Monthly Archives: May 2010

Off the Bench Begins

Darlings:

This year has been a wild ride. I made the transition from bench scientist to program administrator/outreach maven/boss-type-person. I know some of you want to make a similar move, and I want to help you. So, I am starting a column called Off the Bench that will detail for you what this transition has been like, what has worked, and what hasn’t. I tell you, there is a lot you need to know that you ain’t learning in grad school. It’s a shame it’s so hard to learn the soft skills that really make a difference when you are in a new position (these help you whether you’re taking the tenure track or going outside the hallowed halls of the academy), but you need them regardless, so you better find a way to pick them up.

So, here’s the background:

I earned my Ph.D. from the University of Chicago in 2009 in Molecular Genetics and Cell Biology. It became increasingly apparent throughout grad school that science outreach was my thing. Not that research isn’t-it totally is. I have done research in a lab since I was 19 years old, and worked on projects in labs since without pause. I love to do science. I love to ask questions, design experiments, test hypotheses and formulate models based on data. I love to sit for several hours a day taking in the literature on a research area I enjoy (Fig 1.).

Fig. 1: Thesis writing carnage.

Fig. 1: Thesis writing carnage.

I love writing about science, condensing the work of several years into six concise figures. But I also love people, helping others, seeing tangible results every day, and was moved by my own experience to help others who might have professional aspirations in science themselves, as well as my uncontrollable craziness for bringing science to the public. It’s out of control, I tell you. I also have a gregarious and social nature that sometimes competes with the side of my personality that loves to slap my iPod on and crank through a solid session on the electron microscope until 2:30 AM without a soul around in the basement of a science building (Fig. 2).

Fig 2: Extreme isolation, rocking data collection-2:00 AM, sometime in 2009

Fig 2: Extreme isolation, rocking data collection-2:00 AM, sometime in 2009


Make no mistake: those two sides of my personality co-exist, but I left graduate school knowing that I wanted to take a different, but related, path. It’s heresy, but I-wait for it-decided to go for a job that I knew would light me up everyday and skip the post-doc.

You read that right.

I’m one of those.

But read the other part: I got my Ph.D. and took a job that lights me up every day.

So, I want to help you do the same, if that is what you want. If you’re exploring that idea and are not sure how to make it happen, or feeling a little nervous about it, have an advisor who thinks your education is a waste if you don’t take the tenure-track route-which is awesome, but not for everyone, I hope this will help you.

I’ll give you the punchline of the whole thing right now-follow your heart first, and then get the skills you need to make sure you have what it takes to get where you want to go. I warn you, this requires vigilance, self-awareness, planning, and often a feeling of otherness when you are in an intense academic environment. However, you’ll be in another intense environment doing what you love and really happy at the end of all your preparation, so you may as well just go for it, it is worth it. Here’s the other thing: you can learn the other skills, although you don’t want to be missing many of them, but no one can teach you what it is to be a scientist on the job. That, you need to pick up elsewhere. So, pick it up.

In upcoming posts, I will detail what I have learned as I went through this transition, the skills I didn’t pick up in grad school that have become essential to my work in the day-to-day, why I love what I do and what it’s about, and how you can make a plan to get where you want to go.

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Science Explained: Who’s your daddy (genetically speaking?)

The Neandertal genome has been sequenced!  It’s in tomorrow’s issue of Science. I don’t know what kind of dork it makes me that I just screamed this to my office so that they know (I was met with blank stares), but I don’t care.  I’m so excited about this.  It isn’t complete, but a method has been developed to fill in gaps in the genome, and there is enough information to tell us some cool shite.

The History:
Neandertals showed up in the fossil record about 400,000 years ago, lived in Europe and Asia (including the Middle East), and disappeared approximately 30,000 years ago.  It is estimated that Neandertals and modern humans first interacted 80,000 years ago.  So far, only the DNA from the mitochondria, the cell’s power plant, which has its own highly variable mini-genome, has been sequenced in Neandertals.  The problem is that in modern day humans, the sequences are so different (as opposed to the nuclear genome), that trying to match the sequences between Neandertals and humans is not meaningful-there’s too much variation between humans, let alone, humans and Neandertals.  What’s needed is a comparison of the human genome (which we know) with the nuclear genome in Neandertals.  The human genome doesn’t vary much between individuals (relatively speaking), so the comparison could be informative.

Why we want to know:

Simply put, humans and Neandertals look different from each other.  We also look a lot alike.  The genome can help us understand how related are we genetically, which tells us whether the two species bred at one point, at roughly what point in genetic history, and exactly how much we have in common genetically.  Think about it this way: There is roughly 85% similarity (or homology, in science-speak) between human and mouse genomes.  Yet we look pretty different (most of us, anyway).   Without understanding genetics, I certainly wouldn’t have suspected that we had that much in common with mice.  I’m super curious about how much we share with Neandertals to understand where we come from genetically.

The problem:

Neandertals and modern humans share common ancestors in the last 500,000 years, and the known genetic variation between humans and Neandertals isn’t much different from what’s seen between modern humans, at least as detected by previous sequencing attempts.

The solution:

Kick ass technology, that’s the solution.  This research group cleaned up the method of sequencing, DNA isolation, and clean room technology combined with ultra-efficient sequencing methods employed today made the difference.

Methodical details:
1. The genome has been sequenced from three Neandertal individuals from geographically distinct sites.

2. Sequences were compared with each other, five modern-day human genome sequences, chimpanzee, rhesus monkey and mouse genomes.

3.  Bacterial DNA was degraded with proteins that are known to target only bacterial DNA.

4. Mitochondrial DNA told the researchers that the sequences were from three different individuals (it’s super variable, so it is a good marker for different individuals-this is a forensic trick too).

What they found-the short list:

1. Europeans and Asians share 1%-4% of their genomes with Neandertals.  Africans share none of their genomic information (as far as anyone knows) with Neanderthals.  This suggests that Homo Sapiens and Neandertals interbred during migrations of Homo Sapiens onward to Asia and Europe.  White?  Asian?  You’re a genetic mutt, dude.  (But then, aren’t we all?)

Similarity of Neandertal and human genomes.

2. Genetic evidence of positive selection between Neandertals and humans was found.  This means that changes were seen in the human genome that favored positive evolutionary movement toward favorable traits.  This kind of selection was observed in particular for cognitive and cranial development.

What does it mean?

This study can help us think about our own genetic history, develop new ideas about how human migration may have occurred through history, and learn about traits that may have developed through our evolution to the modern human.  It doesn’t mean everything is solved, but it helps unlock the mystery. It helps us begin to understand, genetically, who the Neandertals were, and how we are related, genetically and evolutionarily, to our ancestors.  It informs our thinking about the simultaneous movement of agriculture and our genomes as individuals and populations.  It gives us a different way to look at the world.

If you want to check out the original research, which I hope gets you as excited as it gets me, visit Science’s Neandertal special.

I dedicate this post to Elby Tackett, my high school science teacher, who told us when we hit the chapter on evolution: “I don’t believe in evolution, and I’m not going to teach you evolution.” Pointed to a picture of an ape and said, “that ain’t my grandpa.” Thanks for all you gave me, and thanks for all you didn’t.

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