You'd Prefer An Argonaute

~ Intermission ~

Posted in Blog Affairs by YPAA on March 1, 2012

Cabot Street Cinema, Massachusetts by Hiroshi Sugimoto

This isn’t necessarily the final post for You’d Prefer An Argonaute, but I’m calling an intermission, or hitting the standby button perhaps.

While I’ve thoroughly enjoyed running the blog the past three years, other priorities have taken hold of me, and the blog is getting sleepy, so to speak.

There haven’t been contributions to the RNA Journal Club posts for quite a while. When even I didn’t find the time to do one for my last presentation, it got harder for me to in fair conscience ask others to still contribute. I don’t see a point in continuing to post the papers weekly now that there are no more reviews.

I am extremely grateful to the following people who did contribute: Vikram Agarwal, Josh Arribere, Graeme Doran, Anna Drinnenberg, Robin Friedman, Huili Guo, Allan Gurtan, Mohini Jangi, Carla Klattenhoff, David Koppstein, Madhu Kumar, Charles Lin, Joel Neilson, Michael Nodine, Alex Robertson, Jenny Rood, Noah Spies, Alex Subtelny, Igor Ulitsky, Pavan Vaidyanathan, David Weinberg, Josien van Wolfswinkel, Xuebing Wu, and Muhammed Yildirim.

Pretty much all these people are going to be successful P.I.’s/scientists one day. There’s a significant correlation I tell you!

I hope to still post periodically, things like the annual lists of RNA conferences I compile. And maybe the blog will get its second wind during my postdoc… we’ll see. In the meantime don’t fret about the site disappearing from the web, however, the URL could change if I get sick of paying rent on the domain.

Sometimes I feel like I’ve been writing for an alien audience, because I’ve had practically no contact with viewers. Who and what are you? Spam drones? Bored teenagers?

Well, to the curious, nerdy aliens who landed here for knowledge or laughs, thanks for reading, and stay true in your science.


YPAA Contest #2

Posted in Blog Affairs by YPAA on April 1, 2011

We had our first contest back in November in which an awesome Puffer Hubbard t-shirt was awarded. Let’s roll out Contest #2!

Here are the rules: Answer the three questions below in a comment, and the first two people to correctly answer all three win! It’s that simple.

Question 1

Define “microRNA” correctly in four words or less. No sentence fragments.

Question 2

For every RNase known, list organism from which was first isolated, and briefly describe activity and specificity.

Question 3

Which would win in a three-way fight, ribosome or spliceosome or RNase P? Substantiate your answer carefully and concisely.

Grand Prize: Travel to (no hotel) and one entry to the Creation Museum (Prepare to Believe!) in Petersburg, KY.

Petersburg, KY

First Prize: One unused tube of NEB Buffer 2.

Unused tube of NEB Buffer 2


2010 in review

Posted in Blog Affairs by YPAA on January 7, 2011

The stats helper monkeys at mulled over how this blog did in 2010, and here’s a high level summary of its overall blog health:

Healthy blog!

The Blog-Health-o-Meter™ reads Fresher than ever.

Crunchy numbers

Featured image

A Boeing 747-400 passenger jet can hold 416 passengers. This blog was viewed about 13,000 times in 2010. That’s about 31 full 747s.

In 2010, there were 80 new posts, growing the total archive of this blog to 154 posts. There were 69 pictures uploaded, taking up a total of 51mb. That’s about a picture per week.

The busiest day of the year was January 7th with 144 views. The most popular post that day was Venki Ramakrishnan: the Cadillac of ribosome structure investigators.

Where did they come from?

The top referring sites in 2010 were,, Google Reader,, and

Some visitors came searching, mostly for cadillac, argonaute, fabio, scott valastyan, and harry noller.

Attractions in 2010

These are the posts and pages that got the most views in 2010.


Venki Ramakrishnan: the Cadillac of ribosome structure investigators October 2009


About me and my contributors March 2009


Harry Noller got shafted by the 2009 Nobel Prize in Chemistry October 2009
1 comment


Scott Valastyan teaches Bob Weinberg about microRNAs June 2009
1 comment


The History of the Argonaute, Part 1 June 2009


YPAA’s notes:

The above was automatically prepared by WordPress and emailed to me; pretty nifty it is.

Visitors that arrived through Google searches did come in droves for Cadillac pictures (see above–isn’t she a beaut?), as I noted in an earlier post, and some for Fabio pictures (not to mention Eva Longoria pictures).

I’ll note, however, that the vast majority of Google searches that link to this blog are for more predictable strings (almost always abbreviated/shorthand, and so rarely recur), e.g. on January 5th people searched for “argonaute piwi protein family” and “youd prefer an argo” and then landed here. One thing I have learned blogging is that Google can be a strange beast–at great frequency it gives you the content you want regardless of context, so if you have random pictures on your webpage largely irrelevant to any other content there, like I do occasionally, Google still sends ’em in and then it obviously becomes a reinforcing cycle.

And the Top 5 posts in 2010 were all written in 2009?! Hey, they’re oldies but goodies.

Let’s fill more than 31 747’s in ’11!!!

Fresh tees and blog nogs

Posted in Blog Affairs by YPAA on December 4, 2010

Betta recognize

Neel from Duke was good this year, so now a fresh tee below his tree. (He earned it commenting on my “GWAS” blog post.) This is one of only three that exist in the world right now (the designers of the tee, my friend Calvin and I, are the other two proud owners). It’s a nerdy inside joke around here, a legitimate lab reference we think sounds ambiguously cool and hilarious.

Merry Holidays from YPAA. If you’re cold like I am right now go sip on some egg nogs. Blogs and nogs to warm your insides. 🙂

Rock the Vote, Please

Posted in Blog Affairs by YPAA on August 13, 2010

Update 8/13/10:

This poll has been up for a month now, and to those who voted, thanks! The energy you spent firing your neurons and clicking your mouse was no vain excercise–I’m paying attention to your choices.

To those who haven’t voted yet, no time like the present!

I’ve been occasionally brainstorming what format of interviews would serve the blog best. My standard recipe for each blog post is (at least) 1/2 useful, and the rest humor, simmer for some time, and wah-lah. I anticipate not straying far from this for short interviews. But the thing is, the people I have in mind, you probably haven’t heard of them before, so will you care to read what they have to say? Just trust me on this one. If it ain’t good I ain’t posting it.

The offbeat stuff/humor will continue. Glad you’re enjoying it. Was the last post working for you? I was watching Chappelle’s Show the night before I wrote it (and feeling a bit open access-y), and it popped out.

And brief commentary on papers. My first attempt at this was fun, and not nearly as time consuming as doing one of the full-length write-ups. As you’ve surely noticed, only some of the RNA Journal Club papers get full write-ups. This is because not all presenters are interested in contributing (despite my pleas). This is totally understandable, because all these people are incredibly busy! They’ve already taken the time out of their schedules to present a paper to colleagues, and then to have to write up something about it, it can just be too much. (The corollary to this is that all the people that DO write-ups posted on the blog, noted by their names or occasionally “Anonymous”, are tremendous mega-pimps.) So in the absence of a full write-up, whenever I can easily distill good commentary heard during a presentation, perhaps mixed together with my thoughts, I’ll try to post that. Summaries-schmummaries.

More movement on the above would be happening lately, but gee-whiz, Boston can be mighty nice this time of year, and I’ve been trying to soak more of it in. That’s an excuse. Fall is when shit gets all academic though, and I’ll be out of excuses by then.

Input up to three choices, including entering your own.

RNA JC posts shuffle

Posted in Blog Affairs, RNA Journal Club by YPAA on June 4, 2010

The RNA JC posts for the past month aren’t in chronological order right now. I’m reposting them to the top of the queue when I get summary and analysis to add, rather than burying them down chronologically where you might miss them, a practice I’ll adhere to from now on.

Please enjoy the three most recent write-ups by Pavan and Vikram (below), and Igor (above). They presented three high-impact papers that should be of great interest to you. Kudos to the presenters for setting aside time in their busy schedules to do write-ups.

Click this link

Posted in Blog Affairs by YPAA on May 28, 2010

The allure of Vienna, and regulatory RNAs

Posted in Blog Affairs, Conferences by YPAA on May 22, 2010

I will soon share my thoughts on the Vienna small RNA conference, once I’m comfortably home in my lab computer chair, custom ass-groves and all, but the short of it is “most-excellent.”

In the meantime, hop on over to the “MolBio Research Highlights” blog, run by my blogging compadre Alejandro Montenegro-Montero, to read a guest post I was selected to write, “The allure of regulatory RNAs.” For most readers of this blog, my reasons could sound obvious, but I’m curious to know what you think. So chime in over there, or here, if you wish. At the very least, CLICK THAT LINK.

Now back to more pertinent business: drinking Budvar 12 degree. I’m in Prague right now.

Happy Birthday!

Posted in Blog Affairs by YPAA on March 15, 2010

Today You’d Prefer An Argonaute turns one year old! If you ask me, it’s still as cute as the day it was born. And it’s had an exciting year, with now 93 posts, close to a couple dozen comments, and more than ten-thousand and eight-hundred views.

I’m having a blast rearing YPAA, and a massive chunk of credit must go to these other outstanding nurturers (in chronological order): Anna Drinnenberg (twice), Joel Neilson, David Weinberg (twice), Anonymous 1, Michael Nodine (twice), Robin Friedman (twice), Noah Spies, Graeme Doran, Anonymous 2, Anonymous 3, Vikram Agarwal, Jenny Rood, Igor Ulitsky, and Mohini Jangi. (Thanks also to Margaret for running the MIT RNA Journal Club, YPAA’s baby food.) They’ve help raise this blog to be what I’d dreamt of a year ago–a community effort to highlight and analyze new work in RNA biology. It would be pretty Dubya-ish of me to go ahead and declare “Mission Accomplished,” so I’ll make sure YPAA keeps growing for a while.

If there’s anything you’d like to see on YPAA, or you have suggestions for improvements, just fire through a comment below. If you’re interested in contributing, I’m interested in you contributing (see “How to contribute to YPAA” page in column to the right).

Now back to the birthday celebration–turns out YPAA shares its birthday with other notable folk: an American president, and a couple sex bombs. Fate, I suppose.


Andrew Jackson


Eva Longoria

You'd Prefer An Argonaute

Give YPAA a birthday present by voting below!

My blog is bigger than yours

Posted in Blog Affairs by YPAA on February 25, 2010

Yeah, get used to it bud. We hit five figures. Next stop: six.

You’d Prefer a… Cadillac?

Posted in Blog Affairs by YPAA on February 5, 2010

Try this:

  1. Hop to Google to do an image search and enter “cadillac” as the search term. Yes, as in the the General Motors owned, automobile brand, Cadillac.
  2. Scan the first (or second) page of results and look for the picture of the old pink Cadillac convertible with a grey background.
  3. WTF?

The image is from a post where I compared Venki Ramakrishnan to a Cadillac. Strangely this operation has been contributing many recent blog views, inflating YPAA’s stats, which I find a bit annoying. In general, the search terms that people enter to arrive at YPAA are pretty spot on, in terms of who I target, but apparently sometimes Google redirects the gearheads and classic car lovers to get their learn on, YPAA style.


A new competitor RNA blog emerges?

Posted in Blog Affairs, Open Access by YPAA on January 14, 2010

The new open access journal Silence, which covers RNA directed gene regulation, has a blog. (Hat-tip to my colleague I.U.)

Their first post describes the blog’s aims, some of which bear some semblance to aims I put forth at the inception of YPAA, as here. Their second post covers a “HOT paper”, with a summary and analysis. Hmm… What a great idea!

Two potential explanations: (1) Some people at Silence saw YPAA and aim to replicate it to support their journal; (2) Some brilliant people at Silence haven’t seen YPAA, but independently came up with the idea to start a blog like it.

Either way I’m flattered and I welcome Silence to the blogosphere.

As for the journal itself, I look forward to seeing what it can accomplish. The scientists who founded it, and those on its editorial board, are impressive. It’s peer reviewed. And two thumbs up for being open access! I want it to be successful.

However, while I suppose a journal like this was inevitable, given the explosion of RNAi/non-coding RNA related research in recent years, a potential downside is what it signifies for the importance of the work in the field. Does it denigrate the work of the field if you have to make a new journal to publish it in? Aren’t there enough journals already to publish in? Perhaps some researchers in the field feel a bit like gypsies, without a warm, inviting place to call home when the more luxurious publishing groups say “No Vacancy.”

It’s emergence is probably also a sign of the times. More science by more people means more specialization. More competition at the top, and the desire to have less at levels below. I know near nothing about the current state of publishing, but I imagine even right now some of the more specialized journals (e.g. RNA, NAR) are breaking at the seams trying to pack in all the new RNAi/non-coding RNA papers. The trend toward open access is also present.

During his talk at the Keystone conference last year, Victor Ambros formally introduced Silence and encouraged submissions, providing an anecdote: back in 1987, a famous scientist (I think he said his post-doc adviser H. Bob Horvitz) encouraged him to publish in a new journal called “Genes and Development.” (He did.) It would be great if Silence followed a similar trajectory to G+D’s. If it modeled it’s blog partly after YPAA, I’d say it’s well on its way.

No RNA Journal Club 12/24/09 or 12/31/09

Posted in Blog Affairs, RNA Journal Club by YPAA on December 23, 2009

The RNA Journal Club and YPAA are taking a winter holiday.

As my fellow RNA Journal Clubeans disperse throughout the country and world to rest, the scientific enterprise suffers at the loss of their minds focused on what interests you. As heavy a toll this will take during these two weeks, I offer myself brief respite on two occasions: the assembly and devouring of mouthwatering tamales on 12/24/09, with kinsfolk in Los Angeles; the purchase and consumption of mouthwatering alcoholic beverages, in moderation, with friendfolk in San Francisco on 12/31/09. (For the latter, if you want to join,!)

But 2010 beckons. More greatness to come.