Author Archives: curiouscat

Freeware Math Programs

Maxima – A general purpose CAS (Computer Algebra System) is a program that’s able to perform symbolic manipulation for the resolution of common problems. As a matter of fact, modern CAS covers an extremely wide range of functionalities
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Scilab – Matlab is the standard for numerical computing, but there are a few clones and valid alternatives that are entirely free. Scilab is the closest that you can get to Matlab without spending a penny. It’s very compatible with Matlab (albeit not 100%) but it’s really flexible, powerful and comes with a Matlab converter and Scicos which is a block diagram modeler and simulator.

R – For statistical computing and analysis in the Open Source world, it doesn’t get any better than R. It is a programming language and environment that enables you to do pretty much anything that the commercial software (S-Plus) does. It is so widely adopted that it can be considered a standard in the field.

lpsolve is another one that I like for linear (integer) programming. LaTeX is also a great tool – a typesetting system; it includes features designed for the production of technical and scientific documentation (many will already be familiar with it but if you are not, check it out).

Radical Life Extension

The near-term inevitability of radical life extension and expansion by Ray Kurzweil:

It took 15 years to sequence HIV and from that perspective the genome project seemed impossible in 1990. But the amount of genetic data we were able to sequence doubled every year while the cost came down by half each year.
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If we think linearly, then the idea of turning off all disease and aging processes appears far off into the future just as the genome project did in 1990. On the other hand, if we factor in the doubling of the power of these technologies each year, the prospect of radical life extension is only a couple of decades away.

KurzweilAI.net includes many articles on Kurzweil’s ideas, by him, and others. Major topic areas include: Nanotechnology, Will Machines Become Conscious? and Singularity. The ideas can seem crazy but as Kurzweil discusses the ability to predict with the tremendous increase in the power of technology. I still think many things like radical life extension is unlikely so soon but the ideas presented are interesting and worth thinking about.

Inner Life of a Cell: Full Version

This is an extremely cool 8 minute movie on the inner workings of a Cell. The earlier version we posted about back in September of last year has been one of our most popular posts – see our most popular posts. They have added the scientific explanation that I mentioned I would love to see in the last post.

update: Unfortunately Harvard seems to want to prevent people from seeing this educational webcast. Why they don’t want to promote science education is beyond me. I guess they have better uses for their $35 billion endowment than promoting science. I sure wish they would hurry up and realize this isn’t the 18th century. They say their mission is “The advancement of all good literature, arts, and sciences; the advancement and education of youth in all manner of good literature, arts, and sciences; and all other necessary provisions that may conduce to the education of the … youth of this country…” (Jun 2008). You don’t have to just educate a few privileged soles in ivy covered buildings. You can do that any provide great education material for others around the globe.

Animation created for Harvard’s Molecular and Cellular Biology program:

Harvard University selected XVIVO, LLC, a Connecticut based scientific animation company, to customize and develop an animation that would propel Harvard’s Molecular and Cellular Biology program to the next level of undergraduate education. XVIVO’s recently completed animation, titled “The Inner Life of the Cell”, has already won awards. The eight minute animation transports Harvard Biology students into a three-dimensional journey through the microscopic world of a cell.

DNA Repair Army

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.”
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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.

Communicating Science to the Public

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

Robots Renew Computer Science

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.

Open Access and PLoS

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.

High School Students Interest in Computer Programing

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.

Lego Autopilot First Flight

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.
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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.

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.