Slashdot Mirror
Domain: plosjournals.org
Stories and comments across the archive that link to plosjournals.org.
Stories · 17
-
Cells In the Retina Tile Like Puzzle Pieces
tim writes "Recent work at the Salk Institute in La Jolla, Calif. shows that cells in the retina sample visual space like a multi-layered jigsaw puzzle. High resolution measurements of light response reveal that individual cells have irregular shapes, but together their shapes coordinate to tightly cover visual space. This type of large scale, exquisite coordination could be a general organizing principle of the brain, but no one has seen it previously because technical obstacles typically prevent recording from large cell populations." Here's a link to full paper. -
Scientists Begin Mapping the Brain
Raindance writes "A team at the University of Utah has unveiled a system to map and digitize brain tissue — thus fulfilling one of the long-standing holy grails of neuroscience and enabling for the first time in-depth analysis of how mammalian neural networks function. So far, maps for the entire retina and related neural networks have been released; no ETA on a full-brain digital reconstruction yet. (One of the lead authors hangs out here on Slashdot.)" -
Why Most Published Research Findings Are False
Hugh Pickens writes "Researchers have found that the winner's curse may apply to the publication of scientific papers and that incorrect findings are more likely to end up in print than correct findings. Dr John Ioannidis bases his argument about incorrect research partly on a study of 49 papers on the effectiveness of medical interventions published in leading journals that had been cited by more than 1,000 other scientists, and his finding that, within only a few years, almost a third of the papers had been refuted by other studies. Ioannidis argues that scientific research is so difficult — the sample sizes must be big and the analysis rigorous — that most research may end up being wrong, and the 'hotter' the field, the greater the competition is, and the more likely that published research in top journals could be wrong. Another study earlier this year found that among the studies submitted to the FDA about the effectiveness of antidepressants, almost all of those with positive results were published, whereas very few of those with negative results saw print, although negative results are potentially just as informative as positive (if less exciting)." -
Antidepressants Work No Better Than a Placebo
Matthew Whalley writes "Researchers got hold of published and unpublished data from drug companies regarding the effectiveness of the most common antidepressant drugs. Previously, when meta-analyses have been conducted on only the published data, the drugs were shown to have a clinically significant effect. However, when the unpublished data is taken into account the difference between the effects of drug and placebo becomes clinically meaningless — just a 1 or 2 point difference on a 30-point depression rating scale — except for the most severely depressed patients. Doctors do not recommend that patients come off antidepressant drugs without support, but this study is likely to lead to a rethink regarding how the drugs are licensed and prescribed." -
Scientists Find Believing Can Be Seeing
Ponca City, We Love You writes "Scientists at University College London have found the link between what we expect to see, and what our brain tells us we actually saw revealing that the context surrounding what we see is all important — sometimes overriding the evidence gathered by our eyes and even causing us to imagine things which aren't really there. A vague background context is more influential and helps us to fill in more blanks than a bright, well-defined context. This may explain why we are prone to 'see' imaginary shapes in the shadows when the light is poor. "Illusionists have been alive to this phenomenon for years," said Professor Zhaoping. "When you see them throw a ball into the air, followed by a second ball, and then a third ball which 'magically' disappears, you wonder how they did it. In truth, there's often no third ball — it's just our brain being deceived by the context, telling us that we really did see three balls launched into the air, one after the other." The original research paper is available on PLOS, the open-access, peer-reviewed journal." -
Brains Hard-Wired for Math
mcgrew writes "New Scientist is reporting that "non-human primates really can understand the meaning of numerals." The small study of two rhesus monkeys reveals that cells in their brains respond selectively to specific number values — regardless of whether the amount is represented by dots on a screen or an Arabic numeral. For example, a given brain cell in the monkey will respond to the number three, but not the number one. The results suggest that individual cells in human brains might also have a fine-tuned preference for specific numerical values." The report itself is online at PLoS Biology, Semantic Associations between Signs and Numerical Categories in the Prefrontal Cortex." -
Modeling the Building Blocks of Life
eldavojohn writes "A new research paper is creating some buzz about the roles of computer engineering in biology. Historically, computational techniques in genome sequencing have proved useful in predicting which DNA sequence produces which amino acid and which amino acid sequence produces which protein. Now, this new research is leading towards a robust model of proteins and their messaging systems. This is one step further in understanding the basics of life and, consequently, pushes us closer to being able to emulate organisms entirely from the bottom up instead of our failed prior approaches of from the top down. A long way from perfect, but an opening into a wide field of study and maybe even a new division of biology." -
Avoiding the Word "Evolution"
jakosc tips us to a disturbing article in PloS Biology on the avoidance of the word "Evolution" in scientific papers and grants. From the paper: "In spite of the importance of antimicrobial resistance, we show that the actual word 'evolution' is rarely used in the papers describing this research. Instead, antimicrobial resistance is said to 'emerge,' 'arise,' or 'spread' rather than 'evolve.' Moreover, we show that the failure to use the word 'evolution' by the scientific community may have a direct impact on the public perception of the importance of evolutionary biology in our everyday lives... It has been repeatedly rumored (and reiterated by one of the reviewers of this article) that both the National Institutes of Health and the National Science Foundation have in the past actively discouraged the use of the word 'evolution' in titles or abstracts of proposals so as to avoid controversy." -
Single-Celled Species' Genome As Complex As Ours?
An anonymous reader writes: "A new paper reports on the sequencing and analysis of the genome of a single-celled species known as Tetrahymena thermophila. This ciliate (like the Paramecium people look at in school) has some 27,000 genes, or nearly as many as humans. And despite existing as a single cell, this spcies encodes fantastic complexity and unusual features. For example, it has a primitive immune system that prevents the invasion of foreign DNA. Also, it is able to cordon off its germ cell lineage much as humans do with sperm and eggs. But Tetrahymena does this by having two nuclei within each cell, with one of the nuclei being held in reserve for sex. Basically, this species uses its genome complexity to function like a single celled chameleon, changing its shape and its properties in response to the changing environment. For example, when a new nutrient shows up in its neighborhood this species can build a kit to suck the nutrient in, degrade it, and turn it into cellular biomass quickly. Thus whereas humans use their genomic complexity in part to create a stable environment for the body, this species simply uses a genomic swiss army kit to make do with whatever environment it encounters." -
Single-Celled Species' Genome As Complex As Ours?
An anonymous reader writes: "A new paper reports on the sequencing and analysis of the genome of a single-celled species known as Tetrahymena thermophila. This ciliate (like the Paramecium people look at in school) has some 27,000 genes, or nearly as many as humans. And despite existing as a single cell, this spcies encodes fantastic complexity and unusual features. For example, it has a primitive immune system that prevents the invasion of foreign DNA. Also, it is able to cordon off its germ cell lineage much as humans do with sperm and eggs. But Tetrahymena does this by having two nuclei within each cell, with one of the nuclei being held in reserve for sex. Basically, this species uses its genome complexity to function like a single celled chameleon, changing its shape and its properties in response to the changing environment. For example, when a new nutrient shows up in its neighborhood this species can build a kit to suck the nutrient in, degrade it, and turn it into cellular biomass quickly. Thus whereas humans use their genomic complexity in part to create a stable environment for the body, this species simply uses a genomic swiss army kit to make do with whatever environment it encounters." -
Singing Mice and Brain Chemistry
Shirlockc writes "The Public Library of Science has a research article on how male mice actually sing in the presence of females. They actually posted some of the audios adjusted for human ears as these songs are ultrasonic. The authors are comparing these warbles to bird songs. The songs are quite complex so do the mice learn them and/or improve on them? This can be a potential model for investigating how brain chemistry works during learning." -
Singing Mice and Brain Chemistry
Shirlockc writes "The Public Library of Science has a research article on how male mice actually sing in the presence of females. They actually posted some of the audios adjusted for human ears as these songs are ultrasonic. The authors are comparing these warbles to bird songs. The songs are quite complex so do the mice learn them and/or improve on them? This can be a potential model for investigating how brain chemistry works during learning." -
Nitpicking Wikipedia's Vulnerabilities
tiltowait writes "A lot of Wikipedia critics point to hypothetical situations when giving reasons for not valuing the site. Wikipedia even has a 'Replies to common objections' article set up to field these. I'd rather look at some real examples of applying the same level of scrutiny to materials often held up as the Platonic ideal of 'scholarship,' such as peer-reviewed journals, conference papers, established journalism sources, monographs, and print encyclopedias. Even these have disclaimers because they can be can be vandalized or have their reliability and accuracy questioned. As dangerous as it is to trust unverified information, it can be just as bad to make prior judgments discounting information because the source happens to be anonymous. The above examples illustrate that all materials existing along a continuum of valuable information formats. Wikipedia articles can be useful for quickly obtaining factual overviews or as a starting point to further research. But that's just one librarian's opinion. How do tech-savvy people view Wikipedia?" -
Open-Access Computational Biology Journal Launches
FleaPlus writes "The Public Library of Science and International Society for Computational Biology have published the inaugural issue of PLoS Computational Biology, an open-access journal dedicated to studies which 'further our understanding of living systems at all scales through the application of computational methods.' All works published in the journal are to be released under a Creative Commons Attribution License. The founding editors have some comments on the launch." -
Nanotech Motors, Biotransistors, DNA Fractals
FleaPlus writes "The American Institute of Physics has a news bulletin describing a couple of interesting nanotech advances. The first is the smallest electric motor in the world, made by Alex Zettl's group at UC Berkeley. The second is a single-protein wet biotransistor. Additionally, Technology Research News reports on algorithmic self-assembly of DNA Sierpinski triangles, by Erik Winfree's group at Caltech." -
Wellcome Trust to Require Open-Access Publishing
Lars Arvestad writes "The Wellcome Trust, one of the worlds largest research funding agencies, will require results from research funded by the Trust to be available in public repositories six months after publication. The Trust's policy advisor Robert Terry writes in an article in PLoS Biology that the Trust plans to start its own public access repository where authors are expected to deposit their published works. The repository is modeled after NLM's PubMed Central and is called UKPMC. Terry's article also mentions that a recent Wellcome report found that an author-pays business model has the opportunity for a saving of 30 % on publishing costs alone compared to reader-pays. This contrasts the recent IEEE report (Slashdot story last week) where it was claimed that some universities will face higher costs using author-pays." -
Monkeys Play Videogames With Their Mind
Thanks to IOL/Reuters for their story discussing research on monkeys who control videogames with their thoughts. According to the piece, "Dr Miguel Nicolelis knew he had nailed it when the monkey stopped using her arm to play the computer game. An implanted device had allowed the monkey to control the game using only her thought." The research, to be printed in Public Library Of Science Biology Journal on Monday, is intended to help humans who "have partial or nearly total permanent paralysis."