Open-Source Ecology Takes Root Across the World

October 31st, 2011 by shufei No comments »

This is another case of science going in the “open” direction, trying to harness a network of small experiments. One of the main barrier to science is funding as well as collaboration. This strategy to carry out science aims to lower the barriers in these two dimensions.

The collaboration, called the Nutrient Network—now known as NutNet—has grown far beyond initial expectations, with scientists volunteering at 68 sites in 12 countries. In part, its popular because the simple experiments are designed to answer a broad set of questions about how grasslands respond to global change—without disproportionate effort by any one individual. “Its not a brand-new idea, but its novel that theyve pulled it off,” says Alan Townsend of the University of Colorado, Boulder, who is not involved. The network also provides an easy way for young faculty members, postdocs, and grad students to get involved in a large collaboration and contribute to high-profile papers.

So far, the effort has been funded with just a single $322,000 grant from the U.S. National Science Foundation NSF for coordinating data and analysis, yet already the first few papers have been published over the past year. The most recent, which appeared in Science last month 23 September, p. 1750, challenged a long-standing idea in ecology about plant diversity and productivity. Dozens more papers are in the works, and ecologists enthuse about the networks potential for cost-effective, rapid results. “NutNet has tremendously improved on the way weve done things,” says Alan Knapp of Colorado State University, Fort Collins, another ecologist who is not involved. “Ive been incredibly impressed.”

via Open-Source Ecology Takes Root Across the World.

Citizen Science Takes Off: Could Community Labs Hatch the Next Generation of Bio Innovators?

October 30th, 2011 by shufei No comments »

Applying the concept of “citizen science” in the bioscience field, which resembles the early days of computer science hacker culture, by lowering the barrier to entry into this field.

The BioCurious lab is an extension to the “Science Shop” idea mentioned in Alan Irwin’s book Citizen Science (1995) because BioCurious is set up by grassroots using investment money from KickStarter. The “Science Shop” is started by scientists but allowing citizens to be involved.

Get ready for “citizen science” to transform bioscience. In mid-October, 28-year-old Eri Gentry opened BioCurious, a nonprofit public-use biology laboratory in Sunnyvale, Calif., with 2,400 square feet of “hacker space for biotech.” Similar community labs are sprouting up elsewhere, too. Do-it-yourself biologists are setting up shop in garages, basements, and hacker spaces worldwide. Executive Director Gentry and five co-founders raised $35,000 for the BioCurious lab on Kickstarter.com a site that enables anyone to raise money from the public for creative projects.It all suggests we could start seeing more rapid progress in the biotechnology industry. Publications from USA Today to Nature have heralded the global rise of “biohacker” activities that include personal genome investigations, synthetic biology experimentation, and reverse-engineered research tools. AP journalist Marcus Wohlsen is one of several who have compared DIY biologists to the early code hackers who revolutionized personal computing. His 2010 book Biopunk casts Gentry and her cohorts as pioneers of a movement that is determined to democratize DNA and transform bioscience.

via Citizen Science Takes Off: Could Community Labs Hatch the Next Generation of Bio Innovators? – Forbes.

Open Science Movement seems promising…

September 27th, 2011 by shufei No comments »

The Open Science Movement is a very neat concept (see excerpt from the QUEST interview with Joseph Jackson). Just like the Open Source movement that breaks open more opportunities and more development for the general public to partake in software development, I believe that Open Science Movement can theoretically make science much more participatory to the general public. However, doing science is expensive. The issue of funding, infrastructure, knowledge sharing and other things will need to be ironed out or built up. But just as the Open Source movement didn’t come to establishment over night, Open Science Movement will probably need to experience some ups and downs before it becomes more mainstream and established.

The Open Science Summit gathers a broad coalition of individuals and organizations striving to transform our science and innovation system to be radically more effective. We examine the biggest opportunities for distributed collaboration and problem solving, while considering the barriers and obstacles standing in the way of the transition to a more fully Open Science paradigm. This year’s Summit covers many topics including the future of scientific publishing and peer review (Open Access), data sharing and the future of data driven science, the effects of the patent system on innovation, personal genomics, collaborative (Open Source) models for drug discovery, and new transparent models for clinical trials.

The Open Science Movement – KQED QUEST

A Day with Charis

September 26th, 2011 by shufei No comments »

Last week, I had to stay home to watch Charis, my daughter because my mom went to take the naturalization test, which she passed with flying color. At first, I was thinking that I would be able to put her to sleep and do some work. I was not quite able to do that as she kept waking up and wanting to play. I guess she doesn’t get to hang out with Daddy that often. So, I decided to make the most out of the time I could spend with her by filming her and taking pictures of her. I had a great time with her, and it seemed that she had fun as well. Check out the video clip and the picture slideshow.

SNAMP Last Chance Field Trip (Updated)

September 13th, 2011 by shufei No comments »

On September 12, 2011, I went on my first SNAMP field trip visit the Last Chance, which is the northern site in the project, to see how the treatment has been going. I took a lot of pictures of the place, the treatment, as well as the participants who attended the events. Among the participants were UC Science Team, USFS rangers/managers, Sierra Pacific Industries-the logging industry, environmental groups, as well as, elected representative from the public. We started out by gathering at the Foresthill station. Kim and John gave the opening orientation using the handouts that PPT prepared beforehand. After the initial orientation, we drove to the treatment site, which was about one hour away from the USFS station.

At the first stop, I saw what forest mastication looked like, which was like grounding tree. I also learned that the trees that will be cut down were marked by blue marks. Some questions were raised about how the trees were selected.   Things got more interesting at the second stop where we saw the fellerbuncher at work on one side of the road. It was an eye-opening experience for me as I watched these powerful machines thinning the forest and logging at the same time. On the other side of the road was a pile of logs that were to be burned up in order to reduce the fuel load in that region. At this stop, people asked what SPLAT was, which I was not sure about prior to this. One of the gentlemen (I believe that he’s with  SPI) explained about the economics for using these big machines as well as for using/transporting these fell logs. His analysis on the economics of this operation helps me to understand that it would not be cost-effective to transfer the big pile of refused logs to be burned for energy production. That was why “the best way” (even though it’s still probably a poor way) to handle the fell logs were to burn them, after minimizing the damage to the surrounding and to the soil. I was impressed by how many factors that we need to take into consideration for such an operation.

And then we were taken to close-by site to see the difference between the original forest and the thinned out forest. It was quite a contrast between the before and after treatment. You can see through the woods after the treatment (see picture on the right). At this point, many of the participants asked questions about Lidar. When Maggi and John went over the time table about doing the Lidar by next year, one of the SPI representatives commented that he was able to understand why things had to move so fast. It seemed that SPI probably have never worked on the project where science/research played a factor in their timeline. That is really interesting to me in such a collaborative management project, where multiple processes are happening and different actors who do not necessarily cross path before are interacting with one another. Information flow and dialogue seem to be really important here, and this field trip is clearly fulfill that role.

At the last stop, we were shown a site where underburn would take place. People were able to walk around the area, and many conversations took place in clutters of individuals with the 5 USFS representatives present. And when we gathered back to the trucks that transported us to the site, there were questions about why we should still stick to the 1991 forest management guidelines. One of the older gentlemen questioned who set the guidelines and why we were still following it. The USFS reps explained that they couldn’t do much about it since that was the policy. On the less combative end, one of the elected public representative proclaimed that private homeowners should accept the reality of fire risk in the forest when they first decided to live in the Sierra forest.

Overall, the field trip was very enjoyable and informative. Kudos to the UC Science Team and USFS. There were a lot of open and diverse perspectives and dialogues. The questions and answers seemed to be helpful for everyone who was present.

Android Development Part 1

March 16th, 2011 by shufei No comments »

I finally got my acts together today to set up the Android Development environment on my Windows PC today. The great thing is that it uses Eclipse for development environment, which I have been using to do all my web development. Installation and setup was a breeze without a kink. I am looking forward to building my Hello World Android app soon. The eventual goal is to port the OakMapper iPhone app to the Android platform. I think it will be fun and useful at the same time. 

Android Robot

 

 

Project Noah

March 14th, 2011 by shufei No comments »

Project Noah is a project that is very much similar to iNaturalist and OakMapper, harnessing the power of citizen science. I hope to dig into this more in the upcoming days.

OakMapper Featured in Cal Academy

March 9th, 2011 by shufei No comments »

OakMapper is now being featured by Cal Academy in their recent effort to make the public aware about the spread of Sudden Oak Death disease. I had the privilege to tag along my adviser, Maggi Kelly, in the video interview about SOD and OakMapper. Here is the video:

A short time to love

February 23rd, 2011 by shufei No comments »

I was touched by this video, which emphasizes the point that the time that we have on earth to love one another is very, very short. There is really no time to wait to love others.

Citizen Science Projects – Counting horseshoe crab

February 15th, 2011 by shufei No comments »

Citizen Science attracts young “scientists”…

It turns out that horseshoe crabs are pretty amazing creatures. At over 350 million years on the planet, they are one of our oldest-surviving species. Their shells have been used to make sutures and their blue, copper-based blood is used by pharmaceutical companies to test the safety and purity of drugs, vaccines and medical devices–no other medium works as reliably.

It also turns out that, in recent decades, horseshoe crabs have been disappearing from our estuaries in alarming numbers and scientists want to figure out why. The first step in solving this puzzle was to establish hard data on horseshoe crab populations. Researchers turned to “citizen scientists” to help them establish these baseline numbers–without a dedicated volunteer corps, it would have been prohibitively expensive to complete the initial phase of this study.

via GeekMom » Blog Archive » Citizen Science Projects.

‘Citizen scientists’: Virtual eyes on the skies

February 9th, 2011 by shufei No comments »

What are the conditions that would be suitable for carrying out a “citizen science” project? Perhaps, the following article about recognizing patterns in the space images would give us a clue. Putting this together with the bird count, it seems that one strand of Citizen Science projects is for the public to spot and recognize.

You don’t need to be a scientist to make a valuable contribution to the scientific community. Highly important discoveries can happen in your own backyard or even on your computer screen.

As the universe expands, so does the Zooniverse – an online community of “citizen scientists,” average people getting involved in the scientific process through Internet projects set up by a group of astronomers.

Citizen science is simply asking the public to help by performing basic tasks from the comfort of their own homes – just looking at images and noting what they see.

via ‘Citizen scientists’: Virtual eyes on the skies.

Geospatial Standards: Opening Up the Geosciences | Earthzine

February 9th, 2011 by shufei No comments »

It is important for scientists to begin thinking in terms of Web services rather than file-based computing. Google Maps, for example, is a service offered over the Internet, enabled by the Web. A query returns useful information and little is required of the user in terms of expertise or hardware and software. Wolfram Alpha10 is perhaps a better example, because it is a Web service that provides sophisticated analytical capabilities that operate on many different kinds of data available from government agencies and other sources. The point is that both distributed data and diverse software services can be “in the cloud,” and this rapidly advancing paradigm promises to revolutionize the geosciences.

OGC Web Services standards specify the open interfaces and encodings necessary for building open Web services that provide access to virtually any kind of vector or raster data as well as processing functions that use that data. OGC Sensor Web Enablement standards11 enable developers to make any Web-accessible sensor and/or sensor data repository discoverable, accessible and useable via the Web. This includes Earth observation sensors. Many, but not all, of the standards necessary for chaining of Web services, as in climate models, for example, are available. Others are in development.

via Geospatial Standards: Opening Up the Geosciences | Earthzine.

The Quest for ‘Perfect Climate Information’

July 1st, 2010 by shufei No comments »

The debate over information versus commitment…

What if the world had perfect climate information? If everyone had a perfect understanding of climate science and the threats posed by global warming, would that change most people’s limited commitments to individual action and our ability to implement good carbon-cutting policy? This question is a topic of an informal debate between the one-time NY Times climate reporter Andrew Revkin and Climate Progress’ Joe Romm, and it’s well worth thinking about in order to come to grips with why it is we’re so short of perfect climate information right now . . .

via The Quest for ‘Perfect Climate Information’ : TreeHugger.

BBC News – Viewpoint: Concord, you can give up bottled water

July 1st, 2010 by shufei No comments »

I have built up the bad habit of using bottled water out of convenience. After reading this story, I want to go bundanoon as well.

In Bundanoon we didn’t actually “ban” bottled water. We have no legislation on it, no regulation. It is voluntary.

In bigger towns such voluntary action becomes harder. It’s harder to get every business on side. But remember, by just having good public water sources, you will automatically reduce the amount of bottled water sold.

You will impact upon this most crazy and environmentally destructive of products – a product that is perhaps the ultimate manifestation of the consumer age. Selling people what they already can have almost for free – in bottles produced from oil, 70% of which are never recycled.

via BBC News – Viewpoint: Concord, you can give up bottled water.

30 Hour Famine 2010 – Report

July 1st, 2010 by shufei No comments »

I did my 30 Hour Famine this past weekend along with other people in my church group. The fasting part was relatively painless because I was running around the whole day doing the yard sale fundraiser. I also ran in and out a bit to watch the US World Cup game. Although we lost, I was really proud of the US team.

This was my first time doing yard sale, but my natural, Chinese, haggling instinct came out. It was a lot of fun haggling with my neighbors, also informing them about 30 Hour Famine. I got to know some of my neighbors better through the yard sale. Though I didn’t meet my personal fundraiser goal of $360 (I got $180), my church group, the International Graduate Student Ministry, raised over $9500 altogether.  I heard that World Vision could multiply that amount 7 times, which means that it could feed 182 kids for one year. That’s amazing.

I figure that if we keep doing this every year for 18 years, we could essentially raise a village in 18 years. And that village of kids, hopefully through the message of the Gospel, will learn to be grateful and give back and help fight hunger for their neighbors. I think this 30 Hour Famine can really work!

The Minimalist – 101 Fast Recipes for Grilling – NYTimes.com

July 1st, 2010 by shufei 1 comment »

I love to grill, especially with my gas grill given to me by my sister and my brother-in-law. I hope to try out some of these recipes during this summer.

The Minimalist – 101 Fast Recipes for Grilling – NYTimes.com.

30 Hour Famine 2010

June 24th, 2010 by shufei No comments »

World Vision30 Hour FamineI am participating in World Vision’s 30 Hour Famine, which is
a fundraiser drive that fights hunger and poverty for children worldwide. I will go without food for 30 hours and be hungry for the hungry children.

I’d like to ask for your support toward this effort. You can sponsor me $1/hr, $30 total. Or, you can support me however much you can spare, every dollar helps! On world average, $30 can help feed and care for a hungry child for a month. I am trying to raise $360 to feed one child for one year.

I will not eat from 12am on 6/26 to 6am on 6/27. The money from the skipped meals will be donated. In addition, I and my friends will hold a yard sale to raise more money toward this cause on the day of the fast. (It will also help me get my mind off of food.)

Please support me. THANK YOU!

To donate, click on this link!
http://www.30hourfamine.org/portal/onlinegiving/donate/103131537-078

Donate to 30 Hour Famine

Pitting the Web’s Users Against Its Gatekeepers

May 3rd, 2010 by shufei No comments »

With the majority of Internet traffic expected to shift to congestion-prone mobile networks, there is growing debate on both sides of the Atlantic about whether operators of the networks should be allowed to treat Web users differently, based on the users’ consumption.

While operators have never been required to maintain neutrality, the industry has created that expectation largely by charging users a flat rate for unlimited Internet access.

But there is a big flaw in the concept, according to the operators: Networks have never been neutral. They have always been actively managed to some extent since their inception in the 1980s to ensure that all customers get a basic “best effort” level of service.

The arcane issue of network management, and the free speech and competition issues it raises, has taken on broader political importance as operators have increasingly micromanaged the flow of data, favoring some users over others as they have sought to handle exploding levels of traffic or deliver premium broadband service at guaranteed speeds to heavy users and businesses.

via Pitting the Web’s Users Against Its Gatekeepers – NYTimes.com.

Chinese Rules Said to Threaten Proprietary Information

May 2nd, 2010 by shufei No comments »

China is expected to issue regulations on Saturday requiring technology companies to disclose proprietary information like data-encryption keys and underlying software code to sell a range of security-related digital technology products to government agencies, American industry officials said on Friday.

But they said it remained unclear how vigorously Chinese officials would enforce the new rules, which already are watered down from a sweeping proposal first raised in 2007. Both the American and European technology industries have contended that the rules are unworkable and that they amount to trade protectionism.

One concern is that the rules will allow the leak of crucial foreign technologies to Chinese competitors who are seeking to build a technology industry on a par with the West.

via Chinese Rules Said to Threaten Proprietary Information – NYTimes.com.

China’s Censorship Machine Takes On the Internet

April 29th, 2010 by shufei 1 comment »

The state of China’s internet…

Today, China censors everything from the traditional print press to domestic and foreign Internet sites; from cellphone text messages to social networking services; from online chat rooms to blogs, films and e-mail. It even censors online games.

That’s not all. Not content merely to block dissonant views, the government increasingly employs agents to peddle its views online, in the guise of impartial bloggers and chat-room denizens. And increasingly, it is backing state-friendly clones of Twitter, Facebook and YouTube, all Western sites that have been blocked here for roughly a year.

The government’s strategy, according to Mr. Bandurski and others, is not just to block unflattering messages, but to overwhelm them with its own positive spin and rebuttals.

The government makes no apologies for what it calls “guiding public opinion.” Regulation is crucial, it says, to keep China from sliding into chaos and to preserve the party’s monopoly on power.

“Whether we can cope with the Internet is a matter that affects the development of socialist culture, the security of information, and the stability of the state,” President Hu said in 2007.

via China’s Censorship Machine Takes On the Internet – NYTimes.com.

Challenging the Limits of Open Society

April 27th, 2010 by shufei No comments »

This is a very good piece of critical writing in examining the model of governance for online politics and participation.

The trend toward reappraisal of China comes after hard years for democracy enthusiasts: Iraq and Afghanistan; Hamas’s election; the disappointment of many of Europe’s colored revolutions; persistent repression in Iran and Myanmar; an economic crisis that free societies were unable to prevent and unravel; growing sclerosis in the U.S. political system; and China’s extraordinary success, despite what Westerners have often regarded as a political system incompatible with success.

The question the reappraisers seem to be asking is whether their belief in bottom-up, spontaneously ordering, self-regulating societies blinded them to other truths (as their enthusiasm for China risks blinding them to the cruelty and violence of autocracy). They are asking: Can openness go too far? Can public opinion be measured too frequently? Can free speech sow disorder? Is the crowd really smarter than the experts? Can transparency hamper governance?

In a recent essay in The New Republic, the liberal legal scholar Lawrence Lessig lashed out at “the tyranny of transparency,” criticizing a movement for digitally enabled openness in government that is popular with his liberal colleagues and at present holds much sway in Washington. But Mr. Lessig argued that efforts to require legislators to post schedules online and to map votes against campaign donations, to cite two examples, can leave “a suggestion of a sin” and deprive legislators of breathing room to conduct their work, while eroding the public trust that disclosure was meant to bolster.

At the same time, the just-ask-the-crowd fervor of recent years — reflected in the ascendancy of blogs, citizen journalism, the “Idol” contest votes, Wikipedia, open-source software — appears to be cooling.

via Currents – Challenging the Limits of Open Society – NYTimes.com.

Spammers Paying Others to Solve Captchas

April 27th, 2010 by shufei No comments »

This story presents a dark side of globalization, outsourcing and information technologies. While this line of job may provide some income to the impoverished in the developing country, it makes me wonder if this is an organized crime.

Faced with stricter Internet security measures, some spammers have begun borrowing a page from corporate America’s playbook: they are outsourcing.

Sophisticated spammers are paying people in India, Bangladesh, China and other developing countries to tackle the simple tests known as captchas, which ask Web users to type in a string of semiobscured characters to prove they are human beings and not spam-generating robots.

The going rate for the work ranges from 80 cents to $1.20 for each 1,000 deciphered boxes, according to online exchanges like Freelancer.com, where dozens of such projects are bid on every week.

Luis von Ahn, a computer science professor at Carnegie Mellon who was

phisticated spammers are paying people in India, Bangladesh, China and other developing countries to tackle the simple tests known as captchas, which ask Web users to type in a string of semiobscured characters to prove they are human beings and not spam-generating robots.

The going rate for the work ranges from 80 cents to $1.20 for each 1,000 deciphered boxes, according to online exchanges like Freelancer.com, where dozens of such projects are bid on every

devevising captchas, estimates that thousands of people in developing countries, primarily in Asia, are solving these puzzles for pay. Some operations appear fairly sophisticated and involve brokers and middlemen, he added.

via Spammers Paying Others to Solve Captchas – NYTimes.com.

China Moves to Tighten Data Controls

April 27th, 2010 by shufei No comments »

The increase in security needs to be balanced with China’s economic, scientific, political and international development. That’s the key to China’s control of technology.

“Obviously, it adds another tool that authorities would have to snoop on people,” said Jeremy Goldkorn, publisher of Danwei.org, a Web site about Chinese media and the Internet. “But I don’t think anybody thinks that their communications are safe from the prying eyes of the government, whether it is text messages or any other form of communications.”

Some Chinese legal experts have questioned whether the draft amendment contracts the government’s pledge to be more open and violates China’s constitutional guarantees of privacy and freedom of communication. But one legal scholar cautioned yesterday against judging the amendment before the exact wording was made public.

China’s determination to control cellphone and Internet communications more closely has been increasingly obvious in recent months. A new bureau has been set up to help the authorities monitor social networking sites and other user-driven forums on the Internet. Other measures have been taken to step up surveillance of cellphone text messages, individual Web sites, chat rooms, blogs and other venues.

via China Moves to Tighten Data Controls – NYTimes.com.

Enemy Lurks in Briefings on Afghan War – PowerPoint

April 27th, 2010 by shufei No comments »

This story touches upon the theme of how the design of a technology, upon its adoption, can change the way we do things. It goes without saying that technology has limitation and is designed for specific purposes. The indiscretionary use of technology is the responsibility of the user of technology.

In General McMaster’s view, PowerPoint’s worst offense is not a chart like the spaghetti graphic, which was first uncovered by NBC’s Richard Engel, but rigid lists of bullet points (in, say, a presentation on a conflict’s causes) that take no account of interconnected political, economic and ethnic forces. “If you divorce war from all of that, it becomes a targeting exercise,” General McMaster said.

Commanders say that behind all the PowerPoint jokes are serious concerns that the program stifles discussion, critical thinking and thoughtful decision-making. Not least, it ties up junior officers — referred to as PowerPoint Rangers — in the daily preparation of slides, be it for a Joint Staff meeting in Washington or for a platoon leader’s pre-mission combat briefing in a remote pocket of Afghanistan.

Last year when a military Web site, Company Command, asked an Army platoon leader in Iraq, Lt. Sam Nuxoll, how he spent most of his time, he responded, “Making PowerPoint slides.” When pressed, he said he was serious.

via Enemy Lurks in Briefings on Afghan War – PowerPoint – NYTimes.com.

Big City – 2 Days With No Text Messages for Riverdale Students

April 27th, 2010 by shufei No comments »

Does technology provide freedom or take away freedom? This article suggests that the obsession of modern-day instant communication has taken away the freedom of our youth. But is technology the one to be blamed? Or, is the issue our lack of self-control? For our youth, have we trained them in the area of self-control and time-management?

Boundaries between work and home have long since fallen, so maybe it should not be surprising that the same is true for school and home. But what middle school student 20 years ago would have voluntarily reached out to her mother 10 times between 9 a.m. and 3 p.m.? If school had any universally agreed upon upside, it was that it gave a 12-year-old some much-needed space to revel in independence or struggle with rejection — space in which, presumably, that 12-year-old could start to figure out who she was, or how he wanted to navigate the world.

This text-free Sunday, the Riverdale students said, was unusually relaxing. They were shocked at how quickly they finished their homework, undistracted by an always-open video chat, or checking in on Facebook or responding to the hundred messages they typically get in a day. Kayla and her mother went for a stroll in SoHo, a rare outing, with them both off the computer. “I had to look for things to do,” said Zachary, who ended up watching a movie with his mother.

Fewer than half of the 250 middle school students at Riverdale participated in the experiment, but Julia, for one, found it valuable. Among the revelations was the envious reaction of her father, who pointed at his own BlackBerry and told her, “I’d give anything to put this down.”

Unlike him, she realized, she had a choice, the best youth has to offer: freedom.

via Big City – 2 Days With No Text Messages for Riverdale Students – NYTimes.com.