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Posts from ‘Alexis Carlson’


New Year, More Mushrooms!

You know that feeling you get when you’re in the middle of some much-needed spring cleaning and throw something away and you all of a sudden get a bad feeling about it, but it’s already in the trash bag and partially contaminated with horrible things you left in the fridge over the holidays? I do. Luckily that thing I shouldn’t have thrown away had a twin hidden in the back of a very tall awkward fabric covered growing tent.

But let me back up for a second. This is a mushroom called Lentinus tigrinus. It normally has gills (a form we refer to as agaricoid) but they can also be covered or reduced (a form we refer to as secotioid).

Agaricoid form of Lentinus tigrinus

Secotioid form of Lentinus tigrinus


The past couple of months I’ve been fruiting both types in the lab. Usually the mushrooms look like the previous two photos, but every once in a while I’d get something really funky that looked like it belonged on an alien planet or growing out of zombie that fell into a vat of toxic waste. Anyways, one day I was cleaning off some shelf space, which I try to do regularly to keep the hoarder in me at bay, and I found this odd thing.

Coralloid form of L. tigrinus

Turns out L. tigrinus produces not only an agaricoid and secotioid form but a coralloid form as well! This semester I’m going to be working on replicating this coralloid morphology in order to understand the developmental norms within L. tigrinus, which I’m sure has many more surprises in store for me.


NAMA Foray Magic

Instead of spending finals week piled under review sheets, flash cards and empty coffee cups I attended the North American Mycological Association’s annual foray in Scotts Valley, California. I had never been to Santa Cruz before and was totally and completely blown away. After getting a quick naturalist’s introduction to Santa Cruz I was off with my fellow lab members to explore the redwoods. Here are some photos (there would have been more but everyone’s hands were busy trying to balance collection bags):

Rachael Martin and I at Henry Cowell Redwoods State Park


A mushroom that grows on Rock!

My first find of the day!

Sorting out the collections.


Fall Fest here I come!

With the summer over and my project completed I’ll be spending the next few weeks wrapping up loose ends and putting together a poster for Fall Fest. I want to make sure that I present my research clearly and effectively so I’ll be revising the poster I created for the conference I attended in July. I am planning on having both posters up next to each other so that people can see how the same information can be presented in radically different ways. Lucky for me I will be attending a LEEP workshop this tuesday that will focus on creative communication. I already have a few ideas for the new version of my poster but definitely need to get some feedback before I charge ahead!



Day Two

Today was our second day collecting and after bringing back several duffle bags worth of species the day before, we decided to slow down a bit and limit ourselves to only a few duffle bags. We spent most of our time exploring sites with old growth – we went pretty deep into the forest and I have a terrible sense of direction so I stayed in the middle of our pack for most of the walk (I also have a pretty rotten sense of balance and had a couple of close calls hopping over streams and climbing over rocks). We made a lot of good finds, including 3 more Cordyceps (which are my new favorite fungi). Someone needs to make a horror movie starring them because they are just down right creepy.

Me with a mushroom tiara

Frog friend


Scutellinia - also known as the eyelash fungus

Ramaria sp.



Day One

Rich Lake

Day one in the Adirondacks was amazing! The drive was ridiculously long, but with lots of good music and snacks we managed to make it in one piece. As soon as we arrived at the Adirondack Ecological Center we met with one of the centers directors who showed us to our lab space and sleeping quarters. Once we settled in we took a walk around the property and were pleasantly surprised to find that Rich Lake was only a 2-minute walk from our cabins! The view from the beach was spectacular, and I practically had to be dragged away for dinner (we went back for a swim later though!). Today was our first day out collecting – we hit 2 sites within the Huntington Wildlife Forest and spent about 6 hours out. Once it started getting dark it was time to head back to the lab to sort everything out. As you can see we had quite a lot to work with!


Mycena leaiana

Mycena leaiana

The unloading table

Busy mycologists

Cordycep sp.

Of all the fungi we collected, my absolute favorite was a Cordycep, which I found at the 1st site we visited. Cordyceps are parasitic ascomycetes. The species that I found had parasitized an insect pupae. I had never seen one before and almost tore the mummified body of the host off because I thought it was a pinecone!



Off to the Adirondacks

This week I’ll be going to the Adirondacks with my lab to collect. We will be staying at the Adirondack Ecological Center, which is located in northern New York. I have never been to the Adirondacks and am extremely excited to explore! Last week I went shopping for field pants and boots, because lets face it, sweatpants and converse just won’t do! Now I just have to practice walking in my new hiking boots… wouldn’t want to fall off a mountain on my first Adirondack excursion.


A Busy Month

Yikes! July has been quite a month. Last week I attended the annual meeting of the Mycological Society of America, which was held in New Haven at Yale. I spent the first two weeks of July sketching out poster ideas and trying to create an eye catching layout (which for me is not easy, I am a terrible decision maker – it takes me 20 minutes just to decide between wearing black or dark grey flip flops). Anyways, the first drafts I made were far too complicated and busy, but after a couple of late nights and some feedback I managed to decide on a design. My poster was on the work that I have been doing with Alfredo Justo on the PolyPEET project. We worked with a genus of mushrooming forming fungi called Trametes (which is my favorite fungal genus, although I may just be partial to it because I work with it). If you hike, or walk a lot in woody areas you have probably seen Trametes versicolor, commonly known as turkey tail.

Trametes versicolor

Even though Trametes is extremely well known, its species level relationships remain largely unresolved. Relationships can be resolved by creating phylogenies, trees that help us visualize the evolutionary relationships between species. Phylogenies can be constructed using morphological or molecular data. The phylogenetic study that I worked on was based primarily on sequence data; however, the molecular marker most often used to separate species and clarify boundaries (ITS), did not have enough variation and resulted in an extremely uninformative tree. So for the past year, I have been working with three protein-coding genes (RBP1, RPB2 and TEF1), to see if they were able to provide better resolution within the phylogeny. The results suggest that all three of the protein-coding genes out perform ITS in determining species level relationships.

The conference started on Sunday the 15th of July. I arrived in the afternoon and spent a few hours walking around New Haven and marking down the locations of all the nearby coffee shops on my map. At 6 there was a mixer/reception at the Peabody Museum. It was raining pretty hard when I started walking over which was a shame, especially since it was a 15-minute walk from the dorm I was staying in (but who could turn down free food and drinks, not me that’s for sure). It was really great to have a chance to meet people before all the oral sessions and symposiums began the next day. Monday morning and afternoon were filled with presentations at various locations, one of which was given by a fellow lab member (Dimitrios Floudas). The presentations were fantastic (as was the air conditioning in the lecture halls, New Haven was lovely, but boy was it hot!). Anyways, each presenter had 15 minutes (12 for talking, 3 for taking questions) to speak.

Later that night was the poster session! I was scheduled for the second session (9-10pm) and was extremely nervous. It didn’t help that I had gotten sushi for dinner – stinky breath paranoia and all. I was really anxious all throughout the first session, it seemed like everyone around me had a Ph.D (or was in the process of getting a Ph.D) – I felt like a very small goldfish in a tank of big exotic fish. When my session finally started I couldn’t decide if the feeling in my stomach was good nervous or bad, throw up in the middle of the walkway nervous (thankfully it was not the latter). At first no one came by my poster and I couldn’t decide if I should be thrilled or depressed, but as people worked their way through the room a few people begun stopping and looking at my poster. I fumbled a bit with the first person who stopped by and asked me questions (stuttering, awkwardly twisting my hands behind my back and smiling like a weenie), but by the third or fourth person I had it down. Most people looked at the pictures of Trametes on the right side of my poster first, so I started most of my conversations laying out the broader picture and then moving people over to the phylogenies. I tried to keep reminding myself that less is more and not get too carried away with explaining all the details, but once I had built up my confidence it was hard to stop!

Me grinning like a fool at the poster session


A World of Scientists

Google the word scientist and somewhere in the definition is the word “expert”. There seems to be this ridiculous idea that all scientists are stowed away in crowded laboratories mixing flasks of brightly colored liquid or poking at oddly shaped creatures. Absolutely absurd is what that is, because everyone (you, me, your mother, my mother, the mailman, your 6th grade history teacher, even the president) is a scientist. Whether you are connecting the dots of the fungal tree of life or figuring out who is really sneaking money under your pillow when you loose a tooth, you are using some part of the scientific method.

We use science to discover new things about the world around us. It is a social endeavor that unites us, so even though we may come from different political, socioeconomic and geographical locations, science itself can be used as a means of communication.

But not all of our inner scientists get the nurturing they need. Fear not though, this isn’t one of the cases where if you don’t use it you loose it. The scientist within all of us never slips away. Though in some it may prefer to travel under the grid until it is adequately stimulated. But these days, making sure your inner scientist is up, dressed and ready for anything is more important than ever. Politicians love to twist and obscure scientific findings, which is why it is essential to be able to comprehend primary scientific sources. If we are to make informed decisions about natural world endeavors and ourselves then we must understand the science behind them.

One of the reasons I am so interested in the different ways that science can be communicated is that I will soon have to present research that I am finishing up here at Clark in the Hibbett Lab. Last summer I began working as a research assistant for post doc Alfredo Justo on the NSF supported PolyPEET project. I will explain the project in more detail in a later post, but the goal of the project is to study the taxonomy and evolution of a subset of fungi called the Polyporales.

I usually practice all of my presentations for class on my roommates, which is fun and relaxing, but can sometimes be a pain because I have to explain lots of background information. When I try to explain what I am working on in the lab it gets even trickier because I can never quite do justice to how exciting the project is. For me the excitement of PolyPEET is obvious, it is with me every step of the way. For outsiders it is not so accessible.

I’ve just started reading three books to help me learn how to communicate my research more effectively. The books include: “am I making myself clear? A scientist’s guide to talking to the public” by Cornelia Dean, “Ideas into Words” by Elise Hancock, and “Escape from the Ivory Tower: A Guide to Making Your Science Matter” by Nancy Baron. Hopefully these books will help me increase my proficiency as a storyteller of science in time for the MSA’s annual meeting, where I will be presenting my research.



What is Science?

What Is Science? Seems like an easy question right? Wrong. The quest to successfully define a demarcation criterion that separates science from pseudoscience has been a long and relatively unfruitful one. Individuals like Karl Popper, Imre Lakatos, Paul Thagard, Thomas Kuhn and many others spent their entire lives working within the philosophy of science trying to unveil the answer. And while many of them have thoroughly compelling arguments, getting scientists, philosophers of science and other individuals to agree has proven almost impossible.

So what do we know? For starters, science is an empirical enterprise, it seeks to observe, identify and describe the natural world in order to learn more about it. While some disciplines rely on the abstract, science is based solely on direct observation (each observation has the power to radically alter our understanding). As a result, its body of knowledge is constantly evolving and scientific information and theories are always open to revision in light of new evidence.

At this point you may be wondering why it really matters whether or not we have a logical and concrete demarcation criterion. It matters because we don’t want to end up in a world where mycology and rumpology are receiving similar amounts of research funding.

So to really understand how science differs from other types of alleged knowledge you must take a much closer look at some of the characteristics of its practice. Characteristics that define its practice include: testability, falsifiability, progressiveness, a systematic organization of theories, laws and evidence into research programmes and guidance by natural law (quite a mouthful huh?). And while science is primarily based on evidence and not values, there are a lot of values in science just as there is a lot of science in values. This is not to say that all science and scientific knowledge have this specific set of conditions, but rather that genuine sciences tend to have most of them, while pseudoscientific endeavors seem to lack almost all of them (for some funny examples check out Aqua Mantra, Quantum Jumping and Sacred Geometry). And yet in spite of this, producing a clear and justifiable definition of what science is and what it is not continues to be somewhat problematic. This is because the terms we use to describe and characterize it can mean different things to different people and because scientific knowledge does not always progress and grow in the same way. What is clear is that there seem to be a common set of themes within science and that we somehow know it when we see it (or we at least mostly know).


Pushing the Limits on Communicating Extraordinary Science

But why is your research so important? Gah. Where to begin? How to begin? To some science students such a question is met with discomfort, agitation, and sound effects usually reserved for the moment one finds out a paper is due at the end of a long weekend. The point is, being able to clearly articulate what your research is without causing eyes to glaze is no easy feat. It is however, essential if we want to maintain widespread public support and increase scientific literacy within our communities. Science and the knowledge that comes with it allows us to understand and describe the natural world and to make informed decisions. The problem is that this knowledge is so often so wrapped up in background information and buried beneath heavy layers of complex and abstract terminology that getting to it seems almost impossible. Scientific knowledge is a social knowledge, and in order for it to be used as a resource it must be presented to the public in a language that they can understand.

That is why it is so important to train scientists to be effective communicators, and not just with words, but with graphics, photographs, video and more (for some great film examples check out the Sagan and Feynman series).

Last semester I was fortunate enough to attend a talk given by Chris Linder, an oceanographer and photographer who communicates science through photography as a way to educate individuals about conservation issues. I was completely and utterly blown away by his photographs and how well they captured the essence of the research he was documenting. His presentation wasn’t just informative it was inspiring. It was the type of presentation that makes people want become scientifically literate, to become informed, to ask questions.

This summer I will be looking at the issues surrounding effective communication of scientific research. I am going to be working in the Hibbett Lab here at Clark and will be using my research to communicate what science is and how to best present it to different types of audiences.



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