Lit searches

In bio graduate school, the ultimate sign of success is publishing your scientific discoveries in a scientific journal. In preparation for writing up a paper on my work, I’m reading a bunch of papers related to the work I do. This paper is coming out of collaborative work I started 2.5 years ago, and it’s interdisciplinary, meaning I’m applying skills I have to a different type of biology than I’m formally trained in.

I’m really wishing I’d read some of these when I started the project instead of now, when I’m ostensibly finishing it up. I did read a lot of papers when I started this work, but I missed some really strong ones when I delved in. I think this isn’t surprising — I was learning how to enter a new field and get caught up quickly — but I’m now trying to learn some real lessons from the experience. I’ll be starting a post-doc in the foreseeable future (fingers crossed!), and in doing so I’ll need to once again learn a new field.

For anyone out there who’s switched scientific fields, or changed to any new form of work, how did you learn all the things you needed? Any tips for efficiently finding the most useful resources out there?

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RNA traveling from blood to brain

I’m going to try to start blogging regularly about some of the cool papers that I read. Today’s paper is about a newly discovered way that the immune system can affect neurons during inflammation. Immune system cells can send RNA molecules to the brain! It’s not yet clear what impact those RNAs have, but the idea that RNA can travel between cells is still quite new, and I think very exciting.

Stefan Momma’s group wanted to better understand what happens in the brain during inflammation. Others have reported that the immune system can somehow pass on genetic material to neurons, possibly through the cells fusing to each other. Momma’s group wanted to learn more about how the genetic material was transferred.  Continue reading

On learning to code

When I began grad school, I didn’t know a bit of code. I had never made a computer say “Hello, world” before.

I did know, though, that coding was really important, especially as sequencing got easier and easier. I intentionally chose a project that would force me to learn. The day I  joined my lab, my adviser handed me a book entitled Learning Python. I dove in and read lots about strings, lists, loops, and if statements. I could do small exercises. I was getting confident.

Then I actually needed to write code to analyze my own data, and I had no idea what to do. It was just like I had a read a textbook on a foreign language, then needed to write an essay without any further instruction. I knew some vocabulary and grammar, but I hadn’t quite figured out structure or how to put pieces together.

Thankfully, other people gave me some of their code to help me figure things out. It was like someone else gave me their essay in this foreign language and told me it was okay to copy it, then alter parts of it for my needs, and still call it my essay.

I have improved greatly over the past few years. I’ve also branched out a bit to learning Unix and R. I’ve still not taking any formal classes on coding beyond a short workshop, though, and I’m starting to realize I skipped over some fundamentals along the way. I know how to use while loops, but somehow I never figured out for loops. I hear dictionaries are pretty powerful. Now that I know some of what I’m doing, maybe I’ll go read that Python book again and learn more from it.

I feel like at this point I’ve tried learned from reading a text book and doing immersion learning, but the people I was immersed with speak with some idiosyncrasies. It certainly gets the message across, but perhaps not as elegantly as possible.

How about others? How have you learned to code? Any advice for how I can improve further?

Belonging in college

I just read an article from the NY Times called “Who Gets to Graduate?” which discusses ways to help students who struggle with college to believe in themselves and help them finish their degrees. The article says:

Doubts about belonging and doubts about ability often fed on each other, and together they created a sense of helplessness. That helplessness dissuaded students from taking any steps to change things. Why study if I can’t get smarter? Why go out and meet new friends if no one will want to talk to me anyway? Before long, the nagging doubts became self-fulfilling prophecies.

This article really gave me pause. I was a strong student in college. Considering both my parents went to college, my mom has an advanced degree, and I went to a good high school, that’s hardly surprising. When I got to college, I felt like I belonged there and that I would learn well.

I felt like I deserved my college success. I tried hard and spent lots of time studying. I also joined groups to make my massive school feel smaller (which I recommend to anyone going to a big state school). I didn’t think too hard, though, on the privilege I had from feeling like I belonged. 

I’m glad schools are studying what it takes to level that playing field, to help others, who are minorities and/or first generation college students, reach that same level of belonging. Feeling like you’re in the right place helps you get through the rough patches. I think it makes the rough patches then feel like part of the experience instead of like a sign that you’re not meant to be there.

Intro to gene regulation

I have family in town, which means I have a chance to practice science communication! We visited my lab to see my bench, water baths, centrifuges of various sizes, and gel rigs. I also presented my two posters (pro-tip: if you go to two conferences in one summer, life is easier if you present the same project twice… ). In the process, I tried to explain gene regulation and why we need RNA. Here’s an edited version of my spiel.

Our genomes are a large instruction manual that tell how to make a body. That manual is very bulky and needs to be kept safe, so it’s stored in a special part of the cell, called the nucleus, which is separate from the rest,  almost as if it’s a castle surrounded by a moat, kept safe from intruders.

That instruction manual has the directions for making proteins,  which are the things that do everything. The machinery for making the proteins, however, are on the other side of the moat. The genome needs a messenger to travel and make the correct proteins. In comes the RNA!

Using a messenger doesn’t just protect the genome though. It also gives the cell control over what proteins are made when. That’s because the messenger doesn’t copy all the DNA. It specifically copies the parts  that make the proteins that cell needs. Your eyes are copying instructions for light sensing proteins while your immune system cells copy instructions for disease-fighting proteins. The number of copies made can be regulated, which then influences how many proteins are made.

I study what happens to those RNA copies once they’re made. I want to know how well they  cross the moat, if they’re quickly destroyed, and how they interact with the protein-making machinery. All those events determine how much protein is made from each message.

Developing a profession

I went to a professional development panel today for young biochemists. We got to see this infographic multiple times:

workforce infographic ASCB COMPASS

 

I hope most of my fellow trainees already recognize that the odds of getting a tenure track job these days are pretty tiny. As a result, we heard from PhDs who have a variety of professions — scientist at a basic biotech company, regulatory expert at a pharmaceutical company, seller of scientific equipment, professor at an undergrad institute, researcher at a med school, and editor at a journal.

I noticed two themes in considering non-academic jobs: be prepared to try out jobs but also think deeply about what you want. Regulatory affairs is not a career path people generally think of, but if you have the skills and want to try it out, you might find you love it. Similarly, the editor at Science told me that she gave herself a year to figure out if she liked the position, and she was willing to leave if it didn’t suit her. As it turns out, she loves the job, but that willingness to try a job for a year or so really impressed me. Any job is a chance to better define what you want from a career and make the contacts to help you get that position.

I still dream of an academic job, but it was really useful to hear that perspective. I imagine career paths as being linear (grad school to post doc to professorship). Realizing it doesn’t need to be that way is helpful.

Experimental Biology blogging

I landed in San Diego yesterday for Experimental Biology, so I’m dusting off this blog to share some of what I learn.This is a huge meeting for six different national organizations. I’m here primarily with the American Society of Biochemistry and Molecular Biology. I spent today at professional development panels for trainees (livetweets can be found here).

Later this week, I’m looking forward to getting caught up on lots of RNA research as well as learning more about protein folding, systems bio, metabolomics, and addiction. If you’re working in any of those areas, let me know and I’ll check it out!

Lessons from Scientific Idol

I attended the AAAS meeting in Boston, MA this weekend. Expect a few posts to come from that conference!

The AAAS meeting was fun because they didn’t just have lectures on hard science topics. They also had sessions on effective scientific communication, which were so popular that most had the audience spilling out the door. One favorite was Scientific Idol.

Like American Idol, the scientists had a few minutes in which to impress a panel of judges. In that short time, however, they needed to explain their scientific research clearly and with some detail. The judges wanted to hear why the research mattered as well as how it was done.

All six were critiqued by their three judges Jennifer Bogo (editor for Popular Science), Corey Powell (editor of Discover), and Indre Viskontas (host of Point of Inquiry). They gave very similar commentary on each performer’s act:

  1. Give the audience time to digest information,even though you only get 3 minutes. Less is more (but still be specific)
  2. Anecdotes and narrative structure grab an audience
  3. Use humor

And most importantly: Have a clear take-home message!

I loved watching the contestants. In 3 minutes bursts, I learned about engaging women in sustainability research from Gillian Bowser, how dust storms form and why they’re terrifying from Maura Hahnenberger, sources of gamma rays from Joshua Schroeder, male choosiness during insect sex from Jenna Jadin, a rap about fluorescence microscopy (yes, a rap, it was amazing) from Dan Gerow, and why we should all respect meterology forecasts from Tom DiLiberto. What a fun event!

Intro to sex chromosomes: why my calico cat is a girl

Internet, meet Emmy, the most precious cat in the world. Emmy likes to sit on laps, purr loudly, chew on flowers, and occasionally get so happy that she drools a bit. Most pertinent to this science blog though is that she is a calico. Look at those orange and black splotches.

Emmy the calico

Almost all calico and tortoiseshell cats are lady cats, like Miss Emmy, and if you find a boy calico, he is almost certainly sterile. Why does that happen?

By the way, this is a discussion of biological sex only. Gender is complicated and not the same as sex!

In mammals, females have two X chromosomes whereas males have one X and one Y chromosomes. Those two chromosomes of course determine if an individual develops as a male or females. It also creates a bit of a quandary though.

You see, the 1000 or so genes on the X chromosome could be made twice as much in females as in males because there’s two copies. Making the correct amount of a gene is pretty important though. Females just don’t make twice as much of all those genes as males. Somehow we mammals had to evolve a way for females and males to make the same amount of those X genes.

And that is called dosage compensation, meaning how females make up for having so much more DNA. Sadly, more is not always better.

To make dosage compensation happen, females turn off one copy of the X chromosome in each and every cell. Bam, that chromosome is no longer open for business. Those genes do not get used. The chromosome gets packaged up, almost like putting shoved in a box in deep storage, so it can’t be accessed.

So how does this all relate to my adorable calico cat?

The X chromosome contains a gene for coat color. That gene, depending on its precise sequence, can result in either orange or black fur. One of Emmy’s X chromosomes has the gene type for orange while her other X has the gene type for black. Let’s call them the orange and black chromosomes for short.

As you can tell by looking at Emmy, different X chromosomes get silenced in different cells. In some places, the orange chromosome gets boxed up, leaving the black one active. The opposite occurs at her orange patches. Because she is both orange and black, you can tell she definitely has two X chromosomes.

Sex chromosomes are pretty amazing.  Their evolution, how they get silenced, the regions that aren’t silenced, what happens when someone gets an atypical number of sex chromosomes…many fun subjects! In the future, expect to read about more recent research that’s been done. Find out if the Y chromosome will ever just disappear, how long pieces of RNA are used to turn off a chromosome, and more!

Welcome!

Welcome to my newest adventure…BLOGGING!

You may be asking: Who are you? Are you seeking fame and riches? Will your writing revolutionize my understanding of the natural world?

I understand if you’re not asking those questions. But I’ll answer them anyways.

  1. I’m a graduate student studying molecular biology, specifically gene regulation. I’m especially interested in brain development, RNA, evolution, and mental health.
  2. Currently I’m seeking a chance to practice science writing. I’m delving into explaining complex topics, finding my voice, and choosing a beat (or obsession) to focus on. Perhaps later on, if I’m really lucky, I’ll find some fame and riches. For now I’ll try to have somewhat more reasonable expectations.
  3. A girl can dream! I hope my writing makes someone say “Aha!” or “Oooh, that’s neat” or even “Gross, why would nature ever do that?”.

Thanks for stopping by!