grailsearch.org Researching Engineered Longevity

The National Institute on Aging spends over $1Billion on aging research. The amount invested has grown steadily over the years but flatlined under the Bush administration. Hopefully Obama's pledge to increase R&D to 3% of GDP also lifts this boat.

Attached are the projects that were funded in 2008 in XLS format . The are a good indicator as to where the research emphasis is. Note that there is some overlap between the projects in the two spreadsheets.

Large-scale computing efforts are costly thus doing sizable informatics projects in the "cloud" could be quite cost effective. A couple of U of Maryland students from the Center for Bioinformatics and Computational Biology have been granted nearly $400,000 to test this concept.

The money is part of the larger NSF $5 million funding effort to utilize the joint effort by IBM/Google for developing a cloud-based data center.

So the relevant question for grailsearchers is how does this help accelerate science exponentially? The real gem that could emerge here are standards for doing large-scale informatics projects. When these big players team up, they typically put a good deal of effort into the underlying architectural building blocks such as communication protocols, frameworks, tools, data format protocols, data models, etc. In academic settings, resources are often cobbled together for a one-time run and a paper is published with the relevant science. Standards are used if they can accelerate the publication date of said research but there's little incentive to develop or adhere to standards if the cost of the learning curve is excessive.

If a cloud-based development approach can drive the cost of entire projects down with a recipe-like approach to doing informatics on a large-scale, more researchers might be inclined to try and tackle some of the more sophisticated informatics challenges within the field of biology.

So I went to google dealing with IUB ambiguity codes (they are all the rage, or will be :) ) and as I'm typing, Google's intellisense shows me the issues that other people are trying to deal with:

Death is ranked only #4. People are more concerned with rejection, break ups and difficult people :0

I love Google's intellisense but it can be distracting when you're actually trying to accomplish something. Apparently, dealing with procrastination is a popular search phrase as well but there's something inherently wrong with procrastinating by reading about it.

While twittersurfing I found a quote (below) defining systems biology from a shiny new blog sys-bio.com(it's first post was a few hours before this post). Give the peculiarly ambiguous nature of the field, I thought it'd be loads of geeky fun to round up some other definitions of Systems Biology in order to come up with a more concise definition. So here's what I found:

So keywords that jump out are study, complexity, parts, systematic, interactions. For the sake of brevity, I think a suitable bumper sticker definition would be:

It seems to encpasulate all that other gobbledy gook nicely. BTW, While looking for definitions I found that I wasn't the only one pondering this...

Epigenetics is hot right now and could very well play a critical role in understanding the aging process at the regulatory level of gene expression. Though not necessarily aging related, one of the more interesting items to surface in this field is the discovery of a new nucleotide by researcher Nathaniel Heintz. He found the new nucleotide in Purkinje neuron cells while researching epigenetics. Heintz and others think that this new nucleotide may have a role in regulating gene expression within these particular cell types.

Original Article: Discovery of Sixth Nucleotide Expands DNA Vocabulary

Science Express Report : The Nuclear DNA Base 5-Hydroxymethylcytosine Is Present in Purkinje Neurons and the Brain

Thanks to L. Stephen Coles, M.D., Ph.D from the GRG mailing list for the tip.

Project grailsearch.org is to develop a web portal to support a community of informatics projects targeted at aging research. It is an umbrella project for subsequent informatics projects and expected to be a continuous effort beyond the initial 3 phases:

Phase I (2008-2009) - Prototype CMS (Drupal), blog, forums, list of resources and source code repository (SVN). Research and identify core tools, systems and informatics technologies that will have the most impact on aging research.

Phase II (2009-2010) - Start filling out content in more details, develop prototype bioinformatics tools that are integrated into portal. Start recruiting and fundraising.

Phase III (2011+) - Rollout - Promote to larger groups including students and researchers.

This project is in phase I.

psique is hosting this month's Hourglass blog carnival.

Of particular interest to those interested in the informatics and systems biology of aging is the linkback to Ouroboros who has a nice summary of the excellent work João Pedro de Magalhães is doing @ senescence.info. This is exactly the type of research needed to break down biology's walls of complexity. You can find links to senescence.info and other databases in the left column 2/3 of the way down of this site.

For more information about Hourglass see this.

The site has been upgraded to the latest Drupal CMS version. Our ISP has also moved us to the latest mysql, PHP and Apache. The site needs a new theme though as the last one isn't compatible with 6.x.

New modules installed include some new spam prevention, twitter integration, OpenID support, a forum, some project mgt software and the very cool Drupal Views module which looks like it will come in handy for compiling informatics data down the road.

One idea I've been thinking about is developing bioinformatics modules within Drupal...

Due out in November of '09 this is a book to keep an eye out for. Epignenetics of Aging looks to compile a wealth of data as to how epigenetics impacts aging from the molecular level to various diseases of aging.

I couldn't help but chuckle at the description of session 13 of MIT's OpenCourseWare on System's Biology:

I guess one could argue that slowing, halting and reversing the aging process is sufficiently ambitious (ya think?!?).

The synthetic biologists seeks to add to the the litany of cell functionality by creating new DNA sequences and downstream proteins.

So whose challenge is the greater? The synthetic biologist has the advantage of using rapid evolution cycles to test their new creations which are essentially organically driven robots where failure simply means trash what you have and start over. Compare that to the biogerontologist who seeks to engineer therapeutics for functioning organisms that typically prefer that they are not relegated to the trash bin (go figure).