Slashdot Mirror

An anonymous reader writes "Wired News reports on the growing number of free/open-access academic journals. The Directory of Open Access Journals lists 1527 journals. The Public Library of Science (PLoS) is launching three new open-access journals this year: PLoS Computational Biology, PLoS Genetics and PLoS Pathogens. The National Institutes of Health's (NIH) Public Access Policy is also part of the movement. The traditional academic journals aren't happy, saying that it's unethical to accept money for publishing. But the traditional journals face their own ethical dilemmas by accepting money from advertisers."

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."

DrKyle writes "Another child with "Bubble Boy" disease aka ADA-SCID (adenosine deaminase deficiency causing severe combined immunodeficiency) has been cured by transforming bone marrow stem cells with the functioning gene. Normally toxic levels of adenosine build up in T-cells killing off those important cells required for a robust immune system. While not the first person cured, another successful case of gene therapy goes a long way in encouraging goverments to continue to fund genetic research."

chrisspurgeon writes "The folks at Creative Commons are rolling out a new project aimed at improving the dissemination of scientific publications and data. The National Institutes of Health is already proposing mandated Open Access to all NIH-funded research, and many scientists welcome the free redistribution of their papers, they just don't know the legal details of how to do it. The Science Commons project will take on the copyright problems unique to scientists (things like pre and post prints, and electronic vs. paper journal distribution)."

scupper writes "Infants learn language with remarkable speed, but how they do it remains a mystery. New data shows that infants use computational strategies to detect patterns in language, according to UW's Dr. Patricia K. Kuhl in the Nature article "Early Language Acquisition: Cracking the Speech Code" [PMID: 15496861] Interesting excerpt from the article: 'There is evidence that infants analyse the statistical distributions of sounds that they hear in ambient language, and use this information to form phonemic categories. They also learn phonotactic rules -- language-specific rules that govern the sequences of phonemes that can be used to compose words.'"

cyclop writes "Microbiologists are puzzled by the genome sequence of the giant Mimivirus. It seems this virus has even more genes than many bacteria, is able to synthesize its own proteins and therefore is, by definition, alive. 'We are seeing an organism here. There is DNA, RNA and plenty of proteins,' says Didier Raoult, who reports the work in this week's Science."

meeiw writes "A study from the Institute of Environmental Medicine (IMM) at Karolinska Institute, Sweden found that 10 or more years of mobile phone use increase the risk of acoustic neuroma (slow-growing tumor) and that the risk increase was confined to the side of the head where the phone was usually held."

gtaylor writes "You know that new computer smell? Some people (like me) get sick from it. Can Slashdot readers provide good suggestions for mice or keyboards made from ceramic, unlacquered hardwood, metal, etc, non-plastic headphones and microphones, screens like the new metal-framed cinema display from Apple, etc? (Wood is not necessarily right if it's glued or varnished.) I have a Sharp Plasmacluster air purifier that is very helpful but the fewer volatile organic chemicals released in the first place, the better. I'll also need a chair (leaning to the Herman Miller Mirra chair) and an adjustable metal/hardwood desk. High-density hard synthetics like polypropylene (a popular material at Ikea) or acrylic are also inert enough to be fine if they have no plasticizers - suggestions for a full office set-up welcome."

DrLudicrous writes "According to a recent Reuters article, scientists have been able to cause monkeys to stop procrastinating by blocking the development of a dopamine receptor in the brain. The net result- the monkeys turned into workaholics. An article has appeared in the online version of Nature. Apparently, monkeys, just like human beings, tend to slack off on tasks until the very last minute. They become quite adept at judging how long they have till they absolutely must complete these tasks. The original article appears in the Proceedings of the National Academy of Sciences of the United States of America. An additional blurb appears here courtesty of Science Blog." NIH has a press release.

Manwe's Herald writes "The first draft of the dog genome sequence has been deposited into free public databases for use by biomedical and veterinary researchers around the globe, the National Human Genome Research Institute (NHGRI), one of the National Institutes of Health (NIH), announced today."

Manwe's Herald writes "The first draft of the dog genome sequence has been deposited into free public databases for use by biomedical and veterinary researchers around the globe, the National Human Genome Research Institute (NHGRI), one of the National Institutes of Health (NIH), announced today."

Manwe's Herald writes "The first draft of the dog genome sequence has been deposited into free public databases for use by biomedical and veterinary researchers around the globe, the National Human Genome Research Institute (NHGRI), one of the National Institutes of Health (NIH), announced today."

An anonymous reader writes "Sciencentral has an article saying that many prions, far from causing Creutzfeldt-Jakob Disease are actually responsible for long-term memory storage."

Damek writes "According to UW researchers, prolonged exposure to low-level magnetic fields, similar to those emitted by such common household devices as blow dryers, electric blankets and razors, can damage brain cell DNA. The damage appears to be cumulative, so you'd best get rid of your electric razors & blankets ASAP! The full study is available online now. No word yet for Cell Phone users' brains..."

understyled writes "According to this article, researchers from Fukui Prefectural University in Obama, Japan, and the National Human Genome Research Institute have produced genetically modified zebrafish using sperm cells grown "in vitro." "The secret to our success was the idea of placing a layer of special 'feeder cells' under the spermatagonia in the laboratory dish. These feeder cells, derived from zebrafish testicular cancer cell lines, promote the growth of spermatagonia and stimulate them to mature into functional sperm," said Dr. Sakai, the study's senior author and a reproductive biologist."

understyled writes "According to this article, researchers from Fukui Prefectural University in Obama, Japan, and the National Human Genome Research Institute have produced genetically modified zebrafish using sperm cells grown "in vitro." "The secret to our success was the idea of placing a layer of special 'feeder cells' under the spermatagonia in the laboratory dish. These feeder cells, derived from zebrafish testicular cancer cell lines, promote the growth of spermatagonia and stimulate them to mature into functional sperm," said Dr. Sakai, the study's senior author and a reproductive biologist."

no_demons writes "Along with a selection of other goodies, Apple also unveiled their Xgrid clustering technology from their advanced computation group today. Xgrid can turn a number of networked Macs into a supercomputer, detects nodes automagically via Rendezvous, and can run in or out of a screensaver mode. You can download a technology demo (including a BLAST test app) here."

hedpe2003 writes "'The General Assembly on Tuesday ducked for a year a polarizing debate over human cloning that has set the Bush administration against some allies like Britain and much of the world's scientific community. All 191 United Nations members agree on a treaty to prohibit cloning human beings, but they are divided over whether to extend such a ban to stem cell and other research known as therapeutic cloning. Opponents say total prohibition would block research on cancer, Alzheimer's disease, Parkinson's disease, diabetes, spinal cord injuries and other conditions. The White House says that enough stem cells from human embryos exist for research and that cloning an embryo for any reason is unethical. United States was happy to go along with the one-year consensus but would not alter its stance. 'We will continue to work for a total ban,' he said.' I was just wondering what everyone thought about this. To tell the truth, I didn't know that the US was pushing so hard to ban stem cell research all together."

securitas writes "The Washington Post reports on the first human to be injected with '100 trillion strands of synthetic' Ebola DNA. The DNA in the vaccine has been bioengineered by Vical to remove 'the part that triggers illness and the part that might allow the DNA to recombine with the DNA of some other virus.' The New York Times, AP via ABC and BBC all have stories about the new vaccine as the WHO reports 11 dead in a new Ebola outbreak in Congo this week. If you're interested in participating in the Ebola clinical trials, the NIH needs 27 volunteers. The study only has two. Best quote comes from the NIH vaccine center's nursing director: 'People freak out about Ebola.' Slashdot previously discussed an Ebola/HIV gene therapy."

securitas writes "The Washington Post reports on the first human to be injected with '100 trillion strands of synthetic' Ebola DNA. The DNA in the vaccine has been bioengineered by Vical to remove 'the part that triggers illness and the part that might allow the DNA to recombine with the DNA of some other virus.' The New York Times, AP via ABC and BBC all have stories about the new vaccine as the WHO reports 11 dead in a new Ebola outbreak in Congo this week. If you're interested in participating in the Ebola clinical trials, the NIH needs 27 volunteers. The study only has two. Best quote comes from the NIH vaccine center's nursing director: 'People freak out about Ebola.' Slashdot previously discussed an Ebola/HIV gene therapy."

Daniel B. Cid writes "I wrote the article '8 steps to Protect your Cisco router' (PDF). This small text gives to the reader eight steps (very easy to understand) showing how minimize your Cisco router exposure, by turning off some unused services, applying some access control lists and applying some security options available on that."

scientistguy writes "In case you missed it, Harold Varmus, Nobel prize winning retrovirologist and cancer biologist, former NIH director, and current head of Memorial Sloan-Kettering Cancer Center, has written a review of 28 Days Later in this weekend's New York Times. One would think that his time is more valuably spent running important medical institutions, searching for new cancer insights/cures, etc, but the dude's also an English lit major and has a penchant for sci-fi. 28 Days Later is the new flick from director Danny Boyle (Shallow Grave, Trainspotting, etc.) about a virus termed rage that is advertently released from a Cambridge primate research facility and goes on to devastate much of merry old England more rapidly than the dragons did in Reign of Fire. Although Varmus appears to go out of his way to be even handed, it's clear that he has a problem suspending disbelief on a topic (virology) that is near and dear to him. Reviews from professional movie critics on 28 Days Later have been mixed, but Ebert and another NY Times reviewer were into it. Good, clean summer fun - aside from 'the scenes of maiming, dismemberment, clubbing, shooting, bayoneting and shoplifting'."

goombah99 writes "Nick Bostrom discusses the computational requirements needed to simulate human existence. He offers a proof based on the anthropic principle, that you are almost certainly a computer simulation and not "real". The idea is that given that humans don't go extinct in geologically short time then eventually computer capability will allow complete simulation of the human cortex. Consequently, there must be far more simulations running in future millennia than seconds since you were born. Thus its astronomically more likely you are a simulation than real ... if humans don't go extinct shortly. Recalling the 13th floor, Robin Hanson discusses how one should try to live in a simulation. David Wolpert also weighs in on the physical limits of Turing machines for simulation of the universe. This also may explain why time travel seems impossible: we dont meet visitors from the future since only the present is being simulated."

constantnormal writes "This government study explains a lot of things, from the American public's propensity to elect the worst candidates, to the decreasing fraction of students who bother to study the "hard" sciences, to the overwhelming power advertising holds over their apparently simple minds. I think it was all the leaded gasoline burned in this country prior to the 1970s.
Homer Simpson IS the archetypal American -- Thinking and Reasoning is just too doggoned difficult."

bradbury writes "A host of news sources are carrying news that the gene responsible for Progeria, otherwise known as Hutchinson-Gilford Syndrome, has been identified as Lamin A (LMNA). Sources include a Eureka Alert article, a Science Daily article and a Nature Science Update article. Of interest is the fact that the gene causes at least 6 other genetic diseases. For the hard core science people, an extended discussion of LMNA can be found in the OMIM database here."

spydink writes "The Radio Netherlands website http://www.rnw.nl has a good hour-by-hour listing of potential local time live webcasts from around the world. May be helpful for those who want to raise a glass to the New Year every hour on the hour." (And there's some good news about that, too.) Read on for a few more end-of-year items, which you'll no doubt be seeing more of besides.

SkeeterMac writes "CNN ran an article today listing the top dubious achievements in personal computing for the year... raising again the point that PC speed can not be measured only in megahertz! Too bad the author doesn't think so, because they slam Apple for pricing the iMac around $1,500 for "chugging along at 700 Mhz"..."

cwill1004 writes "Mary Jo Foley has written up a set of predictions for Microsoft in 2003. She suggests that the tablet PC will be a bust, MSN gaining on AOL, and Microsoft getting more flak for its DRM (digital rights management) offerings, much like it did for the Windows Product Activation. It's on Microsoft Watch."

angkor links to Shift's "stupid web moments of 2002."

And the good news -- sulli writes "Just in time for New Year's, the New York Times (register now, use a workaround, or forever hold your peace) discusses at length the health benefits of alcohol. Prevent heart attacks, not with drugs or diet, but with a good California Zinfandel! Avoid strokes with a Perfect Gin Martini! Just don't overdo it, and you'll be fine - too much alcohol, like too much caffeine, has well-known effects. But in moderation, bottoms up!"

Update: 01/01 01:07 GMT by T : Here's another. An anonymous reader submits: "The BBC News has an amusing article titled the 'E-cyclopedia's glossary of 2002'. One wonders what future generations will make of our 'Bollotics' and 'Euronating'... Even Slashdotting gets a mention."

chobee tells us that Apple and Genentech have released an implementation of BLAST, a popular bioinformatics tool, for G4s running Mac OS X. The blastn tool of Apple/Genentech BLAST, used for finding similarities between nucleotide sequences, has been optimized to deliver up to five times the performance of the standard implementation, using the power of the Velocity Engine on the G4. Source code and binaries are available.

Linuxathome writes: "The Washington Post carried an article describing the results of a study linking the average amount of sleep one gets per night with his/her life span. It appears that those who sleep less than 8 hours a night, live longer (optimum is 7 hours). The study (link to the abstract) was aimed at looking at the mortality rate of those suffering from insomnia. But rather than associating insomnia with increased risk of death, it appears that sleeping more than 8 hours carries a much higher risk."

taatacgactc writes: "DARPA (DoD) is now supporting the development of a SPICE equivalent for biological circuits (aka BioSPICE). Best of all, it's to be "open source". Given the hyperexponential improvement in biological technology and the bioengineering efforts getting off the ground, fun stuff should be happening. Of course, there is the "dark side"." More information here. The submitter may be overstating the bit about "open source": the proposal says "All software developed as a part of the program will be open, in the sense that program performers and other DARPA authorized users will have the right to view, use, modify, and distribute code within the program authorized community. All derived works including revision, enhancement, modification, translation, abridgement and expansion of code will also remain open in this sense. ... The DARPA Director reserves the right to approve and exercise licensing arrangements depending on the context and the relevance to national security."

It's the scientific achievment of our generation; what can you say about the mapping of the human genome? But here's a story behind the story. parvati turned us on to this NYT article about James Kent, who wrote the gene assembly program GigAssembler last June. It turns out that, thanks to his code, the public Human Genome Project had actually finished its work three days before the private effort by Celera Genomics -- a feather in their cap and a boon to public science. The head of Celera was "astonished" to learn of this grad student's genius -- ten thousand lines of C in a month, and why? -- "because of his concern that the genome would be locked up by commercial patents if an assembled sequence was not made publicly available for all scientists to work on." (The debate over public vs. private science continues to rage; see this Seattle P-I article, which discusses among other things the ethics of NDA'ing scientific data produced for profit.)

Update: 02/13 02:26 PM by J : Thanks to tlunde for finding the link to GigAssembler and thus clarifying which language it was written in.

Troodon writes " BBCnews SCI/TECH has an item: Screensavers could save lives , anouncing the team up between Parabon Computation and the US National Cancer Institute to apply the idle time of home computers in a Seti@homeesque manner, simulating the responce of cancer cells to potential drugs. The sweetner being the _option_ to receive a payment for your troubles. Other new start ups are jumping on the bandwagon, e.g. Popular Power's choice of contributing to research on Influenza Vaccination, or making a little money with big business. But with these companies potentially looking forward to a healthy cut in the profits of any new drugs developed etc., should us plebs look towards more honourable projects, such as trying to help research into the global warming, that all these boxes dug out retirement are going to contribute to?"

In "one of the most petty and ridiculous issues ever in the history of science" - according to the guilty company's chief scientific officer - federal officials noticed that when Celera uploaded genetic sequences of the fruit fly to a public database, there was some human DNA mixed in. It's now been removed, and everyone seems to think this is not a very significant error. But the harsh exchange and defensive posturing on both sides underscores the edgy rivalry between the government group's slow-and-steady approach and Celera's "shotgun" approach to mapping the human genome. This story is also important because mixing human genes into a fly's genes is freaky cool - someone should make a movie about that.

cjoh345 wrote: "Celera Genomics has just sequenced all the genes in the fruit fly. Apparently the scientists involved are amazed at the genes that we share with this dorm-room annoyance. This discovery also validates Celera's "shotgun approach" to mapping out this stuff. And yes, the genome is available free of charge via Genbank. Good form, Celera!" What would Mendel have thought of this? How about Watson and Crick? This makes me want to break out my copy of The Double Helix .

Albert Hybl is an Associate Professor of Biophysics at the University of Maryland who believes traditional scientific publications are often controlled by editorial cliques that don't necessarily select the best or most original articles available. He says that Open Source, Internet-based scientific journals are the wave of the future. Jon Katz touched on this subject last month. Today Professor Hybl tells us exactly how "Slashdot-style" scientific e-publishing could gradually replace the old way, even though, he says, "this will put a lot of Journal publishers out of business, and they're going to do a lot of kicking and screaming before they go." Open Source Scientific Publication Just as Gutenberg is credited for creating the movable type printing press, Harold Varmus, director of the National Institutes of Health, may be regarded as the creator of the E-Library.

The printing press provided a means to distribute multiple copies of political pamphlets, advertising posters, legal documents, novels -- and Journals containing scientific discoveries.

Scientific Societies use these Journals to disseminate research findings. The expense of Society membership and the additional fees for subscription to multiple Journals has gone out-of-bounds for both individual investigators and institutional libraries. It is just not feasible to expect a scientist/researcher or a member of the public to be able to subscribe to all of them or even to a few specialized Journals.

PubMed provides a powerful search engine for locating biomedical articles. PubMed searches are superior to browsing the specialty Journals. However, once you have used PubMed to find an article of interest you must then locate a library housing the Journal in which it appears, that has a Xerox machine with which to make copies of the sought-after articles.

Harold Varmus proposes that an open access e-repository be established to maintain permanent on-line and downloadable archives of scientific literature. The most obvious advantage of this to the researcher is immediate access to any published report via a hyperlink from the PubMed database. E-reports can also contain more information than print Journals, including larger data sets in various formats, pictures with greater detail, or even movies. Many of the costs associated with the publication of a Journal are avoided. Cited literature [footnotes] can also be hyperlinks, which simplifies in-depth background analysis for serious researchers.

Harold Varmus's proposal describes two methods for submission of a new report that could operate side-by-side. The first is to use the established editorial boards, and the second would be through a publicly available preprint repository.

European backers of Varmus's Proposal tend to favor the first, "closed" method of submission. Their claim is that by sticking to the traditional method there is less chance that the database would be flooded by poor quality reports. A subliminal reason for their desire to maintain editorial control might be that delayed publication gives the group that reviews the data extra time to analyze and extract ideas for future research before it is made available to the world.

With the second submission method, each submitted report would only need to be given a cursory review to eliminate voodoo science (SPAM for health care scams or unhealthy foods, etc.) before it was placed, unedited and unreviewed, into the preprint repository, where any interested party could read it. Each "preprint" report could be given a version number like most Open Source Software projects use. Perhaps the "development" version could show editorial strike-outs and new text in different colors from the original. The next higher, "stable" version would be the reviewed, edited, author-corrected copy. Still higher versions might contain supplementary information. Even after they are published, the lower versions should be archived and accessible for historical use.

The Harold Varmus Proposal would require an article to obtain two favorable reviews, perhaps from members of established editorial boards, before it was transfered from the preprint repository to the general repository. Varmus also touches on the possibility of more open reviewing "in which critiques of the scientific reports are accessible and signed." (Today, most scientific papers are reviewed anonymously.) I suggest that, in addition to solicited reviews, signed, unsolicited reviews should also be considered.

Summary

The electronic submission, publication, editing, indexing, archiving, retrieval and utilization of scientific reports, abstracts, and data is taking a significant turn, and Varmus's Proposal may help make that a turn for the better.

I, like Varmus, believe that since most scientific research is funded by the public, the public should have free access to it from open E-libraries via the Internet, and that the only person who should be allowed to claim "ownership" of a scholarly article is the person who wrote it.

No Scientific Society or Journal Publisher should be allowed to hold a copyright on scientific knowledge. The researcher is the only one who has the right to claim, "I discovered it and I reported it."

Albert Hybl is an Associate Professor of Biophysics at the University of Maryland who believes traditional scientific publications are often controlled by editorial cliques that don't necessarily select the best or most original articles available. He says that Open Source, Internet-based scientific journals are the wave of the future. Jon Katz touched on this subject last month. Today Professor Hybl tells us exactly how "Slashdot-style" scientific e-publishing could gradually replace the old way, even though, he says, "this will put a lot of Journal publishers out of business, and they're going to do a lot of kicking and screaming before they go." Open Source Scientific Publication Just as Gutenberg is credited for creating the movable type printing press, Harold Varmus, director of the National Institutes of Health, may be regarded as the creator of the E-Library.

The printing press provided a means to distribute multiple copies of political pamphlets, advertising posters, legal documents, novels -- and Journals containing scientific discoveries.

Scientific Societies use these Journals to disseminate research findings. The expense of Society membership and the additional fees for subscription to multiple Journals has gone out-of-bounds for both individual investigators and institutional libraries. It is just not feasible to expect a scientist/researcher or a member of the public to be able to subscribe to all of them or even to a few specialized Journals.

PubMed provides a powerful search engine for locating biomedical articles. PubMed searches are superior to browsing the specialty Journals. However, once you have used PubMed to find an article of interest you must then locate a library housing the Journal in which it appears, that has a Xerox machine with which to make copies of the sought-after articles.

Harold Varmus proposes that an open access e-repository be established to maintain permanent on-line and downloadable archives of scientific literature. The most obvious advantage of this to the researcher is immediate access to any published report via a hyperlink from the PubMed database. E-reports can also contain more information than print Journals, including larger data sets in various formats, pictures with greater detail, or even movies. Many of the costs associated with the publication of a Journal are avoided. Cited literature [footnotes] can also be hyperlinks, which simplifies in-depth background analysis for serious researchers.

Harold Varmus's proposal describes two methods for submission of a new report that could operate side-by-side. The first is to use the established editorial boards, and the second would be through a publicly available preprint repository.

European backers of Varmus's Proposal tend to favor the first, "closed" method of submission. Their claim is that by sticking to the traditional method there is less chance that the database would be flooded by poor quality reports. A subliminal reason for their desire to maintain editorial control might be that delayed publication gives the group that reviews the data extra time to analyze and extract ideas for future research before it is made available to the world.

With the second submission method, each submitted report would only need to be given a cursory review to eliminate voodoo science (SPAM for health care scams or unhealthy foods, etc.) before it was placed, unedited and unreviewed, into the preprint repository, where any interested party could read it. Each "preprint" report could be given a version number like most Open Source Software projects use. Perhaps the "development" version could show editorial strike-outs and new text in different colors from the original. The next higher, "stable" version would be the reviewed, edited, author-corrected copy. Still higher versions might contain supplementary information. Even after they are published, the lower versions should be archived and accessible for historical use.

The Harold Varmus Proposal would require an article to obtain two favorable reviews, perhaps from members of established editorial boards, before it was transfered from the preprint repository to the general repository. Varmus also touches on the possibility of more open reviewing "in which critiques of the scientific reports are accessible and signed." (Today, most scientific papers are reviewed anonymously.) I suggest that, in addition to solicited reviews, signed, unsolicited reviews should also be considered.

Summary

The electronic submission, publication, editing, indexing, archiving, retrieval and utilization of scientific reports, abstracts, and data is taking a significant turn, and Varmus's Proposal may help make that a turn for the better.

I, like Varmus, believe that since most scientific research is funded by the public, the public should have free access to it from open E-libraries via the Internet, and that the only person who should be allowed to claim "ownership" of a scholarly article is the person who wrote it.

No Scientific Society or Journal Publisher should be allowed to hold a copyright on scientific knowledge. The researcher is the only one who has the right to claim, "I discovered it and I reported it."