#FF: Using Twitter for Good (Chemistry)

Anyone who knows me personally will by now have been exposed to my (relatively) new Twitter obsession. For that, I apologize.

Only a little bit, though.

The fact remains that Twitter is a powerful engine for rapidly sharing news about any topic in headline format, allowing the reader to make a decision on whether to delve deeper in a matter of seconds. Why humanity has chosen to inundate these spaces with Bieber and pictures of cats is beyond me, but that doesn't mean that your Twitter feed has to experience the same fate.

In the spirit of #FF (Follow Friday), here are 7-ish Twitter accounts you can add to your feed to bring yourself some great chemistry content every day.

Socializing Scientists
I'm going to go out on a limb here and say that you didn't join Twitter to get work done. Scientists, being humans, enjoy having fun with social media. Of course, scientists, being nerds, think that the best way to have fun with social media is to share pictures of their science with as many people as possible. In chemistry, these pictures are all curated and retweeted by @RealTimeChem (#RealTimeChem). From jury-rigged glassware setups to celebrations of that one triumphant spectrum, you're bound to find something interesting here. For example:

All I do is spin, spin, spin no matter what! #RealTimeChem #RealTimeRepetition pic.twitter.com/PkktW3ZhRM
— Tree Town Chemistry (@treetownchem) May 13, 2014

However, scientists on social media aren't only concerned with having fun. There has been a great deal of effort devoted to meeting the needs of underrepresented groups in the sciences in order to promote further participation. Obviously these problems are not yet solved, and conversations continue in a number of venues, Twitter included. The handle that I see most often is @BLACKandSTEM (#BLACKandSTEM), which provides amplification for the voices of black scientists across all disciplines. The handle also hosts frequent chats on universally important topics such as self-promotion and strategies for finding employment.

The American Chemical Society
Most scientific publications and organizations are on social media in some capacity, but the American Chemical Society does a particularly good job of it among chemistry-related organizations. Following @AmerChemSociety will get you access to tweets about high-profile publications from the flagship ACS journals. The best part about following the ACS, though, is that all of the different sub-handles all retweet each other, so by following @AmerChemSociety you'll get information about opportunities for employment, news targeted at graduate students, outreach activities, and more.

Another interesting facet of the ACS social media presence is @ACSReactions, which publishes short pop-science videos giving a chemical explanation for everyday curiosities. It hasn't been active for long, but has already made a big splash with a video about the chemistry of bacon smell.

Chemical & Engineering News
Tweets from Chemical & Engineering News (C&EN) probably make up the bulk of my feed, and they definitely get the bulk of my clicks. As with the main ACS account, the main C&EN account, @cenmag, retweets a large volume of content from its associates. If you're into materials chemistry and emerging technologies, you can't miss.

Additionally, C&EN reporter Carmen Drahl (@carmendrahl) hosts the short podcast Speaking of Chemistry (#speakingofchem), which gives bite-sized recaps of news items in a very accessible video format.

Strictly Business
Do you love to read papers all the time? I'll admit that I've had lunch breaks cut short by a tweet about an interesting paper that inspired me to go out and be productive again. Go ahead and search for your favorite journals - odds are, if they're from the ACS, RSC, or Nature Publishing Group, they're on Twitter. You can use Twitter's Lists function to sort all of the journal tweets out of your feed, which is surprisingly helpful for staying on top of things if you're already on social media fairly often.

While it might be a long way from convincing your advisor that sitting on Twitter is helping you with your degree, following these accounts will give your feed a healthy variety of science news and happenings that you might have missed otherwise. Happy #FF!

Did I miss a good one? If you're following someone great that I haven't mentioned here, feel free to leave a comment!

The Giant De Novo Peptide Review: An Interview with Fangting Yu

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For researchers breaking into the field of protein design, life just got a whole lot easier.

In late March, a massive review of rational protein design ($) entitled "Protein Design: Towards Functional Metalloenzymes" hit the web. Scientists of all levels and disciplines use reviews to figure out where to start on new research projects or to gain a wider perspective of their field, so writing good review articles is an essential part of scientific research. The review was published in Chemical Reviews (ACS) as part of a specially-themed issue on enzymology and authored by Dr. Vince Pecoraro's group at the University of Michigan, along with collaborator Dr. Matteo Tegoni.

Enzymology, or the study of how enzymes do their jobs, is a diverse field of science that intersects chemistry, biochemistry, and biology (for example). Some enzymologists are interested in cataloguing existing functional proteins. Some take those proteins and, by changing their structure or the chemicals available for them to react with, learn the intimate mechanism of their function. Still others apply what is known about how the enzymes work in an attempt to create new enzymes or enzyme-like molecules that function even more efficiently than the natural structure.

The latter group of enzymologists most often utilize the two methods covered by the review: protein redesign/engineering, in which an existing protein is modified to enhance its function; and de novo protein synthesis, in which a functional protein that does not exist in nature is dreamt up and created in the lab.

Dr. Pecoraro's "Protein Design" review was a massive undertaking involving ten authors and over 1,000 cited papers. I sat down with Fangting Yu, the article's lead author and a 5th-year graduate student in Dr. Pecoraro's lab, to learn more about the process of putting the review together.

Fangting Yu, explaining how she uses a device in the lab to synthesize new proteins.
Image credit: Sung-Hei Yau; used with permission.

Getting into the Research
Fangting originally joined the Pecoraro group to work on making inorganic manganese complexes to model the reactivity of the oxygen-evolving complex in photosystem II (PSII). The calcium-manganese cluster in PSII is essential for the final step of photosynthesis in which water is oxidized to the oxygen that we breathe. The mechanism of its action has been debated since the structure of PSI and PSII began to become more clear in the late 1980's (see links).

Fangting got a publication ($) out of the project. However, the manganese project would soon run out of funding. Because of a broad interest in the reactivity of transition metal small molecule centers in proteins, she decided to take up a new project dealing with a more biologically relevant system. At the time, Dr. Matteo Tegoni, an Italian researcher currently at the University of Parma, Italy, and also an author on the review, was a visiting scholar in Dr. Pecoraro's lab. He made progress on a new aspect of de novo protein design involving copper reaction centers. Fangting took over the project as he left and devoted her interests to de novo protein synthesis, resulting in two papers thus far (1 and 2, $).

The All-Important First Draft
Writing a good review can be a huge undertaking, and most graduate students do not have the time to pursue it with hectic schedules and workloads. Fangting was no exception. "We got to write this because of [Dr. Pecoraro]," she said. In addition to de novo design, Dr. Pecoraro has worked on understanding the role of manganese and vanadium in biological systems for the bulk of his 30-year career at the University of Michigan. As one of the leading experts in the field, he was invited by Chemical Reviews to write the article.

Dr. Pecoraro left the first author position open to the student who made the best case for authorship. "I was debating whether or not to take it because that was my fourth year of grad school, and in that summer you can generate a lot of data," said Fangting. However, an instrument critical to moving her research forward broke down near the start of the summer, and she decided to make a bid for authorship.

The writing process began in earnest in May 2013. It took 3 months to put the first draft together for submission, which means it spent about 7 months in review before its publication online.

Collaboration, Here and Abroad
Reviewing a topic as deep and well-studied as protein design requires a ton of reading, and for one person to do it all would be an astronomical task. As such, the paper ended up with ten authors, nine of which are currently in the Pecoraro lab. However, Dr. Tegoni's appointment in Italy put the Atlantic Ocean between him and the rest of the authors.

When I asked if the international collaboration was difficult, Fangting waved the question off. "[Dr. Tegoni] is the person who started my thesis project. We're pretty close - we're both friends and collaborators." Electronic communication made the collaboration easy.

Fangting went on to say that managing multiple authors was not the hardest part of the process. Collaboration is essential for putting together a project of this scale. "One thing that I would advise on multi-author papers is, when you are the point person, you want to be as specific as possible when you give people assignments, and be firm about deadlines."

The Review Experience, In Review
The toughest part of the review for Fangting was deciding what to include. "There's so much out there," she said. "For example, say this protein design paper cites a few other papers that are kind of protein design, kind of engineering, kind of a directed evolution approach." The line of what is in the scope of a review and what is not is never black and white, and those papers fall into the grey area. "It takes time and energy to make a decision on what kind of material you want to include and how you want to connect them together."

Writing the review certainly brought benefits with it. First, in assembling all of the material, Fangting learned a great deal and feels more on top of her field than she did before.

Perhaps more tangibly, though, she feels like she has gotten a head start on her thesis. "Any Ph. D. student is going to have to go through writing a review chapter," she said, referring to the introduction of the final Ph. D. thesis. "It's just a matter of when. I personally think that the intro chapter is the most difficult to write. Deciding what context you want to put your thesis in is the most difficult."

Lessons Learned
Writing the review has certainly given Fangting a head start on her thesis, but has also taught her some valuable skills for tackling large writing projects in general. When I asked her what advice she would pass along to other students engaging their theses or similar publications, she paused and her face became much more serious. "Outline," she said.

"You need to think more than you need to write," she added. "At least for me. I would spend time just shutting down everything and thinking." She paused again. "And outline it."

To learn more about the other authors of the review, and for more specifics on what a rational protein design research project actually looks like, check out the Pecoraro group web page.

ACS - American Chemical Society
PSI/II - photosystem I/II

Join the Fun!

I started Tree Town Chemistry as a way to spread news about graduate student researchers, the social side of science, and other interesting tidbits that interest scientists of all levels, all while building a professional portfolio. So far, it has been a lot of fun and I would call it a success.

But why just me? There has to be someone else out there looking to test the waters, right?

This is an official invitation for guest posts and collaborators - a call for papers, if you will. If you're interested in science writing and want to give blogging a quick try, contact me. Whether you have an idea for a one-shot post or you would like to join the blog long-term, I am interested in hosting your work. More authors means more points of view and a deeper perspective.

Send your ideas in to treetownchem@gmail.com and let's get started.