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Science Writing

I am sharing this guest post of mine that was published in Cell’s Crosstalk: Biology in 3D Blog. Yes, the journal Cell!

Here is the link: http://www.cell.com/crosstalk/why-do-i-blog-about-structural-bioinformatics

Enjoy!

Why Do I Blog about Structural Bioinformatics?:Biology in 3D

When someone says that they have a blog, the stereotypical response would be, “About your travels?” or “Hmmm … Recipes … Must be a delicious blog!” And when one confesses that said blog is about scientific research, the jaw drops. I presume it has to do with the notion that blogging science is not that much fun!

Two things inspired me to become a blogger: (1) an amazing community of scientific bloggers at Research Blogging, who inspired me with their wonderful posts; and (2) my view that structural biology and structural bioinformatics are not getting the exposure they deserve. Thus inspired and motivated, I begun blogging about four years ago, and was able to channel some of my thoughts and energy into my blog, called Getting to Know Structural Bioinformatics.

Guest author and blogger
Raghu Yennamalli

Why do I blog? Blogging is fun! For me, blogging is about sharing with the world recent research and tidbits on structural biology and bioinformatics. Most importantly, it is about sharing the excitement that I feel after reading a paper. In some sense, blogging about research is similar to a journal club, where I am able to share the latest research with my peers. However, unlike a journal club, the audience for my blog is the entire world.

Blogging is also dynamic and interactive, because it allows me to engage in conversation with others (specifically students) when they weigh in with their comments. Below I highlight some of the best practices that I’ve developed over the years that help me with balancing my research, teaching, and personal responsibilities with my blogging.

Selecting the paper

The main way I find articles that I want to blog about is by scouring through the table of contents of the journals I am interested in. Sometimes I also hear about exciting protein structures via friends and other blogs that I follow. I try to have a balanced approach and highlight structural work on systems that are “hot topics” as well as papers that just captured my interest and fancy.

In the early days of my blogging, I was trying to collate and compile tools and techniques that would come in handy for students working with protein structures. I wanted my blog to be a handy place for myself and others to find tips and tricks. Over time, the range of topics and papers I cover has broadened, and although I still cover a lot of method development work, I cover other topics as well. In general, once I make up my mind about the paper I want to blog about, I start reading it, give myself some time to soak in the method and outcome of the paper, and try to think critically as to what possible gaps or methods that the authors could have done to make the paper better. Alternatively, I also analyze the paper’s novelty with respect to structural bioinformatics.

Composing the blog post

I should confess that the monthly posts in Protein Spotlight by Vivienne Baillie Gerritsen are my inspiration while composing posts. I love her writing style and also the manner in which artwork is included in every post, to make it fun to read. Like Protein Spotlight, blogs have the advantage of including other multimedia items, for example using animated gifs and YouTube videos that make the post much easier for the reader. So, I start finding an appropriate image from an art database that best fits the topic (of course, giving credit where it is due). When it is about a tool/software, I figure the best approach is to use said tool/software and include a “first-hand” experience of how I perceived it. Also, I try to include an additional tidbit or information that the authors mention in passing.

Balancing things

With an active teaching and research schedule, finding time to blog does become a challenge. I try to make it a fun process, so that it does not feel cumbersome. If one looks at the frequency of my posts, I try to maintain at least one post per month. Looking at others’ blogs at Research Blogging, I realize that one post a month is a low turnout, and I try to post as frequently as possible. Sometimes, the problem is sheer lack of time or not finding exciting enough material to blog about. However, this does not mean that exciting research is not out there. The key is to find a balance between blogging and other duties. I have had discussions with other bloggers who blog on other nonscience topics, and we observed that the main turnoff in blogging is when one delves deeper and over time a particular post becomes “work.” Maneuvering that roadblock is key to maintaining a successful blog.

In the end, as at the beginning, it all comes down to having fun and sharing with the world my excitement about the type of scientific research I enjoy. I think this is probably the feeling others who blog share as well, and I can see it in some of the blogs I follow, such as the following:


Raghu Yennamalli completed his PhD in Computational Biology and Bioinformatics in 2008 from Jawaharlal Nehru University. He conducted postdoctoral research at Iowa State University, University of Wisconsin-Madison, and Rice University. Currently, he is an Assistant Professor at Jaypee University of Information Technology. He can be contacted at ragothaman AT gmail DOT com.

ResearchBlogging.orgTwo nature news articles make this post. The first one is titled “Scientists may be reading a peak in reading habits”. Read the full news here. With the widespread reading turning towards online rather than the good old library hunting, this is not a shocker. The average time spent on reading is half an hour per article. Now, what they read is not asked. For eg: Did reading a scholarly article mean reading every section or just the valuable snippets of information, mainly from the figure legends? We don’t know.

…The survey defines ‘reading’ as going beyond titles or abstracts to the main body of an article, and so it does not reveal whether researchers are quickly skimming over more articles than they did before…

…Further details from the study reveal that scholars now read more than half their articles on an electronic screen, whereas in 2005, just one-fifth of readings took place on screen…

…Now that researchers can look for articles online, it is clearer that they “power-browse”, says Nicholas, bouncing through a terrain of articles with four or five browser windows open at any one time…

So, what kind of reader are we looking at. IMO, I think I will be looking more into articles that are blogged about. No, I am not saying that the articles need to be have a marketing strategy.  Heavens, No! What I am saying is this lacuna of reading is what research blogging can fill. Whatcha thinking?

The second nature news is a snippet that says that blog citations count towards a research paper!

For 7 of the 12 scientific journals examined in 2009, and 13 of 19 journals analysed in 2010, papers cited in blog posts aggregated by ResearchBlogging.org received more subsequent citations than did papers from the same journal in the same year that had not been cited by blogs.

Isn’t that amazing? In fact, the power of research blogging is yet to catch up with (Ahem!) the people who make decisions.

Hiring and tenure-review committees could use blog citations to assess the impact of recently published papers, suggests co-author Hadas Shema

Anyone listening in the hiring committee? 🙂

Read the full article published in Journal of the Association for Information Science and Technology here.
References:

  1. http://www.nature.com/news/scientists-reading-fewer-papers-for-first-time-in-35-years-1.14658
  2. http://www.nature.com/naturejobs/science/articles/10.1038/nj7486-123a
  3. Hadas Shema,, Judit Bar-Ilan,, & Mike Thelwal (2014). Do blog citations correlate with a higher number of future citations? Research blogs as a potential source for alternative metrics Journal of the Association for Information Science and Technology DOI: 10.1002/asi.23037

Image Courtesy: PymolWiki

It is a fact that there is a non-uniformity with which different space groups occur in protein crystals. For example, the space group P212121 is the most frequent in protein crsytals and occurs almost one-third of the time!!!

Why is this so? This was the question asked by Wukovitz and Yeates in their paper titled “Why protein crystals favour some space-groups over others” [1]
ResearchBlogging.org
Comparing the protein crystals with organic molecule crystals it seems there are marked differences. The rules for organic molecules’ molecular packing was proposed by Kitaigorodskii and it became widely accepted. [2]

However, If we look at the distribution of the space groups in organic molecules and proteins there are marked differences. Thus, the authors argue that same criteria cannot be applied to proteins. One major difference between the crystals is that protein crystals contain 50% solvent by volume, while organic crystals are jam-packed with less space. This results in a higher “coordination number” (10-14) for organic crystals than for proteins, where the number is average 7.5

Based on all these, the authors tried to devise a simple statistical measurement that can answer as to why certain space groups are preferred among the 65 biological space groups.

And the formula is:

D=S+L-C, where

D = Total number of rigid-body freedom
S = number of meaningful degrees of freedom
L = number of independent parameters for describing the unit cell, and
C = minimum number of unique contacts required to make the set of symmetry related molecules

All three are positive integers and are not adjustable parameters. The explanation given by a simple statistical analysis for protein crystals is “For a particular space group only a certain number of rigid-body degrees of freedom are available for assembling the first few molecules before the internal structure of the crystal is completely defined. This number depends on the space group symmetry.”

Three things limit the rigid-body degrees of freedom

  1. number of meaningful Rigid-body DOF for the first molecule in space
  2. the number of independent unit-cell parameters
  3. the number of intermolecular contacts to make a network

How to find C?
The problem of finding C is equivalent to the problem of identifying the minimal set of symmetry elements. For each space group, C can be determined by finding the minimal set of generators for each space group. The numbers range from 5 to 2.

The authors observed that the calculated value of D correlated with the observed frequency of the space group!That is, higher the value of D the most frequent space group.  Guess which space group had a higher D value?

Now the question comes back to “Why P212121 is more frequent?” The reason is that this space group is the least restrictive for the possible orientations and positions of the molecules in the crystal.

The authors do note that their analysis does not take into consideration of the shape of the molecule, energetics, and packing efficiency, which can lead to answers for non-monomeric proteins in the asymmetric unit.  According to the authors, P1 has a D value of 8, and is predicted to be the most used space group for racemic protein mixtures.

References:

  1. Wukovitz SW, & Yeates TO (1995). Why protein crystals favour some space-groups over others. Nature structural biology, 2 (12), 1062-7 PMID: 8846217
  2. Kitaigorodskii AI. Organic Chemical Crystallogrphy (1955) Consultants Bureau, New York (Originally published in Russian by Press of the Academy of Sciences of the USSR, Moscow)

I am back! Feels good to be back.

Image Courtesy: Mr. Jeromy’s Blog

Was looking for some motivation and I saw this blogpost in nature about blogging. Hurrah!

How to learn by Blogging about Science

I had done a previous post on Why blogging research is rewarding. While this is not a research article, it does reiterate the main points mentioned earlier, along with more positive points, specifically the active learning part.

Hope you enjoy reading it as much as I did. Have a great day ahead!

Are you looking for opportunity to hone your writing skills? And at the same time get recognition for doing that? Look no further than the Wiki Contest from Biophysical Society.

http://www.biophysics.org/AwardsOpportunities/SocietyContests/WikiEditingContest/tabid/4125/Default.aspx

http://biophysicalsociety.wordpress.com/2013/02/21/improve-biophysics-information-on-wikipedia-and-enter-to-win/

Share what you know about biophysics with the world by participating in the Society’s Wiki-Edit Contest! The 2013 contest kicked off at the 57th Annual Meeting, and attendees at the kick off event received a button with the image on the left.

Six winners, chosen by a panel of judges who will determine the most improved biophysics-related articles, image collections or other contributions to Wikipedia or Commons, will receive $100 each, a barnstar on their talk page, and free registration to the 2014 Annual Meeting in San Francisco, California.

Visit the WikiProject Biophysics page for more information about the WikiProject. Visit the Biophysics Wiki-Edit Contest page or search WP:BIOPHYS on Wikipedia or Google for information on how to enter the contest.

For helpful tips and tricks for creating a Wikipedia account, adding and editing pages, and more, view the slides presented at the BPS Annual Meeting Wiki-Editing Contest Meet-Up!

The deadline to finish your article is July 15, 2013.

In this age, where many readers have a breath-wise/skimming habit of reading things, instead of depth-wise [Ref 1, 2], blogs are an awesome since you can write as much as you want, post as many pictures one wants to. Blogging by those who are in science is a one of the ways of bridging the gap of communication that is abysmally low between researchers and the non-scientific public. No, not as a propaganda machine, but reaching out to the people who are interested in what one is talking about.

PLoS Biology’s article “An Introduction to Social Media to Scientists” sets the right pitch for those who are thinking of whether they should take the plunge to blogging or not! Read the article here [Ref 3]

Of course, there are other ways of communicating in the social media. But, I will for time being stick to blogs for the two main reasons mentioned by Birk and Goldstein

Longevity; posts are accesible via search engines

Robust platform for building an online reputation.

ResearchBlogging.org

One other effective way of making an online reputation is by editing Wikipedia articles. As of now, I find blogging about research articles to be highly rewarding for the following reasons

  • Sharpening my writing skills (I don’t have to emphasize the importance of this skill for researchers whose native language is not English)
  • Expressing one’s views in a professional manner
  • Making me find more interesting articles that I can blog about, which translates to more reading done as well.
  • For every post, I see my brain working the process of forming an idea, and finally seeing the effort achieve fruition. (This is very helpful to plan the way your write your manuscript with your own results)
  • A sense of satisfaction that comes after clicking the button “Publish”

Read here more about Research blogging!

References

  1. Literacy Debate: Online, R U Really Reading?
  2. What is the Internet’s Effect on Deep Reading?
  3. Bik HM, & Goldstein MC (2013). An introduction to social media for scientists. PLoS biology, 11 (4) PMID: 23630451