About the RWA parody at The Scholarly Kitchen

Interested in scholarly publishing? If you are reading this blog, I’m sure you are (I’m assuming you are a scientist. If you are not, let me know! I’d love to know who else is reading this).

Please take a look at this post by Kent Anderson (CEO/Publisher of the Journal of Bone & Joint Surgery, Inc), entitled “Revisiting a Little-Known RWA of the Past — The Restaurant Welfare Act of 1958“, a “satire” wrote about the Research Works Act. This is at the Scholarly Kitchen blog.

I won’t comment about it here; instead, I strongly advise you to read it, particularly the comments section, in which Anderson takes a swing at the PLoS ONE business model when Michael Eisen starts commenting.
Some of Anderson’s arguments, in which he clearly exhibits his disdain for PLoS One, appeal to a somewhat outdated publishing “world”, in which the internet and its ability to connect scientists from all over the world and find new research articles, regardless of where they are published, is not considered.

He claims that journals serve only two purposes, “quality validation and relevance signaling” and that PLoS ONE does neither. My comment above goes to the 2nd statement. I don’t need a journal to tell me what articles to read. Library days are over. I won’t go the library and pick up a copy of Nature or PNAS (or whatever journal has published an article related to my work, at least once) and hope there’s something there related to my research. I have email alerts now and have all the information, from all journals (currently I’m getting my alerts from Pubmed), so I can find articles related to my research. Hopefully, when I click on the links I get, I’ll be able to download the article in order to evaluate it…

(and before you say anything, no… I don’t think that just by looking at the journals indexed in Pubmed, I’m supporting the ‘relevance signaling’ argument. Do you know how many journals are in there? And PLoS ONE is there too).

This is how Mike Taylor puts it:

As a point of information, the relevance signalling part of this is no longer true (though it used to be). It’s now been many years since I read a paper on the basis of what journal it was published in rather than what it contains. Most papers I read, I am hardly even aware of what journal it’s in.

To which Anderson replies “well, that’s your experience“.

Anyway…. take a look at the parody.

 

Update (14Feb2012). Anderson blocked the comments on his post.

Debating about peer review

Peer review has been under attack lately, particularly due to the whole Arsenic Life story. These criticisms though, are not new, and new approaches have been proposed, for a long time, to address some of  its weaknesses.

I just want to share with you a Nature‘s web debate, consisting of “22 articles of analyses and perspectives from leading scientists, publishers and other stakeholders“, discussing peer review and addressing questions such as “What is the best method of peer review?”, “Is it truly a value-adding process?”, “What are the ethical concerns?”, and “how can new technology be used to improve traditional models?”.

Go check it out!

Also, be sure to follow fellow biologists Jonathan Eisen (@phylogenomics) and his brother Michael (@mbeisen) on Twitter, for more about these sort of debates, and everything related to scientific publishing.

There are far many more that I could recommend, so just get on Twitter and let your timeline guide you through the Science Twitverse.

Boycotting Paper Submissions To Glamour Journals?

Go check these fascinating blog posts (and particularly the comments section), for a great discussion on the subject, which got started by a post on Michael Eisen’s blog.

1) From ‘it is NOT junk’: The widely held notion that high-impact publications determine who gets academic jobs, grants and tenure is wrong. Stop using it as an excuse (which he now has updated, considering all the comments).

Well, not that kind of Glam magazine

2) From Comradde PhysioProffe: Boycotting Paper Submissions To Glamour Journals.

3) Also, on that same blog, the day before, on a post entitled “Boycotting Paper Submissions To Non-Open-Access Journals“, Comradde PhysioProffe says:

And the way that we do this is not by telling one of these poor fuckes not to send their beautiful work to a particular prominent journal for political reasons. Rather, we fight tooth and nail on hiring, tenure/promotion, and grant review committees against the abdication of responsibility for judging the importance and interest of particular lines of research to non-scientist editors at legacy “high-impact” journals.

Nice.

I also want to direct your attention to other quotes from the comments section, which I think either partly convey my opinion or that I simply want to share with you.

In any case, this is what I posted on twitter about it: “The important thing is that people who sit on committees & do the hiring and promotion realize that it’s not all about publishing in Glam J“. Note that I’m not against those journals, just against scientists who consider publishing in those journals (and NOT the candidate’s CV per se) a proxy for excellence and consider that if you don’t have those, then maybe you are not the best candidate for hiring/promotion, or worse, if you have them, even if they don’t even read them, you become to them a serious candidate and disregard others.

Let’s go with the comments. Again I’m not saying I agree with all of them, I just found them noteworthy.

1)

The fact is it does make a difference because too many colleagues are convinced that SNC papers are a proxy for high quality. The argument that some get hired without such papers doesn’t mean that SNC papers do not increase the chances of early stage scientists to get their dream job.

(Sophien Kamoun,link)

2)

But not everyone is privileged like that, and cannot be expected to do the same. I was a post-doc in the just-started lab of an assistant professor with no real reputation and definitively not plugged into the Hughes network. If I didn’t publish the most important part of my post-doctoral work in Nature, I wouldn’t have ever got job interviews at the kind of institution where I am now employed.

(Comrade PhysioProf,link)

3)

Of all graduate students, probably about 10% end up getting a job in academia, if that many. Out of those, there have been rumors that there have been candidates who worked 9-5 and never published in CNS and also got a job. This may be the case, but are you going to bet your rent, food and clothing on that you are going to be one of those fortunate few?

(Björn Brembs,link)

4)

While participating on faculty candidate searches (both as a graduate student representative at one institution, and as faculty at my current institution), I have not only seen the Science/Nature/Cell (and PLoS Biology) effect, but also the “lab of origin” and “institution of origin” effect. That is, the lab (and institution) where you did your PhD and Post-Doctoral work had a substantial effect on how some members of the committee perceived the candidate. While the quality and “substantive” nature of their scientific work was also important, both the journals they published in and where they did the work seemed to (at least sometimes) override other considerations.

(Ian Dworkin,link)

5)

Dude, no one is trying to shoot the messenger. As I have already said, it’s great for people with sufficient institutional and reputational status to tell the glamour mags to fucke offe. But it is wrong to vilify those in weaker positions to go along to get along

(Comrade PhysioProf,link)

A new chapter in the whole Arsenic Life story… yes, this is still going…

OK, so there’s a new chapter on the whole #arseniclife story. Redfield has deposited an article in arXiv (and submitted it to Science at the same time)  in which she challenges the original claim made by Wolfe-Simon et al¹, which is that there is a bacterium that can incorporate arsenate into its DNA.

This is how she puts it: “Our manuscript reporting the lack of arsenate in the DNA of arsenate-grown GFAJ-1 cells is now available on the arXiv server“.

Felisa Wolfe-Simon (Photo: ZUMA Press)

Notably, through an email, Wolfe-Simon now writes that she “never actually claimed that arsenate was being incorporated in GFAJ-1’s DNA”…. which is, to say the least, weird (just look at the article’s abstract!).  See Jonathan Eisen’s post about this.

I applaud the openness of the whole process (see Redfield’s blog), although I’ve always considered that Felicia Wolfe-Simon was treated badly in an unjustifiably way, and at first, the whole idea of going out of your way (when you don’t work directly in that field, see below) to do a series of experiments (and everything that it implies) to disprove a group (or to do the proper controls, however you want to see it), seemed extreme to me, particularly when the funding agencies haven’t give you the money to perform that particular research (which is something she recently acknowledged). But I digress…

Regarding the harsh treatment that Wolfe-Simon has received…. what about all the other authors, all of which are responsible for the manuscript? Apparently, only Wolfe-Simon has been the target of all the criticism and she has stepped up to reply comments and give interviews (See also Redfield’s post about it)

Here’s Larry Moran’s take on this new chapter in the story of one of the most overhyped scientific articles of my time…

Larry Moran: The Arsenic Affair: No Arsenic in DNA!

In any case, I think the matter is far from solved and I’m sure Wolfe-Simon et al will find some problems with Redfield’s approach, which will make this whole story even longer… I’m quite tired of it if you ask me…

–

¹ Wolfe-Simon et al (2010) A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus.Science 332(6034):1163-6

Sadly, it is entirely true…

Sh*t grad students say….

Quotes from the science world: qPCR

Socrates once said, “Know Thyself”… “the unexamined life is not worth living” … well in RT and qPCR …
we must say, “Know Thy Samples” … “the unexamined sample is not worth measuring”

-JMG

 

Bringing a little philosophy to the “art” of qPCR.

(image credit)

The MolBio Hut highlighted in the ASBMB website

First, we know… We haven’t been updating the blog as regularly as we would have wanted, but both Francisco and I are in our last part of our PhDs and time has been scarce. We have, however, a new Direct Connection post in the pipeline, and we  continuously update the “Around the Journals” RSS feed, so you can keep up with the best in molbio research. Further, in our Twitter accounts (@aemonten and @biohighlights), we are regularly posting fascinating molbio-related stuff.

Now, despite our reduce posting rhythm, we have been highlighted in the “ASBMB Today” website! ASBMB “is a monthly publication distributed to all members of the American Society for Biochemistry and Molecular Biology“. In the section entitled “Biochemistry and molecular biology blogs in brief”, Aditi Das described our blog and posteda snazzy picture of Francisco.

Go take a look!

“Around the Journals” gets a Twitter account!

Our fantastic tool, “Around the Journals“, in which we share recent fascinating articles in molecular biology, can new be followed on Twitter!

Just follow @biohighlights for the best research in the field.

The Top 50 Universities in the Life Sciences

Quick post just to direct your attention to the “Top 50 Life Sciences universities” ranking posted at the Times Higher Education site (with data from Thomson Reuters).

From a totally US-dominated ranking (there are only 11 countries represented in the whole list), I’ll just give you a preview of the Top-10:

Harvard University
Massachusetts Institute of Technology
University of Cambridge
University of Oxford
Stanford University
University of California, Berkeley
Yale University
Princeton University
Imperial College
University of California, Los Angeles

Also, there’s a free Times Higher Education World University Rankings iPhone application, “which allows you to change the weightings of our five broad indicators, filter results by country and region, and match your personalised rankings against cost-of-living and undergraduate tuition-fees data“.

Blog about your research and get an Amazon Giftcard!

As you may already know, we’ve always wanted to have a place where molecular biologists can discuss science. That’s why we created MolBio Research Highlights first, and then, The MolBio Hut.

One thing we thought was a good idea, was the “Direct Connection” section in our blog, in which scientists can discuss their own recently published work. This is how we put it when we first launched it:

The “Direct Connection” section at “The MolBio Hut” includes blog posts discussing primary research articles in the field, but these posts are written by the authors themselves. This allows them to discuss the background, results and implications of their work with a wider audience and in a more relaxed format. We hope that this direct link between the authors and the scientific community (hence its name), promotes discussion and interaction with scientists in other fields.

We would like to promote this initiative by inviting grad students, postdocs and even PIs to write a short post discussing their recently published papers. The benefits of blogging are plenty and have been discussed elsewhere (see here, here and here for some thoughts about it), so what better way of getting into it than by discussing your own work?

Just to get things rolling, we will give contributors a 25 USD Amazon Giftcard and we will promote their posts and labs in the web for their research to get the widest dissemination possible (through Twitter, Researchblogging, etc).

By also posting the author’s contact info (twitter account, for example), we hope to create a network of molecular biologists.

So what are you waiting for? Have you recently published a paper in the (wide) field of molecular biology? Then write a short post about it, let people know about your research and its implications and get a giftcard out of it!

Drop me a line with your proposal. We look forward to your posts!