Beyond peer-reviewed journals? | Gene Expression

Joseph K. Pickrell has a provocative post over at Genomes Unzipped, Why publish science in peer-reviewed journals?:

The recent announcement of a new journal sponsored by the Howard Hughes Medical Institute, the Max Planck Society, and the Wellcome Trust generated a bit of discussion about the issues in the scientific publishing process it is designed to address—arbitrary editorial decisions, slow and unhelpful peer review, and so on. Left unanswered, however, is a more fundamental question: why do we publish scientific articles in peer-reviewed journals to begin with? What value does the existence of these journals add? In this post, I will argue that cutting journals out of scientific publishing to a large extent would be unconditionally a good thing, and that the only thing keeping this from happening is the absence of a “killer app”.

[emphasis in the original]

This reminds of the discussion between Melody Dye and Jason Goldman on bloggingheads.tv. After reading Mr. Pickrell’s case, and generally slouching toward a more “open science” stance overall since that diavlog, I think I am now moving toward Melody’s position of “end it,” rather than Jason’s position of “mend it.”

The action in the Genomes Unzipped post is ...

Stephen Colbert Makes A Fracking Mistake | The Intersection

This is a guest post by Jamie L. Vernon, Ph.D., a research scientist and policy wonk, who encourages the scientific community to get engaged in the policy-making process

People wonder why the public is skeptical of climate change. I would argue that it is partly the fault of those on the left who for better or worse get the science wrong when arguing their case. When people go out on a limb to claim that extreme weather is occurring due to climate change without any scientific support, they clearly open themselves up to criticism when cold weather events like “snowmageddon” hit us. Similarly, when the impact of oil spills is exaggerated or endangered species protections are misused, there is a natural backlash, especially when the science says something different. There are metaphors and allegories that relate; chicken little, the boy who cried wolf, Harold Camping, etc.

Indeed, there are cases where the science justifies the outcry. And in those cases, if activists want to win support for their causes, they should ensure they are using accurate arguments. Stay true to the facts. And, if they make a scientific claim, show the evidence that supports that claim. When I say evidence, I mean real, tried and true, peer-reviewed scientific evidence, not a story about your cousin who claimed his toilet water caught fire because it was contaminated with methane gas. There could be other explanations for that.

A hotly contested issue that is popping up in all sorts of places is whether fracking, a process of extracting natural gas, is too risky an operation for Americans to welcome into “their backyards.” The debate is multi-faceted but largely focuses on whether toxic chemicals used in the process are contaminating drinking water in areas close to the drilling. A second issue is whether the fracking process causes natural gas to leak into wells and aquifers. Lisa Jackson, Head Administrator at the Environmental Protection Agency, recently stated in response to a question from the U.S. House Oversight Committee,

“I’m not aware of any proven case where the fracking process itself has affected water, although there are investigations ongoing.”

And yet, opponents of fracking continue to mistakenly claim the opposite is true. Why is the misinformation lingering out there? Without doubt, it’s because many people are motivated for various reasons to oppose any form of fossil fuel use. I can appreciate that. There’s also a problem when community leaders and other activists promote unscientific arguments.

This happened in a recent episode of The Colbert Report, where Stephen Colbert made a fracking mistake. During that episode, he committed more than 5 minutes to the issue. And, in some cases, he ran with material that isn’t supported by the science. In one particular instance, he used a clip from CNN that makes the following unsupported claim,

“The chemicals which are very dangerous, neurotoxins and carcinogens and the gas itself migrate into the aquifers and then you get this kind of situation where people can all of a sudden light their water on fire…”:

That’s just not based on the facts, according to the Head of the EPA. Because Colbert gets it right most of the time, I have to wonder whether this was a genuine mistake or if he has allowed himself to be duped by the anti-fracking voices. Either way, the impact is that millions of well-intentioned viewers are now empowered with false information.

You have to agree, though, the shtick about the coloring book is fracking hilarious!

If we are to take the moral high ground on this issue, we have to wait for the evidence. We should get that evidence from the results of the EPA’s scientific study.

In the meantime, there are issues regarding fracking that merit scrutiny, like where and how do they dispose of the contaminated water leftover from the process and what happens when they have a blowout or a spill. Perhaps, these issues are worthy of opposing fracking all-together. But, it should be our goal to accurately report the science.

Follow Jamie Vernon on Twitter or read occasional posts at his personal blog, “American SciCo.”


Computer Learns to Take Over Virtual Worlds by Doing What Most of Us Don’t: Reading the Manual | 80beats

spacing is importantScreenshot of Civilization IV, a later version
of the game that MIT’s computer played.

What’s the News: Many video gamers scoff at the idea of actually reading the instruction manual for a game. But a manual can not only teach you how to play a game, it can also give you the basics of language—that is, if you’re a machine-learning computer. Researchers at MIT’s Computer Science and Artificial Intelligence Lab have now designed a computer system that can learn the meaning of certain words by playing complex games like Civilization II and comparing on-screen information to the game’s instruction manual.

How the Heck:

The researchers, lead by computer scientist Regina Barzilay, began by giving their machine-learning system very basic knowledge about Civilization II, such as the various actions it can take (moving the cursor, clicking, etc.). The computer also had access to the words and other information that popped up on-screen—though it didn’t understand what the text and objects meant—and it knew when it won or lost ...


Batlantis | Bad Astronomy

This picture of Atlantis approaching the International Space Station made me laugh:

That is all.

[UPDATE: OK, maybe that isn't all. A lot of people don't get why this picture made me laugh; I thought it looked funny because it overflows the frame and is upside-down compared to how we usually see it. It's cute. As for the title, how do bats sleep?]

Credit: NASA


A Closer Look at the House Budget for NASA in FY 2012

AIP Number 90: FY 2012 House Funding Bill: NASA

"There are 14 pages of text pertaining to NASA in the committee report accompanying the FY 2012 Commerce, Justice, Science Appropriations Bill that was passed by the House on July 13. In often great detail House appropriators spell out their recommendations for how the $16,810,257,000 provided to NASA should be spent in FY 2012. Selections from this language, which starts on page 68 of the committee report follow. All figures are taken from the committee report."

Text Of The President’s Call to the ISS

Transcript of President Obama's Call to the International Space Station (with video)

"President Obama: Well, this mission marks the final flight of the Space Shuttle Program and also ushers in an exciting new era, to push the frontiers of space exploration and human spaceflight. You guys will continue to operate, or crew members like you will continue to operate the ISS in coming years, and seek to use it to advance scientific research and technology development. I've tasked NASA with an ambitious new mission to develop the systems and space technologies that are going to be necessary to conduct exploration beyond Earth, and ultimately sending humans to Mars, which is obviously no small feat, but I know we're going to be up to the task."

Last Minute Announcement: NASA Commercial Crew Program Forum

NASA Commercial Crew Program Forum

"The National Aeronautics and Space Administration (NASA) will present a status of the Commercial Crew Program strategy on Wednesday, July 20, 2011. The Forum will be held at the Press Site at Kennedy Space Center from 11:00 a.m. to 12:00 p.m. The Program Forum's key topics will include: Background of NASA's Commercial Crew Strategy, Key Program Attributes, Potential Commercial Crew Program Strategy, Short Q&A session."

Keith's note: 5 day's advanced notice - over a weekend. Too bad NASA hasn't a clue how to plan these things - they had more than a thousand media at KSC just last week and more showing up fo rthe landing. A simple handout could have enhanced visibility for this program immensely. Its hard to play "capture the flag" when you don't let people know where the flag is ... at least they are webcasting it.

President Obama Announces "Capture the Flag" in Space

Keith's note: On Friday President Obama will call the crews of the Space Shuttle Atlantis and the International Space Station from the Oval Office starting at 12:29 pm EDT.

Keith's update: During his call to the orbiting Space Shuttle Atlantis and International Space Station crews today, President Obama mentioned that a special American Flag had been carried to orbit on board Atlantis - a flag that had been carried aboard Columbia during STS-1. According to STS-135 Commander Chris Ferguson, this flag will be left on board the ISS until the next crew of Americans is launched from American soil aboard a commercial spacecraft. The President joked that this is going to become sort of a "capture the flag" game for the commercial spaceflight industry. Shortly thereafter SpaceX tweeted "SpaceX commencing flag capturing sequence..."

And thus the game begins.

NASA Seeks STEM Education Input

NASA Notice of information collection: NASA's education and outreach activities

"NASA's education and outreach activities are funded by NASA's Office of Education, Mission Directorates, and Offices of Chief Technologist and Communications. NASA's Education Coordinating Council includes representatives from each of NASA's field Centers plus the Jet Propulsion Laboratory (JPL), which deliver education and outreach. Data collection to be covered by this request are organized around three goals: (1) Contribute to the development of the Science, Technology, Engineering, Mathematics (STEM) workforce in disciplines needed to achieve NASA's strategic goals, through a portfolio of investments; (2) attract and retain students in STEM disciplines through a progression of educational opportunities for students, teachers, and faculty; and (3) build between STEM formal and informal education providers strategic partnerships and linkages that promote STEM literacy and awareness of NASA's missions."

Webb: Just Send Money

NASA: Extra money needed to launch JWST this decade, Sapceflightnow

"Rick Howard, NASA's JWST program director, said the agency determined the observatory could launch on a European Ariane 5 rocket as soon as October 2018, but it would require fresh funding. And with the federal government focused on wrangling in debt, a budget increase for the troubled JWST project is unlikely. NASA officials were speaking to the agency's astrophysics advisory council, a board of senior researchers chartered to provide advice and input in major scientific and programmatic decisions. "To get to [launch] in 2018, it's going to take a significant amount of new funds," Howard said."

On-Orbit Crew Press Conference (Update)

Joint Shuttle/ISS Crew Press Conference

"The 10 crew members aboard space shuttle Atlantis and the International Space Station will hold a news conference at 8:24 a.m. CDT on Friday, July 15. NASA Television will provide live coverage of the 40-minute news conference."

A Short Chat With Someone Offworld

"If there is one thing I'd say [to policymakers] it is that we need to focus our efforts. I'd appeal to Congress to focus on the long term. They need to look at the horizon - look out 10 years and see where they want the nation to be. We need a coherent space policy that will take us 10 to 15 years out - a decadal plan - and then make it a law so that we have to follow it so that Congress and future administrations are obliged to follow the policy that we, as a nation, have set forth."

NASA KSC’s Office Chair Failure Analysis Team In Action

Failure Analysis of an EckAdams Office Chair from the Maintenance and Operations (M&O) Building,
NASA Engineering Directorate Materials Science Division Kennedy Space Center, Florida

"A 17 year old EckAdams model number 5353 chair was submitted for failure analysis when the cylinder of the chair failed during use. Both macroscopic and microscopic indications of fatigue were observed on the cylinder fracture surface, indicating that the cylinder progressively failed due to the bending stresses imparted on the cylinder during a reclining motion. The stress on the cylinder was likely exacerbated by failed welds that were observed between the chair back mounting plate and the base plate, which ...."

Keith's note: Yes, NASA KSC actually did a full-blown failure analysis of an old piece of office furniture that broke. That's right - an old office chair broke (surprise) and the rocket scientists descended upon it as if it were a Mishap Investigation Board - like the kind that you set up after a rocket blows up. Included in this analysis were detailed SEM (Scanning Electron Microscope) and stereo microscopic imagery analysis. I would be willing to bet that the cost of this analysis certainly exceeded the cost of simply replacing the broken chair and that it vastly exceeded the actual value of the 17 year old chair itself. You hear people defending the way that NASA operates and then something like this shows up. You have to wonder if there is any common sense in the management manuals they use these days. I wonder if KSC PAO can dig up the actual cost of this CFA (Chair Failure Analysis).

Attempt to Save Webb From Cancellation Fails

Schiff Amendment to Provide FY 2012 Funding for James Webb Space Telescope Rejected

"The full House Appropriations Committee had been meeting for almost 3 1/2 hours yesterday when Rep. Adam Schiff (D-CA) rose to offer an amendment to provide $200 million for the James Webb Space Telescope in the FY 2012 Commerce, Justice, Science Appropriations Bill. A vote was pending on the House floor, and House Appropriations Committee Chairman Harold Rogers (R-KY) was ready to take a final vote to pass the bill. After brief comments by Schiff and Commerce, Justice, Science Appropriations Subcommittee Chairman Frank Wolf (R-VA) a voice vote was called, and the amendment was rejected. Schiff's amendment would have moved $200 million from NASA's Cross Agency Support budget, for which the bill allocated approximately $3 billion. This amendment was one of several that sought to transfer money from this budget category to other programs. All were rejected."

Congress Continues to Push on Space Launch System Release

Senator Hutchison Calls for Immediate Action on Space Launch System

"No one questions the need to ensure the best understanding of program costs. We do that every year on an ongoing basis with every major NASA program, as we set spending levels in our annual budget. There is simply no need to defer announcing the vehicle design decision while awaiting yet another cost review. "To do so only increases the real human cost that NASA employees and contractors are experiencing in the face of continued uncertainty about the future. Without a decision we will continue to lose skilled workers that we need to build the shuttle replacements. Besides the toll this will take on workers and their families, who have contributed so much to science, our national security, and the economy, it will be difficult and more costly to replace this invaluable human capital. "We have the information to make a decision now, and I call on the Administration and OMB to immediately make public and approve NASA's technical design decision on the heavy lift vehicle."

Video: World

NASA today debuts an inspirational video featuring the International Space Station and its crews set to the song "World" by recording artists Five for Fighting. The video features imagery of both the space station and the space shuttles that have served as the workhorses of space station construction and resupply. It uses selections from orbit as well as Earth-bound training and launch activities to communicate the importance of space exploration and its benefits for future generations. Intermixed are selections of video that show the beauty of planet Earth as seen from the space station and scenes of children inspired by space exploration. The lyrics emphasize that "history starts now" and invite listeners to ask the question, "What kind of world do you want?"

The video ends with a reminder that although STS-135 is the final space shuttle mission, the International Space Station will continue an uninterrupted human presence in space. The video will air on NASA Television at 7:15 p.m. CDT. For NASA TV schedules, downlink information and streaming video, visit: http://www.nasa.gov/ntv

To watch the video online, visit: http://www.nasa.gov/multimedia/videogallery/index.html?media_id=100242111

NASA also has released a new 26-minute video about the history, research and promise of the International Space Station. During the past decade, 15 nations have come together, setting aside boundaries and differences, to create the largest and longest inhabited object to ever orbit the Earth. To view that video, visit: http://www.nasa.gov/mission_pages/station/multimedia/first10next10.html

For more information about the space shuttle and the space station, visit: http://www.nasa.gov

Prox Ops at Vesta

Dawn Spacecraft to Enter Orbit Around Asteroid Vesta on July 15

"On July 15, NASA's Dawn spacecraft will begin a prolonged encounter with the asteroid Vesta, making the mission the first to enter orbit around a main-belt asteroid.
The main asteroid belt lies between the orbits of Mars and Jupiter. Dawn will study Vesta for one year, and observations will help scientists understand the earliest chapter of our solar system's history."

NASA Shines on the Big Screen

In less than two weeks, “Transformers: Dark of the Moon,” has grossed more than $261 million at the box office. And along with the big-name actors involved, other stars of the movie are NASA workers, locations, and technologies.