Archive for March, 2008

Big Cruncher

March 27, 2008

Rosetta@home top computers

I love distributed computing. It’s a great way to help science even if you don’t work in a lab or don’t have lots of money to donate.

The only project I’m crunching for right now is Rosetta@home (I’m waiting for Orbit@home).

I’m excited about it because computational protein/enzyme/RNA design has the potential to move biotech forward a great deal and cure many terrible diseases, help with bioremediation and clean fuel production, and increase our understanding of biology in general.

So I was surprised when I looked at Rosetta@home’s Top Computers list and saw that my new Mac Pro ranks #4. That probably won’t last forever since the project has almost 200,000 users and is still growing at a good pace, so I took a screenshot for posterity (above).

Technology Review recently published a piece about Dr. Baker’s work (the head of Rosetta@home and of the Baker Lab at Washington University) and what they call “a major step forward for computational protein design”. Check it out, and if you aren’t already crunching, I strongly encourage you to join a project.

Idle CPUs are sad little unproductive things, wasting their potential. Give yours something interesting to work on.

Interview with Michael Anissimov

March 26, 2008

Future Blogger has a very good interview with Michael Anissimov. It covers a lot of ground. Check it out:

V: What do you do and how is that related to the future?

MA: I am a blogger, fundraising director for the Lifeboat Foundation (LF), a director of the World Transhumanist Association (WTA) and a science/tech writer. All of these are related to futurism – my blog discusses futurist issues, the LF looks at future risks, and the WTA represents the futurist philosophy of transhumanism. As a science/tech writer, I do some writing about the latest technologies and materials, like carbon nanofoam or hypersonic flight, but equally enjoy writing about the frontiers of the sciences like paleontology, astronomy, and biology. Not everything I do relates to futurism, but much of it does.

Continue reading.

My Defective Copy of Gödel, Escher, Bach

March 14, 2008

Godel, Escher, Bach (GEB)

Ten minutes ago, I was lying comfortably in bed, reading Gödel, Escher, Bach by Douglas R. Hofstadter. I turned a page and the text stopped making sense.

“Maybe it’s another one of his games,” I thought.

I looked at the page numbers and they went from 82 to 51.

“Clever! He’s doing a recursive motif to illustrate his point.”

But sadly, that wasn’t it. Pages from 51 to 82 are printed twice, and pages from 83 to 115 are missing. Argh. Such a brilliant book too… No choice but to go cold turkey.

Can’t wait for the replacement to arrive.

Update: I received another copy of the book and all the pages are there! Also in the same package: Angela Hewitt’s interpretation of Bach’s Well-Tempered Klavier and Pierre-Laurent Aimard’s recording of Bach’s Art of the Fugue.

Dead Geniuses

March 13, 2008

Wolfgang Amadeus Mozart drawing image

Mozart was 35 years old when he died. By that time, he had composed about 600 musical pieces (that we know of). He started playing the piano at 3, and at 5 he was composing. As those who have seen the movie Amadeus know, he died before he could finish one of his greatest compositions, his Requiem. It didn’t happen like in the movie (which is fiction, based on a play), but he did die of a strange illness:

The cause of Mozart’s death cannot be determined with certainty. His death record listed “hitziges Frieselfieber” (”severe miliary fever”, referring to a rash that looks like millet seeds), a description that does not suffice to identify the cause as it would be diagnosed in modern medicine. Dozens of theories have been proposed, including trichinosis, influenza, mercury poisoning, and a rare kidney ailment. The practice of bleeding medical patients, common at that time, is also cited as a contributing cause. However, the most widely accepted version is that he died of acute rheumatic fever; he had had three or even four known attacks of it since his childhood, and this particular disease has a tendency to recur, leaving increasingly serious consequences each time, such as rampant infection and heart valve damage.

Could modern medicine have saved him? Probably. What if he had lived to be 77 like Haydn, 65 like Bach, or even 56 like Beethoven? What if he had lived to be 120? What if he was still alive and healthy (not a frail decrepit old man) today? What if these other genius composers I just mentioned also had lived longer or not died? That’s worth imagining, no?

Some individuals definitely contribute more to humanity than others (lets not kid ourselves). These statistical aberrations don’t happen very often, and it is regrettable to see them extinguished by random diseases, caused by old age or not. Don’t get me wrong, any loss of life is sad (except for some evil tyrants, maybe), but some deaths create bigger ripples in humanity’s pond than others.

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Longevity Research Needs your Help

March 10, 2008

Scott over at WRevenue posted something interesting about longevity research, along with an interesting challenge.

I decided to accept the challenge and write a bit about that topic here because I want to donate his $20 to the Methuselah Foundation, an organization that does cutting-edge anti-aging research (the real deal, not anti-wrinkle cosmetics).

A lot has been said about the subject and I don’t think I can do a better job of introducing it to you than Aubrey de Grey, so a good starting point would be the talk he gave at TED about his Strategies for Engineered Negligible Senescence (SENS). For a longer, but slightly less polished talk, see his Google Talk. But the best way to really get familiar with SENS is to buy Ending Aging: The Rejuvenation Breakthroughs That Could Reverse Human Aging in Our Lifetime. The biology might be a bit challenging for most people, but everything is explained clearly and it is the best way to make up your own mind.

You can also read more about the objections to longevity research (both technical and philosophical) at SENS.org and FightAging.org (see the “Required Reading”, “On the Causes of Aging” and “Objections Answered” boxes on the top left).

But what I want to talk about here is not SENS and why defeating aging (defined as pathologies caused by accumulated damage resulting from normal metabolic activity) is desirable.

The point I want to emphasize is that unlike religious belief in some kind of better future, research into healthy long-life doesn’t depend on supernatural or “out of our control” elements. Just like the discovery of antibiotics or heavier than air flight, it will require us to do something and solve problems. It is not unavoidable (unfortunately), and each day that it is delayed, at least 150,000 people die of age-related diseases, millions suffer and humanity loses greatly. There are no higher goals for those who want to reduce human misery.

If we don’t encourage and fund research and do our best to inform the general public about it, it might not happen (or at least, not in our currently limited lifetimes). This is too important for it to become a spectator sport.

That’s why I strongly encourage you to get informed, make up your own mind, and if you become convinced as many of us are, spread the word and donate generously to the Methuselah Foundation (anything you donate will be matched to 50% by a $3 million donation by Peter Thiel). Few investments have the potential for such high returns, for you and for those you love.

Update: I’d like to thank Scott for keeping his word and sending the money. I kept mine and donated the $20 the Methuselah Foundation.

Even if you can’t give much, it all adds up and increasing the total number of donors helps with further fundraising efforts.

Made me Smile

March 9, 2008

From the preface of Roger Penrose’s The Road to Reality: A Complete Guide to the Laws of the Universe:

Road to Reality by Roger Penrose, preface

Considering the current state of my math skills, I expect to look like the third drawing most of the time.

The Global Viral Forecasting Initiative

March 8, 2008

Diseased monkeys

The Economist has a piece on the Global Viral Forecasting Initiative (GVFI):

Dr [Nathan] Wolfe, [a virologist at the University of California, Los Angeles], is attempting to create what he calls the Global Viral Forecasting Initiative (GVFI). This is still a pilot project, with only half a dozen sites in Africa and Asia. But he hopes, if he can raise the $50m he needs, to build it into a planet-wide network that can forecast epidemics before they happen, and thus let people prepare their defences well in advance. [...]

The next stage of the project is to try to gather as complete an inventory as possible of animal viruses, and Dr Wolfe has enlisted his hunters to take blood samples from whatever they catch. He is collaborating with Eric Delwart and Joe DeRisi of the University of California, San Francisco, to screen this blood for unknown viral genes that indicate new species. The GVFI will also look at people, monitoring symptoms of ill health of unknown cause and trying to match these with unusual viruses.

More here. See also the Lifeboat Foundation’s BioShield program.

This was cross-posted on the Lifeboat Foundation blog.

Orbit@Home News: New Servers Installed

March 2, 2008

Orbit at Home Server

The Orbit@Home site was updated with some news today:

On February 28th, 2008 we’ve received the new orbit@home server. It has 2 quad-code Xeon CPUs, 8 GB of memory, fast SCSI raid disks, and is powered by a dedicated UPS unit. Right after receiving it, we’ve deployed it in the Planetary Science Institute’s IT room, and installed the Linux Ubuntu Server OS on it. This initial phase took only just over two hours. After that, we’ve installed all the software necessary to operate a BOINC-based project, including the web server and all its components. At this time (March 2nd, 2008), all the components are in place, BOINC is installed, and we plan to publish the complete system tomorrow. The main page of the project is handled by the Drupal CMS, an excellent piece of software that will help us communicate the mission of this project and its result to the public.

The project, when running, will calculate the orbit of as many near Earth objects as possible and report quickly the results so that - if need be - we can act.

See also: