“The science you do not understand looks like magic” – sometimes true even if you understand it

Posted on May 14, 2012 by juliamallen

Science majors in college, in the last years of the undergraduate degree, suddenly realize the value of “experience”. But what is this elusive “experience” that all job applications talk about, without specifying what they actually require you to know? How do you get it? There are basically no entry-level science jobs out there; everyone wants you to already have “experience”. It is scary, when you first realize, that to be able to do anything with your degree, you need to already work in your field, and have all kinds of skills that nobody taught you in class. That is what “experience” is all about. Your classes, your grades do not really matter in the long run, you need to be able to DO things.

So, basically, experience equals doing. Doing science! Well, hopefully that sounds like a lot of fun to a science major, assuming that the reason behind choosing this major was because they like it. I sure did some exploring in different fields, before I settled with my major, and even then one was not enough, and I ended up picking a second major two semesters before graduation. They were both science though, because I love the exploration, the hunt, the quest. Science allows you to ask questions that interest you (and perhaps others as well), and then go ahead and find an answer. Then writing about science is an attempt at convincing others regarding the answers found. It is a never-ending challenge. Hmmm, never-ending, that may make it sound not that attractive for all, but it may just be a special motivation knowing that there is always something else out there that you can pursue.

But I digress, back to experience. So, I realize that I want to DO science. Where to start? Here is how I did it, and would recommend doing it. The easiest way to get started is the departmental list of labs and graduate students. With luck, you just contact them, and you will find a herd of people, eager to get help from you. Manpower is what you can first provide, and you will get skills in exchange, and you will find out whether you really like DOING this. I was already working on a project with birds, running around on campus. Then during the nights, I helped my bird-mentor sort through samples of powder that contained lice collected from birds in the tropics. That is how I met Julie. Since Julie is into lice… she likes them a lot. We started talking about host-parasite coevolution, and what we could do with all the lice that we found. She mentioned that they were looking for somebody in the lab who could help out with a project on Anoplura (those are sucking lice; I had no idea either…). Paying job!!! That is the best way to get the elusive “experience”. Finally, becoming a professional, and getting paid to work on science. This meant a lot of autoclaving, solution making, but also learning: DNA extractions, PCR, a bit of cloning. Part time position, so it allowed me to keep on chasing birds around on campus. It was perfect.

Once I had the basic lab skills down, I started working on the project of Red Colobus (those are monkeys; I had to look them up – way cuter than lice…). Same skills, just different organism, different questions too.  Julie was great at guiding us through troubleshooting, and there was a lot of trouble. Lab work seems to have its own black magic. You can do everything according to the book, follow the recipes, and you just do not get anywhere. Staring at blanks. However, once you get the hang of things, get rid of contamination, make new primers, new water, freshly autoclaved tubes, pipette tips, recalibrated pipetter, fresh dye, fresh TAQ, and the right constellation of stars comes together, then, finally, it is really rewarding to load your samples into those 96 tiny wells on the tiny plate. Magic is necessary. I am not complaining, I am just describing how I gained “experience”; and learned the magic of troubleshooting. It is similar to your computer misbehaving, and the best solution being unplugging and plugging it back in. Simple magic.

The TV shows out there really glorify labwork. Everything works so quick, you load a sample, and out comes a printed sheet with results on it that help you identify the victim, catch the criminal, diagnose the disease, isolate a compound. With “experience” you learn though, that it is not that easy. It is a challenge, it is a leap of faith, and it can be frustrating. It can also be glorious, and rewarding. The reality of first working in a lab as an undergraduate is mostly figuring out what you like, and what you do not like. You have a mentor, or sometimes even more than one. Your mentor(s) guide you, reward you, discipline you, teach you, and if you are lucky like me, they become your best friends. Friends for life.  Because the skills you pick up while getting experience, they stay with you for life. Every time I have to deal with troubleshooting, I think of Julie, my labwork-mentor, and all the things she taught me; but I also remember the shrine of trinkets from all over the world proudly displayed on and around the thermocycler, to please the machine, to give an offering to the forces that allow the primers to sit down in the right places and make your sample DNA elongate. Nobody teaches you that in class…

I still do labwork, and with “experience” I have learned, that I enjoy chasing birds a lot more. It is not enough though, I want the magic of the invisible, the answers hidden in the genes, the things I can only find if I work in the lab. It allows one to look deeply. Deep in time even. Doesn’t that sound like magic?!

Judit Unvari-Martin is a PhD student at the University of Florida. She studies the genetics of birds that live in the Amazon. To do this she spends 6 months of every year in Peru trapping birds and hiking around the rainforest. 

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Are all homophobic politicians gay?

Posted on May 8, 2012 by juliamallen

Doesn’t it seem that every time we hear a politician rant about how we should deny rights to the gay community, he turns out to be gay? From Phillip Hinckle in Indiana to Mark Foley in Florida, time and time again politicians with anti-gay voting records frequently get caught engaged in homosexual activity.  As scientists, we are taught to notice patterns and then pose scientific questions. This is a good example of a pattern that begs for a scientific question. In this case, the question would be “Are all homophobic politicians gay?”

On the surface it seems difficult to answer this question because we need to know politicians’ actual sexual orientation which may differ from what they say it is. Only then can we contrast their sexual orientation with their speeches and voting records on bills that provide equal rights to members of the LGBT community.  A recent NY Times article reported on a study that attempts to answer this question.

Here is the idea behind the study. Dr. Weinstein and colleagues wondered if parents who are homophobic or are not supportive of their children honestly expressing their true attitudes, will have children who demonstrate “reaction response” in which they adopt behavior that is opposite to how they really feel (like being really homophobic to hide their homosexuality).  This response is an attempt to protect themselves from being disowned by their parents or from backlash in the community.

How do you come up with a scientific experiment to test this idea?  How do you figure out what someone’s actual sexual orientation is.  Here is what Dr. Weinstein’s team did. They conducted what is called a reaction time test to determine an individual’s sexual orientation.  Men and women were asked to place words or pictures into one of two categories–homosexual or heterosexual.  The words were “gay, straight, homosexual and heterosexual” and the pictures were of gay and straight couples.  They then measured the time it took the participants to respond. However, immediately before participants began the task, the researchers subliminally flashed either “me” or “others” onto the screen. The research theory was that homosexual participants would take longer after they see the word “me” to put things into the heterosexual category. Similarly, if they are heterosexual, it will take them longer to put things into the homosexual category after seeing the word “me” on the screen. The researchers then asked them questions designed to indicate how their parents feel about homosexuality, how they feel about homosexuality and of course their own sexual orientation.

The results were really interesting.  There was no correlation between participants’ measured sexual orientation and what they said their sexual orientation was unless their parents attitudes towards homosexuals were added to the mix . For people whose parents were not homophobic and were open to their children expressing themselves, measured sexual orientation matched their stated sexual orientation. For people whose parents were outwardly homophobic, measured sexual orientation only matched their stated sexual orientation if they were straight.  However, if their measured sexual orientation was gay or lesbian, they were more likely to say that they were straight. This suggests that people are taking on behaviors that are the opposite to how they really feel if they do not think they are supported by their parents.

More importantly, researchers found that if participants’ measured sexual orientation did not match their stated sexual orientation, they were more likely to be homophobic.  This could explain why our politicians often get caught in homosexual activities when they have extensive anti-gay voting records. They might be trying to hide their sexual orientation to protect themselves from perceived risks such as constituent backlash or parental rejection. This research helps us to not only understand the motivations behind certain behaviors but also brings up other interesting questions. What could we learn about school yard bullies who pick on other students for being gay? What are their parents thoughts about equal rights for the gay community and how does this impact their children’s behavior? Ultimately this research suggests that homophobia might be gay…

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When I Grow Up….

Posted on May 2, 2012 by juliamallen

“Many people don’t know what they want to be when they “grow up”, and I am no exception.  When I started college, I decided to study Biology because I was fascinated by things I had learned about the natural world, about the diversity of life, and about the way organisms have adapted to succeed in their environments.  I had no idea what I could do as a biologist, and had vague thoughts about being a wildlife veterinarian, or perhaps working in conservation.  Then I stepped into the Reed Lab at the Florida Museum of Natural History, and was introduced to a world of research I never knew existed.

During my first summer in the lab, I was trained on molecular techniques including DNA extraction from a bit of tissue, amplification of pieces of DNA using PCR, visualizing PCR products using gel electrophoresis, and sequencing those pieces of DNA for use in phylogenetic analysis that would tell us something about the evolutionary relationships and histories of the organisms in question (in this case, humans and their head lice!).  I have never quite gotten over my fascination with the idea that, in such a short time, I can go from a tiny piece of tissue to data that answers questions about the history of life! (so much so, that 6 years later I find myself in graduate school using many of the same tools (and new ones that continue to be developed) to answer ever more interesting questions about ever more interesting systems).

But molecular work was not all I found in the Reed Lab.  During my 3+ years there I was able to help the graduate students with fieldwork including catching bats in Puerto Rico, and the Florida mouse nearby.  My time in the lab opened up opportunities like studying marmot behavior in the Colorado Rockies, and rainforest birds in the Peruvian Amazon.  I also had the opportunity to complete my own project for an Honors Thesis, in which I studied the genetic relationships of pocket gophers across geographic space using historical museum skins.  Most importantly, I found myself being part of a lab, a group of people who teach you, encourage you, and criticize your work, all contributing in some way to your development as a scientist.  And of course they are there at the end of the day for some cervezas or Argentinian wine-tastings to help you relax and de-stress!

Now here I am in grad school, gearing up for a field season that will take me all over the Southeastern U.S. to study the genetic structure of frogs, also eager to get back to the pile of sequence data that will hopefully be waiting for me to analyze and write up with my advisor and undergraduate co-authors when I return.  As the semesters roll by, it becomes more and more clear that there is another decision somewhere in the distance – what to do next?  Post doc in another research institution?  Teach at a community college or primarily undergraduate institution?  Work at a wildlife agency, conservation non-profit, or natural history museum?  Well, I’ve got a couple more years of catching frogs, teaching, and mentoring to think about it.

So I still may not know exactly what to do when I grow up, but I’ve sure found a pretty fantastic way to appreciate life (and hopefully contribute a little something to our knowledge about it!) while I figure that out.”

Lisa Barrow finished her undergrad degree in Biology and is now a graduate student at Florida State University, where she runs around studying the genetics of frogs.  Here she writes about her experiences doing research as an undergraduate.

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The Black Death

Posted on April 23, 2012 by juliamallen

How does one study an ancient disease? How do you study something that is no longer around? What kind of information do we want and how do we get it? As a geneticist I always want to look at DNA because DNA is an excellent source of information. It can tell us things like was it a virus or a bacteria?  Is it closely related to bacteria that are around today? What made it become an epidemic? The real question though, is how do you get your hands on DNA of an ancient disease?  Well,  you rob graves of course.

The Bubonic plague is probably one of the most famous epidemics of all time. It was also called the Black Death and killed ~25 million people which was around 30 – 50% of Europe’s population in the 1350s. The disease has many symptoms but two of the most famous were the swelling of lymph nodes (ew) and where the tissue in the extremities (like fingertips, arms and nose) would get gangrene and this rotting tissue would turn black (double ew). This symptom is what gave the disease its lovely name the Black Death.  Apparently these symptoms would occur within just a few days of getting the disease and people would die a very painful death soon thereafter.

The disease is thought to have been caused by a bacteria called Yersinia pestis. Although there have been reports of the plague occurring more recently it has been debated whether it is actually the same strain of bacteria as what caused the major epidemic ~600 years ago. One of the things we could do with the ancient DNA is to find out if the plague is still around, of course to find this out we need to get our hands on some of its DNA.

Bos and colleagues took a really interesting tactic to getting this DNA. They wanted to know how its DNA changed to make it go from a regular old bacteria to one that is capable of killing millions of people. To figure this out they had to get DNA from the actual bacteria that was killing people in the 1350s to see what it looked like. So where to find it?  Well, one of the big problems they had during the epidemic in the 1300 hundreds was what to do with all of the bodies, and one of the things they did was to create mass graves just for victims of the Black Death (awesome). Bos and colleagues took advantage of that and went to one of these old gravesites and actually dug up bodies and took teeth from five individuals and got DNA of the bacteria from those teeth (I wonder what they said they wanted to be when they grew up?).

What does the ancient DNA tell us, well to understand this we need to know a little bit about bacteria genomes.  Bacteria have really cool genomes, they have one circular chromosome (different from our 23 pairs of chromosomes) and they have other little pieces of DNA called plasmids. Plasmids are little circles of DNA that can be easily passed from one bacteria to the next.  These plasmids have been really important in the evolution of bacteria. For example, if a gene that makes a bacteria resistant to an antibiotic is on a plasmid and that plasmid gets transmitted to new bacteria then the new bacteria is instantly resistant to antibiotics. This is thought to be one of the reasons we have so many problems with antibiotic resistance.

The genome of Yersinia pestis has one large bacterial chromosome and two plasmids. Boss and colleagues found that the DNA from the ancient strain of bacteria is different from the strains of Yersinia pestis that are around today, but that it is likely that all of the strains that are around today are descendants of the ancient bacteria.  What is even more interesting is that they did not find any single spot on the chromosome or on the two plasmids that could explain why the bacteria became so infectious.  Instead they suggest that there were a lot of other things going on during that time period that added to the problem of this disease, like maybe people were more susceptible to getting sick, and the conditions were just right for spreading the disease.

It is fascinating to think about the issues around diseases and that many times other factors must fall into place for a disease to be really successful (and not necessarily just a genetic change), things like sterility, medical applications and knowledge, human health, and how the disease is transmitted. It may be that some bacteria or virus could be completely capable of causing a huge epidemic but we have other things in place that prevent those things from happening. The recent Cholera epidemic in Haiti is a good example of this. We have known what Cholera is and how it is spread since the days of John Snow, but we still were unable to prevent this problem in Haiti because the conditions were right for the disease to be spread.

 

Paper Referenced: Boss et al. 2011. A draft genome of Yersinia pestis from victims of the black death. Nature 478: 506-510.

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The Real World

Posted on April 22, 2012 by juliamallen

“As soon as you enter University the pressure is on to figure out what you want to do with your life and to gain as much knowledge and experience as possible in those four short years before you enter “the real world”.  I have always known that I wanted to do science; I was fascinated by the natural world around me.  So, the hard part was figuring out what really interested me (the natural world is quite a big place) and how I was going to get any real experience to figure it out.

First semester sophomore year, I was lucky enough to have a fantastic biology TA.  She made biology lab extremely interesting, and best yet, she got me in touch with her advisor about getting some lab experience!  I was finally going to start getting some practical experience so I could start the process of figuring out where my interests lie.  I found out that the lab mainly researched lice (umm…pretty sure that’s not where my interests lie) but that the research was actually using the evolution of lice to look into human evolutionary history (way cool!).

After hours of pipetting tiny amounts of liquid into tiny tubes to the musical sounds of the PCR machine, I had decided that molecular lab work wasn’t for me.  That doesn’t mean I didn’t love every minute (nearly) of it though!  There is something extremely satisfying about putting in a lot of hard work and time to turn on the ultraviolet light and see the genes you were looking for amplified on the gel.  Just knowing that I contributed to research that could shed light on how humans evolved makes me feel pretty important.

So the moral of the story is to take every opportunity you can in college to learn and experience new things.  Even if what you are doing doesn’t directly lead you to your dream job, you still might find yourself involved in something that could change how we think of the world.”

Lauren Long was a former student at the University of Florida. She currently lives in Auckland, New Zealand where she works on public policy issues for the Auckland Council.  Here she writes about her experiences working in research as a college student.

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What’s In Your Guts?

Posted on March 27, 2012 by juliamallen

We are not alone. In fact, we are far from being alone. We live surrounded by all sorts of other organisms. In a given moment, like right now, we have 10 times more bacterial cells in our body than our own cells. We are like walking, talking robots for bacterial communities. We have heard all the hype about good vs. bad bacteria. On the one hand, we are supposed to use anti-bacterial hand sanitizers to kill the bad bacteria; on the other hand, we are told eat yogurt to increase our good bacteria. We know that bacteria are important and have had a huge influence on our daily lives, but we are barely beginning to understand the role bacteria have played in our evolutionary history.

Bacteria have profound effects. For example, the bacteria species Yersinia pestis was the cause of the Bubonic Plague that killed one-third of Europe’s population in the 1300s. Not only do bacteria influence us, they also influence many other organisms as well. In fact, bacteria have been evolving with other organisms for as long as there have been other organisms, and they have played a large role in other species’ evolution. One famous example is the mutualist bacteria that live inside insects, where they furnish nutrients that the insects do not get in their diet. These bacteria are thought to be partially responsible for the huge diversity of insects we see today. However, despite these remarkable examples, we know relatively little about the influence bacteria have had on other organisms. In fact, we do not even know where our own gut bacteria come from.

Ruth Ley and colleagues attempted to answer this question. They wanted to know where the bacteria found in mammal’s guts come from. They suggested two possibilities. First, that gut bacteria come from our diet, meaning that bacteria in and on our food stay and live our guts when we eat them. Another option is that that we are born with these bacteria, meaning we get our gut bacteria from our mothers. They tested between these two possibilities by asking the question in a different way: do animals with similar diets or those that are more closely related have the same bacteria? Using this approach, they surveyed a bunch of animals to get a pretty good clue as to where gut bacteria come from.

They went to a bunch of zoos and collected feces (yes, feces) and identified all the bacteria in them. The idea is that, because feces are a direct product of our guts, they should contain some of these bacteria. They then compared bacteria from animals with different diets, like leaf eating monkeys and omnivorous monkeys. They also compared animals in zoos with closely related animals in the wild, like the Asian elephant from the St. Louis Zoo with its wild relative the African Elephant.

What they found was really interesting, not only did closely related animals have some of the same bacteria, but animals with similar diets also had similar bacteria. This means that our gut bacteria likely come not only from our diet, but we are also born with some of them as well. This research suggests that what we eat is really important for shaping our gut microbial community but that it is not the whole story. Some of our microbes have always been there.

Now that we have more of an understanding of where our gut microbes come from, the next step is to understand what they do and how to maintain a healthy gut community of bacteria. What kinds of foods can we eat to maintain the good bacteria, and how can we help to foster the bacteria that we were born with? What do all of these bacteria do, and how do they work together? We are definitely not alone, and in terms of food digestion, this is likely a good thing.

Article Referenced:

Evolution of Mammals and their Gut Microbes (2008) Ley et al. Science.

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Everyone Should Think Like a Scientist

Posted on August 21, 2011 by juliamallen

The word scientist may bring up interesting ideas about what scientists are and what they do.   Perhaps you think of someone wearing a lab coat and doing crazy things with test tubes.  I certainly did at one point.  However, as I went through graduate school and into my postdoc, my whole impression of scientists and science itself has changed, and this process has changed me.

What is a scientist?  Scientists are people who have been taught to think critically about the world: taught  to ask a question about how life works, collect the appropriate data to answer that question and interpret the results in a way that helps to explain something about the world.  Being a scientist means always questioning why things are the way that they are …..  essentially critical thinking.

Critical thinking is for everyone, but this type of thinking does not come easily at first. It means trying to understand a problem from all angles  and being creative about the types of questions you can ask. This includes everything from explaining why the world is green to trying to understand the facts behind a news story. This type of thinking influences the way we make decisions and approach problems.  Scientists are taught to find information themselves and interpret that information.  Critical thinking takes practice and effort but does come easier with time. Everyone should approach the world with this same attitude.

Critical thinking even allows you to be more understanding with people: to think critically about their point of view and why someone may act or do something that does not make sense to you immediately. Most importantly, it allows for a sense of self confidence. It will give you the ability to believe you have the skills to solve a problem and trust your conclusions and ultimately yourself.  This  is the most rewarding and life-changing part.

Everyone should think like a scientist.

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Sucking lice and their mutualistic partners

Posted on November 14, 2010 by juliamallen

Insects are one of the most successful animal groups on the planet.  They have evolved into almost every habitat and every niche.   In fact they are the most diverse land animal group, and are the primary competitors of humans. Insects have done extremely well at exploiting niches that other animals cannot.  For example many insects have nutrient poor diets like plant sap, wood and even vertebrate blood.  The reason they have been able to feed on these diets is because they have had help from a mutualistic partner.  They have a bacteria that lives completely inside of them that makes important nutrients for the insect.  These bacteria are called primary – endosymbionts. P-endosymbionts live in an enlarged cell called a mycetome, and are transmitted from mother to offspring through the eggs.

Sucking lice are an example of one of these insects.  They feed on mammalian blood, which is missing some important nutrients, and it is thought that all sucking lice have a p-endosymbiont that supplements their diet.  Interestingly, the p-endosymbiont in the human head louse was first described over 300 years ago by Robert Hooke, who was looking at head lice under a primitive microscope, but until this research started the endosymbiont in the human head louse or any other sucking lice had not been characterized or named.

Insects and their primary endosymbionts have had a long coevolutionary history.  Many groups of insects that have these bacteria all have the same lineage of bacteria.  Aphids, for example, all have the same genus of bacteria called Buchnera. This pattern suggests that an ancestor of aphids acquired this bacteria and was able to feed on a new diet, in this case plant sap.  This aphid ancestor then radiated into this new niche passing the bacteria from mother to offspring, and as groups of aphids spread out they became different species over time and each new species then still had the same lineage of bacteria. When we look at these bacteria from different species of aphids they are all closely related to each other supporting this hypothesis.  We wanted to know if all of the bacterial species in sucking lice were closely related suggesting an ancestor of lice acquired this bacteria and radiated out in just as in aphids.

However, we found a completely different pattern in sucking lice. In looking at only a few species of lice I have identified at least eight lineages of bacteria.   We know this because all of the endosymbionts from lice are not closely related to each other.

This finding is interesting because it is very different from what has been found in other insects with primary endosymbionts and begs the question of what is going on in lice.  How many lineages of bacteria are there in sucking lice? Why do they have different lineages of bacteria when most insects with p-endosymbionts only have one lineage? What does this pattern tell us about the evolutionary history of lice and their bacteria?  Our future research on lice is trying to answer some of these questions.

Papers coming from this research:

Allen J.M., Reed D.L., Perotti M.A., and Braig H.R. 2007. Evolutionary Relationships of “Candidatus Riesia spp..,” Endosymbiotic Enterobacteriaceae Living within Haematophagous Primate Lice. Applied and Environmental Microbiology. AEM 73(5):1659-1664.

Perotti M.A., Allen J.M., Reed D.L. and Braig, H.R. 2007. Host – Symbiont interactions of the primary endosymbiont of human head and body lice. FASEB 21(4):1058-1066.

Allen, J.M., Light, J.E, Perroti, M.A., Braig, H.E., and Reed, D.L. 2009. Mutational Meltdown in Primary Endosymbionts Selection Limits Muller’s Ratchet. PLoS ONE: 4(3):e4969doi:10.1371/journal.pone.0004969.

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