‘Fold It’ Media Coverage Clearinghouse

I wouldn’t normally do this, but my Fold It: The Protein Folding Game post generated quite a bit of attention, and it is obvious that many people are curious about the protein-folding game. So I figured that a central repository of media coverage might be helpful – more information might push a few people over the edge and convince them to try the game. Here’s what I’ve found so far:

• University of Washington Official Announcement (which was reprinted on Science Daily and Physorg, among others): Computer game’s high score could earn the Nobel Prize in medicine
• Howard Hughes Medical Institute Announcement: Researchers Launch Online Protein Folding Game
• The Economist: Return to the fold
• Technology Review: Biologists Enlist Online Gamers
• Slashdot (misleading title): Folding@Home 2.0 – An Online Protein Folding Game
• Penny Arcade (last paragraph): Je Parle Un Peu
• Nature Magazine Blog: Addictive protein folding game
• Seattle Times Blog: Free video game from UW: Wiggling and shaking for science
• Kotaku: Foldit Makes Protein Folding A Game
• Seattle PI: Scientists tap gaming’s power

If you see Fold It mentioned in the mainstream media or on a popular website, let me know in the comments and I’ll add it to the list.

Fold It: The Protein Folding Game

Fold It is a game developed by the Rosetta@Home team (learn more about distributed computing) under the direction of Dr. David Baker at the University of Washington.

It features 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.

Interview with Biogerontologist Aubrey de Grey

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.

Longevity Research Needs your Help

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.

More Methuselah Foundation Good News

I’m happy to report that December 2007 year-end donations to fund the Methuselah Foundation’s Strategies for Engineered Negligible Senescence (SENS) research program succeeded in matching two consecutive $25,000 matching grants from Michael Cooper and Doug Arends. Many thanks to all the donors who helped to make this possible!

There’s more to come, however. Looking to the year ahead, and plans for expansion into new branches of SENS research, Foundation supporter Ryan Scott has set up a $100,000 matching fund for all research donations made in 2008. The same rules apply as for this past December: donations are first matched 100% by Ryan’s fund, and then that total is matched again at 50% by Peter Thiel’s $3 million matching fund. That means that all your SENS research donations will be tripled – a $100 donation becomes $300 for new research into longevity medicine.

Jump on in! These are the early years in a steep growth curve – and it’s up to all of us to help make that statement true. Donations to help bring about a future of greater health and longevity can be made at the Methuselah Foundation website, where you can also learn more about how funds are spent and the results achieved to date.

Be generous. Invest in something that could have hugely beneficial returns for all of humanity, including yourself.

See also: The Most Important Thing That Happened In 2007 at Fight Aging.

Update: The Economist has an article about the fight against aging and SENS.

To better understand what the Methuselah Foundation is about, check out this Aubrey de Grey speech. There’s a longer speech he gave at Google here. You can also read Aubrey de Grey’s book.

Also on this blog:

• A Message from Aubrey de Grey
• Cemetery Excursions: Hunting Bacteria to Help LysoSENS
• LysoSENS Update

A Message from Aubrey de Grey

I’ve written about the Methuselah Foundation in the past. I think they are doing extremely important research and they should be supported.

Here’s a email from biogerontologist Aubrey de Grey:

Hello Michael,

I’m writing to you about a great situation the Methuselah Foundation find itself in until Dec 31, 2007.

You might recall in 2006 that Peter Thiel made a 3 million dollar Matching Challenge to SENS Research, where he matches 50% of donations to research until the end of 2009.

Well our performance and Thiel’s example have prompted a supporter and Three Hundred Member, Michael Cooper, to join Peter Thiel and he is offering a $25,000 Matching Challenge of his own until the end of this month.

What’s great is the donations are matched cumulatively. That is, a $1 to research is first matched with $1 from Cooper. This $2 is then matched by Thiel’s Matching Challenge with $1 bringing the total donation to $3.

In this way, a donation of say, $100, is TRIPLED to $300.

…but this multiplier only lasts until the end of this month.

Perhaps you might be interested in helping Cooper and Thiel move along in generously turning their matching challenge dollars into research?

Cheers,

Aubrey

I’ve made my first small donation a few weeks ago, and I’ll make another one before the end of the month. I encourage you to do the same.

If you want to learn more about Aubrey’s work and theories, a good introduction is this TED video. For more in depth information, see this longer talk at Google or Aubrey’s book.

See also:

• Cemetery Excursions: Hunting Bacteria to Help LysoSENS
• LysoSENS Update

LysoSENS Update

This is a follow up to Cemetery Excursions: Hunting Bacteria to Help LysoSENS.

Today I received a email from John Schloendorn (interview with him here) from the LysoSENS research project at the Biodesign Institute in Arizona:

Hey Michael!
All your 3 samples had degraders of an advanced glycation end-product [AGE]. Such degraders are quite common, but three in a row is pretty good. Perhaps that is a point for graveyard-soil. I still need bigger statistics to answer that. I also don’t know yet if they eat it in the right way. Anyway, thanks for this & I hope we can pull their genes out some time not too far away. cheers,
j

I was quite happy to learn that my samples were not useless.

When I first went out to dig, I had only read about Aubrey de Grey‘s theories about cemeteries, so that’s where I went. But in the days following the shipping of my samples, further reading seemed to indicate that high soil biodiversity was the most important factor, and I can certainly think of places around here that are better in that regard than boring homogeneous suburb cemeteries. If after further tests these samples turn out to be really interesting, I’ll be happy to go hunt for more promising sites in the region.

John also said he liked the Toblerone chocolate I included in the package.

Cemetery Excursions: Hunting Bacteria to Help LysoSENS

Today, I did something a bit special. I went out with a pointy little gardening shovel and some plastic bags to get soil samples for the LysoSENS research project.

LysoSENS is the latest Methuselah Foundation initiative aimed at tackling age-related storage diseases. These diseases, informally also called “junk” diseases, are caused by the accumulation of some pathogenic material in the body. With advancing age our bodies cannot degrade or remove this junk. Examples of candidate age-related storage diseases include

* Heart disease and stroke – cholesterol and oxidized cholesterol in the artery wall
* Alzheimer’s disease – Beta-amyloid plaques and neurofibrillary tangles in the brain
* Age-related macular degeneration – Lipofuscin of the retinal pigment epithelium
* Diabetes – Extracellular matrix protein crosslinks, due to exposure of the tissue to high sugar levels

In every case, it is thought that the selective removal of the respective substances would be extremely beneficial, although obviously nobody has directly tested this. LysoSENS is an attempt to do just that, in the worst case paving the ground for rethinking what age-related storage diseases are all about, and in the best case providing a cure for them.

So how is LysoSENS supposed to work? In brief, we are looking for enzymes capable of selectively degrading the respective target material in the environment. This idea is heavily inspired by the field of environmental bioremediation (using microbes to degrade environmental contaminants). We are working in the lab of Bruce Rittmann, a well-known environmental engineer, as he has the expertise to find microbes that degrade weird stuff. We hope that we can isolate enzymes from these microbes and deliver them in a manner similar to current FDA-approved treatments for heritable lysosome storage diseases, where the missing enzyme is tagged with certain sugars for targeting and then injected into the bloodstrem. You can learn more about the LysoSENS strategy from its originator and Methuselah Foundation chairperson Aubrey de Grey here (quick and easy) or here (detailed and technical).

Since they are looking for bacteria able to eat “junk” that our bodies are not able to degrade, a good place to look is cemeteries because we know that decomposing bodies don’t leave behind that “junk”; meaning that some organisms have filled that niche and are having lunch on it.

So I went out to three different cemeteries around town and collected soil samples. I took some notes on where and when I picked them up, packaged the whole thing (including a mini-Toblerone chocolate bar for the researchers) and mailed it to the Biodesign Institute in Arizona. It’s an easy way to help, and the more samples they get from varied and exotic ecosystems around the world, the more chances they have of finding the right bacteria and enzymes to cure these horrible age-related diseases mentioned above.

I encourage you to do the same, especially if you live somewhere interesting from a biodiversity point of view (near hot springs, near historical mass-graves, in a tropical jungle, etc). But even if you live somewhere “boring”, give it a shot. You never know, maybe your sample will contain the holy grail of junk-eating bacteria.

All the information you need, including instructions on how to collect the samples and where to mail them, is on this webpage: LysoSENS.

Update: LysoSENS Update.