Thursday, July 30, 2009

A few ideas for grad students in the life sciences to keep in mind

After 4 years of undergraduate education and a year in the US and here in Chile working as a tech, I finally applied and successfully made it into grad school, some time ago. I remember how anxious we all were (me and my new classmates) back then about entering a PhD program in molecular genetics and start doing research at this fascinating time in molecular biology.

I remember talking to a lot of professors about grad school and reading a whole lot of papers about life as a grad student before I started. Everyone has an opinion regarding the do’s and don’ts of grad school and a recent blog post over at BiteSize Bio [Pointers for New Graduate Students] prompted me to write down a few ideas and concepts I think should be considered by grad students in the life sciences.

So, let’s get down to business.

In my opinion, the most important decision in grad school is to choose the right lab, and more importantly, the right PI. Not only will it be important during your time in grad school, but for your life as a scientist after you graduate.
Of course the lab’s research topic should be appealing to you (you’ll be working for 4-5 years on that) but if your PI has no interest in you or your work, you’ll never get anywhere and you’ll surely be miserable.
So, what makes a PI the right one? You want an interested supervisor, who cares and genuinely gets excited with your research, who gets involved (although not too much, however this depends on your own needs), who is in the country more than he is abroad during the year, or that when away, can easily be contacted (through Skype for example) and is respected (and you should not confuse this with being an “old”, well-established professor; newly appointed assistant professors can also be well-respected, particularly in a small field in which their postdoc work has had some major impact).
Moreover, you should be able to talk to your supervisor without fear! If you are sweating bullets before entering a one on one meeting with your PI, maybe he’s not the right PI for you (See “Psycho” in the figure). You should be able to discuss your results (and science in general) comfortably with your supervisor, the person controlling an important part of your near future. I’m not saying you should be pals (in fact, you shouldn’t), but having a nice, open relationship with your PI is a very important aspect of your formation.
Nine types of principal investigator. Created by Alexander Dent (
I remember Bruce Alberts once told me over coffee that you should run away from labs where your supervisor’s door is always closed or if there is a secretary between you and him/her. He said this not to be taken literally, but to emphasize that you should be able to talk to your PI whenever you need to.
Also, Jonathan W. Yewdell wrote
“(…) generally, you should run from laboratories where a PI is referred to as Doctor X and not by his or her first name” 1.
I’ve found this to be a more US-oriented recommendation, as in Chile, we generally don’t refer to our supervisors by their first names, but also, not as Dr X. “Prof” is something we usually use. Nevertheless, the point remains: if everyone is your lab must refer to their supervisor as Doctor X, you should be cautious.
Also important when choosing a lab is its environment. Are the people happy and enthusiastic about their research topic? Do they help each other out or is just an “every man for itself”-kind of environment? Is there a good “vibe”?
It’s a good idea to visit potential labs, talk to grad students and postdocs and ask them not only about their relationship with their supervisor but also with their peers. I can’t emphasize enough how important is to work in a “nice” lab.
Of course this is mostly wishful thinking, and maybe you won’t find a PI or lab with all the things you would want them to have, but my objective here is to let you know what things to look for so you’re clear in what you don’t want. 

Also, do rotations (if possible). Make use of this opportunity to get to know the inner workings of some of the labs you are considering. You won’t get a sense of how it is to work in a particular lab, until you do.
After covering (albeit briefly, I agree) on the most important aspect of grad school, namely, choosing your advisor and lab, I have a few more tips for grad students.
Sometimes you’ll read a paper that describes the technique you were looking for to solve all your problems. Neither you nor anyone in your lab or department has any expertise with it, so you consider that visiting the lab where the technique was developed could be a good idea. Be proactive regarding collaborations. Don’t expect your PI to do it for you; he/she has enough on his/her mind. Present the idea to your PI, make all the arrangements, contact the other lab, look for travelling fellowships, etc. This is something that you should do.
Attend the seminars in your school. This IS important. You can’t become a good scientist if you are completely isolated from other advances in biology. You never know… a major breakthrough in another field can have important, yet unobvious implications to your research, which could go unnoticed. Also, seminars in other areas can help you broaden your mind and make you reanalyze some results that have been in your mind for a while, with a different and fresh perspective. I’m including not only seminars given by people from other schools, but also departmental seminars. Maybe a technique you need has recently been standardized by a lab in other department.
Maybe there was something that you didn’t quite get at the seminar you just attended. Then, ASK. If you’re shy (or more typically, you don’t want to ask what you consider could be a “silly question” in front of faculty members), then approach the speaker afterwards, but don’t leave with the doubt.
The same applies when at conferences. Talk to people. Talk to other professors with whom you share research interests. Many of them will be excited to be approached by a young student. Lots of scientists (including myself) LOVE to talk about our own research, so use that. I generally approach PIs at meetings and this almost always leads to very interesting and provocative discussions.
Along the same lines, network: meet people and make connections. Sometimes, PIs have poster presentations, and poster sessions are great for talking to people in a relaxed environment, so this is a good chance to talk to them.
Another thing I consider important is to participate in scholar activities at your school. Are there graduate student seminars (GSSs)? Then attend, and more importantly, give a seminar yourself. GSSs provide a nice environment to discuss science in a friendly, relaxed way. You’ll also get to meet fellow students and learn about their research topics.
As a scientist, you’ll have to present your results to the scientific community, both as oral presentations or actual research articles. This tip is particularly direct to grad students whose primary language is not English: learn how to write and speak perfectly in English early in your career. There’s nothing worse than attending a seminar where you can’t make sense of what the speaker is saying. Further, you can’t ask him afterwards either. Everyone (including you) will benefit from a clear presentation: you’ll be able to present your work, answer questions and, as I’ve stated before, talk to people at conferences.
Also, if you can’t speak English, you won’t understand the seminar!
Having an English level that allows you to “understand papers” is not enough. If you can’t understand a seminar or talk to people, you’re doomed. This is a major aspect of a scientist’s life in the English-dominated life sciences. The same happens with writing. Train yourself in writing. Write a blog, for example. Talk to other members in the lab and ask them to review your writing. If you can afford taking an English course, do that: consider it as an investment.
Writing and speaking fluently in English is one of the most important things for a non-native English speaker scientist to develop.
I hope this short list can give some guidance or be of some help to grad students in the life sciences. I know I’ve left a lot out of this brief list, but it should be taken as a starting point. I particularly welcome any input on this topic as I’m far from being the most appropriate person to give tips (as I’m still in grad school). Nevertheless, I wanted to share my opinion with you and importantly, hear from you!
So, what do you think? What would you consider as important and useful tips for grad students in the life sciences?

1 Nat Rev Mol Cell Biol. 2008 May;9(5):413-6

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Monday, July 27, 2009

JANE: Journal and Author Name Estimator

I've just read over at Scienceroll about two tools that “help you determine which journal you should choose for publication”, based on your abstract or keywords [See Journal and Author Name Estimator and Huge Steps in Changing Science].

The first one is part of ResearchGATE (a “scientific network that connects researchers”) and the second one (which has been around for some time, since early 2008) comes as a standalone web application called "Journal and Author Name Estimator" (JANE). Note that to use the tool at ResearchGATE you must sign in.

Browsing around its site, I noticed that JANE was described in an article published in Bioinformatics in 20081, so I read the article and gave it a little try.

Here’s JANE’s description from its website:
Have you recently written a paper, but you're not sure to which journal you should submit it? Or maybe you want to find relevant articles to cite in your paper? Or are you an editor, and do you need to find reviewers for a particular paper? Jane can help!
Just enter the title and/or abstract of the paper in the box, and click on 'Find journals', 'Find authors' or 'Find Articles'. Jane will then compare your document to millions of documents in Medline to find the best matching journals, authors or articles
Also, here’s how it works (again, according to the info on its website -more details in the article-):
How does Jane work?
Jane first searches for the 50 articles that are most similar to your input*. For each of these articles, a similarity score between that article and your input is calculated. The similarity scores of all the articles belonging to a certain journal or author are summed to calculate the confidence score for that journal or author. The results are ranked by confidence score.
* For the computer geeks: we use the open source search engine Lucene. Queries using keywords are parsed with the QueryParser class, titles and abstracts are parsed using the MoreLikeThis parser class.
It’s hard for me to picture a submitting scientist SO lost that he/she  has absolutely no idea which journal publishes articles related to the work he/she is doing and with no clue whatsoever where to submit his/her work, to the extent that he/she would have to rely on a web-based application to enlighten him/her. I mean, surely he/she must have read an article or two for his/her own research and then have some sense of where he/she could submit. I agree that selecting a particular journal to submit your work is not a decision to be taken lightly, and in our case, after putting some thought into it, we generally narrow it down to 2-3 journals, but surely we know what journals have published work related (even remotely) to our own research in the past, from which we can pick our top 3.
In my opinion, using JANE for this is definitely not the way to go. I think it’s wiser to talk to colleagues at your department or at conferences. Their input will be more valuable and practical; some may have even submitted to some of the journals in your area and know a little about the inner workings of that particular journal. Also, at some conferences you can meet with journal’s representatives and discuss if your work would be suitable for their journal, or if you are lucky, they will approach you!
I tried JANE with several abstracts as query and it was kinda hit or miss: it generally gave the correct journal where the manuscript was originally published (not surprisingly, though) but some of the other journals in the list of “recommended journals” were not particularly related to the query as a whole, but to some particular words. This led JANE to propose journals (and this proposal was based on certain articles supposedly related to the query, published in those journals) that were way off.
Nevertheless, you will generally find journals that are indeed related to your input. The good thing is that you can check which articles JANE used to recommend the journals listed, so you can see if they are related as a whole or just because of a particular keyword in the abstract used as a query.
Furthermore, I fail to see an improvement large enough to justify not using directly Pubmed for this. If you put your keywords (although not whole abstracts) into Pubmed, you’ll get a series of articles with their respective journals and also, related papers. The way the authors justify using JANE over Pubmed is in no way satisfactory.
Despite all this, I think this tool can be useful for two things.
The first one is to discover “new” journals or to become aware of other journals (not from your typical selection) that have published related work in the past, so you can have a larger pool where to choose from. Also, you can narrow down your search to find Open Access journals, which is always good.
The second one is directed to editors or grant-awarding institutions: due to its “Find Authors” tool, it can help in finding reviewers for a particular article or grant.
Nevertheless, journals typically have a database with reviewers they generally use, but maybe a new journal (or editor) can benefit from this. I tried it with several articles in the different research areas I’ve been involved, and it generally turned up with a list of relevant researchers who would be appropriate for reviewing them. In my opinion, this is the best use for this tool.
In conclusion, I think that using this tool for “finding the most appropriate journal for publishing your results1 is definitely not the way to go, but I see some potential in using it to find related alternatives and, more importantly, as a tool for editors to find potential reviewers.

1Schuemie, M., & Kors, J. (2008). Jane: suggesting journals, finding experts Bioinformatics, 24 (5), 727-728 DOI: 10.1093/bioinformatics/btn006

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Friday, July 24, 2009

Tom Cech on catalytic RNAs

Tom Cech is someone that doesn’t need much of an introduction around here. Due to the "discovery of catalytic properties of RNA", he won the Nobel Prize in Chemistry in 1989 (along with Sidney Altman). Tom and his coworkers discovered self-splicing as a property of the pre-rRNA transcripts of the 26S rRNA gene from Tetrahymena: the intron was excised from the pre-rRNA and the exons were spliced together in vitro, in the absence of any protein1,2,3. In other words, the 26S rRNA precursor was able to splice itself in vitro.

We conclude that splicing activity is intrinsic to the structure of the RNA, and that enzymes, small nuclear RNAs and folding of the pre-rRNA into an RNP are unnecessary for these reactions. We propose that the IVS portion of the RNA has several enzyme-like properties that enable it to break and reform phosphodiester bonds. The finding of autocatalytic rearrangements of RNA molecules has implications for the mechanism and the evolution of other reactions that involve RNA.”1
This was the first example of a particular class of self-catalytic (self-excising) introns we now classify as “group I introns4.

I first met Tom at the Twelfth Annual Meeting of the RNA Society in 2007, where he gave the keynote lecture ("From the RNA world to the RNP world") and later on in Argentina in 2008, at a Gene Expression and RNA Processing meeting, where this picture was taken (back when I still wore my hair long).

Here’s a short interview by Richard Sever, where Tom discusses, very generally, RNA as a catalyst. He talks a little about the seminal discovery stated above, compares RNA- and protein-based catalysis and briefly discusses the evolution of catalytic RNAs.

I recommend that you download the video (rather than wait for it to load), as it is a 125Mb file.

1Kruger K, Grabowski PJ, Zaug AJ, Sands J, Gottschling DE, Cech TR (1982) Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena. Cell 31(1):147-57

2 Inoue T, Sullivan FX, Cech TR.(1985) Intermolecular exon ligation of the rRNA precursor of Tetrahymena: oligonucleotides can function as 5' exons. Cell 43 2:431-7.

3 Sullivan FX, Cech TR. (1985) Reversibility of cyclization of the Tetrahymena rRNA intervening sequence: implication for the mechanism of splice site choice. Cell 42(2):639-48.

4 Some group I introns can self-splice in vitro, but almost all are thought to be assisted by proteins in vivo.

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Monday, July 20, 2009

The Scientific article of the future

Cell Press has always been innovative [See Another one from Cell Press: free symposia! and references therein]. As a collaborative effort to redefine the way a scientific article is presented online, integrating the tools and capabilities of the online environment, Cell Press and Elsevier have launched a project called Article of the Future at its Beta Prototype site.

Together, they've compiled two prototypes with several features.
Some of them are:

A graphical abstract allows readers to quickly gain an understanding of the main take-home message of the paper. The graphical abstract is intended to encourage browsing, promote interdisciplinary scholarship and help readers identify more quickly which papers are most relevant to their research interests.
This is great as it helps you get the idea of the paper and its implications graphically. Note that this does not replace the written abstract; it's just an addition.

Research highlights provide a bulleted list of the key results of the article.

A figure that contains clickable areas so that it can be used as a navigation mechanism to directly access specific sub-sections of the results and figures.
And many others.

You can check the prototypes here. I particularly liked Prototype #1.

I think that taking full advantage of the most important platform used nowadays to search for and read articles (that is, online), is a great idea. As some have stated in the past (including my former PI) the print version of journals is inevitably heading towards disappearance unless it can find a way to compete with the complete set of tools provided by the Internet (commenting, sharing, rating, audio and video, etc) that enhances the reading (and science communicating) experience. Although I like my print version of Nature, as it allows me to read the News & Views section and editorials during my daily commute, I hardly use it to read the articles related to my research. I'd rather download them, file them, attach comments, etc and save them for good, without worrying about spilling my coffee over them or leaving them behind somewhere. Also, there's some great reference-managing software around nowadays to help you cope with the increasing amounts of articles being published so you can find a particular article in seconds, leaving the old days of diving into piles of photocopied articles to find the right one or visiting the library, behind.

But what about reading the articles online? Is it the same as downloading the article and reading it offline? This new approach by Cell Press and Elsevier, says no. The idea is to take advantage of the capabilities the online environment provides and to "allow readers individualized entry points and routes through the content, while using the latest advances in visualization techniques". Something not available in a simple PDF file.

You can download it just to have it backed up and organized and read it offline if you want to (although, who works offline nowadays?), but the idea behind the project is to enhance the reading experience by taking advantage of what the Internet has to offer.

I think that journals integrating and taking advantage of all the tools the online environment provides, benefits us all and can lead to better science communication.

Be sure to provide feedback to this project.

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Saturday, July 18, 2009

On Science cliches

Betsy Mason just published an article in Wired Science entitled "5 Atrocious Science Cliches to Throw Down a Black Hole" (thanks to @boraZ for the tweet).
In a nutshell, she argues that there are some "annoying and ubiquitous clichés" generally used in science writing that should be eliminated for good (the terms under fire are "Holy Grail", "Silver Bullet", "Shedding Light", "Missing Link", and "Paradigm Shift").

A few minutes later, a blog response at Mad Scientist Jr. called for the importance of these phrases in communicating science to the general public [In Defense of Cliches].

He says:
"(...)We need cliches. We depend upon cliches, and cliches are quite useful in the proper context. While it may be true that the above terms do get thrown about quite a bit, they're still quite useful. Science journalism is already a convoluted field that must continually walk the line between being too esoteric for its mainstream, non-scientist audience and maintaining proper accuracy to satisfy its scientific constituents, which keeps information flowing. Banning the use of any widely understood vehicles for explanation just raises the barrier to effective communication between science and the public. And when we, as a scientific community, have already made it clear that we're not usually pleased by the transmission of our findings to the public through the prism of science journalism, do we really need to throw in even more barriers? (...)"
I posted a comment at his blog post, which I share with you. Please note the text in blue was added for clarity and did not appear in the original blog response:

"(...) Even though I didn't initially think about this in terms of how we communicate science to the general public [I was thinking on their use in scientific papers, see below], the case you are making, makes complete sense and some of these so-called "cliches" may be, in this context, useful.

On the other hand, in technical writing [scientific papers, subjected to peer-review, published in scientific journals], some of those concepts may rightfully be discarded, but others (for example 'shedding light'), are, in no way misleading, ambiguous or confusing, and in my opinion, pose no problem to the way we write about science. In fact, in some cases are even welcomed, as they bring life to some very dull manuscripts. As long as they don't lead to any conflict or misunderstanding of the scientific ideas being discussed (and an example of such a conflicting term is indeed "missing link" -ugh-), I have no problem with them".

What do you think?

Note: for concepts that have been used loosely in primary research literature see [What is Epigenetics? An operational definition] and references therein.

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New journal from CSHL Press

A new review journal, covering all aspects of molecular biology, has recently been launched.

Cold Spring Harbor Perspectives in Biology (CSH Perspectives) is a monthly online publication from CSHL Press, with an outstanding editorial board (featuring renowned scientists like Tom Cech, Mark Estelle, Peter Lawrence, Tom Misteli, Paolo Sassone-Corsi and David Spector just to name a few), analyzing progress in emerging areas of molecular, cell, and developmental biology, genetics, evolutionary biology, neuroscience, cancer biology, and molecular pathology.

Interestingly, articles will be organized as "Subject Collections", which will "gradually accumulate articles as new issues of the journal are published and, when complete, each will represent a comprehensive survey of the field it covers".

This is a very attractive feature and I'm confident, considering its board, that the journal will keep up with the rapidly advancing pace of molecular biology.

Also you can follow the journal on twitter ( which is always a great addition.

We'll keep our eyes open.

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Tuesday, July 14, 2009

Great tweets of science

"Sckt it, Pauling!" lol.
(note the dates...)


(See it from its original source at PhD Comics)

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Sunday, July 12, 2009

The 100th post at MolBio Research Highlights

Our latest post, a discussion on the Cancer Stem Cell Hypothesis [Cancer Stem Cells: the root of all evil?], marked our 100th post.
I considered this to be a good time to talk a little about the ~7 months this blog has been around.

The blog, MolBio Research Highlights, was initially born to compile a list of articles, tools, websites and news in molecular biology I considered of interest [See So exactly, what is this blog about?]. With time, I decided I wanted to comment a little more extensively on the items I was posting and eventually these comments got lengthier and richer, as I sometimes discussed not only the item being highlighted but also related stuff. Indeed, some techniques in the field have also been posted, as an aid for interested young researchers [For example, see Analyzing the genome-wide chromatin landscape: ChIP-Seq].

As primary research literature in molecular biology was sometimes discussed, I decided it was a smart move to join, where blog posts on peer-reviewed research on different topics, are aggregated. Indeed, this attracted a whole lot of traffic to the site and also, through this initiative, I got the chance to learn about several science-related blogs with some very interesting writing. In this sense, I think MolBio Research Highlights stands aside, and through its novel approach joined a particular group of blogs: blogs where the content is written by scientists and more interestingly, for scientists, differing from many other blogs, for example, where science is discussed by some very talented, yet non-scientist/researcher bloggers, and are aimed at the general public, or others which are written by scientists but aimed at the general public. I consider all of these approaches valuable and needed at present, each within its particular niche.

Around that same time, Francisco Barriga, a cancer researcher at IRB Barcelona, joined the blog and his interesting insights in cancer biology have broadened our scope. Indeed, MolBio Research Highlights was featured for the first time in the Cancer Research Blog Carnival [Cancer Carnival #23] and we hope to participate in future editions.

I sincerely hope other young molecular biologists will follow Francisco’s example and get interested in participating in our blog to discuss new research and advances at this fascinating time in molecular biology. The doors are open.
You don’t have to be a regular writer to be featured here; if you occasionally find an article you’d like to write a post about, you are most certainly welcome to contact us with the idea.

We feel very satisfied with the way the blog has developed over the course of these few months, and even though we acknowledge there are still many things that can and must be improved, this has been a good start, in our opinion. We are particularly proud of some of our most-read articles, What is Epigenetics? An operational definition, On PLoS' article-level metrics and the rapid blogosphere hit Cancer Stem Cells: the root of all evil?

Please feel free and encouraged to comment on our posts and also to let us know who you are; do you also have a blog? Let us (and everyone else) know about it!

We hope to have been an interesting addition to the science-related blogosphere during these few months and to improve within the next ones.

Thanks to everyone who has been reading our blog.

[Image credit: Multitema]

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