DNA Repair Army

Posted on May 31, 2007  Comments (1)

Analysis Reveals Extent of DNA Repair Army

Elledge’s group studied human cells in culture and mapped their response to ionizing radiation and ultraviolet light. Specifically, the group looked to see which proteins in the cell were chemically altered by the enzymes ATM and ATR, finding 900 sites on 700 proteins that changed in response to DNA damage. The discovery that so many proteins are involved in the process, Elledge said, was a big surprise.

Also see: Cell Cycle Regulation and Mechanisms of DNA Repair:

Despite the abuse our DNA endures, our individual genomes usually stay basically intact because DNA has a remarkable capacity for repair. Our cells have built-in, highly efficient machinery that finds and fixes “genetic typos.”

Researchers have learned much about the complex genetic machinery that cells deploy to fix broken, cut, mutated, and misplaced genetic materials. Out of that evolving understanding has emerged a deeper awareness that DNA is truly dynamic and that responses to genetic damage are nearly as fundamental to life—and health—as is the genetic code itself.

Related: DNA Transcription WebcastNew Understanding of Human DNA

Communicating Science to the Public

Posted on May 30, 2007  Comments (1)

Webcast above: Speaking Science 2.0 by Matthew Nisbet, School of Communication, American University, and Chris Mooney, Washington Correspondent, Seed Magazine, speak at the AIBS annual meeting, May 2007, in Washington DC. They discuss how to improve the transfer of science knowledge to the public (an important topic and one I am interested in). More on The American Institute of Biological Sciences conference: Evolutionary Biology and Human Health.

via: Framing Science

Open Source Education Curricula

Posted on May 30, 2007  Comments (0)

Curriki Global Education and Learning Community

Our mission is to improve education around the world by empowering teachers, students and parents with user-created, open source curricula, and it’s all free! We believe that access to knowledge and learning tools is a basic right of every child. Our goal is to make curricula and learning resources available to everyone.

Another promising looking effort, though they do need to improving the editing of content. They also need to add tools to make it easy to find the content others have found most beneficial. And they should improve the accessibility of the content – all of it should be available using a browser (now some content is presented only as zipped files, some are word documents…). 200 science and 150 math documents are available now including: Big Cats and Intro to Electricity . The site includes content hosted itself and links to content hosted on other sites.

Related: Open Access Education MaterialsOnline Mathematics TextbooksEncyclopedia of LifeMIT for Free

Robots Renew Computer Science

Posted on May 29, 2007  Comments (0)

Robots put the cool back in computer science (page deleted by CNN so I removed the link):

Georgia Tech, which has branded the robot the “new face of computing,” is hoping that the class can be a new national model to teach students computing. To Microsoft Corp., which is investing $1 million to jump-start the program at Georgia Tech and Bryn Mawr, it’s investment in what could become its work force.

Outside groups have applauded the effort, too. “In fact, computing is a tool that can be used for virtually every application — from entertainment to medicine,” said Virginia Gold of the Association for Computing Machinery. “And the Scribbler helps show how pervasive computers are in everything.” The computing industry has a reason to be concerned about the future.

The number of new computer science majors has steadily declined since 2000, falling from close to 16,000 students to only 7,798 in fall 2006, according to the Computing Research Association. And the downward trend isn’t expected to reverse soon. The association says about 1 percent of incoming freshmen have indicated computer science as a probable major, a 70 percent drop from the rate in 2000.

Related: Electrical Engineering vs. Computer ScienceComputer Science RevolutionDonald Knuth – Computer Scientist2007 Draper Prize to Berners-Lee

Open Access and PLoS

Posted on May 28, 2007  Comments (2)

In An Open Mouse, Carl Zimmer discusses the conflict between closed journals and those that support open access.

And what do I now hear from PLOS? Do I hear the grinding of lawyerly knives? No. I hear the blissful silence of Open Access, a slowly-spreading trend in the journal world. PLOS makes it very clear on their web site that “everything we publish is freely available online throughout the world, for you to read, download, copy, distribute, and use (with attribution) any way you wish.” No muss, no fuss. If I want to blog about this paper right now, I can grab a relevant image right now from it.

His post mentions the recent bad publicity Wiley received. It seems to me the Journals still don’t understand that their copyright of research results paid for by public funds are not going to continue. And that open access science is clearly the way of the future that their continued failure to deal with is increasing the odds monthly that they will find themselves on the outside of those practicing science in the 21st Century.

PLoS on the other hand recently hired Bora Zivkovic as PLoS ONE Online Community Manager. He will be great and continue to build PLoS into an organization supporting free and open science. I loved PLoS proactive action recounted by Bora, he posted that he was interested in the job:

Next morning, I woke up to a comment by the Managing Editor of PLoS ONE asking if my blog-post should be considered as a formal job application. My comment in response was a Yes.

Related: The Future of Scholarly PublicationAnger at Anti-Open Access PR

High School Students Interest in Computer Programing

Posted on May 27, 2007  Comments (5)

Interesting post on Keeping students interested in Computer Science by an 11th grader:

Most students coming into a high school computer science course are expecting to be able to program mind blowing 3D games within a semester. When most find out that they won’t be able to come close to doing so within their single course of computer science class, most bid adieu to it and move on. Students learn that playing video games is a very small subset of computer science, and find this fact discouraging. This is where many students also lose a lot of interest in computer science. They don’t care about sorting through arrays or lists of data, or coming up with algorithms to solve problems. For this reason, a balance must be found between teaching computer science concepts, and applying the learned concepts in an engaging manner.

Very true. Engaging students, as with all teaching, is critical to making learning not just tolerable but fun.

Related: Electrical Engineering Student by college studentInspire Students to Study Math and Science by another high school studentA Career in Computer ProgrammingProgramming with PicturesWant to be a Computer Game Programmer?

Lego Autopilot First Flight

Posted on May 27, 2007  Comments (0)

Chris Anderson continues his progress with the sub $1,000 autonomous flight vehicle (using lego mindstorms at the core). He has created a site to track the progress and provide information resources to others: DIY Drones. Very cool.

Lego autopilot first flight:

My kids and I actually had the first successful test flight of the sub-$1,000 UAV two weekends ago, but I haven’t had time to edit the video properly until now. The good news is that a) it didn’t crash, and b) it works. We tested stabilization, autonomous navigation (only using compass headings this time, although GPS is in the works), and the real-time video downlink. Everything worked well enough that we’re able to see what we have to improve, which is the definition of a successful test.

The main aim of this project is to both make the world’s cheapest full-featured UAV and the first one designed to be within the reach of high school and below kids, as a platform for an aerial robotics contest. Like the Lego FIRST league, but in the air.

Related: The sub-$1,000 UAV ProjectLego Autopilot Project UpdateBuilding minds by building robotsFun k-12 Science and Engineering Learning

Evolution In Action

Posted on May 25, 2007  Comments (1)

Evolution In Action

the way they watched the process was to sequence the whole genome of each bacterial isolate. What they found were a total of 35 mutations, which developed sequentially as the treatment continued (and the levels of resistance rose). Here’s natural selection, operating in real time, under the strongest magnifying glass available. And it’s in the service of a potentially serious problem, since resistant bacteria are no joke. (Reading between the lines of the PNAS abstract, for example, it appears that the patient involved in this study may well not have survived).

The technology involved here is worth thinking about. Even now, this was a rather costly experiment as these things go, and it’s worth a paper in a good journal. But a few years ago, needless to say, it would have been a borderline-insane idea, and a few years before that it would have been flatly impossible. A few years from now it’ll be routine, and a few years after that it probably won’t be done at all, having been superseded by something more elegant that no one’s come up with yet. But for now, we’re entering the age where wildly sequence-intensive experiments, many of which no one even bothered to think about before, will start to run.

Very interesting. He is exactly right that the technology advances continuing at an amazing pace allow for experiments we (at least I) can’t even imagine today to become common in just a few years. And the insights from those experiments will allow us to think of new experiments… Wonderful.

Related: How do antibiotics kill bacteria?Drug Resistant Bacteria More CommonStatistics for Experimenters

Finding Open Scientific Papers

Posted on May 25, 2007  Comments (2)

Sandra Porter has posted a series of posts on finding scientific papers for free: A day in the life of an English physicianWhat’s the best way to find free scientific publications?My new favorite methodone more experiment

via: Finding scientific papers for free

Related: Get research papers freeOpen access science and engineering postsOpen Access Engineering JournalsCurious Cat Science and Engineering Search Engine

Extensively Drug-resistant Tuberculosis (XDR TB)

Posted on May 24, 2007  Comments (2)

Superbug poses dire threat to Africa

The journey to Dr. Moll’s terrifying discovery began in early 2005, when he noticed something peculiar. The staff at his hospital had become accustomed to the marvellous “Lazarus effect” of anti-retroviral treatment for AIDS: seeing desperately sick people quickly start gaining weight and return home or go back to work. But now, in his ward, he had two men in their 30s on ARVs whose HIV infections were suppressed to undetectable levels. Yet their TB, which would normally have cleared up in a matter of weeks, kept getting worse.

He suspected multidrug-resistant TB, or MDR, believed at the time to be as bad as the disease could get. So he collected sputum from 45 patients and sent it off to a lab in Durban for cell culturing. (The only way to tell if a TB strain is drug-resistant is to grow cultures from a patient sample, zap it with the different drugs and see which, if any, fail to kill it.) The process takes six to eight weeks. “In that time, we more or less forgot about it,” Dr. Moll said. One of his two young men died.

But the phone call from the lab, when it eventually came, slammed the issue to the top of their agenda: Of the 45 samples, 10 were indeed drug-resistant. But they weren’t resistant to just one or two of the drugs used against TB. They were resistant to all six medications available for use in Tugela Ferry. In other words, there was nothing to cure that TB at all.

As we have discussed previously, antibiotic resistance is a huge problem today and especially looming in the future. Perhaps we will find new fantanstic cures but the failure to take sensible action puts us at great risk.

Related: Deadly TB Strain is Spreading, WHO WarnsCDC Urges Increased Effort to Reduce Drug-Resistant InfectionsEntirely New Antibiotic Developed

New Neurons in Old Brains

Posted on May 24, 2007  Comments (0)

More research on feeding your newborn neurons, New Neurons in Old Brains Exhibit Babylike Plasticity:

Using a retrovirus that targets dividing, or reproducing, cells, the team tracked new neurons in the hippocampus (a midbrain structure involved with learning and memory) from their births to their deaths. The scientists could determine the behavior of cells by measuring their electrophysiological activity during different phases. “In young animals, cells are very active, very plastic, and they can change their properties readily,” he says. “This whole process [also] happens in the environment of adult circuitry.”

The team found that there is a two-week window, or critical period, about a month after these new cells hatch during which they act like the neurons of a newborn baby. The researchers cued the new cells with a pattern of electrical activation that mimics the sequence that takes place in the brain of a mouse as it learns about a special spot (such as a corner in its cage where it may receive food or a shock). During this time, the cell synapses (connections that allow neurons to communicate with each other) that are artificially stimulated become stronger.

Related: No Sleep, No New Brain CellsHow The Brain Rewires Itself