Nature's Editors on Paper Selection

For many researchers, perhaps especially for those in graduate school, the successful publishing of a paper in a journal such as Nature or Science is the pinacle of professional success. General wisdom, backed by hard numbers, shows how difficult it is to publish a paper in such high impact journals. But is that difficulty solely do to the immense competition for limited space? Or are researchers also battling a specific editorial agenda that seeks to pick papers for publication based upon a set of limited criteria. According to the editors of Nature, the answer to those questions is no.

Today in Nature, an editorial discusses the journal's paper selection process. The editorial seeks to address several "myths" about the selection process at Nature, including that "Nature's editors seek to inflate the journal's impact factor by sifting through submitted papers (some 16,000 last year) in search of those that promise a high citation rate", or that the editors "allow one negative referee to determine the rejection of a paper".

The editors seek to dispel these myths using specific examples and descriptions of their role during the paper submission/ peer review process. In the end, the editors claim, the choice to publish a paper in Nature is not based on the authors identities, the potential impact factor, or the opinion of any particular referee. Instead, they "make the final call on the basis of criteria such as the paper's depth of mechanistic insight, or its value as a data resource or in enabling applications of an innovative technique."

While their statements are interesting, I find it highly doubtful that any single editorial will dispel the pervasive and proliferative myths that will inevitably surround the process of entry into the upper echelon of published authorship. What is interesting to me are the potential motivations behind the publishing of the editorial. What stressor triggered Nature's editors to publicly refute these (rather specific) myths? The first paragraph of the editorial states that "as the current headlines make all too clear, controversies over scientific conclusions in fields such as climate change can have the effect — deliberate or otherwise — of undermining the public's faith in science." Are the editors of Nature reacting to events such as the high-profile retraction by Lancet of the Autism/MMR Wakefield study? Do they believe their reputation is at risk due to "number of false impressions that [they] have become aware of in and beyond the research community"? How specific are the reputations of scientific journals such as Nature outside the research community? Can we expect the general public to differentiate specific scientific journals, or is it more realistic to expect a more generalized view of the publication process?

What are your thoughts? For those researchers out there, thinking back to the days before you made your living doing research, do you remember paying attention/having a decided opinion about one scientific journal over another (or any scientific journal for that matter). Does anyone have friends/relatives/spouses/acquaintances who are both members of the general public and followers of the publications in Nature/Science/scientific journal X?

Nature's Choices. Editorial. Nature. 63, 850 (18 February 2010) | doi:10.1038/463850a

Renovating Stanford Hospital

For the past year, I've been hearing murmurs concerning a planned renovation of the Stanford Hospital. And as fond as I am of its odd exterior and asbestos ridden basements, Stanford Hospital is long overdue for a major renovation. This afternoon, I just happened to virtually stop by the Stanford Hospital website. While there, I found evidence that this much needed renovation will actually be occurring at some point, in the form of a dedicated website. This website presents the cunningly branded Project:Renewal, and claims that Stanford Hospital is slated to be rebuilt, with the Packard Children's Hospital getting an expansion. Also,  "outdated laboratories at the School of Medicine" will be "replaced". Judging from the project side map and pictures (see below), new Hospital Building will be built nestled amongst current buildings.

(A side note: is it just me, or does the intersection of Pasteur Drive and Quarry Road involve some creative reinterpretation of reality? Along the same vein, its possible the outdated laboratories previously mentioned are Edwards, Lane, and Alway.)

The Project:Renewal website features several artists renderings that are fully drool-worthy. Some of them are below.

Koala's Call: Making Love Not War

Aficionados of cute animals may know that the koala, the officially adorable Australian marsupial, will, upon occasion, bellow. Previously, it was believed that these deep groaning noises produced by male koala's were used for announcing territorial information. However, a terrestrial ecologist at the University of Queensland, William Ellis, has used GPS and cell phones to show that the bellows are, most likely, actually mating calls used to attract females in the small hours of the night. The research, presented at the Society for Integrative and Comparative Biology, is described in greater detail in Science by Elizabeth Pennisi.

Koalas Calling, by Elizabeth Pennisi. Science News Focus, Science, 327(5967): 777, DOI: 10.1126/science.327.5967.777

The Birth of Haematopoietic Stem Cells: The Movie

Today, Nature published a paper describing the generation of haematopoietic stem cells from aortic endothelium. During embryonic development, haematopoietic stem cells arise during four disctinct stages, the last of which involves the dorsal aorta. Previously, it was not known exactly what this involvement entailed. The paper, by Bertrand et al, shows that aortic haemogenic endothelium directly converts into baby haematopoietic stem cells, which eventually grow up to found the entire adult haematopoietic system. To do this, Bertrand et al conducted confocal time-lapse imaging in zebrafish embryos (on cmyb:eGFP; kdrl:memCherry double transgenic animals, to label the baby haematopoietic stem cells and the aortic endothelium, respectively). Excitingly, the authors include videos of this process as supplemental figures, which can, and should, be viewed, here (remember, green=stem cells, red=endothelium).

Their results, showing that haematopoietic stem cell generation requires a transition through a haemogenic endothelial intermediate is expected to help in researcher induce haematopoietic stem cell formation from pluripotent precursors, which previously has not been possible.

Bertrand JY et al. Haematopoietic stem cells derive directly from aortic endothelium during development. Nature advance online publication. doi:10.1038/nature08738;

William Gilly on Science Friday

A head's up for all you fans of Stanford's William Gilly : he appeared this morning on NPR's Science Friday. He and Ira Flatow discussed the invasion of jumbo squid off the California coast. The Science Friday Archive: Squid Invasion off California Coast, containing video of jumbo squid, and at some point, a link to the podcast.

Another Wakefield Study Retracted

In the aftermath of the retraction of the controversial Wakefield MMR/autism study by Lancet, the journal NeuroToxicology has just withdrawn another study by Wakefield, this time one on the effects of Hep-B vaccines on the brains of primates. Retraction statement from NeuroToxicology.

Thanks to @bengoldacre and @coxar on Twitter for the tip.

Genes Underlying Stuttering Identified

Today the NIH reported the first identification of genes underlying stuttering. In the study, published today in the New England Journal of Medicine, researchers identified three mutations on the GNPTAB gene, which is responsible for encoding an enzyme that assists in the lysosomal breakdown/recycling of cellular components.

The two other genes identified by researchers are GNPTG (which works with GNPTAB to encode the enzyme mentioned above), and NAGPA (which encodes another enzyme immediately downstream of GNPTAB).

Interestingly, mutations in GNPTG and GNPTAB have already been implicated in the lysosomal storage disorders mucolipidosis II and III.

This discovery may pave the way for treatments for stuttering similar to those already used to treat lysosomal storage disorders (injecting missing enzymes directly into bloodstream).

Kang et al. Mutations in the Lysosomal Enzyme-Targeting Pathway and Persistent Stuttering. NEJM. 10.1056/NEJMoa0902630

Using MRI to diagnose Vegetative States

Today, the front page of the NYTimes website hosts an article describing a study published in the New England Journal of Medicine, wherein doctors took MRI scans of patients in a vegetative state, and asked yes or no questions. Depending on which areas of the patients brain lit up, the doctors declared that the patients were, or were not, correctly diagnosed as vegetative. This research comes from a group that in 2006 published a paper wherein they asked a non-responsive patient to imagine walking through her house, and recorded areas of her motor cortex lighting up. In the current study, the researchers asked vegetative patients hooked up to the MRI machine to complete two imagery tasks:

1. "imagine standing still on a tennis court and to swing an arm to "hit the ball" back and forth to an imagined instructor."
2. "imagine navigating the streets of a familiar city or to imagine walking from room to room in their home and to visualize all that they would "see" if they were there."

The paper reports that from the pool of 54 patients, 5 were identified that could modulate their brain activity in response to the imagery tasks (with their brain activity compared to that of healthy subjects).

In addition, patients were asked to complete a communication task. An excerpt from the paper's methods explains the generation of control data from healthy participants:

Before each of these imaging sessions, participants were asked a yes-or-no question (e.g., "Do you have any brothers?") and instructed to respond during the imaging session by using one type of mental imagery (either motor imagery or spatial imagery) for "yes" and the other for "no." The nature of the questions ensured that the investigators would not know the correct answers before judging the functional MRI data. Participants were asked to respond by thinking of whichever imagery corresponded to the answer that they wanted to convey.

Then, in the case of one patient in a vetetative state:

In this patient, the activity observed on the communication scan in response to five of the six questions closely matched that observed on one of the localizer scans (Figure 2A and 2C and Figure 3A and 3C). For example, in response to the question "Is your father's name Alexander?" the patient responded "yes" (correctly) with activity that matched that observed on the motor-imagery localizer scan (Figure 3A). In response to the question "Is your father's name Thomas?" the patient responded "no" (also correctly) with activity that matched that observed in the spatial-imagery localizer scan (Figure 3C).

The paper presents their methods as a novel use of functional MRI, and appears to have a high success rate for identifying brain activity in patients previously diagnosed as vegetative. The authors seem keen upon their use of MRI as an important diagnostic tool to "bridge the dissociation that can occur between behavior that is readily observable during a standardized clinical assessment and the actual level of residual cognitive function after serious brain injury."

However, the brain, and consciousness are undoubtedly more complex than "yes" or "no" questions. With no good handle on how consciousness is generated in the brain, is it too early to say that we can image a brain and determine state of mind?  Is the (relatively simplistic) model of equating brain activity to conscious identity one that will be lodged into the public mind? With the high-profile nature of the article help enhance public awareness of the importance of neuroscience research and the complexities of the brain and its activity, or will it focus public attention even more on the blind use of fMRI to solve problems ranging from whether a person is lying to whether a person is still a person at all?

Trace of Thought is Found in "Vegetative" Patient. Benedict Carey for the NYTimes.

Monti et al. Willful Modulation of Brain Activity in Disorders of Consciousness. 10.1056/NEJMoa0905370

counter-anti-progress Progress?

Thanks to Brittany for this tip:

It took 12 years, but the medical journal the Lancet has retracted once and for all a controversial paper that drew a link between vaccines and autism and helped fuel a backlash against immunization of children.

Now we shall see if the anti-vaccine armada, all evidence eradicated, is prepared to press forth on a truly science-less sea of supposition, filling their sails solely with their own hot air.

I'm not totally convinced that with all the science-bashing they've happily engaged in, they'll be much phased by the retraction of the original paper sparking this nonsense. But there's always hope!

NIH seminars available online

Today during the Tsien lab meeting, one of the post-docs mentioned an online repository of video/postcasts of NIH events and seminars. Intrigued, I harnessed the power of Google to find the NIH VideoCasting and Podcasting website, brought to us by the Center for Information Technology. The website contains a library of seminars, recorded in both video and audio forms, on subjects in Neuroscience, Bioethics, Career Development, and Evolution and Medicine.

Some examples from the list of available Neuroscience seminars:

• Molecular neurobiology of social bonding: implications for autism spectrum disorders, by Larry Young.
• Selectivity of local circuits in the neocortex by Stanford's own Shaul Hestrin.
• Receptors, Synapses and Memories by Richard "Not-to-be-confused-with-Huguenard" Huganir
• Common Mechanisms of Axon Guidance, Axon Regeneration and Vascular Patterning by Marc Tessier-Lavigne
• The Ins and Outs of Glutamate Receptor Synaptic Trafficking by Roger Nicoll
• Plasticity and Processing in the Whisker Map in Rat Somatosensory Cortex by Dan Feldman.
• Recurrent Inhibitory Circuits in the Cortex by Massimo Scanziani
• Synaptic Plasticity: Multiple Mechanisms and Functions by Rob Malenka

The list goes on. In short, a rich repository of fascinating talks given by experts in the field of neuroscience.

Again, these talks are available online at the NIH VideoCasting Website.