The importance of the first page, or judging a book by its cover

http://www.phdcomics.com/comics/archive.php?comicid=1531

This blog post has been a long time coming (just realized last post was in August!) and it will be obvious why I’ve been lax writing here. I am at the point in my PhD where I not only need to be frantically doing lab work, analyses, and writing for my dissertation, but also writing and applying for grants, fellowships, and advertized post-doc positions so I can be employed after I graduate. This is both exciting and frustrating at times. With my first big grant proposal turned in this week, I finally have the time to write down some of the things I’ve been thinking about in terms of writing a good grant, and maybe get this online to help those of you writing DDIGs, NSF Pre-docs and other grants due in this fall’s grant cycle. You can of course take any of my advice with a grain of salt, these are just some broad ideas that have been useful for me and you may be advised otherwise..

The whole time I was writing the thing going through my head over and over was “the first page is so important, got to hook ‘em in the first page.” One of the things learned in my first semester when I was writing my first NSF grant (thanks, Spencer!) was that you need to basically say everything that a reviewer needs to assess your project in the first page. These people read tons of proposals during these review panels and if they haven’t been convinced your project is worth funding after the first page, it is going to be tough to convince them in the subsequent pages. For example, anyone who has graded a lab report knows that you can tell if the student knows what they’re talking about after you’ve finished reading their first page, sometimes the first paragraph. I think this must be similar to how it is reading these proposals, although this time with a much higher bar than what we expect for undergrads, hopefully.

You should be able to describe what are the big questions you want to address, why does it matter, and how you are going to accomplish it, within the first page of the proposal, with the rest of the document following up on the details that will probably just confirm that you are capable of actually doing what you propose.

The first paragraph should state clearly what the big issue, knowledge gap, or question in your field is that needs attention. Here it is important to remember that an issue that may be obviously interesting or important to you or someone in your immediate field. You are likely (probably 100% likely) to have a reviewer that is outside of your discipline a bit, and that you will need to make this issue relatable to someone who hasn’t read all the papers you’ve read, etc. For instance, why should a plant-fungal ecologist or climate modeler think my project investigating co-infection patterns and immune function in rodents is important? Even better, if you can describe how your work will influence people outside the scientific community (remember those “broader impacts”) that would make this first paragraph even stronger. Using some well-placed references in this section can help make your argument stronger.

Shortly after the first or second paragraphs you should directly state what your research questions/hypotheses followed by a brief description of how the proposed project is an innovative way to answer these questions. You need to convince the reviewer that what you want to do is new and exciting enough that it is worth funding. You do not need to go through every detail of the proposed methods, but you should mentioning the general plan so they know you have thought out how you are going to accomplish what you propose. Also, if you are good at summarizing your methods in a way that is clear for an expert and a non-expert, you are probably going to have a good complete description later in the proposal. This will also make the reviewer want to keep reading and be interested in learning more about this super-awesome project you just introduced them to. Mentioning previous experience that will make you the best person to successfully accomplish your project could also be beneficial here.

One thing to remember as you are figuring out the best ways to get your ideas out on paper is that they are not only funding your project, they are funding you as a scientist (thanks to friend and former IU EEB student Britt for reminding me of this). They want to see in your proposal that you are thinking about your research in an interesting and innovative way. The NSF loves things that are “transformative” and “interdisciplinary” and it doesn’t hurt to use those buzz-words strategically if you think your research in fact is. What I think is exciting is when someone takes old/established ideas and integrates them with new methods and findings that somehow makes a complex problem seem simpler or more tractable. Go figure, I am a disease ecologist and I think it’s totally awesome when theories describing population or community dynamics that have been around for the last 40-50 years overlay onto disease systems and perfectly (or close to perfect) illustrate host-parasite interactions.

When I was writing my NSF proposal it was kind of exhilarating, scientifically, to get out my community ecology notebook, check out Jared Diamond’s book on community assembly from the library, and refresh my memory on some hard core ecology theory, and see how these concepts I had learned about when I started grad school I could now see through my host-parasite lens. These moments remind me that I am doing what I want to do, that I think my research is important, and that all the pain and stress is worth it (hopefully).

Also, go through as many drafts as possible with your advisor, lab-mates, and other science friends as you can. But, also know when it is time to stop editing and let it be. This will probably happen the day before the deadline. I did some last-minute editing the day-of this time, and I’m not sure if it was the greatest idea. If you have worked hard on it, it is probably in great shape the couple days before the deadline and anything you turn in would be a good representation of what you want to do.

I hope this is helpful to anyone going through this process right now. However, this will probably make any non-academics reading this happy they don’t have to sing for their supper continually. I have to keep thinking this process is making me a better writer, communicator, and scientist and that it pays off when I graduate and become a more independent scientist. Fingers crossed for funding for me, and you too! 

Science on the move, again!

The summer is (sadly) coming to a close, which means its time for ESA, the Ecological Society of America conference. This is a huge meeting, around 3,000-4,000 people attend, from all kind of ecology. Going to conferences in an integral part of being a scientist because this is where you hear about the newest stuff going on in the field and get to talk to people about your and their science, hear about new methods and research projects you may have never known about before. This meeting consists of talks and posters and the meeting lasts a whole week. This meeting always takes place is huge conference centers and there are tons of sessions going on at the same time and you have to do some homework with the program to figure out what you want to see and when. Because this meeting is so big students have the opportunity to present their research when there may not be as much opportunity at smaller meetings.

This meeting can be overwhelming to some, especially if you are a plant ecologist and there are tons of overlapping sessions with talks you want to see, but I really enjoyed my first attendance last year. The disease community is still small enough that there is usually only one, sometimes two, concurrent sessions with disease ecology talks and most of the people I see at this meeting I’ve met before, so its another opportunity to see friends and hear talks from more people than there is room for at EEID. Also, since very few people get talks at EEID and even fewer grad students, this is the only national meeting I will give a talk at this year.

I will be giving a talk on the data I collected in last year’s field season on patterns of tick burden and immune function within individuals over time, trying to address the questions: “Are some hosts consistently more parasitized than others?”, and “Is there a relationship between host’s tick burdens and innate immune function?”. I have some top professors in the field giving talks in the same session as me, which is both awesome and a little terrifying.  I need to keep telling myself that I am the one that knows my data the best and I just need to tell everyone a good story about it. Hopefully the nerves will stay under control, I can get way more nervous than I expect at these things.

The meeting this year is in Portland, OR which I am super excited about. Last year it was in Austin, TX, which is a great city, but it is f-ing hot there in August! Portland may be a little warm for them now, but I think it will still be a pleasant chance of scenery. I have heard nothing but great things about the city. Plus, they are a great beer town so I am sure there will be plenty of mixing beer and science, which is one of main point of going to these things.

I plan on updating my Tumblr account with pictures and thoughts from the meeting, since it is a little easier than uploading directly to the blog. So, subscribe to my page if you want to see updates. The hashtag #ESA2012 is being used by tons of people who will be posting stuff about the meeting. I am always optimistic about mobile blogging and such from these meetings, but I always seem to end up having way too much fun actually being there to talk about it online. We’ll see what happens this year. I leave tomorrow at 6:00am (yikes!) but am very excited to present my research and get tapped into the disease ecology world once more before the fall semester starts.

Chiggers: making field work less fun since…forever!

I got a request to do a blog post on chiggers from a Bloomington community member, James, when he came to talk to me at a nature outreach table I did in collaboration with my friend who is an environmental educator for the Bloomington Parks and Rec Department at our local farmer’s market a couple Saturdays ago. I figured, why not!

Anyone who has done field work in Indiana and other places in the more southern US have experienced them and their terribly itchy, lingering bites. They always seem to be in those places where you never want bites, like under your arms and along the waistband of your pants and other places where your clothes are up close to your skin. You never seems to get the bites until the day after you’ve been outside, which is quite annoying, and sometimes you get more bites even though you haven’t been outside again. These bites also stay itchy for way longer than mosquito or tick bites, and itch a lot more, so really the worst kind of bites.

Some of the questions James asked me where, what are chiggers exactly? Can you see them? What causes these bites?  Is there a way to get rid of them or prevent being bitten? These are all great questions and there are a lot of misconceptions about them too, which I will try to address too.

Chiggers are the larval stage of a trombucid mite, sometimes called “red bugs.” The nymph and adult stages eat plant material and do not interact with host animals. The larvae are very small and are difficult to see with the naked eye. One of my lab-mates did see one crawling on her leg and scraped it off onto a microscope slide and then we could look at it under a microscope. This was the first time I actually saw a chigger, it looked very similar to the picture above.

Unlike ticks, these mite larvae feed on the skin cells of their hosts. They use their mouthparts to burrow into the skin of the host and uses a specialized enzyme to liquefy the outer layer of skin so it can be ingested, creating a stylostome (kind of a tube into the host’s skin). This is probably why the bites are sooo itchy and stick around for a long time, because there is more damage or manipulation of the host skin, as opposed to insertion of the mouthparts of a tick or mosquito. The bites also look like they have a red dot in the center, which is the stylostome, and sometimes the mite itself. The host’s immune response to the chigger saliva and to the bite that can cause irritation too, which is similar to other ectoparasite bites. The bites usually form after the mite has extracted itself from the stylostome. However, if the chiggers aren’t washed off the skin they can move around and create more bites even after you come back from being outside. Some people say putting nail polish on the bites will suffocate the mite and kill it, since they are still inside the bites when they appear. This might work to stop them itching, or stop you itching them, but since most of the mites would have removed themselves before you see the bites it won’t kill them.

The places that are usually the worst for chigger bites are scrubby areas with a lot of grassy or brushy vegetation. The old-wives-tale is that blackberry patches are the worst for chiggers, which is kind of true, and this may be because blackberry bushes provide good habitat for animals like mice and rabbits that chiggers use for hosts. A traditional preventative measure against chiggers is to put sulfur power into something like an old sock and sprinkle it around your wrists and ankles. The chiggers don’t like the taste or smell of the sulfur and are deterred from biting. This works pretty well, and a Bloomington soap maker makes a soup that has sulfur inside it, which is a must for people who do field work. This soap doesn’t make you reek like rotten eggs, you can smell it if you put your nose up next to your skin, but it does do a pretty good job of at least reducing the number of chigger bites you’ll get. My same lab-mate that put the chigger on the microscope slide did a little experiment with this soap. Half of her field crew used the soap before field work and half didn’t, and the ones that used the soap had many fewer bites. That’s good enough for me, and I stock up on this soap before each field season! Taking a shower as soon as you come back from being outside and scrubbing hard with something scratchy, like a brush or a luffa, can help scrape off any chiggers that are still on your skin. Chiggers can hang out on your clothes too, so putting them in the freezer for 24 hours or washing them on hot can kill them.

So, while chiggers are related to ticks, they are the larval stage of a mite and do not suck blood. Most chiggers don’t transmit any diseases because they don’t come into contact with the hosts’s blood (some chigger species in southeast Asia can be disease vectors, but none are in North America). We sometimes find them on our rodents. There probably isn’t a way to avoid getting any bites, but you can do a few things to prevent them. Hopefully this comes soon enough for some of you to reduce any painful side-effects of spending time in the great outdoors!

Some of my sources, in addition to talking to some of the local ectoparasite experts over the years:

http://en.wikipedia.org/wiki/Trombiculidae#cite_note-url-14

http://science.howstuffworks.com/environmental/life/zoology/insects-arachnids/chigger3.htm

Its summer, off to the races!

The spring semester has ended again and its time for the summer, when those of us who teach during the school year get the majority of our work done. It is also time for summer traveling, sometimes for fun but definitely for work.

I am attending the Ecology and Evolution of Infectious Disease conference and workshop this year in Ann Arbor, MI and am excited to geek-out about parasites and disease ecology. Because I am the only person studying disease ecology in mammals and ticks at IU right now, these meetings are always fun because I get to talk to other researchers who work on similar systems. This meeting is also relatively small, which means you can get face-time with “famous” professors, and get to meet a lot of really awesome students from all over.

This summer’s meetings have a bit more pressure than usual. I am hoping to graduate next spring or summer, so this summer my job is to talk to possible post-doc advisors and give people a face to put with my name if I show up on any of their job searches. I hope I can wow them with what I have been doing for the last few years and talk about possible future collaborations and projects.

I will be mobile-blogging while I am away, mainly through Tumblr I think, but I will try to have posts copy to my blog here as well. Also, International Towel Day is in a week and will happen while at the meeting, so I hope to post some Douglas Adams homages while away.

Happy spring!

We are history!

I haven’t been able to write the blog for a good while now, research and other things keep getting in the way even when I think about topics I’d like to discuss and write about. But, I have something I don’t really think needs a lot of up-front writing or analysis from me, just maybe some prompting to muse and think.

I have been listening (for the 3^rd time or so) to the audiobook of Terry Pratchett’s book A Hat Full of Sky, the second book in the Tiffany Aching series. These may be my favorite books that he’s written and I love them every time I hear/read them. I have been thinking about the excerpt below quite a bit lately. I’ve been teaching a vertebrate zoology lab this semester, so I have been thinking about phylogeny and evolution more than usual, so I’m sure that’s one reason. But also I was just thinking about how beautifully this section describes what is means to be human in a greater biological context, considering the remarkable history of life on earth and the ways that humans are different from other animals. And while we are always being reminded about how much trouble and damage humans cause the world and the other organisms we share the earth with (as being something that really does set humans apart from other living things), this is one of those passages that reminds me of the why humans are special, in spite of how extremely similar we are to other living things, there are some vastly important differences that have led to us being who we are.

So, take a minute to read this passage and see what it makes you think about. After Douglas Adams in Dirk Gently’s Holistic Detective Agency, writing about Bach being the music of the world and the “fundamental interconnectedness of all things,” this is one of my favorite excerpts about the wonder of the natural world. Let me know what your thoughts are, I would love to hear them! And pick up one, or I would recommend many, of Terry Pratchett’s books if you haven’t already done so!

(a bit of context: Tiffany is talking to a “hiver,” which is an entity that takes over the bodies of animals or people, and then “becomes” everything its ever taken over, and almost always kills whatever it is embodying. So, the hiver has all the memories and experiences of every animal or person it has ever been. It cannot think of itself as “I” or one living thing, because it is everything all at once. It cannot figure out how to die, to stop killing things, because it doesn’t know what it is.)

“Here is a story to believe,” she said. “Once we were blobs in the sea, and then fishes, and then lizards and rats, and then monkeys, and hundreds of things in between. This hand was once a fin, this hand once had claws! In my human mouth I have the pointy teeth of a wolf and the chisel teeth of a rabbit and the grinding teeth of a cow! Our blood is as salty as the sea we used to live in! When we’re frightened, the hair on our skins stands up, just like when we had fur. We are history! Everything we’ve ever been on the way to becoming us, we still are…I’m made up of the memories of my parents and grandparents, all my ancestors. They’re in the way I look, in the color of my hair. And I’m made up of everyone I’ve ever met who’s chanced the way I think. So who is ‘me’?”

“The piece that just told us that story,” said the hiver. “The piece that’s truly you.”

“Well…yes. But you must have that too. You know you say you’re ‘us’—who is saying that? Who is saying you’re not you? You’re not different from us, we’re just much better at forgetting. And we know when not to listen to the monkey.”

“You just puzzled us,” said the hiver.

“The old bit of our brains that wants to be head monkey, and attacks when its surprised,” said Tiffany. “It reacts. It doesn’t think. Being human is know when not to be the monkey or the lizard or any of those other old echoes. But when you take people over, you silence the human part. You listen to the monkey. The monkey doesn’t know what it needs, only what it wants.”

-Terry Pratchett, A Hat Full of Sky, p. 240-241

(http://books.google.com/books/about/A_hat_full_of_sky.html?id=dmc3CVG-aqgC)

I *heart* Data

PhD comics never fails to have an appropriate image. (http://www.phdcomics.com/store/mojostore.php?_=view&ProductID=12631)

 A while back I said I would discuss what “comes next” after all the field work. Well, I have started the next big project: identifying all the ticks I collected from the mice and voles we trapped over the summer. This is a big project because I collected over 670 ticks, and these are larvae and nymphs, the younger life-stages of the tick, and are really small and can only be identified under a dissecting microscope. It is important to identify all these ticks to species and life-stage because there are different assumptions about previous host interactions and possible infections for each group. To catch everyone up, here is some background before we get too deep into things.

This is a diagram of the Ixodes scapularis lifecycle. It is a "cool season" tick because its adults are active in the fall. Most of the ticks in Indaina have all life-stages active in the spring and summer.

To review, ticks are ectoparasites of vertebrates that have a 4-stage life cycle: egg, larva, nymph, and adult. These parasites need to bite a host and obtain a blood meal in order to molt and transition to the next life-stage. This is somewhat unique because other common vectors like fleas and mosquitoes only feed on a host directly in the adult stage. This means ticks can have many interactions with host over their lifetime and have the opportunity to become infected or pass on infection many times. The larvae emerge from eggs uninfected, besides obligate bacterial symbionts, so the larva can pick up a pathogen infection during their first blood meal. When these larvae molt into nymphs they become infected with whatever bacteria was picked up during the previous blood meal and can transmit to an uninfected host. This same thing can happen with adult ticks, but they have had two possible times to pick up an infection. The adult female ticks then feed to produce eggs, the males mate with the females during this blood meal and they rarely feed themselves. Then the females drop of the host and lay thousands of eggs in a “mass”. The larvae then emerge in the spring and the cycle starts all over again.

Mouse with a lot of engorged nymphs on its back.

The rodent hosts that I am interested can be hosts to the larval and nymphal stages. In the part of southern Indiana where I conducted these surveys have three main species of tick, but only two have been found using rodents as hosts, Ixodes scapularis (blacklegged deer tick) and Dermacentor variabilis (American dog tick). The main character that differentiates larvae from nymphs is that larvae have 6 legs while nymphs have 8 legs (as well as the adults). Each species has some unique features that I use to discern between the two.

My lab bench

The tools I use when identifying ticks are a dissecting microscope, this is a microscope that doesn’t need a specimen to be prepared on a slide. It used an external light source to illuminate a whole sample. I manipulate the ticks mainly with a paintbrush. This is a common tool for people who handle fragile invertebrates in the lab because it can move and stick to the specimen but won’t accidentally damage it like a normal pair of forceps. There are also “soft” forceps that are made from a flexible metal that are useful for samples that are too heavy for the paintbrush to grab on to. I covered my whole bench in white bench paper. This helps keep my workspace clean, and if any ticks fall or get dropped they will show up better on the light background. My scope to chair hight ratio is still off a bit, the chair is too high so I have to hunch to look into the dissecting scope, which can be a little painful after a long time. I’m going to have to figure out the best solution to this problem (a shorter chair or raising up the scope on a platform or something).

Dermacentor is the most common tick we’ve found on the rodents, from our previous surveys and from the data I’ve collected from this past year so far. Its mouthparts are somewhat rounded, the body and legs are a light brown color, and the shield on the back (dorsal) side comes away from the body in a straight line.

Ixodes seems to be somewhat less common on these hosts, but still very present. This is of particular interest to many because this species can carry Borrelia burgdorferi, the bacteria that causes Lyme disease. These ticks have longer, straighter mouthparts, are usually darker, blacker in color (the legs in particular, especially in the larvae), and the shield is rounded all the way around. The picture I have below compares a nymph from each species. See if you can see some of the differences I listed.

These little rodents are kind of teeming with parasites, and ticks are the only ectoparasites I collected from them. Fleas and mites were fairly common, but are harder to collect because they don’t attach to the host so they are freely moving through the host’s hair and around the body while you are trying to grab them with forceps. These parasites are important because they can also carry pathogens that can infect wildlife and humans (remember theplague post?). Analyzing the blood samples we collected in 2009 showed that many hosts are infected with Bartonella, a flea-borne pathogen, so fleas may be really important in this disease community.

Flea from a mouse, most likely Orchopeas leucopus.

Fleas and mites look really different from ticks and each other. I know fewer details about these creatures, but I do know they look pretty nasty. Fleas are covered in these little hairs which make them really sticky to the host fur (and hard to handle with the paintbrush, my usual tool for this). They look like they're "swimming" through the hair when you see them on a host, its pretty crazy.

I couldn't get the whole mite in focus at once. The left picture shows its arms in focus, while the right picture shows the little hairs that cover its back.

I think mites look like little monsters with their front set of legs reaching above their head. I’m sure many of you think these guys all look like monsters, but I get so used to looking at ticks I’m not phased by them anymore (what a strange state to be in, huh?).

If I haven't completely grossed you out with this post, stay tuned for more on parasites!