History of the planet in 60 sec

Seed has a video posted showing the history of the planet scaled to 60 seconds. It is worth a look here.

What if you had access to unlimited DNA sequence data?

As odd as it may seem to some, the possibility of having as much DNA sequence information as you want is not too far away. The human genome project , in an effort to sequence a single, full, human genome (~ 3 billion base pairs long), took 13 years and cost 2.7 billion (1991) dollars. Today, human genomes are being “resequenced” using new technologies for on the order of tens of thousands of dollars. We are not to the point where we can easily get any sequence data that we want but we are surely getting close.

Sequencing technology has come a long way in the last few years, with massively parallel sequencing becoming the norm. While you get shorter sequence reads (35 – 400 base pairs) relative to traditional sequencing technologies (700 – 900 base pairs) you get millions of reads at one time. Especially in cases where there is a good reference genome (the ones you hear about in the news – humans, drosophila, gallus etc..) you can line up your short reads to the reference genome and get a newly sequenced individual in a matter of days for a few grand.

This begs the question – In a decade or so when biologists are no longer limited by what DNA they can sequence, what questions do you ask? What does perfect DNA sequence knowledge give scientists, and what does it not give.

There are already a wealth of projects using the new sequencing technology to address fundamental questions. People are using resequencing projects to look for polymorphisms in sequences within populations (in a population of drosophila, or humans), allowing for finer resolution mapping studies to look for genes associated with a diversity of traits such as human disease. Instead of relying on culture methods, or expensive and time consuming clone libraries, microbiologists are able to metagenomics on environmental samples (water, soil etc..) to determine the diversity of microbial communities. Researchers are measuring gene expression with sequence-based technologies rather than hybridization technologies, allowing for a much higher throughput.

Imagine a time where a biologist can go out into his or her favorite field site and get complete sequence information for all individuals in the population. What are the questions to ask?

My answer would include the high resolution mapping of traits of interest to the genome. Also, you could do real-time, whole-genome assays of selection accross generations. Whole genome mapping of fitness would be phenomenal.

What other ideas are out there?


Avak Kahvejian, John Quackenbush, John F Thompson (2008). What would you do if you could sequence everything? Nature Biotechnology, 26 (10), 1125-1133 DOI: 10.1038/nbt1494