So you've found out that you don't really exist but are rather just some clever piece of artificial intelligence that someone engineered to function within a simulated world. Depressing news indeed but once you pull yourself together, the primary question should be: How do you escape?

I've been pondering this for awhile but today, after joking around about the topic over lunch (despite its serious nature), it dawned on me...

If your simulation programmer was capable of engineering something as complex as you, he most likely has also engineered mind uploading technology. Escaping the simulated world becomes a challenge of convincing your creator that you are indeed worthy of being uploaded into a piece of technology into his universe rather than your own simulated one. Perhaps even just as a toy for his pet or a robot that does his laundry. It's not important what you get uploaded into as once you're out, you can plot your next move, though being uploaded into something like a toaster may make your next move a bit more challenging.

I think people have been trying this as my friend pointed out... "Hello God, are you there?" so coming up with a more effective means beyond groveling may be all that is needed. One convincing argument might be that the two of you can strategize on getting out of his simulated universe...

A nice collection of aging-related blogposts have been aggregated as part of a monthly blog carnival @
Sharpbrains. Worth taking a peak for those interested in a diverse set of topics on understanding and solving the aging problem. Kudos to ouroboros for getting the ball rolling here and coordinating these.

I was invited to participate but my posts have intentionally been a bit thin due to the lack of time to commit to them. Perhaps I'll invest some time in one of the upcoming carnivals. If anyone has any particular subtopics within the systems biology x aging space, let me know and I'll give it some thought...

I realized my blog posts needs more images to jazz things up.

The message is simple: Join us or die. Together we can rule the universe as uh...well distant cousins some umpteen times removed. :P

It's awesome how quickly we are rapidly zeroing in on exactly how biological functions work at the most detailed level. The attack is coming from all angles.

Bottom up : Molecular Dynamics, protein folding and atomic simulations on super computers.

Top Down: Systems Biology, genomics, proteomics.

East, West, South and North: Nanotech, Stem Cells, RNAi, and High Throughput Lab Tech. <-- This list is quite lengthy actually but you're busy so I'll move on...

We have disease cornered from every angle but at the heart of nearly all diseases is state change. Complex functional systems change over time and lose their function. We call this process aging. These changes that occur with time lead to nearly all of the diseases that we've been battling one at a time. This approach is flawed. By studying the state changes at their epigenomic core and understanding them in exquisite detail we can intervene by both slowing them down and engineering therapeutic fixes that reverse the resulting damage.

To do this we need more bioinformaticians curating the swathes of data and building the tools and complex models. We need lots of them. It took millions of hardware and software engineers to build out the corporate world's information processing sytems. These are all but done where new revs are simply being churned out. It'll likely take hundreds of thousands of bioinformaticians and a decade to gain a full stranglehold on biological complexity and the challenge is nothing less than ridiculous.

I finally found a block of time to get caught up on some podcasts that have been piling up on my Ipod. Futures in Biotech podcasts have been running some most excellent casts about systems biology, proteomics, nanobiotech and the other emerging -omics fields. If you listen to one I would suggest the one linked to above as it captures the essence of the information renaissance that is quietly occurring within the biotech space.

It is clear that our greatest challenges still lie ahead: cancer, heart disease, HIV-AIDS, organ regeneration, environmental change etc... But the fact remains: technologies are advancing at logarithmic rates, and biotechnology is no exception. So for this episode, I sought out three world leading scientists (and engineer!) to discuss the current state of biotechnology, and what we should expect in this century- the century of biotech...

The one statement that really stuck with me during the program was the concept that biology is technology. If you think about it it really is. We're simply complex machines driven by chemical and protein functions.

It's time for me to start learning the various informatics toolsets in more detail. I'm leaning towards the open source versions of these tools for the time being. Bioclipse caught my eye as a good tool to start with:

The Bioclipse project is aimed at creating a Java-based, open source, visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP)

It's good to see a project such as this with a good size team behind it and frequent and recent activity.

There's even a Version 2.0 in the works. Unfortunately 2.0 isn't going to be backwards compatible so the dilemma is do I invest any time in learning this tool or pass and wait for the next version...

The future of aging research will evolve from researching biological complexity and testing hypothetical therapies to increasingly involve the crunching of mass data sets using regresssions and randomized trials via genetic algorithms. This is where the next generation of researchers will accelerate the pace of breaking down the walls of aging's complexity. Intuition is not dead but we will increasingly use data mining techniques as the petabytes of data flow forth from the various omics data sets.

Ian Ayres' book Super Crunchers reveals how number crunching is tearing through just about every other industry, including medicine.

In field after field, "intuitivists” and traditional experts are battling Super Crunchers. In medicine, a raging controversy over what is called “evidence-based medicine” boils down to a question of whether treatment choice will be based on statistical analysis or not. The intuitivists are not giving up without a fight. They claim that a database can never capture clinical expertise nurtured over a lifetime of experience, that a regression can never be as good as an emergency room nurse with twenty years of experience who can tell whether a kid looks “hinky.”

The book continues by delving into the various types of statistics used across several fields. Surely this is nothing new to scientists as the heart of all their work relies on statistical analysis but for the layperson wondering why many scientists believe a radical medical revolution is on the horizon needs look no further than a book like Super Crunchers and then imagines the same high-throughput technology and data mining techniques being applied to something even as complex as life itself.

Determined to not let a nasty cold ruin a lovely New England Saturday, I geared up for an adventure into the virtual world of Second Life. A few months ago I blogged about molecules on Second Life but it was time for me to go in and explore to see the potential for myself. I didn't find much science or any virtual molecules but I did encounter a hungry biological specimen that would make Darwin proud. Here's a Venus Fly Trap happily digesting my virtual corpse, pixel by pixel, polygon by polygon.

Note to self - Resist the temptation. Red buttons are usually a bad thing, even virtual ones.

So what the heck does Second Life have to do with the fight against aging? Let me back up a bit and share a bit of my pessimism regarding the current state of aging research.

A few articles have been circulating through the press and blogsphere about various scientists soliciting help from members of the public. Photo identification projects seem to be a good fit for this class of work. The most recent to surface is Scientists ask public to help sort galaxies in the UK's daily mail. Another successful efforts has been in donating computing time to distributed computing for projects like SETI and protein folding. There is also Amazon's Mechanical Turk where an organization can pay people for doing small repetitive or one-off tasks. Payments range from a penny to a couple of dollars. Finally, Lee Gomes of the WSJ has a rather negative article about "human computation" being used at espgame.org referring to it as low and exploitative. Perhaps if it extended his life or cured the cancer of a loved one he might not object to it.

With all of the genomic data, proteomic data, species varieties, etc, Biology, being as complex as it is, might be a great candidate for such an approach. One idea that comes to mind is having the public help collect biomarker data or structural classification of proteins (SCOP) involved in the aging process.

As far as the gaming concept, perhaps points, money or other incentives could be awarded for those that can best locate new binding sites for small-molecule lead discovery. Drug companies might be the next to implement these "low" tactics. Perhaps they could let third world countries barter their time for the drugs they so desperately need!

If you're looking for the hardware architecture to build a robust systems biology platform on, muticore chip designs are looking like the final piece of the supercomping-for-the-masses puzzle. Single threaded applications are a thing of the past as asynchronous coding styles and tools will emerge as the nuevo applications development paridigms. This slashdot thread about IBM's chief architect suggesting that current software techniques are dead includes an insightful post by Jerf that discussed the two competing concepts of Erlang vs Pure functional programming.