own advice. You see, I have a problem with my boss. I need to publish at least one first author paper in order to graduate. I will have done enough work for (hopefully) three first author papers by the time I'm ready to graduate. My boss has some weird aversion to publishing. He doesn't like to read the things you send him unless it's under a deadline. When I wrote a grant with him a few years ago, I was up all night the night before, getting revisions from him until 3AM. Honestly, it was kind of a nightmare since I'm not really a procrastinator. I try to finish things up with plenty of time. So, on top of all the worry and anxiety of dealing with and getting through grad school, I have to now figure out a way to get my boss to read and critique and publish my papers. It's pretty stressful to say the least. I'm also trying to consider where I will go next, what I want to work on, what type of environment I want to look for and where I want to live. Needless to say, I've got a lot of anxiety in my life right now. I've been trying to develop my "patience" skill. I don't have a lot of it, especially since I moved East. It's definitely a skill I'd like to develop! I've also been running a lot. I run at least three times a week. It feels great to get out all that energy and decompress. I don't listen to my headphones, I don't do anything but focus on my breathing and my stride and I run. It makes me feel like a kid again (although I don't have nearly the amount of endurance or energy as I did when I was a kid). I'm not very fast, and I probably have all the wrong form. But it helps. And I just have to trust that when the time comes, things will work out for the best.

40 years ago today....

The Apollo 11 mission left earth for the first manned flight to the moon. Understandably, an unbelievable feat, I just wanted to commemorate the awesomeness of this day. NASA was able to pull off an amazing trip to the moon that was broadcast around the world. I know that I have always been inspired by astronauts and space. Another trip to the ISS is underway today. I was able to watch the live broadcast of the launch last night, and it brought back so many memories. I remember the Challenger blowing up. For some reason, I was at my Grandparents' house that day, home sick from school. The first schoolteacher in space. I remember waking up early to hear the sonic booms from the space shuttle landing. I remember seeing the weird 747 at Mugu, preparing to fly the shuttle to Florida. NASA and the space program have so advanced science and made it open and accessible to the public. What a truly historic day. Congrats, NASA! Here's to 40 more years of exploration (at least!).

This is what I do....

An Historic Day

As I'm sure you can tell, I am a scientist. For the past 8 years, I have watched in horror as the Bush Administration dismantled scientific inquiry and made policy changes relying on falsified and incorrect scientific data. The state of science is something that worries me, not only for my future career, but also for the future of medicine and medical care, the prevention of diseases, the maintenance of health, the production of preventative care, our future generations, the health of the planet, environmental conservation and so on and on. There has been a marked shift in the way science is treated with the election of Obama, illustrated today by the reversal of Bush's ill informed ban on federal funding of research on human embryonic stem cells (hESCs). In no way do I want to tout the amazing things stem cells can do - they cannot. At this time, we know very little about what hESCs could possibly do. There are still vast limits on what we can and cannot do with hESCs. However, I do want to say that the possiblilites are endless; you just have to give us some time. I think it's amazing to have a President who values scientific inquiry. As much as Bush's policies tried to ignore veritable, actual science (endangered species, anyone? global warming? hello?), Obama tries to put scientific policy in the hands of scientists. I am nothing but thrilled and hope this is the beginning of a beautiful science/political relationship.

Happy Birthday, Darwin!

Today marks the 200th anniversary of the birth of Charles Darwin, the writer of On the Origin of Species and the "Father of Evolutionary Theory". Very few scientists of modern day have changed the face of science like Darwin did. Although a reading of On the Origin of Species is quite dry, it lays the foundation for entire regions of modern day science practiced today. Darwin, in hismost famous voyage, travelled upon the ship the Beagle to such places as the Galapagos Islands, where he came up with ideas as to how species form and how particular traits can be selected for (called natural selection). For example, finches live on many of the Galapagos Islands, and some have thick beaks and some have thinner beaks. Where the thick beaked birds live, there are only nuts and hard shelled seeds to eat. Where the thin beaked birds live, the food is more diverse, with bugs and flowers serving as a source of food. One can imagine that as birds settled these islands, those with thicker beaks did fine on the islands with only nuts to eat, while the thinner beaked ones died off, as they were unable to eat the nuts (and thus, unable to survive and reproduce). These types of things happen daily, as certain areas see more or less precipitation, as invading species eat particular foods, as humans encroach more and more on habitat. Species adapt to their environments, a central idea in Darwin's theory (and one of very many). As you can probably tell, I am fervent defender of science education and I truly believe our education system needs to be improved in a multitude of ways. One of the most important battles we as scientist (and logical thinkers) have been fighting of late is the ridiculous idea of "Intelligent Design" - a thinly veiled attempt at teaching Creationism (and thus, religion) in our public schools. Don't get me wrong, I value religion and I find it definitely has it's place in society. I also value the study of religion and feel that children should be allowed to study different types of religions and their dogmas in school. I do not, however, condone the teaching of a fake idea like Intelligent Design alongside tried and tested scientific theories like Evolution. And, so, on this anniversary of Darwin's birth (apparently now referred to as "Darwin Day"), I would just like to remind you that we are fighting on in this battle that's been going on for 150 years now. We are fighting for the integrity of science, for the separation of church and state (as afforded in our Constitution), and for the intelligence of our children and our future. It's a battle that's been going on for centuries. And we're not about to quit now.

CSI: Reality

I don't really watch much TV. Cable here is really expensive and I haven't got the time. I'd much rather delve into a book or Vanity Fair than watch some lame TV shows. However, I did take in one recent episode of CSI and I've got to tell you: wow, is that show terrible! I'm a big fan of reality - don't really buy too much into science fiction. Sometimes I am able to suspend disbelief (like, in the case of Harry Potter), but usually I am a stickler for details. I didn't love Spiderman because they showed a spider biting him and then the spider's DNA intercalating with Peter's DNA and that's how he became Spiderman. From a scientific point of view, I can't even tell you how many wrong things there are with that picture....
Anyways, I get off topic easily. Back to CSI. In it, there is a crime committed, the people in the lab examine some inconsequential piece of evidence (rapidly, I might add) and discover the true identity of the killer. While some of the things they do on CSI are plausible (for example, you can extract DNA from smaller and smaller pieces of tissue left behind - but the results are neither rapid nor without fallicy) most of the things they present cannot and do not happen. Trust me, you CANNOT look in a microscope and be able to tell whether DNA is human or animal. DNA is DNA is DNA. You also cannot look at a drop of blood under the microscope and tell what species it comes from. Sequencing DNA is a long and arduous process, we don't put some tubes in a machine and have a read-out right away. The truth is that police departments around the nation are strapped for cash. Unless a crime committed is unusual or involves a celebrity or rich person, there are not enough resources to do all the things that are done on a case in CSI. While I hope the majority of people realize this, it can lead to a serious problem.
I served on a jury over a year ago. It was a really interesting experience, and I highly recommend it if you can do it. The suspect was charged with possesion and intent to distribute crack cocaine. The only witnesses were cops on a stakeout who both observed the suspect opening the door to a known crackhouse and busted the suspect in the crackhouse later on. A large amount of cash was found on the suspect. Drug paraphernelia and the drugs themselves were found at the house. The jury ended up being a hung jury (for several reasons, really) but we kept coming back to the fact that NOTHING had been fingerprinted. Wouldn't that have sealed the case if the suspects fingerprints were on the bag of drugs? If they were on the paraphernelia? We kept talking about it, saying we had seen it on TV, why couldn't they have done something so simple? Well, the truth of the matter is that the Philadelphia police department is hard up for money, just like every other place in the country. They can't afford to run tests like fingerprinting, DNA tests, etc. These tests cost tons of money. Take it from me, I could blow a grand in a day buying reagents for my experiments. It concerns me that we can't afford to pay for simple lab tests to proporly prosecute criminals. It also concerns me that innocent people could be convicted of crimes they did not commit because of circumstantial evidence. I can only hope that the future will bring cheaper, faster lab tests to be used in law enforcement. And that people take everything they see on CSI with a grain (or perhaps a bag) of salt.

Science Education Thursday

As graduate students at Penn, we are required to complete yearly bioethics training. Due to this training, I attended a symposium last night entitled "Vaccine Mandates and Children". It was a pretty interesting discussion since the majority of people attending seemed to be pretty educated on vaccines and scientific theory. But there were the requisite crazies there too, which made me want to write a little bit about how science works. In general, scientist do experiments in order to answer some type of question. For example, if a gene is thought to be involved in some process, scientists can knock down or knock out the function of that gene in order to determine if it's involved in a certain process. Really, any type of science involved hypothesis (question) driven work, including population trends, clinical trials (does this drug treat the problem it says it does?), etc. Once we have gathered enough information, a "story", if you will, we begin the process of publishing our work in peer-reviewed scientific journals. The peer review process is extremely important because it involves prominent scientists who are experts in the field you are publishing in. They read your paper, critique your data, and send you feedback as to whether the journal should publish your work, or whether you should do more experiments to prove your point. Sometimes, you might miss a control, your interpretation of the data can be explained in several different ways, etc. This part of the process of publishing papers is so important because otherwise, science would not be regulated. As such, scientists self-regulate themselves, push each other to do better experiments and create an open dialogue about science and experiments. Without this regulation, scientific papers would merely be opinion of the writers of the paper, with no input from the scientific community. Once papers have been reviewed, the paper is sent back to the authors with important changes to be made, or it can be accepted or rejected on first submission. More often than not, papers are sent back to the authors for some changes and extra experiments. Once your changes have been made, your paper is sent back to the journal and sent out for re-review. If the reviewers are satisfied with the changes you have made, your paper will usually be accepted for publication. If not, it can again be rejected and new experiments may be suggested. Why I'm telling you this is because it's an important part of science that is not usually discussed. If you see a news story about an article in the New England Journal of Medicine you can be assured that article was peer-reviewed and passed the test for having proper controls, had a logically designed set of experiments, and the sample size was large enough to draw conclusions about the larger population. However, when a study was published in a journal that does not peer review articles, or worse, is published in a book (also not peer-reviewed) then you can be assured that the study was not done properly. The reason I am stating these things is because the unsubstantiated link between vaccines and autism came up last night (of course). People are refusing to vaccinate their children because they think vaccines cause autism. The link has never been proven, even though large studies have been carried out in multiple countries looking for a link, correlation, anything. The few people at the talk last night who still believed this cited a study that was not peer reviewed, was not published in a peer reviewed journal, had multiple, fundamental flaws, but was able to draw a link between autism and vaccines. Basically these people were citing faulty research. Just because someone with the title of "Dr." publishes a study does not mean you should entirely trust everything they say in their study. However, when articles are peer-reviewed, you can at least be assured that prominent scientists agree with the findings, the proper controls were done, and the proper number of experiments were carried out. It's unfortunate that the internet allows for people to get a hold of faulty research, so please, please do your research yourself.
Vaccines do not cause autism. More than likely, autism is caused by a combination of genes and the environment we live in. The first few weeks of pregnancy are extremely important, basically when all the "good stuff" happens. Like the formation of the brain, the nerves, your internal organs. If you face an environmental insult during this time period, or in later stages when the "fine tuning" is occurring, we have no idea what effect this has on a developing fetus. More than likely, this is when autism is started, but we have no way of assaying its development until a later time period, when language skills are developing and interpersonal interactions are becoming more obvious. The truth is that vaccines have saved lives and that having even a few un-vaccinated individuals in a classroom can nucleate an outbreak of a disease that should be preventable. The truth is that children should be vaccinated and parents that refuse to vaccinate their children are putting the rest of the human population at a huge risk for outbreaks of eradicated disease that can kill people.