Tuesday, October 29, 2013

Fall in Boulder

I just found this photo that I took a few years ago. It seems appropriate for late October in Boulder.

Monday, July 29, 2013

Signing on and reading up

OK, so I have finally taken some steps toward keeping up on the literature and staying aware of this crazy industry called Academia.  I've subscribed to paper versions of the Chronicle of Higher Education and Science, and signed up for emails from ArXiv about quantitative biology and e-alerts from Nature Publishing.  I regularly peruse the Science sections of the BBC and NYTimes.

What else do people do to stay up to date on general science developments?  I'm open to more suggestions, though I'm not quite sure I can stomach an RSS feed.  I'm looking more for a sprinkler system of relevant, edited science news rather than a fire hose.

Thursday, July 18, 2013

Short Course on Complexity

The Santa Fe Institute (SFI) is an institution and think tank focusing on complex systems and transdisciplinary research.  SFI is hosting a short course in Austin, Texas that should be excellent.  The program coordinator is Dr. Melanie Mitchell, author of "Complexity: A Guided Tour" (which is an excellent introduction to complex systems).  My advisor, Dr. Aaron Clauset, will be speaking, along with Drs. Chris Moore, Luis Bettencourt, Simon DeDeo, Jennifer Dunne, Paul Hines, Bernardo Huberman, and Lauren Ancel Meyers.  More info here: http://santafe.edu/education/schools/short-course-complexity/

Friday, July 5, 2013

Alessandra Volta and the invention of the battery

I have spent the past two weeks in Como, Italy for a wonderful conference called Quantitative Laws of Genome Evolution.  I will write more about it later, but let me at least thank Marco Lagomarsino for organizing such a wonderful conference.
The location was ok, too.  Como is a beautiful place; I was in the region 15 years ago and was eager to return in the name of science.  However, during my first visit to Lombardy, I wasn't aware of the rich scientific history in the region.  Como was the home of Alessandro Volta, who discovered the first battery by creating a continuous current between two metals and stacking these in a voltaic pile.

Today I visited the Tempio Voltiano to try to glean some details of Volta's life from the Italian descriptions and to look at his instruments and early batteries. I was attracted to the exhibit after learning that Volta discovered the battery in 1800.  I found out that Volta was an interdisciplinary scientist, tinkering and building eudiometers, investigating "inflammable gases" (e.g., methane), studying atmospheric conditions, building capacitors, etc., all from materials such as wax, clay, wood, stone, metal, paper, and glass.  It seems miraculous to me to design something as complex as a battery from these supplies without any post hoc knowledge.
Tempio Voltiano

There were also displays about the study of "animal electricity," the view supported by Volta's rival Luigi Galvani, including many mummified frog legs and one manta ray preserved in formaldehyde.  What an interesting time to be studying the movement of electrons!  Did energy come from the dead animal itself?  Or was the animal just a vehicle?  Volta was inspired to build his voltaic piles to prove his rival wrong, ultimately inventing an incredibly useful technology.  He received recognition in his time, as well, demonstrating his early batteries to Napoleon in Paris.

And now I leave you with a few pictures from the museum. Enjoy!

Earliest voltaic piles

Volta demonstrated the voltaic piles on the right to Napoleon.

The first chemical battery.

Tuesday, June 18, 2013

Wednesday, June 5, 2013

Statistical packages and Mac computers

So it turns out that lots of statistical packages and programs are not compatible with Macs.  I have a hard time understanding why this is.  Right now, I'm working through Andrew Gelman and Jennifer Hill's book, "Data analysis using regression and multilevel/hierarchical models." They do a wonderful job incorporating R code into the book.  But...they specifically say, in the appendix about software, to download and run R and BUGS "on your Windows computer."

I have to ask: why?  Why can't we be inclusive?  I'm sure there are good reasons, but this level of uncompatibility is just really frustrating for me.  I wish there were some brilliant programmer out there who would fix this.  I'm getting really sick of reading R forums and StackOverfow. 

OK, back to the troubleshooting. *end rant*

Tuesday, May 28, 2013

Microbes and indoor ecology

This photo is from the NYTimes article's video, "The Jungle Indoors."
Great article in the New York Times yesterday about a collaborative effort among ecologists to map the microbiome in homes and other built structures (e.g., hospitals).  Last week, the American Society for Microbiology held its annual meeting in Denver, CO, and I was lucky enough to meet some of the participants. One, Dr. Jack Gilbert, was kind enough to offer some suggestions on my research.  He is also mentioned in this article for his research into the infection of a new hospital wing by its patients.  Basically, researchers are reproducing E.O. Wilson and Daniel Simberloff's classic island biogeography experiment, where mangrove islands in the Florida Keys were fumigated to eliminate all arthropod life, and then the recolonization dynamics could be observed over time.  However, this time, scientists are looking at biogeography and colonization dynamics of built spaces by microbial species.  It's a whole new area for ecologists for explore, with plenty of applications for human health.  Also, much of the research is being done by CU's own Noah Fierer, who is an incredible microbial ecologist.

Tuesday, May 21, 2013

Time saver

Credit for this post goes to my labmate Daniel Larremore.  For those of you out there like me who grew up in the age of Facebook, it can be difficult to just close the window and step away.  I know, I know, I get my news there too...my friends post fascinating articles, and so many of my college friends are studying such interesting topics in their own grad studies: stem cells, behavioral ecology, sociology, public health.  But, checking multiple times a day doesn't do much for my productivity.

Enter LeechBlock.  Best app ever.  I have blocked Facebook between the hours of 9am and 5pm.  When I type facebook.com into my search bar between those hours, I see this screen:
Yes, I can wait 60 seconds and get access...but usually I don't.  Time saver, willpower enhancer, all around great app.  Thanks, Daniel. :)

Wednesday, May 8, 2013

Franco Pacini, 1939 - 2012

In preparation for my trip to the Quantitative Laws of Genome Evolution workshop in Como, Italy next month, I was reflecting on my last trip to Italy five years ago.  During that trip, I stayed near Greve, but the highlight of my trip was my visit with Dr. Franco Pacini and his family in Florence.  I recently learned that Dr. Pacini passed away last year.

In homage to this incredible man, I mention two stories.  The first is documented in this blog post, when Franco gave me and my family a private tour of Galileo's home.  It was one of the most incredible experiences of my life, for someone who wrote a 3rd-grade report on the famous astronomer.  My second story about Franco took place in my childhood home in Vermont, when I was a senior in high school.  I recall that my father came home from work one day and informed my mother and me that we would be watching this specific episode of Nova on PBS, because his friend Franco was a speaker on the program.  What an incredible surprise; not only did my father have a friend in Italy who was an astrophysicist, but he was on NOVA, the PBS show that we watched almost every week, and he was talking about science to the general public!  He was an incredible role model for a burgeoning scientist such as myself.

Rest in peace, Franco, and thank you for your contributions to science and the pursuit of knowledge.

Wednesday, April 10, 2013

My google profiler thinks I'm male

In the category of weird machine learning applications, I learned today that Google uses its information about your search history to infer your age and gender...and Google got it wrong!

I guess my search history just doesn't seem very female-ish: sports, computers & electronics, politics, mortgages, dogs.  I wonder whether it is Reddit's fault.  In any case, you can check your google ad profile here.

Monday, April 1, 2013

A short rant about science journalism

I can't resist...a good friend of mine linked to a Discover magazine blog today.  The blog was covering a recent Correspondence piece in Current Biology.  Basically, the authors have been studying a local population of swallows for the past 30 years and have noticed a decrease in swallow roadkill as a proportion of the total local population.  They found and reported a correlation between longer wings and victims of roadkill.  The blog coverage, however, basically reported that rapid evolution is causing swallow wingspan to decrease, which allows swallows to avoid traffic more efficiently. 

This is a classic example of a science journalist taking a suggestive science article (which was already of questionable quality) and spinning it into a narrative for the public. And this is why we have science illiteracy in the US

...Or is it? I can't know the precise causative agent(s) for my generalized sense that many Americans experience confusion around scientific topics.  Why?  Because correlation does not imply causation.  *end rant*

Wednesday, March 27, 2013

Curing cancer

Leukemia cells
Today I hung out with a good friend of mine who transferred from the Evolutionary Biology department at the University of Colorado to University of Sheffield in England.  While on a walk, he mentioned the latest news from the biology grapevine: researchers at Memorial Sloan-Kettering in NY have developed a new treatment for a certain type of leukemia, genetically modifying patients' own T-cells to attack the cancer.  Pretty impressive stuff, and seems like it could be quite a breakthrough for cancer research.  Check out a good summary article here.  And remember to hang out with your friends in other disciplines -- you never know what you'll learn from them!

Thursday, March 14, 2013

Bacterial close-ups

When I was doing my master's research on the ecology of speciation in Bacillus subtilis - B. licheniformis, we had an undergrad working in the lab who took some of my plates and ran them through an electron microscope to see what the bacterial colonies looked like.  Here is one of the photos he took.

I was reminded of this photo from this National Geographic piece, showing lots of different bacterial species through an eletron microscope.  Check it out.

Sunday, January 20, 2013

Political impact on research funding

This is an interesting and scary article in Forbes magazine about the impact of the Congressional budget negotiations on biomedical research.