Science reporting….

Just three cartoons on the matter.

From xkcd

From PhD Comics

 

From SMBC

I’ll take my sequence to go please…..

Oxford Nanopore Technologies has revealed the initial results from its GridION system and they look pretty exciting. They also presented MinION™, a sequencer the size of a USB memory stick. You can read all about it here, here and here.

The most striking thing about their announcement is that they claim that their technology, based on nanopore sequencing (you can check videos of the technology here), will allow them to sequence a human genome in just 15 minutes.

This announcement was made at the Advances in Genome Biology and Technology meeting in Marco Island, Florida. You can follow this meeting through Twitter, using the hashtag #AGBT.

The Lab Grammys 2012

The Grammy Award Ceremony was just held, but left out an important category for us molecular biologists: science parody of the year.

That’s right. Due to this unfortunate oversight, Biotechniques has decided to hold their own award ceremony “to honor this year’s best song parodies about our love-hate relationship with lab“.

I’m sure we all can relate.

Go check the nominees here!

Update: And the winner of this year’s Science Parody award was….

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(Image credit)

Quotes from the science blogosphere

An IF of 4.4 for a journal less than 5 years old, that does not pump up its IF by publishing review articles, and that does not pre-screen for scientific impact, is nothing less than remarkable

-Alex Merz (referring to PLoS ONE), in a comment at the Scholarly Kitchen

The ideal postdoctoral candidate

From Nik Papageorgiou’s blog.
You can follow him on Twitter, too.

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…

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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….