Planet SciFoo

P. Z. Myers: Cutest little bugs ever

2008-01-26T17:29:23+00:00

So what if they want to chew your face off? They're being the best Japanese Giant Hornets they can be.

P. Z. Myers: An exemplary Christian science fair project

2008-01-26T16:31:32+00:00

It's getting to be about that time: science fair season. I'll remind you all that we have an infamous local event, the Twin Cities Creation Science Fair, in which real live homeschooled creationist kids will present their experiments at the Har Mar Mall, on 16-17 February. I'm hoping to make it this year, but I've got a lot of other traveling to do that week, so I'm not sure that I'll be able to make it…if I do, though, I'll let you know.

Because I have to deal with this all the time, I'll also remind everyone that the Objective: Ministries Creation Sciende Fair page is a satire, OK?

This, however, is real: Possummomma finds a lovely example of Christian "science". A sixth-grader in her area decided to test the hypothesis that "unchristians" are less moral than Christians with a questionnaire — a badly done questionnaire. Some amusing bits: the student had his subjects report on their amoral behaviors, and didn't keep their answers anonymous. Cool. That could add some fun to a community event.

The other amusing thing is the conclusion: everyone failed the morality test. The answer, then is that we are all sinners, so we'd better become Christians.

The kid ought to come on up to Minnesota — he'd fit right in.

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P. Z. Myers: Should I be afraid to go to the coffee shop?

2008-01-26T14:40:59+00:00

There might be crazy Christian ladies there!

Nah, I know there are crazy Christians there, but they're mostly fairly cool…I haven't seen any eruptions like this one.

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Alex Palazzo: Drugmonkey got Swallowed by Scienceblogs

2008-01-26T14:35:36+00:00

I often read these guys - the lives they describe are something that any struggling young scientist trapped in the web of academia and the NIH can relate to. Since their move to Sb, they've even managed to post on grant writing. Go check 'em out.

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Bora Zivkovic: ClockQuotes

2008-01-26T09:03:36+00:00

The best thing about the future is that it comes one day at a time.

- Abraham Lincoln

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Jean-Claude Bradley: Andre Brown's Talk on Science2.0

Jean-Claude Bradley — 2008-01-26T06:06:32+00:00

From Bora Zivkovic's A Blog around the Clock:

Here is a video of SPARC-ACRL Forum '08 on 12 January, 2008 at the Pennyslvania Convention Center in Philadelphia:

The SPARC-ACRL Forum at ALA '08 entitled "Working with the Facebook generation: Engaging students views on access to scholarship." Panelists discuss the merits of student activism, patent reform, blogs as a communication medium for scientists, and students as active members of a discussion about the right to access information for scholarly work. Features Andre Brown, Nelson Pavlosky, Stephanie Wang, and Kimberly Douglas as panelists.

Pay particular attention to Andre Brown and minutes 42-55 as he talks about science blogs and Science 2.0 including
mentions of all the usual suspects (Jean-Claude Bradley, Rosie Redfield, Reed Cartwright, Bill Hooker, Peter Suber and me):

SPARC-ACRL Forum '08 from Matt Agnello on Vimeo.

Andre Brown does a really good job of summarizing the key points of the potential of social software in communicating primary research.

UsefulChem gets a mention around minute 50 and Gus Rosania is used as an example of how blogging about science can facilitate collaboration (minute 52).

Andrew Walkingshaw: Links for 2008-01-25 [del.icio.us]

2008-01-26T06:00:00+00:00

RDF Vocabulary Description Language 1.0: RDF Schema
Main Page - N2 wiki
Talis platform documentation

Deepak Singh: Loic Le Meur with Linda Avey at Davos

2008-01-26T04:45:53+00:00

Wanted to link to a post on Seesmic by Loic Le Meur, where he ~~interviews~~ chats with Linda Avey from 23andme

Technorati Tags: 23andme, Linda Avey, Loic Le Meur

Bora Zivkovic: My picks from ScienceDaily

2008-01-26T02:11:44+00:00

EDGE Amphibians: World's Weirdest Creatures Just Got Weirder:

A gigantic, ancient relative of the newt, a drawing-pin sized frog, a limbless, tentacled amphibian and a blind see-through salamander have all made it onto a list of the world's weirdest and most endangered creatures.

Scientists Look At Those In Evolutionary Race Who Don't Make It 'Out Of The Gate':

In the race of evolution, scientists until now have only looked at winners and losers. Now, they've come up with a way to look at the contenders who never made it out of the gate. It's the organisms -- in this case lizards -- that die early in life, before scientists can even assess what they might bring to the reproduction game, and that have gone uncounted in the effort to quantify genetic fitness. This group has been dubbed the "invisible fraction." Andrew McAdam, assistant professor of fisheries and wildlife and zoology at Michigan State University, has co-authored a paper in the Jan. 23 Proceedings of the Royal Society which brings that elusive fraction to light.

World's Aging Population To Defuse War On Terrorism:

Changing demographic trends will impact the future of international relations, according to the latest issue of Public Policy & Aging Report (PP&AR). Several hotbed areas in the world that offer the motive and opportunity for political violence are due to stabilize by the year 2030.

How Much You're Willing To Pay Depends On What You Were Just Doing:

Your shopping buddy turns to you and asks, "Which one of these would you get?" Or, you're talking with your spouse about which candidate you'd like to vote for before switching on the nightly news. Turns out simply being asked to make a choice-- especially if you're in a hurry or have something on your mind -- will make you like the next thing you see more, says a new study from the Journal of Consumer Research. The researchers found that asking people to choose among things primed them to think about positive attributes -- and caused them to be in a positive frame of mind when evaluating the next item they saw.

Extinct Marsupial Lion Tops African Lion In Fight To Death:

Pound for pound, Australia's extinct marsupial lion (Thylacoleo carnifex) would have made mince meat of today's African lion (Panthera leo) had the two big hyper-carnivores ever squared off in a fight to the death, according to an Australian scientist.

Secret Of Scottish Sheep Evolution Discovered:

Researchers from the University of Sheffield, as part of an international team, have discovered the secret of why dark sheep on a remote Scottish Island are mysteriously declining, seemingly contradicting Darwin's evolutionary theory. Dr Jacob Gratten and Dr Jon Slate, from the University's Department of Animal and Plant Sciences, led the team, which found that the gene responsible for dark coat colour is linked to other genes that reduce an animal's fitness.

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Bora Zivkovic: 'Working with the Facebook generation: Engaging students views on access to scholarship'

2008-01-26T01:00:01+00:00

Here is a video of SPARC-ACRL Forum '08 on 12 January, 2008 at the Pennyslvania Convention Center in Philadelphia:

The SPARC-ACRL Forum at ALA '08 entitled "Working with the Facebook generation: Engaging students views on access to scholarship." Panelists discuss the merits of student activism, patent reform, blogs as a communication medium for scientists, and students as active members of a discussion about the right to access information for scholarly work. Features Andre Brown, Nelson Pavlosky, Stephanie Wang, and Kimberly Douglas as panelists.

Pay particular attention to Andre Brown and minutes 42-55 as he talks about science blogs and Science 2.0 including mentions of all the usual suspects (Jean-Claude Bradley, Rosie Redfield, Reed Cartwright, Bill Hooker, Peter Suber and me):

SPARC-ACRL Forum '08 from Matt Agnello on Vimeo.

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Corie Lok et al.: News recap: 1000 genomes, rejecting organ rejection and MIT energy funds

2008-01-25T23:42:28+00:00

One of the big science news stories this week was the announcement of the 1000 Genomes Project. The goal: sequence the whole genomes of 1000 people from around the world, using newer, faster, cheaper sequencing technologies (not the traditional Sanger method) and use them to map in more detail a wider range of genetic variations than in previous projects (such as the HapMap project, which looked only for single nucleotide changes).

But already, according to this Nature News story, there’s doubt about how accurate the sequences will be, given that the budget for it will be a mere $30 to $50 million. David Altshuler of MGH/Broad is one of the chairs of the consortium of researchers involved.

Steve Jurvetson: Zeno - Robotic Friend [Flickr]

jurvetson — 2008-01-25T22:27:45+00:00

jurvetson posted a photo:

Zeno’s face is soft frubber and quite expressive. He tracks you with in-eye CCDs to maintain eye contact. He is developing a natural language conversational interface. He comes from the mind of Hanson Robotics (photos of Eva)

The body looks similar to a dancing Robonova.

And he comes with a back story, immersive world, and movie script. (Zeno’s World)

Here’s a video of Zeno too.

Steve Jurvetson: Blinded by the Light [Flickr]

jurvetson — 2008-01-25T22:25:30+00:00

jurvetson posted a photo:

Zeno stares into the Powerpoint projector on the conference table.

His eyes have embedded sensors for facial recognition and maintaining eye contact.

Julia Whitty: $1 Ethanol Isn't Innovation, It's a Commitment to Business as Usual

2008-01-25T22:10:28+00:00

Americans do not reduce. We may reuse, and we may recycle, but our economic system is predicated on steady consumption. So it makes sense that while trying to invent our way out of the consequences of global warming, we would seize upon those ideas that encouraged us to, well, consume. In other words, business as usual.

Today's quick fix is brought to us by Coskata. This Illinois-based energy startup, thanks to a hefty investment from GM, has already announced its triumph in the race for a new global energy source. The winning product? Bargain ethanol. Coskata's innovative technology, which lets anaerobic "patented microorganisms" eat syngas (a carbon monoxide and hydrogen compound formed by processing biomass such as corn husks), allows the company to produce waste-free ethanol from almost anything you give them: tires, factory waste, switchgrass, you name it.

What's more, says the company, because its process can convert so many different types of material into essentially pure ethanol, the fuel could be locally produced anywhere in the world. Each gallon will generate nearly eight times as much energy as it takes to make it, and the product reduces carbon emissions by 84%. The production cost of this miracle fuel? $1 per gallon.

P. Z. Myers: Typical.

2008-01-25T20:30:54+00:00

This is a painting Our President loves; it's called "A Charge to Keep," and GW Bush even used that as the title for his autobiography.

Here's what Bush himself says about the picture.

I thought I would share with you a recent bit of Texas history which epitomizes our mission. When you come into my office, please take a look at the beautiful painting of a horseman determinedly charging up what appears to be a steep and rough trail. This is us. What adds complete life to the painting for me is the message of Charles Wesley that we serve One greater than ourselves.

Bush got it wrong. The painting has been traced back to its source, and it turns out it doesn't portray a Methodist missionary spreading the word on the Texas frontier…it's something far more appropriate.

Only that is not the title, message, or meaning of the painting. The artist, W.H.D. Koerner, executed it to illustrate a Western short story entitled "The Slipper Tongue," published in The Saturday Evening Post in 1916. The story is about a smooth-talking horse thief who is caught, and then escapes a lynch mob in the Sand Hills of Nebraska. The illustration depicts the thief fleeing his captors. In the magazine, the illustration bears the caption: "Had His Start Been Fifteen Minutes Longer He Would Not Have Been Caught."

I laughed and laughed. It epitomizes their mission, alright.

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Gregg Favalora: What J-Fav doesn't know about Thanksgiving, 1984

G-Fav — 2008-01-25T20:13:49+00:00

Hi -

I thought I'd step outside the usual link-posting to share something that I'm not sure J-Fav even knows about me, which is the significance of Thanksgiving, 1984. You know, as it relates to time travel.

When I was younger, but old enough to know that my engineering mindset would land me somewhere in engineering/science-ville, I wondered for a moment about time travel. Since, obviously, if time travel became a common mode of spatio-temporal transportation, I'd be working at the time machine factory or have time-traveler buddies. (Look, I thought a lot of weird stuff up in fifth grade.)

So, the logic went: The popular press said that although time travel into the future is unlikely, perhaps one could skip back to the past. Somehow. I don't know how, something about spinning massive chunks of ultra-dense black cylinders near the mouths of black holes or something like that.

Then I wondered if I really would ever get to travel back in time.

Then I wondered if there was I way I could make sure to find out that I'd travel back in time, such as hiding a note near a landmark, or winning the lottery and saving the money for myself somewhere.

I finally decided that I would pick a date and location that I would travel back to if I ever had the chance, and meet my younger self there, and then as my (original) younger self grew up, I'd always remember that event. Since I'm bad at remembering just about everything, I figured the name of a holiday and an important-sounding year would be easy enough to reference back for a date.

So I picked Thanksgiving, 1984, in the town of West Orange, NJ.

Then I realized that if I was destined one day to travel in time, I'd be able to find out ahead of time - immediately - as soon as it was clear that I've fixed that date and location in my brain. Right? As long as it's after Thanksgiving, 1984, and assuming I won't forget that date, if I suddenly have a recollection of meeting my older self over Thanksgiving dinner in fourth grade, then I've proved that I will at some point in the future travel backwards to meet myself.

Except there's one problem.

There's, like, 100 places much more interesting to visit than that.

And then I start feeling guilty, because in 1984 I feel like there are a bunch of people I could run to and say very important things to that would change the course of their lives, and how selfish it would be of me to squander my one chance for time travel on mere tourism.

So, I suppose that it's insufficient for me to simply remember a date and place. I must still convince myself that's where I'm going, and not be seduced at the last second into traveling somewhere more interesting. Assuming I do get a chance to turn back the clock, I'd need to stop waffling about my destination if I want to know ahead of time if I'll get that chance.

In retrospect, this feels a lot less logical than it did in fifth grade.

g-fav

Julia Whitty: Insects Creep Out of Asia—And Into Your Backyard?

2008-01-25T19:42:14+00:00

Invasive species like the Asian tiger mosquito are on the rise in Europe, French researchers recently reported. Nineteen new invasive species made Europe their home every year from 2000 to 2007. (From 1950 to 1975, only about 10 species per year established themselves.)

Tim O'Reilly (et al.): Books that make you dumb

Artur Bergman — 2008-01-25T19:11:35+00:00

By Artur Bergman

Wikiscanner hacker Virgil Griffth told me a while ago about his latest data mining project, to visualise the relationship between books and SAT scores. Today he released his findings at Booksthatmakeyoudumb.

He does this by cross referencing the 10 most popular books at every college, as given by Facebook, and the average SAT score. He then presents it all in this nifty little visualisation.

I find it somewhat amusing and surprising that erotica takes top and bottom positions, with Lolita at the top and the author Zane coming in last (perhaps it says something that the lowest scoring book is actually miscategorized.) The book named "I don't read" also comes pretty far down.

In all, the results aren't that surprising, but as Virgil said to me; "but isn't it wonderful to have concrete data to back it up?"

Julia Whitty: Antarctica Is Melting, After All

2008-01-25T17:44:02+00:00

A while back, I blogged about how global warming skeptics were all smug and glowy (and wrong) about how Antarctica's not melting. If the sea ice in the South Pole is actually increasing, the reasoning went, then how could the planet be warming? Huh? Huh? Well, for a number of reasons, that logic is false, but guess what? It may be moot point anyway, since it turns out that the western part of Antarctica is melting—and fast: Ice loss in the region has increased by 75 percent over the past ten years.

A team of researchers led by scientists from UC Irvine discovered that the underlying cause for the melting was accelerated glacier flow, which is, in turn, caused by warming oceans. All that melting means higher sea levels:

They detected a sharp jump in Antarctica’s ice loss, from enough ice to raise global sea level by 0.3 millimeters (.01 inches) a year in 1996, to 0.5 millimeters (.02 inches) a year in 2006.

That level of melting puts western Antarctica almost on par with Greenland, a dubious distinction, to say the very least.

Tim O'Reilly (et al.): GoogleMapsVision: A Semi-Realtime Edits Viewer

Brady Forrest — 2008-01-25T17:33:27+00:00

By Brady Forrest

Google Maps just released a semi-realtime viewer of user edits. Sometime after the edits happen they pop up on the map in little balloons. It's very similar to Twittervision (or Flickrvision -- Radar post) in that you get a sense of what locations your fellow internet users find important. Aside from gaining buzz the viewer will also encourage people to edit locations (there's a handy box in the top right). Watching the screen for a little while compelled me to correct the placement of my house.

P. Z. Myers: Say howdy to DrugMonkey

2008-01-25T17:28:14+00:00

Sure enough, we actually have a new scibling in the borgosphere: DrugMonkey. It's OK if you encourage them.

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P. Z. Myers: Why teach biology?

2008-01-25T16:55:01+00:00

I've been tagged with a teaching meme: I'm supposed to answer the question, "Why do you teach and why is academic freedom critical to that effort?". We science types are late to the game; there are already several examples online, mostly from those humanities people.

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P. Z. Myers: Evolution in 5 minutes

2008-01-25T16:34:30+00:00

OK, it's cute and catchy, but it's also got a very awkward sudden jump from the mammal-like reptiles to the primates, and unfortunately it perpetuates the "evolution as a process on rails" concept by showing a single lineage — ours, of course. Why not show a progression to a modern rose, or a fly, or a fish? Or better yet, illustrate evolution as an ongoing explosion of diversity? I know, I know, it isn't as engrossing to self-centered humans, the market for this sort of thing.

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Maxine Clarke: Researchers like the peer-review system

Maxine Clarke — 2008-01-25T16:32:50+00:00

The Publishing Research Consortium publishes a study this month (January 2008) in whch more than 3,000 senior authors, reviewers and editors were asked about the peer-review system. The conclusions are that researchers want to "improve, not change, the system of peer review for journal articles". According to the report, a summary of which is available (1.7 MB; PDF), more than 93 per cent of respondents believe that peer review is necessary, and more than 85 per cent say that it helps to improve scientific communications and increases the overall quality of published papers.
Although many respondents pointed out the operational difficulties in double-blind peer review, two-thirds of respondents felt that it is the most objectively fair system, compared with single-blind (the current prevalent system). Alternatives such as post-publication and open peer-review were not popular.
While of the majority of respondents saw peer review as an effective filter for research, some did not think it was effective at detecting plagiarism, fraud or misconduct. Interestingly, most reviewers among the respondents thought that paying peer-reviewers would be too expensive for publishers; most of them said that they perform reviewing as part of their support to their research community.
The full report is available here (1 GB; PDF). According to the Publishing Research Consortium, the main objective of the study was "to measure the attitudes and behaviour of the academic community with regard to peer review. This will inform debate concerning peer review, and underpin discussions, either in discussion lists or at future workshops/conferences."
This new report comes as the NIH (National Institutes of Health) finish analysing the thousands of responses to their assessment of grant peer review. Lawrence Tabak and colleagues are filtering the list into a set of key recommendations, which will be given to Elias Zerhouni, director of NIH, at the end of February.

Bora Zivkovic: Welcome the newest SciBlings!

2008-01-25T15:45:52+00:00

Go say Hello to DrugMonkey and PhysioProf, the newest acquisitions by The Borg, at DrugMonkey blog. Both are regular readers and commenters on this blog, always providing thoughtful and intelligent (and provocative) additions to the conversation. A great addition to the scienceblogs.com universe!

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Jean-Claude Bradley: We Have Anti-Malarial Activity!

Jean-Claude Bradley — 2008-01-25T15:40:54+00:00

The results are in.

Jiri Gut from the Rosenthal group has run 2 of our Ugi products and they both show inhibition of falcipain-2 (EXP165) and Plasmodium falciparum (EXP166) in the micromolar range.

To put this in context the activities are roughly 2 orders of magnitude lower than the positive control used for the enzyme inhibition and chloroquine for the parasite.

But it is a start. And we have officially closed the Open Science Loop for the malaria project, meaning that we have openly documented the docking results from Rajarshi Guha (D-EXP014), our syntheses (EXP148 EXP150) and testing (EXP165 EXP166) in the Rosenthal group.

We can't tell much about the validity of Rajarshi's docking model from the results of two compounds but as more data come in the situation should become clearer.

However, Jiri did make this interesting observation:

The food vacuole abnormality, which is indicative of cysteine protease inhibition was not observed in the parasites, suggesting other mode of action.

Vaughan Bell (et al.): Griefer madness

2008-01-25T15:00:00+00:00

You know it's a bad day when it starts raining penises during a media interview. Wired has an article on the 'griefer' subculture, sociopaths of the virtual world.

Essentially, they are virtual world vandals, or online versions of those local kids on the street who love shouting abuse and messing the place up.

Like most other aspects of human behaviour, antisocial behaviour transfers from the offline to the online world.

But like many subcultures on the internet, it is a new phenomenon in that people who would never normally get a chance to meet many others who share their socially unpopular beliefs, suddenly have access to a huge, distributed community of such people.

One of the most notorious 'griefer' attacks, before the term was even conceived, was described in the landmark article 'A Rape in Cyberspace', and describes an antisocial user taking over a text-based environment

It was one of the first pieces to convince people that internet interactions could have serious emotional effects, and is widely cited in the internet psychology literature.

The Wired article discusses the motivations (and even, the 'philosophy') behind these groups, as well as their impact on the increasingly commercial virtual worlds.

Link to Wired article on 'griefer subculture'.

P. Z. Myers: Inappropriate iconography

2008-01-25T14:57:18+00:00

A reader sent me an example of religious kitsch, but just to be on the safe side, I'm going to have to put it below the fold. There's nothing obscene about the work in question, but I dare you to look at it and not have wildly inappropriate thoughts skitter through your brain.

I think we need a caption contest for this one.

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Bora Zivkovic: New and Exciting in PLoS Community Journals

2008-01-25T14:17:20+00:00

Friday - time to take a look at the new articles in PLoS Computational Biology, Genetics and Pathogens - check them all out, but here are a couple of picks:

Exploration of Small RNAs:

There is substantial interest in noncoding RNAs (ncRNAs), which play an essential role in complex biological systems without encoding for proteins. Only a limited number of ncRNAs, such as ribosomal RNA (rRNA) and transfer RNA (tRNA), have previously been characterized in any depth. Recent studies revealed many novel ncRNAs, covering a wide range of sizes [1]. RNA molecules have several functions including catalytic activity and ability to act as a structural component. Of these functions, the ability to specify a nucleic acid sequence is superior compared to proteins. A common way in which ncRNA contributes to biological processes is through the ribonucleoprotein (RNP) complex, where its role is to guide recognition of nucleic acid target sequences relying upon sequence complementarity [2]. Small RNA molecules are widely utilized in this type of machinery, and are involved in important biological processes [3]. Exploration of novel small RNA species and their functions attracts substantial interest. The advent of recent technologies to profile cellular RNAs, such as high-throughput sequencing and microarray, coupled with computational analysis, has contributed to rapid progress in this field. Here, we review the recently discovered small RNA species and their pathways in a view of conservations and differences between higher eukaryotes. We also summarize recent exploration efforts of novel small RNAs based on devised technologies to provide a perspective for the future.

Why is Real-World Visual Object Recognition Hard?:

The ease with which we recognize visual objects belies the computational difficulty of this feat. At the core of this challenge is image variation--any given object can cast an infinite number of different images onto the retina, depending on the object's position, size, orientation, pose, lighting, etc. Recent computational models have sought to match humans' remarkable visual abilities, and, using large databases of "natural" images, have shown apparently impressive progress. Here we show that caution is warranted. In particular, we found that a very simple neuroscience "toy" model, capable only of extracting trivial regularities from a set of images, is able to outperform most state-of-the-art object recognition systems on a standard "natural" test of object recognition. At the same time, we found that this same toy model is easily defeated by a simple recognition test that we generated to better span the range of image variation observed in the real world. Together these results suggest that current "natural" tests are inadequate for judging success or driving forward progress. In addition to tempering claims of success in the machine vision literature, these results point the way forward and call for renewed focus on image variation as a central challenge in object recognition.

Getting Started in Text Mining:

Text mining is the use of automated methods for exploiting the enormous amount of knowledge available in the biomedical literature. There are at least as many motivations for doing text mining work as there are types of bioscientists. Model organism database curators have been heavy participants in the development of the field due to their need to process large numbers of publications in order to populate the many data fields for every gene in their species of interest. Bench scientists have built biomedical text mining applications to aid in the development of tools for interpreting the output of high-throughput assays and to improve searches of sequence databases (see [1] for a review). Bioscientists of every stripe have built applications to deal with the dual issues of the double-exponential growth in the scientific literature over the past few years and of the unique issues in searching PubMed/MEDLINE for genomics-related publications. A surprising phenomenon can be noted in the recent history of biomedical text mining: although several systems have been built and deployed in the past few years--Chilibot, Textpresso, and PreBIND (see Text S1 for these and most other citations), for example--the ones that are seeing high usage rates and are making productive contributions to the working lives of bioscientists have been built not by text mining specialists, but by bioscientists. We speculate on why this might be so below.

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Bora Zivkovic: Today's Carnivals

2008-01-25T13:58:47+00:00

Carnival of Space, Week 38 - The Adventures of Shorty Barlow, Private Eye - is up on Sorting Out Science

Friday Ark #175 is up on the Modulator

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P. Z. Myers: Salvage Florida thread

2008-01-25T13:32:35+00:00

It bodes ill for a certain southern state that my mailbox overfloweth with tales of idiocy from Florida … it's gotten to the point where I cringe a little bit when I see "Florida" in the subject line, because I know it's going to be another delusional school board, another wacky letter to the editor, another Floridian complaining that his state isn't as stupid as it sounds from all the news. Even the Florida Citizens for Science blog is a reservoir of terrible stories right now.

So I'm going to abstain for a little while from the Florida bashing and give the good guys a chance to catch up. How about telling us some good news? I'm sure there are intelligent, progressive people down there gearing up to fight for science and reason, so let's hear the positive news from the Florida creation wars. If you want anonymity or don't like commenting, go ahead and email Florida stories with a hopeful bent to me and we'll try to present the other side of the state.

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Alex Palazzo: My Day

2008-01-25T12:21:23+00:00

Wake up, make breakfast. Espresso, two slices of bread from a French batard from Clear Flour Bread with some mouhamara spread from Arax. In the newspaper I read about the primaries, the financial crisis and nothing too important. I waste an hour with email, signing up to some HHMI online system, reading teh intertubes and blogging. Time to work on the grant. I read the background and significance section ... did I compose that crap? After rewriting a bit I move down to preliminary data. Not so bad. I add some clarifications here and there ... man I have to finish the methods section and it's already noon! Eat a quick lunch - I finish the batard with some mortadella, some crotonese cheese and a tomato. Back to writing. No no all this is wrong. Damn. Write write write. What the hell am I proposing? Call up baymate. "How did you do that?" "I got the prep from her, check the paper" I look at the pdf. "were prepared as previously described by Walter et al. 83" Do I have that? No. And the reference is some methods paper not available online. Damn. Look at Dirk's paper. Ah yes, exactly. Write write write. Oh yeah mention p180. Go onto pubmed. Hmm no one's done that? strange. Read some obscure manuscript (well ok it wasn't so obscure - JCB '02) Wow! This could actually be it! Email baymate. Go back look up p180's sequence. Hunh? p180 and only 980 amino acids? That's too small. And where are all the famous repeats? Click, click, click. I don't get it?

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Timo Hannay (et al.): Some papers are more equal than others

2008-01-25T12:05:18+00:00

There's a Commentary in this week's Nature about detecting plagiarism in scientific papers (free access this week) by using eTBLAST, a strange but seemingly effective hybrid of alignment search and heuristics originally designed to help search PubMed. Basically you give...

Bora Zivkovic: ClockQuotes

2008-01-25T08:54:45+00:00

You have played enough; you have eaten and drunk enough. Now it is time for you to depart.

- Horace

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Vaughan Bell (et al.): 2008-01-25 Spike activity

2008-01-25T08:00:00+00:00

Quick links from the past week in mind and brain news:

The fantastic Claudia Hammond explores the curious psychology of disgust on BBC Radio 4's science programme Frontiers.

Advances in the History of Psychology notes the passing of Paul D McLean, creator the the "Triune Brain Theory". Every time you hear the phrase 'reptilian brain', that's McLean at work.

AI learns to play Ms Pac Man. Presumably, it will soon by driven insane by the annoying music.

To the bunkers! Charmingly wide-eyed transhumanists discuss the 'singularity' - supposedly when computers will overtake the abilities of the human mind.

No really, to the bunkers! Israel intend to deploy an AI-controlled missile system that "could take over completely" from humans. Not that anyone would notice if it went bezerk I guess.

Neurophilosophy looks at a case of epilepsy triggered by hip-hop. As we noted back in October, the Beastie Boys created hip-hop triggered by epilepsy.

Dave Munger of the mighty Cognitive Daily reviews the new book by the Blakeslees on embodied cognition over at The Quarterly Conversation.

Which self-help books for depression do psychologists recommend for depression? PsyBlog looks at an interesting study on the most effective bibliotherapists.

A link between walking speed and mental quickness in the elderly is reported in an intriguing study covered by the BPS Research Digest.

The philosophy of friendship is discussed in a podcast from Philosophy Bites

Cognitive Daily examines the 'remember / know' distinction, one of the most important ideas in long-term memory research.

The myth of the mid-life crisis? An article in The New York Times questions one of our most persistent cultural clichés.

The Frontal Cortex has an interesting meta-piece on whether neuroscience is being overly popularised.

Dr Pascale Michelon writes her first article as one of Sharp Brains expert contributors on neuroimaging and the '
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">cognitive reserve'.

Scientific American's Mind Matters blog discusses how to create out of body experiences in the lab.

Immanuel Kant, or can he? Fragments of Consciousness has a great post on philosophy teams.

Tim O'Reilly (et al.): Slow Comments on Radar

Brady Forrest — 2008-01-25T07:54:58+00:00

By Brady Forrest

We have turned off auto-publish on Radar comments. We have been using reCAPTCHA, the human-detection system that assists in the translation of books, and it appears that there is currently an exploit. Our internal team is working to make our commenting system secure again (thanks Jennifer, Dave and Laura!), but for now all comments will be approved manually (sorry!). Hopefully there will be a fix soon.

Deepak Singh: Waiting for the crash?

2008-01-25T06:13:33+00:00

The way consumer genomics companies are popping up left, right and center, we’re soon going to stop keeping track. Folks its really hard to maintain mindshare in a crowded market. Unless you’re offering something compelling don’t bother. Today’s Consumer Genomics company, SeqWright.

It will be interesting to see where the market ends up by the end of 2008. I have my misgivings about the sustainability of some of the companies. There is room for only so many providers. It’s one thing to have the technology. The keys to success will be ownership, privacy, and usability. The companies that do the best job of providing information that can be of use to the layperson and do so securely, while allowing the consumer to own the data will be the ones that make the cut. No, giving away free kits at Davos doesn’t make the cut. The people there can actually afford them.

Technorati Tags: consumer genomics, personal genomics

P. Z. Myers: A nice perspective

2008-01-25T06:06:18+00:00

This is a good opinion piece in the Charlotte Observer by an Englishman residing in the city. He states right up front that he likes the city and sees a great deal of promise for the future in it, but he has one reservation: the region's religiosity.

To a foreigner like myself, it's disturbing that a majority of Americans don't believe in something as fundamental as evolution (in a CBS/New York Times poll, 55 percent said God created humans in their current form). This erosion of belief in science and rationality is especially troubling for a prosperous region such as ours. American action is vital if we are to defuse the looming crisis of global warming, and Charlotte's rise as an emerging global city gives us special responsibilities to play a leading role in solving this challenge. But solutions will be impossible without informed debate based on rigorous science.

It's a polite piece that makes a solid point, that common American attitudes about science and religion are becoming an obstacle to economic progress.

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Andrew Walkingshaw: Links for 2008-01-24 [del.icio.us]

2008-01-25T06:00:00+00:00

Good Math, Bad Math : Databases are hammers; MapReduce is a screwdriver.
About the recent critique of MapReduce. One of the best articles I've read on MR, actually...

Deepak Singh: BioBricking at UCSF

2008-01-25T05:18:36+00:00

On March 1, the BioBricks Foundation is organizing a Technical & Legal Standards workshop at UCSF. I hope to be there (need to clear out a couple of things from my calendar), so if any bbgm readers are planning to be there, let me know.

The BioBricks Foundation is a non-profit founded by Drew Endy and others, and “encourages the development and responsible use of technologies based on BioBrick™ standard DNA parts that encode basic biological functions.”

What are BioBricks? BioBricks is a standard for interchangable parts, developed with a view to building biological systems in living cells. You can find out all about them at the Registry of Standard Biological Parts.

Why am I interested? Well, partly cause Drew Endy is involved. I don’t know him personally, but I have heard him talk and anyone with that level of involvement with OpenWetWare gets a huge plus in my book. Most importantly though, I am fascinated by biological engineering. I have always believed that biological systems are marvels of design. Not always perfect, but fulfilling a purpose. The ability to engineer such systems has therefore always been of significant interest (just don’t call it nanotechnology, which drives me nuts). Drew’s approach to bioengineered systems is very interesting, but like in many other areas, I remain “skeptically” optimistic. As fascinating as molecular machinery is, biological systems are also very complex and we don’t quite understand how things work.

What is also important is that we understand the risks and implications. As responsible scientists and citizens, we must self-police, otherwise the naysayers and alarmists become louder and louder and then the regulators come into play, a surefire way to stifle innovation. Not sure how much value my opinion has, but hopefully with my little experience in nanotech and regulatory affairs, there will be something to add.

Technorati Tags: Synthetic Biology, Bioengineering, Drew Endy, BioBricks

Bora Zivkovic: My picks from ScienceDaily

2008-01-25T04:59:02+00:00

Seismic Images Show Dinosaur-killing Meteor Made Bigger Splash:

The most detailed three-dimensional seismic images yet of the Chicxulub crater, a mostly submerged and buried impact crater on the Mexico coast, may modify a theory explaining the extinction of 70 percent of life on Earth 65 million years ago.

Jacky Dragons Are Born When The Temperature Is Right For Their Sex:

An Iowa State University researcher spent four years in Australia studying reptiles. Dan Warner, a researcher in the ecology, evolution and organismal biology department, has been working with the jacky dragon, a lizard found in Australia, to discover if egg incubation temperature and sex affects the viability of the lizards.

Adaptive Functional Evolution Of Leptin In Cold-adaptive Pika Family:

Researchers at the Northwest Institute of Plateau Biology, Chinese Academy of Sciences have put forward the viewpoint for the first time that adaptive functional evolution may occur in the leptin protein of the pika (Ochotona) family, a typical cold-adaptive mammal. They speculated that the cold, rather than hypoxia, may be the primary environmental factor that drives the adaptive evolution of pika leptin.

Forests Could Benefit When Fall Color Comes Late:

Do those fall colors seem to show up later and later--if at all? Scientists say we can blame increasing amounts of carbon dioxide in the atmosphere for prolonging the growing season of the trees. And that may actually be good news for forestry industries.

Changing Fashions Govern Mating Success In Lark Buntings, Study Finds:

A study of how female lark buntings choose their mates, published in Science, adds a surprising new twist to the evolutionary theory of sexual selection. Researchers at the University of California, Santa Cruz, discovered that female lark buntings show strong preferences for certain traits in the males, but those preferences change from year to year.

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Tim O'Reilly (et al.): iPhone 1.1.3 Jailbreaked

Brady Forrest — 2008-01-25T02:25:11+00:00

By Brady Forrest

I mistakenly upgraded my iPhone last week (un-jailbreaking it) to get MyLocation (works some of the time; interesting to play with) and the ability to send SMSs to multiple people (godsend). When I did this I gave up the ability to make sketches, record voice notes, auto-upload images to Flickr and make my friends smile by using the iLevel app.

Now on Techmeme I see that I was too hasty. There's a jailbreak out for iPhone version 1.1.3, but you need an already jailbreaked iPhone (and a willingness to try barely tested hacks). Now I am on the hunt for a way to un-jailbreak.

Nate True on Cre.ations.net has the instructions.

Nate True is going to teach a tutorial on iPhone hacking at this year's ETech. Early registration ends Monday, January 28th. Use the following code: et08rdr for a 20% discount. ETech is March 3rd to the 6th in San Diego, CA.

P. Z. Myers: The fashion accessory Ben Stein really needs

2008-01-25T01:29:00+00:00

It's a lot cheaper than making a movie and trying to persuade all those scientists to shut up.

Let's be fair — somebody used a little photoshop on me, too. But really, my head isn't that small, I'm not quite that chunky, and I'd never use a gun.

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Tim O'Reilly (et al.): Seattle Startup Weekend... This Weekend!

Brady Forrest — 2008-01-25T01:07:46+00:00

By Brady Forrest

Starting tomorrow night 125 developers, designers, UX gurus, legal eagles, PMs, new media marketers, and biz dev folks will conceive and build a web app as a part of Startup Weekend Seattle. The goal is to launch by Midnight on Sunday the 27th. We're sponsoring along with Adobe, Madrona, Lockergnome, UW, and Sun.

Much like Ignite, Startup Weekend has been spreading from city to city. Seattle is just the latest in a series, as is explained in their about page:

Founded in 2007 by Andrew Hyde, the weekend is a concept of a conference focusing on learning by creating. It is known for its quick decisions, ‘out of the box’ thinking, unique facilitation technique and letting the founders show what they can do. The program has already met with success in Boulder, Toronto, New York, Hamburg, Houston, West Lafayette, Boston and DC and is expanding to 10 other cities. These cities include San Francisco, Boston, DC, Atlanta, London, Dublin, West Lafayette, Chapel Hill, Austin, Portland, and Seattle with more cities signing up weekly.

I also noticed this clause on the ownership:

Founders receive equal shares of founder stock of the company they create (see the FAQ’s for a full explanation). 5% of each company created goes towards Startup Weekend.

Seems like the Startup Weekend crew are creating a mini-Incubator while invigorating local start-up communities. If even one of the weekend's creations do well they'll be paid back quite a bit.

Though they are technically sold out I was able to secure a spot for Radar readers. Leave your best start-up pitch in the comments by noon tomorrow. Organizer Hans Omli and I will award the best one with a spot.

Also, they are short on designers and will be willing to make exceptions for you; ping Hans at shoestringventures dot com if you are interested.

Peter Murray-Rust: APE2008 - Heuer, CERN

2008-01-25T00:32:26+00:00

APE (Academic Publishing in Europe) was a stimulating meeting, but I wasn’t able to blog any of it as (a) there wasn’t any wireless and (b) there wasn’t any electricity (we were in the Berlin-Brandenburg. Academy of Sciences, which made up for the lack by the architecture and the legacy of bullet holes in the masonry). So I took notes while the battery lasted, but they read rather staccato.
The first keynote was very exciting. Rolf-Dieter Heuer is the new Director General of CERN - where they start hunting the Higgs Boson any time now. CERN has decided to run its own publishing venture - SCOAP3- which I first heard of from Salvatore Mele - I’m hoping to visit him is CERN before they let the hadrons loose.

So my scattered notes…

SCOAP requires all COUNTRIES contribute (i.e. total commitment from the community and support for the poorer members)
closely knit community, 22, 000 ppl.
ca 10MEUR for HEP - much smaller than expts (500MEUR) so easy for CERN to manage (So organising a publishing project is small beer compared with lowering a 1200 tonne magnet down a shaft

22% use of Google by young people in physics as primary search engine
could we persuade people to spend 30 mins/week for tagging

what people want
full text
depth of content
quality

build complete HEP paltform
integrate present repositories
one-stop shop
integrate content and thesis material [PMR - I agree this is very important]

text-and data-mining
relate documents containg similar information
new hybrid metrcs
deploy Web2.0
engage readers in subject tagging
review and comment

preserve and re-use reaserach data
includes programs to read and analyse
data simulations, programs behind epts
software problem
must have migration
must reuse terminated experiments

[PMR. Interesting that HEP is now keen to re-use data. We often heard that only physiscists would understand the data so why re-use it. But now we see things like the variation of the fundamental constants over time - I *think* ths means that the measurement varies, not the actual constants]

preservation
same reesearchers
similar experiements
future experiements
theoretic who want to check
theorist who want to test futuire (e.g. weak force)
need to reanalyze data with time (JADE experiement, tapes saved weeks before destruction and had expert)
SERENDIPTOUS discovery showing that weak force grows less with shorter distance

Raw data 3200 TB

raw-> calibrated -> skimmed -> high-leve obj -> phsyics anal - > results
must store semantic knowledge
involve grey literature and oral tradition

MUST reuse data after experiment is stopped

re-suable by other micro doamins
alliance for permanent access

PMR: I have missed the first part because battery crashed. But the overall impression is that SCOAP3 will reach beyond physics just as arXiv does. It nmay rival Wellcome in its impact on Open Acces publishing. SCOAP3 has the critical mass of community, probably finance, and it certainly has the will to succeed. Successes tend to breed successes.

… more notes will come at random intervals …

Peter Murray-Rust: Richard Poynder Interview

2008-01-25T00:09:25+00:00

I was very privileged to have been invited to talk to Richard Poynder at length in a phone interview. http://poynder.blogspot.com/2008/01/open-access-interviews-peter-murray.html.

I am impressed with the effort that Richard put in - it is a real labour of love. We’ve not met IRL and hope to do so some day.

Internviewers of this quality provide very useful checkpoints - in going over some of the points I was able to realise what might be consistent and contradictory. And there is an objectivity which an individual cannot create for themself.

So many thanks Richard.

Gregg Favalora: How lenses are made...

G-Fav — 2008-01-24T22:56:17+00:00

...or as J-Fav might call it, "optics porn."

The folks at Gizmodo linked to a YouTube clip from the Discovery Channel showing how multi-element lenses are made. Craftmanship!

With all the attention given to dust, it's funny how the technicians don't have to wear hairnets and are allowed to wear jewelry on their hands (e.g. large wedding rings). In any case, you can't argue with the final result.

Looks like this was filmed at JML Optical.

g-fav

Corie Lok et al.: Events alerts: pub night and Euro career fair

2008-01-24T22:15:15+00:00

Make room in your calendars…the monthly Nature Network Boston pub nights are starting up again this year. The next one will be next Tuesday at 6:30pm at the Middlesex Lounge near Central Square in Cambridge. Please come, bring labmates and scientists-friends. Details and RSVP here.

And later next week, the European Career Fair will be held at MIT (Feb 1-4). They call themselves the largest career fair in the US featuring employers based in Europe. About half of the companies are in the life science/engineering/technology sectors.

I had lunch a couple of weeks ago with one of the organizers, Wiep Klaas Smits, and he told me, to my surprise that most of the people registered to attend the fair are NOT homesick Europeans. According to the organizers’ stats, only about a third of registered attendees declare themselves to be from Europe. One third say they are American and the other third from other parts of the world.

I found that interesting. In science, the conventional thinking has been that you go TO the US (or STAY in the US) to further your career. Is the flow of traffic reversing now? Are more scientists finding Europe to be a more attractive place to work and live? Why? Is it just for the superior wine, cheese, bread? :)

Wiep Klaas has started a group here on NNB for anyone attending the career fair. Join the conversation there about why you might be interested in careers in Europe.

P. Z. Myers: We made the Knoxville news

2008-01-24T22:13:51+00:00

It's all about that goofy Abunga bookstore nonsense — I love how a couple of paragraphs and a few hundred comments can make the zealots swoon.

There are lots of comments there, too, most seem to either dislike Abunga's model, or are defending it on false pretenses: "we MUST maintain the integrity of our free enterprise system"!!! It seems to me that having a swarm of people using their rating system exactly as they designed it is perfectly fair and a fine example of free enterprise in action.

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Richard Akerman: library 2.0 presentation from GTEC 2007

Richard Akerman — 2008-01-24T21:16:46+00:00

A Google search for library 2.0 books happened to turn up this presentation

Library 2.0 Library Services & Web 2.0 (PPT) - GTEC conference - October 16, 2007

by Donna Bourne-Tyson of Mount Saint Vincent University (MSVU) in Halifax, NS

A couple things I hadn't known

NRCan libraries in delicious - http://del.icio.us/nrcanlibrary

Dalhousie University implementation of LibGuides - http://libguides.library.dal.ca/

Deepak Singh: Toby Segaran joins Freebase

2008-01-24T21:09:26+00:00

Toby Segaran, the author of one of my favorite books, Programming Collective Intelligence is joining Freebase. That’s what they call heavy artillery.

I really need to get my act together about using the service for something concrete instead of futzing around every few months

Technorati Tags: Toby Segaran, Freebase

Tim O'Reilly (et al.): Survey: what benefits do online communities bring?

Andy Oram — 2008-01-24T21:03:28+00:00

By Andy Oram

If you're part of a community that comes together mostly or entirely online, you can help The Civil Society Project research what happens on that community. They have a simple survey of about 10 questions that ask why you participate in that community, what good and bad things happen there, etc. Their essential question is whether people can bond and grow in these communities just as they do in face-to-face communities.

P. Z. Myers: What is part of their job description?

2008-01-24T20:59:25+00:00

Both the Republic of Ireland and Northern Ireland are making a reduction in the legal blood alcohol driving limit from 0.08 to 0.05%. This is facing opposition from an unexpected quarter: Catholic priests are concerned about driving home after Mass. Well, now, how terrible for them.

"Perhaps it could be enough for you to fail a drink-driving test," the Rev. Brian D'Arcy, a priest from Enniskillen, told the Irish Times. "I don't like to use the word wine, as it is Christ's blood in the Eucharist -- but it still has all the characteristics of wine when in the blood stream."

So it's OK to drive if it's Jesus who has lowered your response time, diminished your coordination, and addled your perceptions, but not if it's alcohol? And do these guys seriously believe that that's Jesus's blood in your circulatory system afterwards? Weird.

I did learn something new…

Priests say the new limit would put them over the legal limit after fulfilling their duties during the Mass, which include drinking all consecrated wine not distributed during communion.

What a racket — here I thought godless evilutionists had it easy, what with their porn and moneybags, but the Catholics have made gurgling down any leftover wine an official duty. At the next EAC meeting, I'm going to have to move that we make it Official Policy that atheists are allowed to eat the last office donut, they are required to bogart that joint, and even if they are the last man or woman on earth, you must have sex with them.

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