In the past, I have read many journal articles that describe research that happened several years before the paper was published. It used to make me wonder, what was the delay? Why did it take so long to go from collection to publication. As I go through my journey toward a PhD, I can finally say that I understand. There are many steps in the process. I'll try to walk you through them.
(1) Learn what you know and what you don't. There is no point in doing scientific research on a topic until you've figured out what has been done. Along the way, make note of things that maybe should have been done differently and thoughts on other questions that the prior studies bring to mind. These will be the basis for finding the niche of your work. As I get further in my career, I expect that this will take less time, unless the direction of the research takes a big turn.
(3) Processing samples can take a lot of time. Scientific knowledge is generally gained not one sample or site at a time, but hundreds of samples from dozens of sites at a time. Depending on the methods and equipment available, determining how much of a certain chemical is in a water sample can take several minutes per sample. So if you have 90 samples and are testing for 4 parameters that take about 5 minutes each, you are looking at about 30 hours of work, not including running controls, cleaning glassware, ensuring proper waste disposal, etc. In my experience, the most convincing studies have far more samples than this.
I am currently focused on sorting invertebrates from sediments in a set of samples collected using a Hess sampler. This process can take between from 2 to 20 hours per sample. Part of me wishes I had been tracking this so I could tell you how many hours have been spent on sorting, but I think I'm better off without this knowledge. Identifying the individual invertebrates to genus or species will take many more hours. Multiply these many hours by the number of sites and samples and invertebrates needed to reach an acceptable sample size and this can result in thousands of hours of work.
(4) Quality number crunching is vital for successful science. You know how I posted about the bajillion hours it takes to process the data needed for most good science? Well, nobody wants to look at all of that data until it is pared down to a few highly relevant numbers and a couple of figures and tables. Statistical analyses fit in here, too. Properly summarizing data into these smaller pieces is really a work of art when done well. When done poorly, it is a horror to behold. It takes time to reach the artistic stage and I don't claim to be there yet, but I think I'm beyond the nightmare stage.
(5) Writing is a process that is not for the faint of heart. There are many wonderful articles, blogs, Tweets, and other bits of wisdom that can be found on the internet or in your favorite bookstore about writing. There are strategies for making yourself start writing, for taking breaks when writing, and for knowing when its time to just stop writing. I don't feel the need to go into that here, because everyone writes differently and plenty of other people can provide far better insights than I.
(6) Still not done! So, you've written a manuscript chock full of references to the latest research, well-executed field collection and lab analysis, and artful statistics and figures. Says you... Now it is time to send it for review. Even on the most excellent papers, this process can add months to the time before publication. The editor must get the manuscript to reviewers. The reviewers must find time in their busy schedules to read and comment on the manuscript, the comments are compiled, and (unless the work is outright rejected) it is all placed back into the hands of the author for minor or major revisions. I've heard rumors of manuscripts being accepted the first time with no changes, but I have trouble believing that...
So, the process of taking a project from idea to publication can be lengthy. If this is the only thing a researcher has on their plate, then they are fortunate. Most researchers are balancing this process with teaching, networking, mentoring, grant-writing, collaborating, learning, presenting, doing other research, and (hopefully) living a life outside of their discipline. I am glad that I've been learning to juggle!
As you may know, I've been doing a lot of work at the microscope these past two months. I have been taking advantage of this time to catch up on some reading I've been wanting to do. You may be thinking, "Reading? At the microscope?!" Well, yes. I have been a fan of audio books for many years and have recently listened to a couple of classics: Mark Twain's "A Connecticut Yankee in King Arthur's Court" and Harriet Tubman's "Uncle Tom's Cabin." I recently expanded my audio enjoyment to a few news and science podcasts to brush up on world affairs and scientific happenings. As much of the science air-space was taken up with tributes to the 50th Anniversary of the Apollo 11 mission in July when I began listening, I went to some of the older material to start with. This is not to say that I dislike space science or that I have anything against that mission. I just wanted a little variety (though I admit that I did enjoy the bits I heard about human waste disposal in space).
One great thing about science podcasts is that you can start on any episode. If they do a good job of listing the topics in each, you can pick and choose anything in their archives, which is especially useful if you are caught up with all the the current offerings. Here are a few of my favorite science podcasts so far:
There is a lot of scientific work going on out there that I know nothing about. This includes work in urban streams (an area of expanding knowledge that I try to focus on), prairie restoration (an interest to me because of my work with the Missouri Botanical Garden), other biological areas of study where I have less experience (birds, microbes in the soil, mammals, genomics, the animal microbiome, etc.) and a wide array of scientific disciplines outside of biology that are too numerous to list. I am hopeful that listening to these podcasts will both inspire me to ask new questions and make me better informed about these disciplines that are complementary to my own.
If you have a favorite podcast, please tell us about it in the comments below!
This month the Knouft lab has been hosting Tony Dell, Ashley Olson, Maria Kuruvilla, and Andrew Berdahl who have been taking advantage of some of our under-utilized lab space. They represent a collaboration between NGRREC and the University of Washington (Seattle). It has been great to see the fascinating work they are doing!
These researchers are collaborating on a project to see how temperature impacts the behavior of fish that experience the appearance of an aggressor. In this case, the aggressor is a video played on a tablet. In this video, a small dot hovers in the middle of the screen. After a prescribed period of time, that dot grows larger, resembling an advancing predator. The response is video recorded, allowing the team to make very accurate measurements of parameters like time to response and distance moved.
The video below shows a demonstration of the predatory dot in action. The tablet at the top shows the dot which begins to grow at about 9 seconds into the video. See how these fish respond!
The team will be completing their work soon and will be returning to their respective homes. I have enjoyed the chance to see this study develop and will miss their enthusiasm and creativity.
Since the semester ended, I've spent a much larger portion of my time at the microscope sorting and identifying aquatic invertebrates. Here are a few photos of what I've been seeing in the microscope. With the exception on the scud (Gammarus minus), these are some of the animals I've not seen very often. Enjoy!
You may have noticed my absence from blogging in December (or, maybe not). I wish I could attribute this to an overwhelming abundance of festivities and merry-making, but that is not the case. Don't get me wrong, there were festivities, but that did not delay my blogging; it takes more than a few parties to keep me away from my adoring reader. (See you on Tuesday, mom!)
The Biology Department at Saint Louis University was displaced about 18 months ago by a fire. Nobody was hurt - unless you count the tears and heartache of years of lost work for some faculty and grad students. Anyway, we've been in temporary dwellings across campus while Macelwane Hall was repaired and renovated....until December. About half of the department, including yours truly, were moved back into the newly renovated space last month, so we spent the first part of December packing our desks and lab spaces. That, and running one last toxicity experiment before the upheaval.
Megan and I finished the last of our packing and prepared to take a last look to make sure everything was properly labeled for the move. Fortunately, we were only responsible for the packing and unpacking (still to come). A couple of companies were hired to actually move the boxes and furniture from place to place.
Our newly renovated biology building is fantastic! Well, it will be when they finish getting the kinks out. My shared office space has no functioning outlets, the air lines and water treatment system for the aquatics lab are not installed yet, and the shelving units in the lab are missing some parts. While we wait for the details to come together, I've been fairly productive in my temporary home office. I have to share the space (see photo), but my table-mate is generally quiet and well-behaved (although at the moment she is playing with a bit of caulk she removed from the bathroom, but that's another story).
But the new building... when it is done, it will be great!! There is a lot of natural lighting on the three upper floors and even in the windowless basement, the fixtures make it feel like daylight. The lab space for our group is bigger than before with separate spaces for our GIS work and wet-lab efforts. The aquatics lab has a huge sink with an industrial sprayer and will be equipped with a high-quality water filtration system. The mud room for our field gear is spacious and has room to both clean and store gear. There is a new space for biological collections, something that was distinctly lacking before. The graduate student offices are near their labs (often with windows into the lab space) and are equipped with printers, refrigerators, and (coming soon) coffee makers. All in all, it is a state-of-the-art building that will serve the department well in the coming years. I can't wait to tell you all about it!
The lab I work in has been a very busy place for the past few weeks, especially for my lab-mate, Megan Pagliaro. She is studying how fish from streams and lakes respond to long-term increases in water temperatures. The expectation or hypothesis is that fish living in places where summer water temperature is warmer will be able to survive higher peak temperatures better than fish from places where where summer temperatures are more moderate. This is kind of like saying that someone from Oregon will be better suited to a Texas summer than someone from Alaska. Megan is using the existence of the urban heat island effect in St. Louis as the source of the temperature difference.
Over the summer, Megan captured fish from sites in about 16 lakes and 14 streams. Each of these sites has also been home to a temperature logger that has recorded hourly temperatures. The expectation is that the lakes and streams that are closer to the city will generally be warmer than those that are farther from the city; factors like lake size and the presence of springs in some streams may influence the water temperature and mute the urban heat island effect. The data from the temperature loggers will help Megan place the sites on the heat island temperature gradient and relate the fish responses to the actual conditions in their home waters.
So how does one go about testing the temperature tolerance of the fish? With a test of the Critical Thermal Maximum (or CTMax). I can share the basics of how Megan did it. First, she acclimated all of the fish to the same moderate temperature. Then she put some of them (11 or 12 at a time) in individual small containers in an aquarium so that all of the fish in the aquarium would experience the same rate of temperature change. Water was pumped through a heater and back into the aquarium to gradually increase the temperature. She would then watch the fish until they experienced a loss of equilibrium (this means that they couldn't stay right-side-up anymore). The temperature when each fish lost equilibrium is the CTMax for that fish. Megan then repeated the test on additional groups of fish. Each test took 2-3 hours, so this process went on for a couple of days.
Megan just collected the last of the dataloggers from the lakes last week and some of the ones in streams are still in the field. I hope to share her results in the future, so be sure to check back in the coming months!