What is a "least publishable unit"?

I've recently linked to a Letter in Science arguing that there's nothing wrong with the publication of “least publishable units” (LPUs) and that we needn't worry about a hypothetical paper glut and it's alleged effects on paper quality, provided a rigurous peer review system exists (See Quotes from the science world). This was published as a response to this letter. 

Dave Bridges posted the following comment on my entry:

(...)to me the question boils down to what the least publishable unit is. Can you publish a single well controlled experiment. Or does it have to be in the context of a story?

So, I wanted to get your impressions on this matter. What do you think constitutes a LPU? How do you feel about these sort of articles, particularly in the context of the advancement of science?

Be sure to check the comments on my last post  and the two related Letters in Science (see here and here).There are pros and cons, obviously, so I wanted to know what fellow scientists think about this interesting subject, which has been discussed at length before, but for which new readers can have interesting insights.

Comment away! Also, follow me on Twitter, as fantastic discussions usually take place through it. 

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UPDATE: There are some comments over at Friendfeed.

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2010 - A year in review. We are now 2 years old!

Another year has gone by and it’s time to evaluate how 2010 was for us. Yesterday was my blogoversary, making MolBio Research Highlights 2 years old. In these two years, a lot has happened and this blog has evolved from being a place where I linked to papers I considered interesting, to a full blog where we discuss primary research articles in the field, link to interesting things in the web (including molbio blog posts), organize the MolBio Carnival, discuss life as a scientist and more (See here).

Let’s talk about some of this blog’s highlights for 2010 and some things worth mentioning about my professional life.

1) We were finalists for Best Expert Level Blog and I was a finalist for Research Twitterer of the Year in the 2010 ResearchBlogging Awards.

This was awesome. Even though we didn’t end up winning these awards, being a finalist among several candidates was enough for us.

I use Twitter a lot for topics surrounding research in the life sciences (I think the award was given to a “Science” Twitterer, rather than to a “Research” Twitterer, but anyway), and yesterday I used an application to make a word cloud for my Twitter updates for 2010.

The resulting cloud speaks for itself: I-tweet-science (see also below, where I discuss my Twitter use on an interview for Wiley). So, if you are interested in the life sciences I invite you to follow me!

As I tweet a lot about articles I consider interesting, let’s see what this cloud has to say regarding the topics I discussed in 2010.

Genome, transcription, genetics, RNA, chromatin, microRNAs, cancer, evolution, and lately, arsenic, are some of the most used tags.

Also, apparently I laughed a lot (I see “haha” in there) and talked to Chris Dieni and Psi regularly.

2) We started a series of posts under the title “The hottest molbio topics: the next few years”, which until now, has featured David Garcia and Keith Robison

We had a poll inviting people to vote for what they thought were going to be the hottest topics in the field in the next few years (see Which will be the hottest topic in molecular biology in a few years? The results), and I decided to share the results by accompanying them with blog posts by experts in the respective areas.

So far, David Garcia from You'd Prefer An Argonaute and Keith Robison from Omics! Omics! have talked about small RNAs and new sequencing technologies, respectively. Fascinating posts. Go check them out!

3) I got invited to write an article for LabTimes because of my blog post on Yeast Recombinational Cloning

I wrote a post discussing a very simple and efficient cloning strategy that we routinely use in our lab, called “yeast recombinational cloning” (See here). Some time after that, I was contacted by the people at Lab Times (“a new, free, Life Science journal for the whole of Europe”), and invited me to write an article for them discussing this methodology. I immediately accepted, wrote the article and it was featured in their 03-2010 issue. You can check it out here.

4) We took a top place in the 2010 HAL Medical Blog Awards, sponsored by Apredica, under the "Future Leaders of Biomed – Best Blog Award" category

As taken from their website:

“A search for “medical blog” in Google will get you more than 175 million results.

But of those 175 million results, which should you actually read? The 2010 HAL Medical Blog Awards, which highlight the very best blogs in health and medicine, aims to answer that question.”

Someone nominated us and we got a top place in the “Future Leaders of Biomed – Best Blog Award” category, which “recognizes the top blogs covering biology and medical issues that are by graduate students with exceptional promise”.

See my post about it here.

5) We started the “Direct Connection” Section

We created “Direct Connections”, a section which includes blog posts discussing primary research articles in the field, written by the authors themselves (see below). We have many of these in the works, but the first post of this series was written by Chris Dieni, who discussed his paper entitled “Regulation of glucose-6-phosphate dehydrogenase by reversible phosphorylation in liver of a freeze tolerant frog”.

Take a look at his post.

6) I was invited to write a post for Benchfly!

In early 2010, Benchfly organized the “Model Organism Week”, in which fellow science bloggers were invited to talk about some of the many organisms that have been instrumental for our current understanding of biology.

I wrote a piece for this initiative entitled “The Almighty Fungi: The Revolutionary Neurospora crassa”, in which I gave a historic view of the importance of this fungus for the advancement of modern molecular biology.

Go check it out!

7) We organized The MolBIo Carnival and hosted its first issue

A blog carnival discussing molecular and cellular biology was missing, so together with LabRat, Lucas Brouwers, Psi Wavefunction and Alex Knoll, we organized The MolBio Carnival, which groups together posts discussing peer-review articles, techniques, books and related topics in the field.

We hosted the first ever issue of this Carnival back in August (See The MolBio Carnival: the first edition) and this has been going one since then. The 6th one goes live on January 3rd, so there’s still time to get your posts in!

You can take a look at the Carnival’s history on its website.

8) I got interviewed for an article in Nature

That’s right. I was interviewed for an article discussing the "internationalization of science", which was part of a supplement entitled "Science masterclass", which commemorated the 60th Lindau Meeting of Nobel Laureates.

I won’t get into much detail and I encourage you to take a look to this article which was published back in October.

Francisco actually attended this meeting. Read his post entitled "My impressions on the recent Lindau Nobel Laureate Meeting"

9) I was selected as an Advisor for Wiley and was interviewed for their “Advisor Spotlight” section

The Wiley Science Advisors initiative aims to start a correspondence with young scientists and hear their perspectives on a variety of topics in science and publishing.

I’m currently involved in this program and recently, I was featured in their “Advisor Spotlight” section, for which I answered some questions regarding my online presence, i.e my blog and Twitter use.

Take a look!

10) I was interviewed by the PostDoc Forum

My interview for the PostDocs forum has just been published. I was kindly invited by Susan Steinhardt, who, despite of my "inattention to schedule", was continuously interested in featuring me.

Thanks Susan!

11) I’m a Mendeley advisor

This year I was selected as a Mendeley University Advisor. Mendeley “is a free reference manager and academic social network that can help you organize your research, collaborate with others online, and discover the latest research”.

I’ve given some talks in Santiago to fellow researchers on the benefits of using Mendeley and actually convinced some people to switch from other platforms to Mendeley. If you have any questions regarding Mendeley, please send me an email or contact me through Twitter.

12) I won a F1000 twitter contest

Back in March, Richard Grant organized a fascinating Twitter contest, in which the idea was to "post your most embarrassing scientific error or egregious lab-based manipulation to Twitter with the #scifubar hashtag".

I contributed with this little thing…

Undergrad said he couldn't "paint" the black lines on the autoclave tape as good as his supervisor (he even bought a black marker) #scifubar,

which got me first place!  Read about it here.

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Well, I guess that’s it. A whole year in review.

Thanks to everyone who has helped us throughout these two years and we hope to continue to be of service to all of our loyal readers.Yes, to all three of you :)

Happy holidays!

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Generation X-change

A few months ago, I was interviewed for an article to be published in Nature, on the topic of the "internationalization of science". Basically, the idea was to interview scientists from different countries to address "whether or not the exchange of people and ideas is changing how science is done in countries all over the world".

The article, entitled "Generation X-change", was published today as part of the Nature supplement "Science masterclass", which commemorates the 60th Lindau Meeting of Nobel Laureates.

Go check it out... there's free full access to all articles in the supplement!

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My impressions on the recent Lindau Nobel Laureate Meeting

I recently attended the 2010 Lindau Nobel Laureate Meeting, a “globally recognised forum for the transfer of knowledge between generations of scientists”. This exciting and mind-broadening conference was enriching in many ways (with actual science being only one of the many fantastic things about it), and in this post I’d like to share with you my impressions of it.

First of all, the historic city of Lindau (Germany) is a beautiful place, located near the Austrian, German and Swiss borders. The 2010 edition of this meeting was the 3rd one to be formatted in an interdisciplinary way, bringing together Laureates and young researchers working in biology, chemistry and physics. This made it all the more interesting since I had the opportunity to meet people from different fields and with varied backgrounds. 

Aerial view of Lindau Island (Image credit)

The meeting itself has been going on for 60 years now and it was started  after the Second World War as a way for scientists to meet each other and exchange ideas. The concept of also inviting students was put forward by one of the meeting's founders, the late Count Bernadotte. Interestingly, it wasn’t until 10 years ago that non-German students have been invited to participate. This year, notably, 70 different countries were represented at the meeting (or maybe I should say 71, because for some reason I was enrolled as a Spanish instead of a Chilean student), highlighting the global nature of this conference.

The lectures are available online, so if you are interested in the scientific aspect of the meeting, I encourage you to take a look at 3 that I considered to be among the most interesting ones in the biology field: Roger Tsien’s lecture (Laureate in Chemistry, sharing the Prize for GFP), Jack Szostak’s (Laureate in Physiology or Medicine, for his work on telomeres) and I highly recommend watching Oliver Smithies’s talk, which in my opinion, was really inspiring (you can comment on it here after watching it online).

The famous harbour entrance of Lindau (Image credit)

Besides getting to know more about the science behind a Nobel Prize, the thing that I considered to be most fascinating was the humane side to all of it. How researchers stumble upon findings (and most will tell you was sheer luck), and basically, how they went after the things they considered interesting and fulfilling. The take home message is this, then: work on whatever makes you happy and forget about prizes, they rarely come and if they do it is not by following any guidelines.

The other major aspect of the meeting is getting to know other students (undergrads, grad students, post docs and occasionally a young PI) from all over the world, which is always something exciting. The mixture of cultures, lifestyles and even research topics was remarkable. On this note I’d like to add that if you ever have the opportunity to attend this meeting (or another one of similar characteristics, if there is such a thing) I highly encourage you to attend: you won’t regret it.

In a nutshell, I learned 3 things from this meeting:

1) Work on interesting problems that make you happy.

2) Don’t be focused on awards and...

3) Do NOT walk from Lindau to Austria at 3 am (it was a 7 km walk back to my hotel!)

-Francisco

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(Top image credit)

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Where you end up publishing your paper...

...is not what's most important. Focus your time and energy on trying to do a good job and on being thorough and analytical about your research, rather than on worrying about metrics and whatnots....

I've just read a short article while browsing around the latest issue of LabTimes and wanted to share this short quote with you.

“Don’t worry about it, old chap. Your article is good, actually very good. And these days, good articles will be read – and cited – wherever they appear.”

Ralf Neumann (See the short story here)

This is actually very true in this day and age, when many life scientists find out about new articles through PubMed or other databases, rather than by browsing through the print issue of their favorite journal (or the corresponding electronic Table of Contents). At least in my case, I learn about new articles important for my research through customized PubMed searches (the results of which are sent to my email) and not by reading the Table of Contents of a few hand-picked journals. This would just be silly...

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(Image credit)

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A Biologist's Mother's Day Song

This is just awesome...

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So you want to work in Nature or other NPG journal...

As some of you may know, I have a deep interest in science publishing and a few days ago, I posted this question over at the "Ask the Nature Editor" forum.

I was wondering which of these two hypothetical scientists would have a better chance of entering the editorial team either at Nature or some of the other NPG journals.

a) Scientist with a recently awarded PhD degree. Published 2-4 papers during his/her formation. Works as an editor in a journal of a competing publisher for 1-2 years after obtaining his/her degree (the journal is one of his/her area of expertise). Applies for a job at NPG.

b) Scientist with a recently awarded PhD degree. Published 2-4 papers during his/her formation. Works as a postdoc for 1-2 years, publishing 1-2 more papers.
Applies for a job at NPG.

Both scientists are non-native English speakers.

What do you think? Who would have a better chance? Please post your thoughts!

You can then check Maxine Clarke's response here.

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Rules for presenting at Experimental Biology

Stop whatever you are doing! Yes, stop!... and go over to Professor in Training and read her hilarious post: Rules for presenting at Experimental Biology.

I especially liked the first one, because it's something that I generally have to remind my colleagues about:

1. Do not use comic sans on your slides. It sucks. And it makes you look stupid.

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After a long day...

After a long day, which included Neurospora crassa RNA extraction and cDNA generation (from several samples), picking transformants into slants (way too many...), Neurospora transformation (again, several samples), reading papers, mentoring undergrad and a lot more (I had lunch about 3 hrs later than usual), there is nothing better than relaxing in a nearby bar with friends...

I think I'll start things off with a nice piscola

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(Top image credit)

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Lab retreats: yay or nay?

Lately, I've been hearing a lot about lab retreats, mostly from labs abroad and I've been wondering why we don't have them here in Chile (or at least, it's not an activity that most labs here integrate into their yearly plans).

Is it because some PIs think it's a waste of "bench" time, or maybe because they think that lab meetings are enough to discuss the research of the different lab members, or maybe something else?

So, the following question is directed to fellow scientists working in labs that do have lab retreats. Why does your lab have lab retreats? In your opinion, what do lab retreats contribute to the advancement of the lab that weekly lab meetings can't? Do you like having them? Do you feel that every lab should have them? On the other hand, have you ever felt like the time spent in the retreat could be better spent in the lab? What about having them every other year, rather than every year, would this be better?

And to those who work in labs that don't have them, would you like to have them, or are you better off like this?

Please note that I'm all for lab retreats and I actually want to make them part of my lab's activities: I feel it's a good time to discuss new strategies, new directions and new techniques.
Anyway, I felt it was important to get input from people that have actually experienced lab retreats on a yearly basis.

Feel free to comment!

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(Image credit: both images are from lab retreats at Eric D. Brown's lab, which has a great website, by the way)

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Talking about a great work space....

Now THIS is the proper size for a desk in the lab (and the proper lighting as well)...

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(Image credit: the Nedivi Lab)

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Rant!

Next, me ranting:

If the email address the corresponding author provides for a publication is no longer valid after ONLY two years, then he/she should be arrested and beat senseless. Even more so, when he/she doesn't even have a personal website.

Thank you.

-AMM

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(Image credit)

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That struggling life in the lab...

I found this at the You'd Prefer An Argonaute blog and wanted to share it with you.

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Reposted from You'd Prefer An Argonaute:

Laboratory biological science hasn’t changed much in the last 40 years:

"What, the reader may ask, did we do in the 6 years between starting C. elegans genetics and publishing the first article on it? Since the animal has a short life cycle of 3.5 days, it should not have taken all that much time just to complement and map the mutations. Many visitors who came to the MRC Lab in Cambridge thought that we spent far too much time eating, drinking, and talking. Observing us only during normal working hours, you could see their point. If one arrived at the lab at the reasonable hour of 10 am, there was just time to open one’s mail before adjourning to the canteen for morning coffee, usually prolonged by a very interesting discussion on some aspect of science. This did not leave much time before lunch, which naturally was also accompanied by discussion that was terminated only by rushing off to attend an afternoon seminar on the Bohr effect in hemoglobin or the like. That brought one to afternoon tea and after that there was hardly enough time to start anything in the lab before adjourning to the pub for liquid and intellectual refreshment. It was only after dinner that the real work started and the lab then filled up with the owls. Even these bouts of work had to be interrupted, of course, for midnight coffee and more discussions".

Sydney Brenner, from In the Beginning Was the Worm . . .

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The Simpsons: PhDs and Grad Students

Here are the Simpsons mocking grad students and postdocs...




BTW, I make more that US 600 a year and I got rid of my pony tail BEFORE grad school, OK? :)

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What does Spring Break mean to grad students?

This?

Not quite.

To us, spring break, is just that time of the year when:

1) we don't have to wait in line at the University cafeteria
2) we can park wherever we want
3) we can sit wherever we want at the library
4) your PI spends more time at his/her office and thus, pops up in the lab asking how experiments are going, more frequently

(From Phd Comics)

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Yes we can! (work in a developing country)

(...) We showed unequivocally that working in a developing nation is no bar to doing excellent science. (...) Our key strategy was to work as a team with an innovative horizontal philosophy that involved people from different areas of research in various countries.

Such multinational collaborations are crucial to the success of science, technology and innovation in developing nations.¹

Exactly. Multinational collaborations are indeed required and not only in the context discussed in the article, but in general. Collaborations are, in my opinion, our best approach to the advancement of science.

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¹ From Nature 464, 486 (25 March 2010) | doi:10.1038/464486c

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10 Web tools, programs and applications that keep me sane

The very first thing I do every morning when I get to the lab is turn on my laptop (this is unless I did a bacterial transformation the day before, in which case the first thing I’ll do is check the incubator). Then, I usually review a number of things: I check my email, check the latest updates from my favorite journals/blogs, manage my PDF library, etc., in addition to organizing my lab day (although I usually do this the night before). To keep track of all this (which can be a lot) I use several tools and applications without which I would be a mess. Here’s a list of some of my favorites.

Let’s start with the Google stuff:

1) Gmail. OK, this is fairly obvious. I did try some alternatives, but let’s face it: Gmail rules.

I have customized my Gmail homepage though, using some gadgets from “Gmail Labs” (check for this logo () in you Gmail page):

a) Right-side chat: Moves the chat box to the right side of the inbox. This gives you some extra space on your left sidebar to put other things, for example:

b) Google Calendar gadget: Adds a box in the left column which shows your Google Calendar. See upcoming events, locations, and details (See image on the left and #4)

c) Google Docs gadget: Adds a box in the left column which displays your Google Docs. Shows recent docs, starred docs, and has fast search (See image on the left and #2).

d) You can add other stuff, by using “Add any gadget by URL”: adds a "Gadgets" tab to Settings, where you'll be able to specify the URL of any gadget. This gadget will show in a box in the left column. There are several third-party applications that you can add.

e) And finally, “Navbar drag and drop”: Allows you to reorder the items in your navbar using drag and drop.

2) Google Docs. As you can “create and edit web-based documents, spreadsheets, and presentations and store them online so that they can be accessed from any computer”, it is ideal for documents that are frequently used and updated by all lab members. Be sure to back-up frequently: you never know.

3) Google Reader. Fantastic web-based aggregator to keep track of all your favorite journals, blogs, news, etc. You can easily add subscriptions, email content to colleagues, add tags, share with friends, organize using folders, etc. You should definitely use this or some other sort of RSS aggregator/organizer (if you don’t even know what RSS is, see here).

4) Google Calendar. I use it to schedule meetings, appointments, etc. A great thing about Google calendar is its very customizable “Notification” system. You can ask for pop-ups, emails and even free SMS to be sent to you at any time you specify before a scheduled event.

Note that all of these fantastic tools and many other Google applications work on phones (and not only iPhones). Check Google Mobile for more info.

OK, enough with the Google stuff. What other tools and applications do I use?

5) Remember the Milk (RTM) A great customizable task manager (like a to-do list). Normally I’d simply use pencil and paper to organize my daily tasks (e.g. Neurospora transformation, colony PCR, etc), but this has worked great for me: no risk of losing the sheet of paper.

A cool thing about it is that you can add your list as a gadget to your Gmail homepage (see image on the right and #1d), so you can check and manage your tasks, email, calendar and access your shared docs all in the same place (your Gmail page). Some may argue that this is the same idea behind iGoogle, but the gadgets in iGoogle, particularly Gmail, are very limited. You can also access RTM through your phone and it's compatible with Google Calendar.

RTM is free, but you can pay for some additional functions.

6) Tweetdeck. I really like this (free) software for managing my Twitter account. It has a multiple columns format, an in-built URL shortener, and many cool features. Further, I like the interface. It’s also available for the iPhone.

7) Mendeley. Free reference management program. I only use it to manage my (huge) PDF library and access the articles quickly (like “Papers”, but for Windows PC). Its MS Word plugin for managing references in a document isn’t quite there yet: it still can’t manage journal abbreviations, so, for example, it won’t give you a bibliography in Nature’s format. For managing references in documents I use Endnote (and Endnote Web), although I may try CiteSmart soon: it seems simpler and quicker (both Endnote and CiteSmart are non-free).

Note, however, that the “Journal abbreviation” feature has already been suggested at Mendeley’s website.

8) Foxit Reader. A (free) small, fast and rich PDF reader (there's also a paid version with more functions).

9) Mozy. An online backup service. You can select what folders to back up (backup your lab folder!), and the software will do that on their servers automatically. If you have more than one computer and need backup and syncing, you may find DropBox more useful.
Free and paid plans.

10) Microsoft OneNote. For those ready to make the jump to a digital lab notebook, this is a very good choice. I must admit that there are several other alternatives out there that I haven't tried yet, but this works fine.

You may find many more useful tips, tools and applications over at ProfHacker (which you can also follow on twitter @ProfHacker), Lifehacker and Hackademe.

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(Image sources: RTM Gmail Gadget, Calendar and Docs gadgets)

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