Tricks of the Trade: LaTeX

Ok, guys. I’ve been studying as a baby statistician (scienctician? statscientist? ecologitician?)  for a little while now and I’m here to share some of their secrets. Before I started here at Penn State I had a couple ideas about what other grad students in my department would be like. First, everyone would be computer masters of any and all statistical programs: R, SAS, others that I hadn’t even heard of yet. Second, they’d all be completely on top of everything in all of our classes because they all would’ve completed undergraduate and master’s programs also in statistics. And thirdly, it’d be really hard to relate to other students because of my background in biology and my love for the outdoors (because clearly they’d all prefer sitting inside in front of their computers, right?). Thankfully, I was way off base and not only am I not left in the educational dust, but my cohort is full of awesome students with a wide variety of strengths and abilities. And I must collect them all. Yea, my new goal is to be like some sort of awesome Anna-Paquin-as-Rogue statistician and glean all of the amazing abilities and knowledge while I can. Except I think I’ll stick to taking the time to learn and practice things...instead of the whole touchy hurty thing she does. One of my absolute favorite new acquires is the ability to write and code in LaTeX.

Cover Letters of Interest

Once you've gone through the process of finding potential grad school advisers, the next step is to contact them. It can be quite scary. That fear that you'll craft a seemingly marvelous letter, attach your well-written CV, send it off, and then…hear back nothing. Or worse, you'll hear back, but they aren't interested in your obvious brilliance. Try not to get in your own head too much. Think of it more as the start of an epic journey towards the next step in your blossoming academic career. The professors that show the most interest in you are going to be the ones that are the best fit for your unique interests and skills. Writing about yourself is hard, but now is the time to brag on yourself a bit. Say it with me, “I am a badass science baller and all the profs want me.” Keep in mind that this letter does not need to be perfect. I just looked back at the cover letter I sent to my MS advisor (keep anything you write about yourself!) and it’s nearly 2 full pages long with way too much information. Thankfully, she wasn't bored, and I had a wonderful, productive Master’s experience.

Say it again!

Collaboration Station: Google Drive

Collaboration is a vital part of the scientific process. Do you think I’m going to save the world on my own? Nope. I’m going to need at least a little bit of help. The more great minds working on a project, the faster advancements may be made. And we need advancements (I’m look at you, self-driving car peoples)! Any sort of collaboration is difficult across distances. Technology has made the process easier and email is currently the main tool for communication for researchers. While I’m really proud of the older generations of scientists for getting on track with email, I’m afraid I’m going to have to ask them, and everyone, to utilize Google Drive for their collaboration needs.

Being able to access my Google Drive from anywhere keeps me productive!

Cool Stuff Sunday 8

Really cool week, so some really Cool Stuff to share with everyone! I've got another wide range of articles and videos for everyone. One article was actually sent to me by a friend who knew I loved these types of reads and shared them with everyone. Thanks! Everyone is encouraged to send submissions for Cool Stuff Sundays!! Doesn't even have to be something you think would specifically interest me, if you think it's Cool Stuff, then it is!

Unknown mathematician (Yitang Zhang) published paper that takes us
leaps forwards in understanding twin prime conjectures. 
(Thanks, Mike for sharing this one!)

I'm also very VERY excited to share with everyone a recent publication from an
 Ecology friend of mine, Colin  Kremer. We studied together in 2007 at
Kellogg Biological Station, where he has since continued as a PhD student.
His paper: Coexistence in a variable environment: Eco-evolutionary perspectives.

Usually I have Stuff that primarily relates to STEM fields of interest, however this Cool Stuff is a
 book recently published by an old college friend. I remember being in awe of his poetry at slams
 and can attest to his talent and voice. 

Filmmaker, Samuel Orr, has been working on a one hour documentary on Cicadas 

since 2007, and now has a Kickstarter to help with funding. I really hope you 

check out this moving video and consider donating to his cause!

Credit: ACS Nano
RNA laced bandages could treat wounds on the genetic level. What?!

Question of the Day:

What topics interest you? What would you post in your own CSS section?

Borrowed from PhD Comics: The Higgs Boson Explained

Yet another example of how I am constantly amazed by people's ability to distill down difficult topics and concepts and present them in an understandable and entertaining manner. Jorge Cham of Piled Higher and Deeper  intersperses comics inspired by life as a grad stud with interviews at various universities and research institutions. This week he traveled to CERN to interview Particle Physicist Daniel Whiteson about the Higgs Boson and how the LHC is attempting to find it.



The combination of visual and audio information presented in such a unique and entertaining way gets me excited to learn about a new topic. I recommend watching the video in full screen to get the entire experience.

*       *       *

Don't forget to vote in this weeks poll. What sort of posts do you want to see on this blog? More like this one? Your opinion is important to me!

Guaranteed to Lift You Up

No long post today. My thesis needs some undivided attention.

However, in an effort to not leave you empty handed, please enjoy this video as much as I did.



If I'm ever lucky enough to have such an experience I hope it's caught on tape so I can share it.

Question of The Day:
What are some of your more memorable experiences to date?
What are some you hope to have?

Scale Matters: Applying the Concepts

If you haven't checked out Monday's, Tuesday's, Wednesday's and Thursday's blog posts, it'd be best to start there! This week we're having a series of posts discussing scale and size. I'm hoping you all still have your imagination hats handy. 

The concepts we've learned about during this week's series, space and time, hold a very important role within scientific research, more specifically, within experimental design. We may also refer to these aspects as spatial and temporal factors, respectively.

An important question to ask in research: So What?

Researchers need to be very mindful of these scales when asking their research questions. This questions will lead to treatment  and experimental structure.

When scientists study genetics, they use fruit flies and not elephants. Life span is important.

When entomologists study insects, they often have to consider multiple life stages that occupy both aquatic and terrestrial habitats. Some insects live days, while some may live over a decade.

When climate researchers collect data, they do so over centuries. Perspective related to time is important. Repetition is vital to minimizing experimental error.

100+ years is a long time! Certainly longer than any one researcher could record. (Dang, that would be one heck of a PhD project). However, as science is a field of collaboration, communication, and networks, people have found a way to develop approaches to address the limitations our lifespans present. Long Term Ecological Research (LTER) is currently being conducted at 26 different sights in the U.S. that spans multiple ecosystem types, environmental conditions, and varying levels of human domination of the landscape.

Different Scales within Research

Grand Canyon Temporal Scale - Click for Full Size

But even looking at data that span a hundred, or even a thousand years becomes less impressive when you start talking to a geologist. A great way to visualize the time frame geologists must consider is to imagine the layers of rocks in the walls of the Grand Canyon. Geologist can match each rock type and layer position to a point in our Earth's history. The further down the rock layer, the older it dates. 

You may also confer with a planetary scientist. Or an astronomer. Even a cosmologist. They deal with temporal time scales that stretch back millions or billions of years. Even to that very first moment, the Big Bang. 

This week has been a great experience for me. I'll try and do series like these every so often. Next week, we'll return to more sporadic topics for posts. Feedback on these posts is greatly appreciated. Just a head's up, the next application announcements may occur this week. 'Mid-April' is a little vague, but I'm feeling very optimistic. Keep reading, sharing, and commenting if you'd like to read along while I'm on (fake) Mars!

Questions of the Day:

If you are a scientist conducting research, what are some of the spatial and temporal scales that you've had to consider?

If not, can you think of the spatial and temporal scale necessary if someone wanted to study you?

Further Reading:
Implicit Scaling in Ecological Research
Choosing appropriate temporal and spatial scales for ecological research
Relative Importance of Spatial and Temporal Scales in a Patchy Environment
Expanding the Temporal and Spatial Scales of Ecological Research and Comparison of Divergent      Ecosystems: Roles for LTER in the United States

Stuff Your Face Saturday

When you are a grad student, weekends take on a whole new meaning. Especially when you are nearing your Defense Date. Weekends become those enjoyable 2 days where you can be in the lab all day with no one around to distract you. (I really think I might be the only person in my building right now.) Also, you get to park anywhere!

Working on campus is certainly not the most ideal way to spend your weekends, but this time of year is crunch time. You may think you have plenty of time to finish everything, however something will always come up. Other students are defending, taking their comprehensive exams, and celebrating their victories and you'll want to take time out of your day to attend or celebrate with them! Certainly others be doing the same when it's your turn at bat.

Once you are sucked into research and thesis writing to this degree, it becomes harder and harder to find time to feed yourself. You may find yourself drawn to fast food and junk food, because of its convenience. But, if you make time in the mornings and evenings to prepare snacks and meals in advance, you may still have enjoyable, healthy food to keep you going.

Here are a few tips and ideas that have helped me:

Prepare Ahead of Time
I can be very bad about just wanting to lay down and relax after the day is over. However, I also want to lay in bed until the last possible moment the next morning. Something has got to give. How hard is it to whip together tomorrow's lunch though? A sandwich. A salad. Some quinoa and whatever delicious things are around the kitchen.


Snacks

Red Pepper Hummus

Try bringing some of these with you in some reusable containers:

• cut up veggies and hummus 
• chips and salsa
• peanut butter and apples
• crackers and spread
• hardboiled eggs

Leftovers
Never underestimate the power of leftovers. Getting full while dining out? Don't keep eating just because its there, ask for a box or some foil. BAM - tomorrow's lunch. Also, don't be afraid to make a recipe larger than you'll need for that meal. You can store it in meal sized containers that are easy to grab for lunch on campus.

Curry

Crock Pot Breakfasts/Dinners
Slow cookers can be your best friend. All you have to do is throw a bunch of ingredients in and when you get home dinner is waiting for you. I've enjoyed making vegetarian chilies, pasta sauces, curry, and beans in my crock pot. I also have a list of recipes waiting to be tried. Including an apple pie oatmeal.

Questions of The Day:
What do you do for meals during your busiest days?
Will you try any of the tips here? Tell me how it goes!

CSULB: Graduate Research Project

My time in Long Beach has come and is now fleeting with a speed that terrifies me. Does time speed up in the months before your defense? How cruel. I still have so much to do! A short, but very sweet, adventure has produced some fun posts. This will be my last Spring Break post and since I'm graduating soon, I don't know when I'll even have another Spring Break! Oh, Real World, you are trying to get a hold of me and I won't let you!

We've talk about lab and field work in the previous posts and today I'll wrap up the series with one more spotlight on research. My friend, Rachel, was kind enough to take time from her insect identifications to answer a few questions about her research. 

Rachel displaying proper bird handling.

Rachel's Master's Thesis research studies the impacts of an invasive weed species, Lepidium latifolium, on marsh food webs. For her, 'the field' is a brackish marsh on Rush Ranch Open Space Preserve, a component of San Francisco Delta Estuary. She measures environmental parameters of the vegetation, in addition to sampling birds (via blood and feathers), invertebrates (bird food), and plants (invertebrate food) for stable isotope analysis.      
                                                                                            More fancy science talk. Stable isotope analysis. This technique follows the notion that you are what you eat. Isotopes of certain elements (Carbon and Nitrogen, in Rachel's research) get passed along when organisms are consumed and become incorporated into the predator's tissue. Rachel can compare the plant, bug, and bird isotopes to figure out the food web.

Marsh at Rush Ranch Open Space Preserve. White 
plants are the invasive weed species she studies.
 Photo Credit: Christine Whitcraft

Rachel's field component in the marsh requires a seven hour drive into northern California. With drives that long, she has to concentrate her efforts for the weekends. A typical outing includes measuring environmental parameters of vegetation, and the aforementioned sampling for isotope data. She has modified a leaf blower so now it serves as a 'bug vacuum' for collections. Her lab work consists of lots and lots of processing. According to Rachel, "It's just the right amount of mix between the two, by the time I'm tired of being up at 4 am, it's time to be in the lab for a while. When I'm sick of being indoors it's time to go out to the field again." In addition, she must also devote several hours per week with other graduate students in her lab working on the restoration efforts mentioned yesterday.

Questions of the Day: 
Do you know of any invasive species in your area?
Have they caused problems for the natural flora and fauna? 

Lab Visit: CSU Long Beach Wetlands Ecology Lab

Blog post ideas come to me in a variety of different ways. On the more frustrating days, I sit and ponder and worry and formulate and brainstorm until I have something. On pleasant days, such as today, the post  practically writes itself. My Long Beach friend, Rachel, let me tag along with her to work this week and I feel more like her annoying little sister, instead of a fellow graduate student friend.

"What does this do? Do you work with this thing? Can I touch every single thing in here? Oh, look at this cool thing! What kind of bug is this? And this one? What about this one?"

This is exactly the sort of passion and interest I want to share with my readers. Science involves some cool cool stuff. So I'd like to start a new tradition of exploring new labs that I visit and sharing with ye ol' readers via a photo post!

California State University at Long Beach - Wetlands Ecology Lab

Researching within the Biological Sciences, you are going to be exposed to many types of working environments. Many projects require you to venture out 'into the field' for experiments, sample collections, or recording observations. But often, a lot of processing, identifying, and analyzing takes place back in the lab. Most labs are unique and reflect the diversity of research conducted by their members. 

A brief bio of the lab's Principle Investigator and their research. 

Questions of the Day:

What is your favorite part of the CSULB Wetlands Ecology Lab? 

What items would you like to know more about?

What would your lab's mascot be?

Click the link below to see the rest of the photos!

Some labs have mascots to represent the research conducted. Icky the Isopod keeps moral up during late nights in the lab.

Rachel (left) and a fellow lab mate (right) use their creativity to design decorations for the lab.

It is often very important to keep track of lab utensils. Some samples in this lab are preserved with certain chemicals, and would contaminate samples used for stable isotope analysis. This spoon is marked 'Dead' to denote that it should only be used on preserved samples. 

You never know what supplies you might need during your research. It's also difficult to keep track of instruments and tools in busy labs if lots of students are in and out. An organized lab with a sign out sheet will run smoothly.

Macrofauna can be difficult to identify. Microscope time is vital, yet sometime straining. The ability to take pictures of samples help the identification process. Photos can be saved as references or sent to colleagues for confirmation. Shown is a polycheate. 

Infauna vouchers. (Invertebrates kept to use as a comparison for later identifications.)

Meticulous record keeping is a good trait to master. Write everything down! You never know when you might need to look back over your notes. Trust me, you'll forget things.

What marine focus lab would NOT have a calendar with tide charts?

You don't realize all of the different tools you'll need during your research. I am sure I've used everything in this photo in some form back at my own lab.

Cool toys are another perk of the science life. This unit takes light saturation points for leaves. The map shown above is of Huntington Beach Wetland Complex. This lab is monitoring restoration of this area. Tidal influences have been reintroduced to this area.

Working to Save the Planet

One of the many requirements for participants in this food study is a Bachelor's degree from an accredited institution, preferably in engineering, biological or physical sciences, mathematics, or computer science. All applicants were required to propose research to be conducted during their time in the Mars Analog Habitat. For the results of the food study to be applicable, the working conditions of the participants must closely resemble those of astronauts who conduct research in space. 

I received my Bachelor's of Science from Western Kentucky University, where I majored in Biological Sciences and minored in Mathematics.

Currently, I am a second year Masters student at New Mexico State University in the Fish, Wildlife, and Conservation Ecology department. I plan on defending my thesis and graduating this May (remember Zing Phrase #13? Graduation or Death!) Since the research I proposed to the Hi-SEAS review committee is a continuation of my present research, I feel it would be helpful to introduce you to the world of algae cultivation for biodiesel production. 

Nannochloropsis salina and other organisms

Perhaps you've heard of ethanol, or another source of renewable biofuel? The energy stored in algae lipids may be refined in a similar process to create biodiesel. Microalgae are ideal sources of energy because they are capable of year-round production, require less water than terrestrial crops, and produce valuable co-products.

The main goal of my project is to address limitations of algae cultivation methods through an aquatic ecology approach. Increasing lipid production in these systems while minimizing the invasion of non-target algae will improve the cost of algal biofuel. The simplest approach would be to manipulate environmental factors to simultaneously promote algal growth and limit competitor or predator growth.

'Invading organisms' are usually dispersed by the wind (and right now New Mexico has plenty of that to go around) and can include diatoms, rotifers, ciliates, and cyanobacteria. They are pests to the algae industry when they munch all the nutrients meant for the target algae or munch the target algae themselves!

Our species, Nannochloropsis salina, was selected due to exhibit high growth rates, lipid productivity, and a wide tolerance range for different environmental parameters. Meaning, these guys might be small, but there is strength in numbers and they'll be tough against competitors and predators. Salinity, pH, and temperature are valuable environmental parameters to utilize for our purposes. Each parameter is the focus of a pair of experiments:

2012 Temperature Experiment

1. Nannochloropsis Growth and Invading Organism Occurrence at Different Levels of [Salinity, pH, Temperature] 
2.   Nannochloropsis Lipid Accumulation 

Samples from these experiments are later quantified by some very diligent and helpful undergraduate students. Imagine spending a few hours with your eyes glued to a microscope counting little green circles! (Note: I do not actually glue my undergrads to their microscope...yet.) Other samples are taken to a special lab on campus where I work with some very knowledgeable and helpful researchers to determine lipid accumulation. They even go a step further and investigate what different kinds of lipids are present!

2010 Salinity Experiment

Once experiments are completed and data is collected and analysed, there still remains the process of writing everything up into a concise and informative manuscript. When I am ready to defend I will have a thesis with three separate chapters that cover everything I have worked on during my time at NMSU. Before I may graduate my committee must read it all and I will present my findings in a 40 minutes presentation. Eventually, each of my three thesis chapter will be reformatted into journal articles that may be submitted for publication, along with other papers I may write with data from other research endeavors. 

I hope you now feel confident with your new algae cultivation knowledge. More important than being able to conduct research is being able to communicate the concepts and results to the public successfully. I hope I've been able to do that today. Please ask questions if you are interested in learning more!

I will try to speak more in depth about different aspects of the life of a graduate student. But for now, thanks for reading along with me. Please also check out my new 'Experiences' tab for a taste of the fun life as a scientist can entail!

Question of the Day:
Was this post helpful and informative or do I need to work on my science communication skills?