Thursday, August 23, 2007

Nature precedings?

I was catching up on the latest Nature, reading about mice with OCD and how we graduate students are all doomed because only 30% of PhDs have jobs in academia (or if you really want to be depressed read the comments on pharyngula), when I noticed an add for nature precedings. Now there is a small explanation on the site of what the purpose of nature precedings is, but judging from the content it resembles PLOS ONE. Except there is no peer review.

"Nature Precedings is a place for researchers to share pre-publication research, unpublished manuscripts, presentations, posters, white papers, technical papers, supplementary findings, and other scientific documents. Submissions are screened by our professional curation team for relevance and quality, but are not subjected to peer review."

It seems you can just submit a paper and then people can vote on it, and discuss it. Most of the popular papers are about H5N1. I can see the usefulness of rapidly sharing some information, such as polymorphisms and possible antigens. Information sharing is key if an epidemic is ever to occur. And this type of information can probably get away with not having been peer reviewed. But when I perused the cancer section I noticed some strange papers. Take this one for example "metastasis as a faulty recapitulation of ontogeny". It reads more like an OP-ED than a review or paper. The premise is that transforming somatic cells with oncogene is like bringing back the cell to its original progenitor-like state. For example some lung cancer cells look like the embryonic cells that give rise to the alveolar epithelium. Well nothing new here. He author argues that these "progenitor-like" cells will behave like their embryonic counterparts and migrate in a similar fashion. Well nothing outlandish here either. He also argues that some of the metastases may implant in different organs and assume the identity of that organ and maybe remain unnoticed. While this is all somewhat interesting I doubt any of the ideas are novel enough to actually get published in one of the "real" nature journals. In fact that paper could have easily been published on a blog . Is this the future of science publishing? Is it a good thing?


Anonymous Coward said...

already there are some pretty shady things on there:
"According to our new viewpoint, Neandertals were neither one of our direct ancestors nor a different species. Their origin was not in Europe 150-200 or 300 thousand years ago. As for the origin of H. sapiens, it was neither in Africa roughly 2 million years ago nor roughly 200 thousand years ago. In other words, both the Multiregional model and the recent African origin model seem wrong. Our own species arose in the Middle East approximately 150 thousand years ago and split into two subspecies: Moderns and Neandertals."

Anonymous Coward said...

"...the paper was a poorly written intelligent design argument, thinly disguised as a research paper on ancient skeletal remains. [...] After wading through all the junk, I decided to find out who one of the co-authors, Omer Faruk Noyan, is. A google search turned up this petition questioning the validity of Darwinism."

The Key Question said...

Wow, that was quick!

As for the observation that graduate students are all doomed - I only have one things to say:

The palm trees whisper softly
In the scented balmy breeze
The clouds lean out to sea
With sound of luscious leaves

Oh Singapore Oh Singapore Oh come to our fair shore!

Oh Singapore Oh Singapore Our island we adore...

It's a song.

Bayman said...

Regarding science jobs. You don't go into science to get a job. No scientist in history to produce original work has ever had this motivation. Science is about pursuing an interest, not having a guaranteed paycheck and a nice little office. Scientists, like artists and writers throughout history, have been driven by their passion, an incessant need to question and understand their world, and an inescapable compulsion to learn and help others do the same.

Sure, many scientists end up with tenure and a yacht, but this is once the science is done, that it is so obvious that the scientist has contributed valuable knowledge to society, that universities feel they can get some added prestige to paying these people to hang around. This is also when the creativity ends.

Young students in science or any other field should not go into grad school because of the perceived guarantee that "the system" will provide them with a particular job or some sort of security or payback. This is not trade or vocational school. It is about learning to think and discovering how your mind works. Like scientists before us, we should be prepared, when our degrees are done, to continue to innovate and come up with creative ways of doing science while exploring the context of our society and how we can use our abilities to contribute to the people around us.

It is a common myth today that the role of universities is to "produce" "knowledge workers" that when finished are ready to "plug and play" so to speak to play their specific role in the "system" or "global marketplace". But if even the most educated of our society buy into this pre-determined way of life, how can we as humans ever hope to ensure the "system" functions to our collective benefit?

A utopian life of guaranteed security, prosperity and perfect health life can never be real, these are illusions - I hope our scientists and students of the future will continue to be able to see through the false promises and continue to help humanity learn about the real world, with all its flaws and imperfections.

Anonymous Coward said...

And that's why we love you Bayman, you're a dreamer and an idealist. Yes science is the worst possible way to get a job. Yes you should be in it because it's a passion, because you're curious, because you seek the truth. But at the end of the day you still need food on your plate.

Bayman said...

Food on your plate? Or maybe just beer in your belly?

You're right though, reality is a balancing act, and the scientific ideal is no more of an absolute reality than any other. One can pursue the ideal, but each must find their own path and sometimes make compromises along the way to the sake of survival.

But when I read articles saying there aren't enough ready-made jobs for PhD graduates I have mixed feelings. On one hand, we need to convince governments in particular, to invest much more in scientific research. But this is mostly our job - no one except scientists can really be expected to convince society of the rewards of their specialty.

All too often however, these types of articles smack of a sense of entitlement, that if you go into a PhD, the tenure-track, cushy academic jobs should just be there waiting for you when you graduate.

This type of naivety is most damaging to students themselves, making them ripe for exploitation as they slave away in the lab dreaming of the paradise-like afterlife of academia they are headed for upon graduation.

Ask any religious leader - people will do anything if they believe it will get them into heaven.

Anonymous Coward said...


Bayman said...

That said, there might just be some tenure-track openings here at the bayblab one day in the future, and linking to the bayblab or commenting on a story would certainly not worsen one's case when it comes time to review one's application....

Anonymous said...

Regarding the very last part of the post and the philosophy of peer-reviewed publishing, Bora and the folks at BPR3 have been having an interesting discussion about what exactly constitutes peer-reviewed research. It's an interesting read, and there are some other links in there as well. Check it out.

Anonymous said...

(I am a product manager for Nature Precedings.) In regard to the submission on Nature Precedings, I wanted to mention a corresponding discussion in our Nature Network forum where we responded to the allegations by Selena (the blogger quoted in the first two comments):

I'd encourage you to read the paper yourself and let us know what you think by commenting on the paper. We're especially keen to have researchers who work in this area comment on the paper.

Bayman said...

Thanks for the comment. I checked out the discussion on your site. Although I am not qualified to comment as an evolutionist on the paper (although I may do so anyway once I read it :) ), the comments bring up some interesting points about open publishing in general (with which I am more interested). In particular, Kojiro Yano makes a nice point we didn't do justice here:
"If someone finds problems with a preprint, s/he should criticise the publication rather than the publisher of the server. Of course publishers should implement certain quality control but I believe readers should also take some responsibility to maintain the quality of preprints to make the system work."

It's a good point, if we really want open publishing we can't cry out whenever a sketchy paper gets published, we just have to hope the expert commenters point out it's flaws appropriately.

That said, I think even open publishers need to have some level of filtering; perhaps this paper is evidence that Nature Preceedings has set the bar too low. That would be unfortunate, because if an open-access journal with the notoriety of Nature attached to it fails, there could be devastating consequences for the whole idea.

Anonymous said...

Hi Bayman,
Thanks for taking the time to read the discussion and respond--We also thought that Kojiro made a good point. ;)

I wanted to clarify one point--Nature Precedings is not a publication or a journal, and is not peer-reviewed, but a pre-print server similar to the physics pre-print server ArXiv. It is in some ways a step closer to the vision you described in your later comment (here): "a do-it-yourself process with a minimal need for organizing structures".

Precedings is focused first and foremost on facilitating scientific communication, and for that reason there may be documents that would not be appropriate for journal publication. The review by Ulf Rapp (mentioned above; also here) is an an example of a document that we thought would be interesting for other scientists working in the field, but would perhaps not be something that you would see in Nature (the journal).

NPG does provide some screening of documents (we basically assess whether the contribution is genuine and from a qualified scientist, which usually requires submitters to have a recognized academic affiliation), but it is the scientists in the community who will be weighing in on the documents and evaluating them.

I also want to point out also gotten some incredibly high quality submissions (some of which have later been published in Nature's own journals). We hope that you will look at other submissions, especially if they relate to your own field of study.

Bayman said...


Thanks for clarifying the objectives of Nature Precedings. I must admit my initial interpretation your goals was off-base. I assumed that the purpose of attaching such a website to an organization such as Nature was to provide some level of quality control typical of an open-access journal, along the lines of PLOS One. I actually think the idea of a using the web to share and discuss "pre-publication" data it a great one, however I'm not sure I see the need to do this on one centralized server such as Nature's. Many scientists are already doing this on their own personal websites or blogs. There's not necessarily a need to have all this information on one server or website, as it can all easily be found through a centralized search engine such as Google.

I guess I had an idea in the back of my mind that the impetus for print journal publishers to get involved in open-access publishing would be to integrate "pre-publication" data discussion and "real publication" into one dynamic process. Pre-publication data would just evolve naturally into a more complete body of work, as the author addresses criticisms posted in an open forum, completes new experiments, and releases follow-up data. The host (ie Nature Precedings) would provide the service of tracking the researcher's progress, feedback and responses that would be needed to provide indicators of productivity in lieu of something like journal prestige or impact factor (ie for those evaluating one's CV).

For Nature Precedings to be useful, I think it needs to be clear that there's an advantage to submitting data to that particular website, rather than posting the data independently using one's own resources. Admittedly I'm not yet familiar enough with Precedings to have an opinion, I guess we will see with time how people like it.

Again, thanks for taking the time to discuss the issue, and I appreciate the challenges you must face in your efforts to improve scientific publishing. Obviously it's much easier to criticize from the sidelines than to take the initiative to make things happen.


Anonymous said...

Hi Bayman,
We do provide some level of quality control, but much less than one would find at a peer-reviewed journal (or even an "internally-peer-reviewed" journal like PLoS One.) Many scientists are already choosing to share documents on their own blogs, however, posting on Nature Precedings means that one doesn't need the overhead of maintaining a blog or website. One can comment on each paper in the same way that one can comment on a blog, and we generally accept comments that are more informal than those that would be expected in peer-review (though more formal comments are certainly welcome).

I do think that Precedings provides some benefits that blogs do not. For every document, we embed DC-based metadata to facilitate indexing by search engines such as Google Scholar. Documents on Precedings receive DOIs (or, in select cases, Handles), which are registered with Crossref and can be used in citations and serve as a permanent identifier for that document. Finally, Precedings ensures that submitted documents are properly licensed and copyrighted, something which many authors do not consider when posting to their blog. (A recent article in CTWatch covers why this is important).

Of course, since material on Nature Precedings can be redistributed, one can jointly post on Precedings and on one's blog. For individuals who do this, we encourage them to submit a link to the blog post so readers will be able to reference both versions.

We are always looking for ways to improve Precedings, so if you have suggestions, please feel free to get in touch, or post in our forum on Nature Network.