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SCOTUS: DNA is information, not a chemical

Shipud Re:Wait, what? And unamimous, no less? (3 comments)

There is a catch. The catch is that the information is still patentable, only in a rather more occluded manner. It seems like Myriad can still patent BRCA1/2 under the new ruling.

about 10 months ago
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Computers May Be As Good As (Or Better Than) Human Biocurators

Shipud Re:Nothing in TFA says the machines are better (35 comments)

If you look at the figures, you'll see that the IEA-evidenced annotations outperform the curated ones.

about 2 years ago
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Tonight is the Meaning of Life

Shipud typos (1 comments)

conict --> conflict.
denitions --> definitions
fl & fi do not cut&paste well from PDF.
Sorry.

more than 2 years ago
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New Top Tier Science Journal Announced

Shipud Re:top tier announced ? (57 comments)

nothing "top tier" ever gets announced. Something becomes top tier because it proofs itself to be top tier.

Counter-example: PLoS Biology was announced as Top Tier, and became so. They made the journal attractive by the editorial board they recruited. This is what the backers of this new journal will do: between Max Planck, HHMI and Wellcome they can get any of the top biomedical researchers in the world lend their names to this journal.

more than 2 years ago
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New Top Tier Science Journal Announced

Shipud Re:Additional work (57 comments)

Dreadful as it sounds, /. is closer to the optimal form of online journal than most online journals, which seem to be trying to emulate the limitations of paper journals as closely as possible. Given that everything is published (made public) in arxiv.org anyway,

Life scientists and medical researchers rarely, if ever, publish in arxiv.org (or have even heard of it), exactly because it is not peer-reviewed. This journal is for life science and biomedical research.

more than 2 years ago
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New Top Tier Science Journal Announced

Shipud Re:Transparency is good, but... (57 comments)

This would be primarily an experimental biology journal. So not exactly feasible to reproduce experiments within the reviewing time/budget.

more than 2 years ago
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RMS Cancels Lectures In Israel

Shipud Re:It's Ironic (609 comments)

It is a fact that Israel is the new apartheid S. Africa with shades of Nazi Germany thrown in (like when the Israeli Jews got caught harvesting organs from Palestinian prisoners for Jewish transplantees-- Israel admitted to it, and "apologized", as if that makes it OK).

You may want to curb your blood-libel tall-tales a bit to make your antisemitism less obvious,

more than 2 years ago
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RMS Cancels Lectures In Israel

Shipud Re:nothing ironic about it (609 comments)

Wow. So many untruths, Where to start?

"What's actually going on is that Israel is forcing foreign scientists wanting to visit the Palestinian territories to travel through Israel, and then saying "oh, we made you come here, why don't you also give some lectures for free". Imagine the US used military force to keep international planes from landing in Canada and then asked foreign scientists diverted through the US to also give free talks in the US; it would be quite outrageous."

It would also be outrageous is Israel is doing it, which it isn't. I would ask you to find citations for that ever happening. And what is this about "Israel paying"? When a scientist is invited to speak at an academic institution the institution is paying. There is zero government involvement. There is also no involvement from other institutes, unless they are pooling resources for an event (say, a conference).

" 'No side trips' is a common condition for invited talks".

I am an associate professor and I have been invited to give hundreds of talks, at institutes and companies in the US and in many other countries. I have never heard of this "Common Condition".

At most I ask my paying hosts for accurate dates, telling them I will be travelling more. I have never encountered any kind of objection to that, nor a request to share the primary travel venue. Of course, I do not ask for extra travel or Room & Board for the "side" travels.

"Apparently, Israel isn't interested in that."

Again what is "Israel" the university of Tel Aviv? The University of Haifa (which, BTW, in which the majority of students are Palestinians)? The Israeli Immigration authorities? The Mossad? El-Al?

more than 2 years ago
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The Neanderthal in us

Shipud Re:Flamebait much? (2 comments)

Nice to see that racists moderate the firehose

more than 3 years ago
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Aphid's Color Comes From a Fungus Gene

Shipud Re:Another challenge to dogma (132 comments)

Actually, it does not refute anything. HGT has been known to exist for a long time in all of life's kingdoms, and has no impact on the Theory of Evolution. It is yet another genetic variety generating mechanism, on top of sex. The authors provide a very plausible mechanism to explain how the gene got fixed in the population. BTW, if you don't believe in evolution, how can you on the one hand accept their inference of HGT which is based on evolutionary considerations (sequence similarity and homology), but on the other hand claim that the conclusion from that inference is that evolution is wrong. that's like saying that You calculate the area of a circle using Pi=3.14, and then claim that Pi=3.5. Doesn't make sense.

more than 3 years ago
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The Journal of Serendipitous and Unexpected Results

Shipud Re:This is a great idea! (153 comments)

"Philosophers, incidentally, say a great deal about what is absolutely necessary for science, and it is always, so far as one can see, rather naive, and probably wrong. For example, some philosopher or other said it is fundamental to the scientific effort that if an experiment is performed in, say, Stockholm, and then the same experiment is done in, say, Quito, the same results must occur. That is quite false. It is not necessary that science do that; it may be a fact of experience, but it is not necessary. For example, if one of the experiments is to look out at the sky and see the aurora borealis in Stockholm, you do not see it in Quito; that is a different phenomenon. 'But,' you say, 'that is something that has to do with the outside; can you close yourself up in a box in Stockholm and pull down the shade and get any difference?' Surely. If we take a pendulum on a universal joint, and pull it out and let go, then the pendulum will swing almost in a plane, but not quite. Slowly the plane keeps changing in Stockholm, but not in Quito. The blinds are down too. The fact that this happened does not bring on the destruction of science. What is the fundamental hypothesis of science, the fundamental philosophy? We stated it in the first chapter: the sole test of the validity of any idea is the experiment." -- (Lecture 2, Basic Physics, from the Feynman Lectures on Physics)

more than 4 years ago
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Unicellular "Enigma" Changes From Predator To Plant and Back

Shipud Re:Is this your blog? (168 comments)

While this is extremely interesting, we need a link to the actual journal article, or to some source material, not just a link to a blog. Without that we can only assume this is an attempt to turf slashdot to drive traffic to your blog and generate ad revenues.

1) The blog has no ads 2) The links to the original article are in the end of the post 3) How do you expect to understand an article in a scientific journal, when your reading skills are so obviously lacking as to not notice (1) and (2)

more than 4 years ago
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The Incredible Shrinking Genome

Shipud Re:Reduced Competition (2 comments)

The problem is that in the original article, the authors speculate that genome size may have been 3 times as large as it is now, prior to the KT extinction. Why did pruning of mobile DNA elements as a fitness increaser apply then, when mammals were competing for teh few neiches left to them by the dinosaurs? Of course, the authors may be wrong in their speculation on pre-KT mammal genome size. If so, your own explanation sounds plausible.

more than 4 years ago
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Why Isn't the US Government Funding Research?

Shipud It is (599 comments)

The National Institutes of Health annual budget: $29 billion. That money funds most of the university biomedical research in the US http://www.nih.gov/about/budget.htm Current NIH funded projects include among other things the human genome, the human microbiome, almost all cancer research in the US, obesity, diabetes, communicable diseases.. The National Science Foundation has an extramural grant budget of $6 billion. The Department of Energy has an extramural research grant budget of $24 billion Among other things they fund alternative energy research, genomic research, You might say the US federal government should be funding more, but you cannot say it is not funding anything at all. The space race and the Manhattan project were both driven by wars: WWII and the Cold War. Maybe that is what it takes for a government to fund major research: fear of losing power and primacy to an opponent.

more than 4 years ago
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Every Man Is an Island (of Bacteria)

Shipud Re:"Biomedicine"? (193 comments)

Quite an accepted term, really. The first google page provides you with two journals having biomedicine in their titles, from Wiley and Elsevier.

more than 5 years ago

Submissions

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Measuring science with a broken ruler

Shipud Shipud writes  |  about 6 months ago

Shipud (685171) writes "How do we assess the value of of a a scientific study? How can we tell "just OK" scientist from "great scientist"? Measuring this intangible is important to funding agencies, university search and promotion committees, and fellow scientist. One way is to look at the journals they publish in. Journals are ranked by a measure called the "impact factor", which is he average number of citations to that journal's articles over a history of two years. Although deferred to almost universally, it is a poor measure by which to assess scientists and their science. The fact that such a poor measure is almost universally used raises the question of how well funding and hiring decisions in science are being made."
Link to Original Source
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Weight gain in ex-smokers may be due to changes in gut bacteria

Shipud Shipud writes  |  about 7 months ago

Shipud (685171) writes "Smokers who quit often gain weight. This has usually been attributed to decreased metabolism, and /or food replacing smoking as a reward system. New research shows that changes in gut bacteria may explain weight gain in those who quit smoking. The changes in the gut bacteria in people who quit smoking are startling. Moreover, the type of bacteria that emerge in the gut after smoking cessation are the same type that have been shown to cause obesity."
Link to Original Source
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Plants communicate using fungi

Shipud Shipud writes  |  about 8 months ago

Shipud (685171) writes "In response to aphid attacks, some plants produce chemicals that repel the aphids and attract wasps, the aphids' natural enemies. Researchers at the University of Aberdeen have shown that plants attacked by aphids can communicate that information to neighboring plants via existing networks of fungi in the soil. Thus fungal symbiosis with plants is shown to be taken one step further: not only do they provide nutrients to plants, they also function as communication hardware."
Link to Original Source
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Sequence squeeze: an open contest for DNA sequence compression

Shipud Shipud writes  |  about 9 months ago

Shipud (685171) writes "Next-generation sequencing machines produce large quantities of data which are becoming increasingly difficult to move between collaborating organisations or even store within a single organisation. Compressing the data to assist with this is vital, but existing techniques do not perform as well as might be expected. The need for a new compression technique was identified by the Pistoia Alliance who commissioned an open innovation contest to find one. The dynamic and interactive nature of the contest led to some novel algorithms and a high level of competition between participants."
Link to Original Source
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New Links Found between Bacteria and Cancer

Shipud Shipud writes  |  about 10 months ago

Shipud (685171) writes "A recent study by a group at the University of Maryland School of Medicine shows that bacterial DNA gets transferred to human cells, in a process known as lateral gene transfer, or LGT. LGT is known to occur quite commonly between bacteria, including bacteria of different species. In fact, that is how antibiotic resistance is transferred so quickly. The team has shown that certain types of tumor cells acquire bacterial DNA that may play a role in tumor progression. Another group at the University of North Carolina, Chapel Hill has shown that gut inflammation leads to a radical change in the microbial population there, which encourages growth of E. coli that can disrupt the inflamed cells' DNA, leading to cancer. Both studies enable us to ask new questions such as: how does inflammation change the landscape for bacterial colonization? Can bacteria indeed harness inflammation — and then cancer — to flourish and remove competitors from their newly found ecosystem? And can we use this information to fight cancer?"
Link to Original Source
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SCOTUS: DNA is information, not a chemical

Shipud Shipud writes  |  about 10 months ago

Shipud (685171) writes "Today SCOTUS ruled that naturally occurring genes cannot be patented. The ruling was made in the lawsuit against Myriad Genetics and their patent on the mutations in BRCA1/2 which are predictive of breast cancer. But what is really interesting is that SCOTUS has treated DNA as a vehicle of information, rather than as a chemical construct. Should DNA be even subject to patent laws? For the purposes of “ownership”, treating DNA as deoxyribonucleic acid is like treating books as collection of cellulose sheets and ink splotches. Nobody does that, and ownership and reproduction rights for books lie within the realm of copyright law, rather than patent law. Copyright law talks about information: who can reproduce what, under what conditions. Perhaps it is time to separate the DNA as a chemical from DNA as information, and move the legal treatment of DNA from the patent to the copyright realm."
Link to Original Source
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The allure of low quality big data in biology

Shipud Shipud writes  |  about a year ago

Shipud (685171) writes "Genomics has ushered biology into the data rich sciences. But genomic data provides us with the instruction book: what the organism is capable of doing based on its DNA. To see what the organism actually does we need to run experiments to interrogate the biological pathways that together constitute life. But biochemical experiments only tell you about a few proteins at a time. Slowly. Much slower than the information gain from genomics.

Enter systems biology with the promise of bridging the knowledge gap by performing large scale biochemistry and molecular biology. High throughput assays such as Yeast 2 Hybrid, Mass Spectrometry proteomics, and RNAi functional genomics have accelerated the rate of data collection in cellular biology. However, a new study shows that the data coming from ‘factory science’ are of a much lower quality than can be used, and these low quality data are taking over what we deem to know about protein function, masking out, by their sheer mass, the higher quality annotations. Contrary to what we hear, systems biology is not quite a BIg Data science yet."

Link to Original Source
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Terrible advice from a great scientist

Shipud Shipud writes  |  about a year ago

Shipud (685171) writes "E.O. Wilson is the renowned father of sociobiology, a professor (emeritus) at Harvard, two time pulitzer prize winner, and a popularizer of science. In a recent article in the Wall Street Journal, Wilson provides controversial advice to aspiring young scientists. Wilson claims that math literacy is not essential, and that scientific models in biology, intuitively generated, can later be formalized by a specialized statistician. One blogger calls out Wilson on his article, arguing that knowing mathematics is essential to generating models, and that lacking what Darwin called the "extra sense" is essentially limiting to any scientist."
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A new genetic code found

Shipud Shipud writes  |  1 year,20 days

Shipud (685171) writes "A group from Oak Ridge National Laboratory, Yale University and the Joint Genome Institute have isolated single cells of otherwise elusive and unculturable SR1 bacteria and sequenced their genomes. They found that SR1 deviate from the genetic code in a way previously unknown: what codes for "stop making proteins" in most organisms, is used differently in SR1, to actually continue making them. This study shows the power of a new technology, single-cell DNA sequencing, to reveal genetic information. SR1 bacteria are found in our mouths, and are suspected to cause periodontitis."
Link to Original Source
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Raytheon's Riot program mines social network data for intelligence agencies

Shipud Shipud writes  |  about a year ago

Shipud (685171) writes "Raytheon has secretly developed software capable of tracking people's movements and predicting future behaviour by mining data from social networking websites according to this story from The Guardian.

An "extreme-scale analytics" system created by Raytheon, the world's fifth largest defence contractor, can gather vast amounts of information about people from websites including Facebook, Twitter and Foursquare.

Raytheon says it has not sold the software – named Riot, or Rapid Information Overlay Technology – to any clients. But the company has acknowledged the technology was shared with US government and industry as part of a joint research and development effort, in 2010, to help build a national security system capable of analysing "trillions of entities" from cyberspace.

The power of Riot to harness popular websites for surveillance offers a rare insight into controversial techniques that have attracted interest from intelligence and national security agencies, at the same time prompting civil liberties and online privacy concerns."

Link to Original Source
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Did viruses evolve from an extinct domain of life?

Shipud Shipud writes  |  about a year ago

Shipud (685171) writes "A study was recently published by a group from the University of Illinois, Urbana-Champaign . The authors analyzed the structures of proteins found in the genomes of organisms from the three domains of life. Those domains are eukarya which includes all plant, animals, fungi and some microbes; bacteria, and archaea which is a group of single-celled microorganisms distinct from eukarya and bacteria. The researchers also included a group of viruses known as NCLDVs (Nucelocyptoplasmic Large DNA viruses), Their conclusion is these viruses may have evolved from a, now extinct, fourth domain of life. Viruses are not considered to be alive, or even to have a place on the universal tree of life, by most researchers. So their claim has far-reaching consequences in our understanding of the origins of life."
Link to Original Source
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International challenge to computationally interpret protein function

Shipud Shipud writes  |  about a year ago

Shipud (685171) writes "We live in the post-genomic era, when DNA sequence data is growing exponentially. However, for most of the genes that we identify, we have no idea of their biological functions. They are like words in a foreign language, waiting to be deciphered. The Critical Assessment of Function Annotation, or CAFA, is a new community-wide experiment to assess the performance of the multitude of computational methods developed by research groups worldwide to help channel the flood of data from genome research to deduce the function of proteins.

Thirty research groups participated in the first CAFA, presenting a total of 54 algorithms. The results are published in an article in Nature Methods. The researchers participated in blind-test experiments in which they predicted the function of protein sequences for which the functions are already known but haven't yet been made publicly available. Independent assessors then judged their performance. The challenge organizers explain that: 'The accurate annotation of protein function is key to understanding life at the molecular level and has great biochemical and pharmaceutical implications, explain the study authors; however, with its inherent difficulty and expense, experimental characterization of function cannot scale up to accommodate the vast amount of sequence data already available.The computational annotation of protein function has therefore emerged as a problem at the forefront of computational and molecular biology.'"

Link to Original Source
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A New Concept in Publishing Science

Shipud Shipud writes  |  about a year ago

Shipud (685171) writes "There are three concerns in publising scientific findings: the quality of the venue, the cost, and the distribution. Some journals are open access, but the publication cost ($2000-$4000) can be prohibitive. Those that are behind a paywall generaly have lower costs to get a paper in, but require high subscription fees from university libraries, and are inaccessible to the public. A new journal, PeerJ is trying a new model to be both open-access and cheap. Everything is published under a Creative Commons license, and the authors pay a one-time membership fee entitling them to a certain number of publications per year. O'Reilly media are backing this venture, and Tim O'Reilly is on the board. The quality is assured by a distinguished line of editors, and 10 Nobel laureates on the board of advisors."
Link to Original Source
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ROSALIND: an addictive bioinformatics learning site

Shipud Shipud writes  |  about a year and a half ago

Shipud (685171) writes "Bioinformatics science which deals with the study of methods for storing, retrieving and analyzing molecular biology data. Byte Size Biology writes about ROSALIND, a cool concept in learning bioinformatics, similar to Project Euler. You are given problems of increasing difficulty to solve. Start with nucleotide counting (trivial) and end with genome assembly (putting it mildly, not so trivial). To solve a problem, you download a sample data set, write your code and debug it. Once you think you are ready, you have a time limit to solve and provide an answer for the actual problem dataset. If you mess up, there is a timed new dataset to download. This thing is coder-addictive. Currently in Beta, but a lot of fun and seems stable."
Link to Original Source
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Can we make accountable research software?

Shipud Shipud writes  |  about a year and a half ago

Shipud (685171) writes "This practices of code writing for day-to-day bioinformatic lab research are completely unlike anything software engineers are taught. In fact, they are actually the opposite in many ways, and may horrify you if you come from a classic software-industry development environment. Research coding is not done with the purpose of being robust, or reusable, or long-lived in development and versioning repositories. Upgrades are not provided and the product, such as it is, is definitely not user-friendly for public consumption. It is usually the code’s writer who is the consumer, or in some cases a few others in the lab. In most cases research results are published without the code that was used to generate them. There are no resources in most labs to make that code fir for public consumption. How can this problem be solved?"
Link to Original Source
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Mother's milk trains baby to fight bacteria

Shipud Shipud writes  |  about 2 years ago

Shipud (685171) writes "It is pretty much common knowledge that mother’s milk is the healthiest food for infants, and that it bestows health benefits upon the baby that formula feeding cannot match. But a recent study of the baby gut metagenome has revealed an unknown benefit: mom's milk enriches a small population of disease causing bacteria in the infant's gut. Just enough to train the infant's immune system, but not enough to cause actual disease. The interesting thing is that the same pathways that enrich the baby's immune system, also help in the development of the gut tissue. An all-around win situation as explained by one of the coauthors."
Link to Original Source
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Music evolving by listeners' taste, with a slashdot history

Shipud Shipud writes  |  about 2 years ago

Shipud (685171) writes "A collaboration between a group in Imperial College and Media Interaction group in Japan yielded a really cool website: darwintunes.org. The idea is to apply Darwinian-like selection to music. Starting form a garble, after several generations producing something that is actually melodic and listen-able. The selective force being the appeal of the tune to the listener. From the paper published yesterday in the Proceedings of the National Academy of Sciences: "At any given time, a DarwinTunes population has 100 loops, each of which is 8 s long. Consumers ratethem on a five-point scale (“I can’t stand it” to “I love it”) as they are streamed in random order. When 20 loops have been rated,truncation selection is applied whereby the best 10 loops are paired, recombine, and have two daughters each." Note that in 2009 the creators of darwintunes harnessed the power of slashdot to help "evolve" their site."
Link to Original Source
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Computers are better than humans at genomics?

Shipud Shipud writes  |  about 2 years ago

Shipud (685171) writes "Sequencing the genome of an organism is not the end of a discovery process; rather, it is a beginning. It's the equivalent of discovering a book whose words (genes) are there, but their meaning is yet unknown. Biocurators are the people who annotate genes — find out what they do — through literature search and the supervised use of computational techniques. A recent study published in PLoS Computational Biology shows that biocurators probably perform no better than fully automated computational methods used to annotate genes. It is not clear whether this is because the software is of high quality, or both curators and software need to improve their performance. The author of this blog post uses the concept of the uncanny valley to explain this recent discovery and what it means to both life science and artificial intelligence."
Link to Original Source
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Video shows the greying of scientists in the US

Shipud Shipud writes  |  more than 2 years ago

Shipud (685171) writes "A video created by the office for extramural research at the NIH shows that the percentage of young (36 and under) biomedical research faculty in the US dropped from 18% to 6% since 1980. Also, it takes much longer for a researcher to set up a funded lab. This means less young blood in research, and that more funds are allocated to well-established labs rather then to promote younger — and perhaps more innovative — researchers."
Link to Original Source

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