Michael Graham Richard

Fold It is a game developed by the Rosetta@Home team (more about distributed computing).

It’s a new approach to protein prediction. Instead of using a more or less brute-force approach, with a CPU trying lots and lots of possibilities and calculating which ones give the best results, the game uses the human brain’s pattern recognition abilities (with help from a few automated tools) to try to find the lowest-energy folded state of a protein.

It has the potential to be on the cutting edge of a new generation of scientific games that are fun to play, teach you things, and can actually help researchers.

Words are inadequate to describe it, so please watch the two videos below to get an idea.

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A recent article in Technology Review by Nick Bostrom generated a lot of discussion about the Fermi paradox, which states:

The size and age of the universe suggest that many technologically advanced extraterrestrial civilizations ought to exist. However, this hypothesis seems inconsistent with the lack of observational evidence to support it.

I’ll add my 2 cents to this discussion by saying that there’s a possibility that any civilization that becomes advanced enough discovers that physical reality can’t hold a candle to virtual reality and makes the transition (alien transubstantiation, to coin a phrase). This could explain why they haven’t colonized the galaxy, or why we aren’t bathed in their radio communications.

Virtual worlds can be, in theory, both much more pleasant to inhabit, with unlimited freedom and none of the downsides of an existence based on crude physical processes, and also much more energy-efficient. Even without cold computing, it would take a lot less energy for an advanced civilization to do all that it wants to do within a simulation than by moving atoms around.

As I mentioned before, they could also think much faster, subjectively pushing back the heat death of the universe (while at the same time making communication with ’slow’ beings almost impossible).

I haven’t read all the serious papers on SETI and the Fermi paradox yet, but I’m pretty sure this is not an original theory. It’s just something that I haven’t seen mentioned yet and that I think deserves thinking about.

Update: Just to make things clearer, the kind of virtual reality I’m envisioning here is not one where you connect a biological body to a machine that sends it sensory information (like in the Matrix, for example). What I’m thinking of could probably be called ‘mind uploading’. There is no physical body, because one is not required. Everything would be inside the virtual world, kind of like how an artificial intelligence would not require a physical presence other than its computing substrate.

For the past few days I’ve been reading (among other things, of course…) Meditations by Marcus Aurelius, a roman emperor who lived from 121 to 180. He is known as one of the most important stoic philosophers.

One thing that has been on my mind while reading this is the fact that many people are very impressed by anything labelled “ancient wisdom” and have a bias towards giving it more weight than more recent thought. Part of that inclination is rational: If something has endured that long, there’s a good chance that it is because of its quality. But another part of it is not rational. It is based on the false parallel between the fact that older humans are generally considered wiser and the fact that the text is old.

From our point of view, the text is old. But from the point of view of human knowledge, old texts are ‘younger’ than modern texts.

So while I appreciate many of Marcus Aurelius’ stoic principles (look for truth, mind your own business, don’t waste your time on frivolous things, clearly define what matters to you so you can better stick to it, be open to have your mind changed by evidence, eliminate the unnecessary, etc), I simply chuckle when I read about his conception of the universe, the gods, reality, destiny, dualism (soul separate from body), death, etc. This is the best information that was available at the time, but compared to what we know now, it’s clearly archaic and if the roman emperor had been born today, he probably wouldn’t believe what he believed then (not to mention his positions on slaves, women, homosexuals, etc).

Yet some people will automatically give more weight to these ideas than to ideas that come from more contemporary sources because they come from “ancient wisdom”. If you suffer from that bias, you should recognize it, look back on how it might have influenced you in the past, and keep it in mind for the future. Judge ideas on their own merit, not on their capacity to endure the passage of time. With some things, it doesn’t matter too much (f.ex. morality). With others, it changes everything (scientific fields such as cosmology, biology, physics, etc).

If more people realized this, fewer Bronze Age myths would be taken seriously.

Here are 7 questions that I would like to ask to the following people: Michael Anissimov, Jamais Cascio, Tom McCabe, George Dvorsky, Steven Smithee, Randall Parker, and ‘Reason’ of Fight Aging.

Guys (no girls in my blogroll, sadly), you don’t have to reply if you don’t feel like it, but if you want to, just post the answers on your blog (I’ll link back to the entry) or in the comments here. Anybody else who wants to participate by answering one or many of the questions is welcome to do so in the comments. Thanks!

1. What would you nominate as the best idea that anybody has ever had? Why?

7. Looking ahead, are you an optimist or a pessimist? Why?

Update: ‘Reason’ from Fight Aging has answered my questions here. Michael Anissimov has given his answers in the comments below (keep an eye out for his upcoming book!), as well as Jamais Cascio. Someone going by the name of ‘Infidel753′ gave his answers over on his blog. Also in the comments are answers by Jeremy Sheperd, Dustin Parsons, and Zach. George Dvorsky also replied on his blog. Many thanks!

My own answers can be found below.

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This story doesn’t seem to have been picked up by the media yet (and maybe it won’t, but these kinds of things usually are because we like to know in which activities we can still beat machines):

PARIS, April 9 /PRNewswire-FirstCall/ — During the Go Tournament in Paris, staged between 22 and 24 March 2008 by the French Go Federation (FFG), the MoGo artificial intelligence (IA) engine developed by INRIA - the French National Institute for Research in Computer Science and Control - running on a Bull NovaScale supercomputer, won a 9×9 game of Go against professional 5th DAN Catalin Taranu. This was the first ever officially sanctioned ‘non blitz’ victory of a ‘machine’ over a Go Master.

That’s impressive on its own, but lets not jump the gun and claim that humans have been defeated at Go in the way that they have been defeated at Chess (Kasparov v. Deep Blue, 1997). The reason for that is that a board game usually has 361 squares (19 x 19), and this one only had 81 (9 x 9).

That makes quite a big difference in the size of the ‘tree’ of possible moves that has to be searched by the computer, which means that the brute force approach is less effective and so the software has to be smarter in how it approaches strategy and tactics to perform well.

Not surprisingly the Go master beat the computer in a game on a 19 x 19 board, and that with a nine-stone handicap. But even after that, he was impressed:

[...] the Go Master nevertheless rated the IA system as ‘approaching Dan standard’ in a performance that promises some formidable battles to come between man and machine.

Formidable battles indeed! The final one will be fought over Artificial General Intelligence (AGI).

Source: Latest Advance in Artificial Intelligence: Computer Wins a Game Against a Go Master

I was reading and article in The Economist about lasers that can pulse extremely rapidly. We’re talking really fast, in the femtoseconds range (one billionth of one millionth of a second).

This got me thinking about the nature of time: Is there a theoretical limit to how fast something can happen? I’m not aware of any, but physics probably gives an answer one way or the other.

Still, even if there’s a limit somehow, there’s still quite a gigantic range. From femtoseconds to how long it takes for universes to die.

What if what we consider to be “real time” - how fast we move, talk, think - happens to be a glacial pace compared to other lifeforms? I’m not sure if biological intelligent life could have a subjective impression of time on such a scale because of limits to the speed of chemical reactions and the minimum complexity required for intelligence, but if an advanced civilization had made the transition to a non-biological substrate (such as super-computers), it would be conceivable that for them seconds could subjectively be the equivalent of millennia (or more) to us.

That would make communication unlikely. It would be a bit like trying to have a conversation with a rock. Even if you knew it was intelligent, you’d probably be bored out of your mind and either you would ignore it, or wait for it to speed up. And even if that’s too anthropocentric a way to look a the situation, there’s still the problem of saying something coherent mentioned below.

There’s always the possibility that such a fast intelligence would remembers how slow it once was, in its original bio-chemical form, and plan for future contact with lesser intelligences. Keep listening on the ’slow lane’, in other words. But even if it did that, could it really communicate with us coherently if between each syllable it had the time to evolve and change a lot (more than Homo Sapiens has had time to evolve so far)? Even if it creates the message in its ‘real-time’ and then slows it down to send it, will the entity that created the message have much in common with the subjectively much older entity that exists by the time the message has been completely sent?

A few months ago I discovered Futures in Biotech, a podcast that “explores the world of genetics, cloning, protein folding, genome mapping, and more” by Marc Pelletier. The episode that first caught my attention was an interview with Dr. Vijay S. Pande of Folding@home. In fact, I might have found Futures in Biotech via a link on the Folding@home blog.

Anyway, I had a look at their archives and saw that they didn’t have anything about Aubrey de Grey or the Methuselah Foundation. I figured it would be a perfect fit and that their listeners would be interested by the SENS platform.

So I found Marc’s blog and I either emailed him or left a comment (can’t remember) suggesting that he interview Aubrey de Grey, and gave some links to check out.

Today, I returned to Futures in Biotech and was very happy to see that their latest episode is an interview with Aubrey de Grey! I haven’t listened to it yet, and I can’t be sure that it was my comment/email that was the seed from which this grew, but whatever the cause was, I’m quite happy that a few more people will be exposed to SENS.

Maybe some of the listeners of that show are biology students or research scientists and this will start a chain of events that will lead them to help healthy life-extension research directly or indirectly, or maybe some of the listeners will donate to the Methuselah Foundation. This can only help.

You can listen to the interview here.

Update: I’ve now listened to the interview and it’s quite good. Unfortunately, the sound quality for Aubrey’s side of the conversation isn’t very good and I missed some of what he said.

I encourage you to listen to the interview, but know that it is not the best introduction to the SENS platform. A better start would by this TED talk, and the most complete and detailed overview is Aubrey’s book.

Last November, I bought Molecular Biology of the Cell by Alberts (5th edition). I’m a few chapters in, and so far it’s an excellent textbook, I recommend it.

But there’s something that has been intriguing me for months: Once every few pages, seemingly at random, there are groups of 4 red letters inside pointy brackets. At first, I thought it was probably formatting meta-data, some kind of printing accident. But the second time the red letter popped up in a weird place, I noticed that the letters were all DNA letters (T,A,G,C).

Could this be a puzzle? Is this some kind of clever biological joke by the authors?

If it is, what do these code for? Some well-known protein?

It’s a mystery so far.

Update: Unless this is a well-known joke among biologists (it’s a common textbook, after all) and someone tells me about it in the comments or via email, I’ll probably compile a sequence of nucleotide letters long enough for it to be unique and then Google it. I had my “duh” moment and realized there’s no need to go through the whole 1000-page book and compile all of red letters…

We often hear about how the deoxyribonucleic acid (DNA) macro-molecule that contains the human genome has about 3 billion base pairs, but we rarely hear about the atoms. I was curious to know how many such a complex structure required…

Warning: Back of the envelope calculations.

Here we go:

3 billion base pairs equals 6 billion nucleotides.

The human genome uses 4 types of nucleotides:

• Adenine (A)
• Guanine (G)
• Cytosine (C)
• Thymine (T)

‘T’ is always associated with ‘A’, and ‘G’ with ‘C’.

Each of these nucleotides is composed of a nitrogen-containing base, a five-carbon sugar, and a phosphate group.

To simplify, we’ll only look at Thymine, which is pretty representative of the others in size.

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I’m realizing more and more than my curiosity has gotten me interested in lots of things, and gotten me lots of places that few people go, but that I need more than that to get to the next level.

Don’t get me wrong, I think it’s great I’ve got this drive to constantly learn new things, and I think I’m pretty efficient at it too. The way it works is, I go through learning phases where I’m very interested by something. It might last anywhere between 2 weeks and a few months, and during that time I usually consume large quantities of information on that thing (thank you, Internet!).

For example, during this winter I went through a photography phase. Over about a month, I went from almost no knowledge to a decent understanding of f/stops, focal lengths, bokeh, the technical specifications of various lenses and cameras, various techniques to take portraits, landscapes, indoor low-light photography, composition, telephoto, high-speed, and some software post-processing. I’ve read dozens of in-depth reviews and specification sheets. I don’t even own a camera yet, but I think I know as much, or more, than many people who own fancy DSLRs.

Another example: A couple of years ago I went through a classical music phase. I went from knowing absolutely nothing except for a few pieces used in Hollywood movies to owning a few hundreds of classical CDs, within about 6 months. I now am familiar with almost all major composers from the Baroque period up to the beginning of the modern post-romantic era. Bach, Mozart, Haydn, Beethoven, Schumann Schubert, Brahms, Tchaikovsky, Shostakovitch, Bruckner, Mahler, Berlioz, Liszt, Grieg, Mendelssohn, Stravinsky, Sibelius, Tveitt, Saint-Saens, Bartok, Holst, etc. Got various symphonies, chamber music, piano sonatas, operas, lieders, etc. Even have more than one interpretations of many pieces, because, for example, I like both the grandeur of Gardiner’s St-Matthew’s Passion (Bach) and McCreesh’s smaller choir and period instruments. During that phase, ArkivMusic.com was almost my home page and I devoured Hector Berlioz’s autobiography to learn more about the musical scene of that time. So in a few months, I learned more (on certain levels) about classical music than some baby-boomers I know who’ve been into it for 35+ years.

Since that phase has ended, I’ve been digesting all that music (it’s not something I could have done fully at the time) and acquiring more albums, though at a much slower pace. But still, nothing compares to the incredible productivity of that initial burst.

That’s just two learning phases I went through. Off the top of my head, I can think of many others that happened at various times in my life: Computer hardware, software, other musical genres (jazz, metal, klezmer, etc), literature (science fiction, etc), environment-related fields (climate science, energy infrastructure, transportation, food production, etc), biology (still slowly getting through a few textbooks), transhumanism-related fields (nanotech, biotech, A.I., longevity science, neuroscience, etc), economics, audio equipment, 20th century history, entrepreneurship/startups, astronomy, fighter planes (as a young boy), etc.

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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.

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.

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.

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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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.

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

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

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.

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:

• Distributed Computing
• Orbit@Home Funded by NASA
• Deflecting Earth-Bound Asteroids
• Near Earth Objects: We Can’t Beat the Odds Forever
• Target Earth
• Near Earth Objects and Asteroids: Are We Whistling in the Dark?