20 Sep

What is a biochemist?

You have arrived at a site named The Absent-minded Biochemist but you are likely wondering what exactly do I do? I once had a professor tell me the great thing about biochemistry is nobody knows exactly what we do so we can do whatever we want. While this isn’t exactly correct, biochemistry does encompass a broad area of study.

Biochemistry is the study of the chemistry of living things. I’m sure when you heard chemistry you thought of someone like this guy:

mad_scientist

A biochemist studies the composition, structure, properties and change of matter within a living organism such as humans, mice, or plants. So now you are probably picturing this guy:

frankenstein-1931

In reality, we are nothing but hard-working scientists that want to understand what makes us tick. Biochemists study everything from how genes are turned on and off during development (that’s me!) to how enzymes (biological molecules that help complex reactions occur at a faster rate than they would on their own) work to drug discovery. You can have ten biochemists in a room, and they will likely all be studying something different.

This diversity is what makes the field great!


Do you have a question regarding biochemistry? Do you want to know more about what I do? Leave a comment below!

 

19 Sep

M.I.A. Again. Decided what I want to be when I grow up!

Hello! My depression took a turn for the worse, and I was struggling daily. My doctor and I have worked hard and seem to have everything figured out. *fingers crossed*

On a side note, I went to The Allied Genetics Conference in Orlando, Fl this past July. While the conference itself was not what I had hoped, I did meet a woman who sent me researching a career path. She works as a program coordinator at a science center. In other words, informal education.

When she described what she does in her position, I just knew that was what I have searched for in a career! So now I embark on frantic last-minute career exploration and strengthening my résumé.

I will likely be obtaining a business certificate (providing my committee is on board) over the next few semesters. I have also purchased several books to help me with my communication and writing skills.

With this career goal, I have decided to reformat my blog. I am going to aim still for three posts a week (maybe more). I would like to write about science topics on all three posts. Is there some science topic you want to be explained? Did you hear something in the news and want to know if it is factual? Leave a comment below or send me an email and I will answer your questions!!

25 Aug

How do you plan crazy?

Whew, what a crazy summer I had! And this fall is going to be even crazier. I am teaching two lab sections that are three hours each plus the extra time to prep lectures and grade assignments. I am also taking a genomics course that is a three credit hour course (meaning we meet in class three hours a week) and don’t really know how much work that is going to take. I have also been elected the outreach officer for the 2015-16 Biochemistry Graduate Association at my school (brand new position so I have no guidance). So far this entails officer meetings of about an hour in length at least once a month, putting together a weekly email of events coming up the following week, and planning our participation in local outreach activities. I am attempting to finish a teaching certificate that our university offers to prepare grad students for a tenure-track teaching position. For this, I have to attend several seminars throughout the year, audit a couple of classes and fill out evaluations, as well as write a teaching philosophy statement, CV and a syllabus.

Oh, and I am also guest lecturing for my advisor towards the end of the semester.

On top of all this, I had a “come to Jesus” meeting with The Boss today and he informed me he wants me writing by next December. This means I should have all my research done by the end of next year.

Yikes!!!

I’m obviously needing to plan out what I want/need to accomplish. I’ve decided that I want to break it down in the following way:

  • Long term: Completing my project by December 2016
  • Long, mid-term: Plan out what I need to complete by the end of each semester
  • Short, mid-term: Plan out what I need to complete by the end of each month
  • Short-term: Plan out what I need to complete by the end of the week

After making this decision, my next step was to head to Google. And boy was I overwhelmed with articles and templates on time management and planning (over 502 million results for “time management” and over 54 million results for “planning dissertation research”). Trying to sort through what is helpful and what isn’t relevant is turning into a task of its own.

As I investigate further, my question to you is this: How do you plan your tasks? What do you use to lay out your goals? Please leave your tips and suggestions, all are welcome!!!

14 Jul

The Science of Tattoos

With some fresh ink on my arm, I thought I’d take a moment and explain the science behind a tattoo’s permanence.

As this fascinating video from TED explains, tattoos are actually a complicated inflammatory process—a delicate balancing act between your body and the dye that’s invading it.

It turns out my fierce samurai is kind of like an infection—and the reason it’s permanent is because your body keeps on fighting it forever.

Tattoo needles punch through the epidermis, the outer layer of skin, and drive the ink into the dermis, the deeper layer that’s mottled with nerves and blood vessels. “Every time the needle penetrates, it causes a wound that alerts the body to begin the inflammatory process,” the video explains.

That signal sends immune system cells racing to the site of the wound (or multiple wounds, in the case of the five-inch dragon breathing fire across your chest). Special cells called macrophages come to the rescue, eating up the dye in an attempt to “clean up” the inflammation it’s causing. The rest of the dye gets soaked up by skin cells called fibroblasts. The fibroblasts, along with many of the macrophages, stay suspended in the dermis in perpetuity. The dye in the bellies of the trapped macrophages and fibroblasts shows through the skin, projecting your Chinese word for “love” or constellation of tiny blue stars to the outside world.

Oh, and just in case you have “ragrets” about your choice, the video explains how you can get that fixed.

“You have no regrets? Like, not even a single letter?”
10 Jun

Troubleshooting experiments, or how to waste your time.

I’ve been doing really well with getting over my mid-Ph.D. crisis (post here) and have been getting in the lab every day to get work done. I have recently begun doing quantitative RT-PCR. I extract messenger RNA from zebrafish embryos, reverse transcribe it into cDNA and then perform specific PCR looking to see if there is a difference in transcript levels of the mRNA.

Anyone who has done qRT-PCR knows how much work goes into setting up the experiment. You have to determine the quality and quantity of RNA you have extracted, determine if there are any inhibitory  components in the sample, design your primers, pick a template for standards and optimization, determine what primer concentration is best and analyze the primer performance in the assay, validate the assay efficiency and sensitivity, and finally perform the RT and qPCR steps. Follow all this up with data analysis and qRT-PCR is quite an extensive process.

I set up my first reaction and my melt curves are off. I run a general PCR and run the product on a gel to see what is going on. Low and behold I have primer dimers. This is where my primers anneal to each other and form products instead of the template and forming amplicons. Big problem if you want to quantitate the amount of template present in a sample. So back to the primer design I go.

In addition to this, I also discovered that either our enzyme or primers are contaminated with DNA as my “no template control” produced a product. I had a just soaked my pipettes, UV’d my bench, and opened a fresh bottle of nuclease-free water. That leaves only enzyme and primers as being the culprit. I guess I’ll find out with the new primers.

Sorry for the very specific rant about lab work. Do you have any tips on setting up qPCR?? If so, I’d love to see your comments below!

3 Jun

Grading and feedback, how to make them meaningful

I received news that my hiatus from teaching will be over this fall and I’m torn on how I feel. On one hand, I enjoy teaching. On the other hand, this means less time in the lab. As I mentioned in my recent post about goal-setting vs. goal achieving, I’ve struggled to multi-task and have recently laid out my goals. Now I will have to adjust these goals to take into account the time needed for teaching.

If I had to state the one thing that I believe takes up the most time for teaching, it is hands-down grading (and most other grad student TAs will give the same answer. Multiple choice questions are easy, its right or not. In science, asking multiple choice doesn’t help the student learn so we tend not to use these types of questions. That means most of what I’m grading is short answer questions. I’ve always been a TA that likes to give feedback when a student misses a question. With a new semester fast approaching and me wanting to spend more time in the lab and less time grading, I’ve decided to look at ways to reframe my approach to grading.

1. Prioritize and write feedback that will have the most impact. This is probably the most important lesson. I’ve decided that I will grade without corrections/feedback first to look for common mistakes amongst my students. Generally speaking, they usually seem to miss the same questions. I can save tons of time by recognizing where my students are struggling as a whole and addressing this in class rather than writing the same comments 15-25 times on their papers. In addition, I will list what my priorities are for what I want out of their answers. Are there keywords that they should include? Is there a particular concept I was wanting them to use? My addressing my priorities first, I can get a large chunk of the feedback out-of-the-way.

2. Feedback is all about Socialization. Most of the students I teach have taken laboratory classes but have not worked in a formal lab. The way we expect them to record data and answer questions in my lab is the same way they would if they were performing research in a lab. I try to explain to my students that, up until this point, they probably have not done much technical writing. They need to be precise. When keeping their lab notebooks, they must write it like a user’s manual. I tell them that I should be able to take their notebook to someone in the hall that has never taken the course and that person should be able to understand why they did the experiment they did and how to perform it. I try to help them “learn the ropes” and guide them rather than act as a gatekeeper meant to keep them out (or passing the course). Keeping this in mind, I plan to be upfront in how I expect them to write their answers and lab notebooks and hopefully remove some of the minor corrections.

3. Work with the student, not just the assignment. Something I’ve been proud of myself for doing in the past is being able to recognize when a student is struggling with concepts. Sure, you have the kids that just don’t put forth the effort but I’m talking about the kids that pay attention during lecture, ask you questions during the experiment but still seem to struggle when it comes around to quiz time. Here are some things that I plan to implement to try to help my students even more:

  • Take a long look at the student’s development in my course and use my feedback as a means of having a conversation about their progress.
  • Make sure I match my feedback to the goals of the assignment. No point wasting my time and confusing the students if what I write doesn’t line up.

What strategies do you find helpful when you sit down to grade student assignments? Please share your thoughts and ideas in the comments below!

24 Apr

This week in science!

This week in science: Chimps look both ways before crossing a road; gazing into your pooches’ eyes increases oxytocin levels; vaccination against ebola; mutation in IRF7 increases risk of lethal flu

Wild chimps have learned to look both ways before crossing a road! Researchers observed wild chimps crossing a busy road in Sebitoli, in northern Uganda’s Kibale National Park. The noted that the chimps would pause at the road and look both ways for vehicles. They would quickly cross the road in small groups while continuing to look for oncoming cars. The researchers also observed that the alpha males of the group would lead the crossing and wait until all members had crossed. Chimps in Bossou, Guinea behave differently as the roads are quieter. Here, they would cross in a single file line. (Cibot, M. et al. American Journal of Primatology (2015), doi: 10.1002/ajp.22417)

Staring lovingly into your dog’s eyes increases oxytocin levels. Gazing is an important part of non-verbal communication in humans. The “mutual gaze” has been discussed as the fundamental manifestation of the attachment between mother and infant, with maternal oxytocin levels rising during the moment. Now researchers have shown that man’s best friend have hijacked this nonverbal cue. Researchers examined whether a dog’s gazing ability affected the oxytocin levels in both the dog and the owner during a 30-min interaction. Indeed, the oxytocin levels in both dogs and their owners was shown to increase. This suggests that humans may feel affection for the dogs in a similar manner felt towards their family members. So the next time someone refers to Fido as their child, they really do feel that way! (Nagasawa, M. et al. Science 348, 333 (2015)

Ebola vaccination protects nonhuman primates against lethal infection with the virus. As we are all aware of, ebola is a very dangerous virus. With the recent epidemic in Africa and with the recent scares we’ve had here in the US, it’s no surprise that research is underway to find a vaccination against the virus. It has already been demonstrated that a vaccine that is based on a replication-defective strain of ebola (it can not make more of itself) can protect mice and guinea pigs against lethal infection with a rodent-adapted ebola virus. Now, Marzi et al. have demonstrated that this same vaccination protects nonhuman primates against lethal ebola infection. The group further inactivated the virus by treating the replication-defective virus with hydrogen peroxide. It has been known for many years that hydrogen peroxide is an effective viral inactivating agent but only recently has it been revealed that this treatment does not affect the antigenicity (or ability to cause a reaction from our immune response) of the virus. This vaccination provides a safe and effective means to vaccinate against ebola. (Marzi, A. et al. Science 348, 439 (2015))

A mutation in IRF7 increases the risk of lethal flu infection. A mutation in IRF7 in an otherwise healthy child has been linked to life-threatening influenza (flu). IRF7 encodes the transcription factor interferon regulatory factor 7 and plays an important role in the expression of virus-targeted genes. With these mutations, the child’s body produces very little type I and type III interferons (IFNs). IFNs are signalling proteins that are released in response to pathogens such as viruses.  This suggests that type I and III IFNs are necessary for protection against primary infection by the flu virus. (Ciancanelli, M.J. et al. Science 348, 448 (2015))

Other random science-related facts:

  • Germany’s political parties have agreed to increase funding to science by $5.4 billion (US) between 2018 and 2028. Now if we can get the US to follow suit!
  • The Center of iPS Cell Reseach and Application (CiRA) of Kyoto Univeristy has partnered with Takeda, a Japanese pharmaceutical firm, to develop clinical applications for induced pluripotent stem (iPS) cells, including treatments for heart failure and diabetes.
  • The CDC has started late-stage clinical trials of a potential ebola vaccine in partnership with Sierra Leone’s College of Medicine and Allied Health Sciences.

 

Did I miss anything you found interesting? Want to learn more about any of these topics?

20 Apr

The perils of tutoring

I love to teach. I always have. My mother has told me (and I vaguely remember) that I used to set up my easel as a kid in front of some milk crates and chairs and “teach” my younger sister and our stuffed animals. I even hijacked my dad’s mechanic manuals to use as textbooks! So it’s no surprise that I’ve actually enjoyed being a teacher’s assistant and tutoring here at my university.

That being said, tutoring is very time and energy consuming. I am in a molecular genetics lab so I don’t use a lot of the biochemistry and metabolism that you learn in the biochemistry classes. I have to spend several hours a week reviewing the material to keep it fresh in my mind. In addition, finding and preparing materials for each student is time-consuming as well. I’m lucky in that I learn very quickly how people learn so I know within a session or two how to present material for each student but this means I might be constructing several different types of material depending on how many students I have. All on top of my responsibilities to stay well-read in my field and keeping my research moving forward.

As a tutor, you rely on your student putting forth a certain level of effort, obviously dependent on the grade that they hope to achieve. Here is where my dilemma lies.

I am currently tutoring a non-biochemistry major student. This is her third time taking the course and she sought a tutor about half way through the semester when she realized that she was, yet again, not going to pass on her own. I gave her the same advice I give all biochemistry students: Start memorizing the pathways the day they are introduced to you. There are numerous pathways, some of which are very complicated and they can not, by the average person, be memorized overnight. As the semester has gone on, it has become obvious that I’m putting more effort into our sessions than she does. She falls asleep during our hour sessions and is never prepared.

So now I’m stuck with the decision of continuing this one-sided relationship or parting ways. What would you do?

20 Apr

Hello world!

Why, hello!

I am the absent-minded biochemist. I am a Biochemistry Ph.D. student at a big state university. The reason I choose biochemistry is pretty simple: most people don’t really know what a biochemist does so you can do whatever you want to do!

I’ve been tossing around the idea of starting a blog as a means to improve my writing. Then I stumbled across a blog post over at Next Scientist by Julio Peironcely. Julio writes about how by starting a science blog, it allowed him to open up to others and it helped him get back on track and regain hope in his PhD. This was the catalyst I needed.

I have two “themes” for my posts that I plan to write:

  1. This week in science/check this out: A weekly post pointing out awesome things that are happening in the field of science. I hope to be able to convey the fascinating and important things going on in the field of science to non-sciencey people.
  2. Grad life: posts relating the struggles and anguish that we all experience in grad school! This will include the struggles of balancing life with school, research woes, and teaching experiences. Most importantly, I hope to include things I wish I would have known when I started.

Let the experiment begin!