30 January 2013



Vote for me, a 5 for me, please for me, Japan for me!!!

It's a Threadless contest where the grand prize is a trip to Japan! Runners up get their t-shirts printed.

My idea is a meeting of mythological creatures - the kitsune (or foxes) in Japan and Bigfoot from America. Bigfoot some how ends up in strange territory and we all know how shy he is, especially when the kitsune light up their foxfires!!

I was inspired by Hiroshige's classic woodblock print called "Fox Fires on New Year's Eve at the Garment Nettle Tree at Oji". I originally drew Bigfoot in a more comic book style, but he's much cuter this way!

29 January 2013

お酒 と きつね!

O-sake and kitsune, that is!

My nascent sake smells amazing and the weather is cooperating, giving us below freezing temps here in CO. Of course, the sake doesn't want to be that cold, but it helps to keep the closet where the sake lives nice and chilly- between 45 and 50, preferably. Luckily, my apt has cinderblock walls, so the chilly air gets in nicely. You might think its odd that I saw "luckily" with regards to my leaky apartment, but in the case of making sake, it is very lucky! I guess you could say that if I had a less leaky apartment, I could spend the extra money I save on the electric bill on store-bought sake, but that's no fun, now is it? Tomorrow begins the preparation for the もろみ Moromi or "dancing ferment".

On the other hand, the ales I'm making do not so much like the cold weather, and we've actually had to raise the thermostat up to a balmy 66 degrees so the yeast don't putter out and give us a stuck fermentation. My heaviest beer to date is currently fermenting, so let's hope the yeast can handle the sub-par temps and give me a delicious vanilla porter!

ANNNNNDDD I am officially a proud submitter of t-shirt designs to Threadless! Hooray! They are having a contest with the theme "East meets West", and I managed to come up with something just under the wire! I had a bunch of good ideas, but only the time to execute a group of Foxfire Kitsune bumping into a lost Bigfoot in a nameless Japanese forest. I think its pretty cute! I will post a link when I get the word from Threadless that its live!

22 January 2013

Microbes in soil can work with plants to fight off disease


It is a very interesting article, albeit long. A summary:

There are 30,000 species of microbes in soil samples, vs 10K in humans. Current ag methods kill most but not all microbes, creating a vacuum for opportunistics.

Tomato plants communicate via a fungal network in the soil. Infected plants grown in the presence of this fungus warn neighbors about the disease, inducing the plant to produce disease fighting proteins.

A beneficial bacteria B subtilis establishes itself in the soil by blocking plant defenses, producing an antimicrobial at the same time, which may protect the plants roots while it is establishing. Other plants that were infected with bad bacteria Pseudomonas produced a sugar food source for B subtilis to encourage it's colonization of the roots. This triggered the plant to produce defensive chemicals. They worked together! Progeny of plants that were grown with B subtilis had better defense systems even if B subtilis wasn't around - it lasts across generations.

Plants grown under drought conditions had more bacteria that enhance growth and photosynthesis, enabling the plant to better withstand drought.

In infected plants, B subtilis colonization induced the plant to close its stomata (the pores in the leaves that allow gas exchange), which would prevent further infection (this particular disease can enter the plant through the stomata).

Microbial communities that were more genetically distinct resisted establishment of pathogens better - there was no niche for the pathogen. However, some communities with "too many" species were less able to ward off pathogens - they were not working synergistically in this case. You can imagine there may be a way to encourage certain beneficial microbial communities to best help the plant.

Of the plots sampled, a plot planted with a mixture of grasses and herbs had the strongest microbial community for fighting off disease.

You can draw a comparison between using antibiotics and the effect on your gut microbes, and the use of fungicides and insecticides on the soil microbes. Studies suggest that crop rotation, tilling and fertilizing are better ways to establish a strong soil microbial community.

Rapeseed seed meal can help beneficial bacteria streptomyces colonize soil and prevent root rot and help the plant grow as much as introducing streptomyces itself. A combination of seedmeals was better able to resist colonization by pathogens, because they contain different glucosinolates that break down, producing a variety of anti pathogen chemicals.

Cultivating healthy soil and hence, microbial communities, can help plants reduce disease, growing better, and curtailing the reliance on blunt-force chemicals.

* * *

I think this research is very interesting because it shows how little we understand about nature. I am not a fan of the cover-all techniques we use in a lot of modern science and I think science is really going to move in the direction of using what nature has already provided via microbes. Microbes are the next big thing!

21 January 2013

So many hobbies!

This was a very busy weekend. In fact, most of my weekends lately seem to be this busy.

This weekend, I wrapped up koji growing for my sake, miso AND shoyu projects. The sake is going very well and I expect it to be a great success. The miso and shoyu, however, are total experiments because of course I went off recipe and used spent grains from brewing instead of more traditional grains for koji. As a result, the grains were too wet I think for really good koji growth. Something was definitely happening, just not sure what. I think it would be cool to be able to sequence some of these home ferments and see what is actually going on in there. Towards the end, I think some yeasts started going to work in the spent grain koji, as it acquired a sort of sharp, alcoholic smell. Well, only thing to do is wait! The sweet miso will be ready in 4 to 6 weeks, the salty miso in some amount of months, and the shoyu in... a year! I tend to think that the salt will prohibit more ethanol production, but thats just a hunch.

ALSO, I am engaging in an expt with my fishtank. The poor fish have been lethargic and have had their dorsal fins down for quite a while. I have switched to a canister filter because I wanted to try to boost my plant growth, by reducing the surface turbulence and trapping the CO2 the fish produce in the tank. My oxygen is suffering, however, because I woke up this morning to heavily breathing fish with dark red gills. Turn on the air stone and they were fine in 15, but it was a little scary. Not sure if I should add more light so that the plants do a better job photosynthesizing - is CO2 still the limiting reagent, or is it light? I think there is a lot of confusion about this on the forums. People inject CO2 into their tanks but then have surface turbulence, which I would think would cause the CO2 to degas and regain equilibrium with the environment. Goldfish are really dirty, so I would think they would produce plenty of CO2. I don't really know though.

Anyway, I think my fish have some sort of parasite, they flash and yawn and twitch. PraziPro didn't clear it up so I thought maybe it is Trichodina? The stupid Petsmart and Petco here didn't have the Malachite Green + Formalin product I was looking for, so I ended up with this herbal stuff. Hopefully it works anyway because I hear the Malachite can stain the sealant in the aquarium. Weird. The herbal thing probably won't work but I guess its worth a shot since it's not an emergency. I turned the air stone back on for the treatment, to make the fish comfortable as well. The plants will just have to wait.

In other news, I have yet to start my presentation for Biophysical Society, which is in 2 weeks. And I also need to finish my design for Threadless so maybe I can win and go to Japan!!! Unlikely, but its worth a shot! Busy busy!

09 January 2013

Surviving Graduate School

Several interesting internet stumbles have appeared since my last post, and in my mind, they are related.

We have the hilarious #overlyhonestmethods Twitter hashtag.

And more seriously, some discussion about mental health in graduate school.
About a panic attack by See Arr Oh
An interchange between someone in and someone out by Chemjobber and Vinylogous.
I prefer the first piece, which was actually written in response the second. It feels totally honest and hit home with me in some ways. The second piece (which is actually a series and as of writing this, is unfinished) asks a lot of good questions but for me, doesn't feel as poignant or compelling.

I guess what prompted me to write this post is that I had similar experiences to See Arr Oh in my time here at graduate school (which continues). There was a period where I felt anxious on a daily basis, developed a social anxiety where I similarly felt trapped in seminars, and felt like the only thing that really helped fight the anxiety was alcohol. It didn't culminate in a panic attack, luckily, but did lead to crying bouts (usually not at work) and unmotivation in lab.

I think what helped me get through that time was a supportive baymate (ie the person you sit right next to in lab, where the benches back each other, like a bay), and past history with worse anxiety that gave me some coping mechanisms. Besides listening to my moaning, my baymate advised me that maybe actually achieving something in lab would help with my motivation. That by staying busy and celebrating small successes, I would regain some motivation. This worked to some extent, but was probably hindered by her enabling behaviors of wanting to drink with me. Obviously drinking is a poor choice in coping mechanism, and was one that developed in graduate school, but during my undergraduate, I had developed others that probably helped keep my head above water.

Bare with me now, but mostly it has to do with how you think of the cycles of anxiety and your mind. Developed from brushes with Eastern-influenced New Age thinking via my mother, I came to see that the thinking that builds anxiety is extremely cyclical and superfluous. In my case, my anxiety revolved around the future and the thoughts were often formed by "what if" questions, the answers to which are unknown - well, because it hasn't happened yet. You can see why this is a self-defeating and pointless circle, but the insidious nature of anxiety is that you get trapped inside and spiral downward. The second important point is that although your mind is very powerful and good at creating these self-defeating cycles, it is also under your control (to some extent). You can let it control you, or you can choose to control it, if its being rowdy. Different teachers have different opinions about what to do with dangerous thoughts, but the point is, you don't have to believe them. Either by pushing the thoughts away or confronting them to see what is really scaring you, you can stop the cycle or at least hinder it before you get too deep.

So, things are mostly better now. I can go to seminars, I'm not a complete alcoholic and I don't have crushing anxiety at every moment. But the anxiety is still there under the surface. One stray thought and it is back, but only as a shadow. There are periods of months where I don't have it at all. I basically have resigned myself to it as long as I'm in graduate school, especially with the uncertainness of my future as it is. Hopefully in the coming months, I will cement down a option for post-graduation.

One thing that I'm a little confused on, though... I continue to have a life outside of the lab which is fulfilling, with various hobbies and friends. However, in my own experience, and by looking at others, thinking about your project outside of lab can lead to much better productivity. In times when I was feeling the best about my project, and things were going well, I would think about my project all the time. So there has to be some tradeoff between hobbies and thinking of research outside of lab. In some sense, I understand profs when they don't want people to have hobbies, because for me, the hobbies are sort of a sign that I'm just not that into my project right now, and that I need other successes to build up my lab-eroded confidence. Of course, having profs require a lack of hobbies is unlikely to work and what probably leads to greater mental decline among students. Who is to say, I don't have the answers though...

08 January 2013

Post-Vacation Grad School Blues

Having recently returned from my vacation (as in, yesterday), I am confronted with the typical post-vacation work-related feet-dragging. There is certain prevalence of the idea that vacation is supposed to "recharge" you for work, that you will return ready to kick science-butt with renewed energy. Instead of being recharged, however, I find myself wondering: who are these people that are recharged after vacation? Does this really exist?

I think for the majority of graduate students, this vacation recharge is a myth.

Case in point.

However, maybe there are people that are truly rearing to go after they get back from vacation. I think that my PI is probably one of them. He let us in on this little secret of his when he told us that he spent a lot of time thinking about the philosophy of graduate school while on his most recent vacation in Mexico. Sitting on a beach, thinking about how best to mold these young minds into great hypothesis-driven, problem-crushing, publication-writing machines. This is a man who obviously enjoys his job.


Of course, it is probably unfair to say that most graduate students fall into the "I'm on vacation, so we're NOT talking about lab" category. I have known some fantastic grad students who remain truly curious about all things science, even while Science slowly erodes their hopes and dreams on a daily basis. They stay upbeat, read journal articles for fun at night, etc. I believe these are the people that are going to make great professors someday.

For the rest of us, it's not to say that maybe we won't be useful scientists or even great professors. I think the issue is more about the work mindset that is necessary to succeed in graduate school. For instance, I now cook as soon as I come home from school, in part because it allows me to achieve something on a shorter timescale. Many of graduate school's successes (for me anyway) are few and far between. It is difficult to celebrate an attractive gel when you have yet to get your first paper published.

For students like me, graduate school is a long and tiresome process. It is a journey. When I was a first-year, I was told by a senior grad student that graduate school is a marathon, not a sprint, and that many of his classmates were no longer there because they didn't have this particular brand of perseverance. This same student also told me that you stay in graduate school either because you love your project, or your professor. If you love both, obviously that is the ideal situation. Of course, I didn't take him very seriously at the time, but it's true that when your project is giving you grief, the only thing that really pushes you to continue with any fervor is your professor. And when your professor is a true pain to work with, genuine interest in the project is the only thing that keeps you there.

So, while I know I don't quite have the right blend of working style and personal attributes to really soar in graduate school, I know it is temporary. And I know the journey will teach me the skills and knowledge to land a career where I may experience that recharged, go-get-em attitude... when I come back from vacation :)