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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.
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of the retraction of the controversial Wakefield MMR/autism study by Lancet, the journal NeuroToxicology has just withdrawn another study by Wakefield, this time one on the effects of Hep-B vaccines on the brains of primates.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.
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).
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:
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
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!
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:
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.
A new review in Neuron attempts to enumerate examples of interesting computation in the retina, arguing that retinal circuitry is much more than an image preprocessor that relays the visual world to higher brain areas. The authors, Tim Gollisch at Max Planck and Markus Meister at Harvard, instead argue that within the retina lies circuitry specifically designed to perform ethologically important computations.
Read MoreAn article in PLoS ONE presents a novel methodology for tracking change in large scale networks. Using the bootstrap statistical method, the authors analyze the citation patterns of 7000 scientific journals over the past decade, finding that neuroscience has transformed into a mature and independent field. The authors point out that the analysis of large-scale network activity is integral to many scientific disciplines, from biological to economical. However, despite the great strides that have been made in tracking that activity, there are no significantly powerful tools for mapping changes to the structure of the network itself. Such a tool is critical if we are to continue to ask questions involving network activity; the authors seek to provide such a tool.
The basis of their method relies upon the bootstrap, "a statistic method for assessing the accuracy of an estimate by resampling from the empirical distribution." The power of the bootstrap method lies in its ability to handle data sets whose underlying distribution is not accessible. The authors developed a 4 set process for analyzing the change in a large scale network:
1. Cluster the original networks observed at each time point. 2. Generate and cluster the bootstrap replicate networks for each time point. 3. Determine significance of the clustering for at each time point. 4. Generate an alluvial diagram to illustrate changes between time points.
To demonstrate their method, they apply it to ~ 35 million citations from ~7000 scientific journals over the last 10 years. By using the citation patterns, they seek to track the flow of scientific ideas over time. The alluvial diagram they generate shows striking changes in citation behavior for distinct scientific disciplines, particularly for neuroscience.
In their citation behavior, neuroscientists have finally cleaved from their traditional disciplines and united to form what is now the fifth largest field in the sciences (after molecular and cell biology, physics, chemistry, and medicine). Although this interdisciplinary integration has been ongoing since the 1950s [17], only in the last decade has this change come to dominate the citation structure of the field and overwhelm the intellectual ties along traditional departmental lines.
The figure above shows an alluvial diagram for a set of biomedical fields for the years 2001, 2003, 2005, and 2007. As someone just starting her career, the obvious, rapid cohesion of citations into a Neuroscience field is thrilling.
The full paper makes for an interesting read, particularly if you are interested in methods of large data analysis, or if you enjoy admiring complex graphical depictions of large data sets.
Research published today in Nature describes the discovery of melanosomes in fossils of several non-avian dinosaurs.
Melanosomes are melanin-containing organelles found in the feathers of birds, and responsible for the colors of those feathers. Researchers looked at the fossils of several non-avian dinosaur species possessing integumentary filaments which had previously (and controversially) been categorized as feathers. The controversy stemmed from the classification of these filamentous structures as feathers, with some researchers contending that the structures were degraded dermal collagen fibers, and not feathers at all.
Seeking to resolve this issue, Zhang et al examined the fossils using a scanning electron microscope, finding evidence of "sub-micrometre-sized bodies" that they interpret as fossilized melanosomes. Furthermore, the researchers identify the specific color associated with the fossilized melanosomes: a reddish-brown to yellow pigment.
Much of the letter is spent providing evidence to back up the claim that the identified structures are melanosomes, and it will be up to the experts to battle out a consensus. But based on their research, Zhang et al conclude the confirmation of the putative evolutionary precursors of true feathers, and the broach the possibility of decoding the external coloration of the dinosaurs. Indeed, the authors suggest some color schemes in the letter:
"Only phaeomelanosomes have been identified so far in filaments from the tail of Sinosauropteryx, and this suggests that the dark-coloured stripes along the tail in the fossil, and possibly also the filamentous crest along the back, exhibited chestnut to rufous (reddish-brown) tones."
For more details of their research, and more potential dinosaur color schemes, the article is available online:
Zhang et al. Fossilized melanosomes and the colour of Cretaceous dinosaurs and birds. Nature advance online publication 27 Jan 2010. doi:10.1038/nature08740
Image by Chuang Zhao and Lida Xing, courtesy of The Guardian, here.
Here's a collection of 3 recently published studies that caught my eye and one recently published case of massive scientific fraud. The Neurophilosophy Blog writes up a recent paper about the discovery of grid cell-like activity in humans. Spoilers: Researchers recorded activity very similar to that of mice grid cells. But with data collected only through population imaging, direct electrophysiological measurements are needed to show the existence of human grid cells.
Updated: Link to the original paper, published today in Nature.
Nature Neuroscience published a brief communication regarding activation of the dorsal amygdala in response to perceived inequality in subjects adverse to such inequality. See the paper for a better description of their methods and conclusions.
Another Nature Neuroscience article describes the neural mechanism behind exacerbation of migrane headaches by light. Spoiler: It's due to posterior thalamic neurons. These neurons receive nociceptive signals from cranial dura mater, but their activity is modulated by projections from retinal ganglion cells. So the light information modulates the nociceptive signal being passed through the thalamus to layers I-V of somatosensory, visual, and associative cortices.
Meanwhile, over at the journal Acta Crystallographica Section E, an editorial published last month reveals some extensive scientific frauds involving papers published during 2007. The editorial states that at least 70 structures were falsified, and that the number of structures will most likely rise. Credit for the discovery goes to Ton Spek. The basis of the fraud involves using a real set of data from a correctly determined structure to produce multiple papers wherein authors changed one or more atoms in the structure to produce a new, wholly imaginary compound. At most, more than 18 fraudulent structures were composed from a common data set.
The editorial states:
"The correspondence authors are Dr H. Zhong and Professor T. Liu, both from Jinggangshan University, Jian, China. The co-authors on these papers included other workers from Jinggangshan University together with authors from different institutions in China. Both these correspondence authors and all co-authors have signed forms agreeing to the retraction of 41 papers published by Dr Zhong and 29 by Professor Liu. Details of these retractions appear elsewhere in this issue of the journal. Having found these problems with articles from Jinggangshan University, all submissions from this University to Acta Crystallographica Sections E or C have now been identified and are being checked for authenticity. Preliminary results indicate that further retractions will result from this exercise."
Editorial by Willian T.A. Harrison, Jim Simpson, Matthias Weil. Acta Crystallographica Section E Structure Reports. Vol 66, pages e1-e2. Jan. 2010. via @bengoldacre
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