Monday, October 8, 2007

Which came first, the chicken genome or the egg genome?

Looks kinda like a chicken, right?

I thought so too. This is genomic duplication data from figure 2 from a Nature Genetics paper published online today.

The title of the press release is: "Which came first, the chicken genome or the egg genome?"

But the paper is really about a different "which came first" question facing scientists? and one that -- if answered fully -- will help to explain exactly how we modern humans came to be. And it will give us a whole lot of new insights on genomic disease as well. The human genome is full of duplicated chunks of DNA that have played important roles in evolution, and which are involved in disease. The new research provides tons of new data on which of the copies of thousands of DNA segmental duplications in the human genome are the originals and which are the copies.

“Identifying the original duplications is a prerequisite to understanding what makes the human genome unstable,” said Pavel Pevzner a UCSD computer science professor who modified an algorithmic genome assembly technique in order to deconstruct the mosaics of repeated stretches of DNA and identify the original sequences. “Maybe there is something special about the originals, some clue or insight into what causes this colonization of the human genome,” said Pevzner.

You can read the press release here. If you're a journalist and would like a PDF of the paper, send me an email at dbkane AT ucsd DOT edu

Below if the full figure 2 from the paper: This colorful image (figure 2 in the paper) illustrates the process of ancestral-state determination for one 750-kb duplication block on human chromosome 2p11. In this example, 15 of 16 ancestral loci were accurately predicted by the computational method.

Do you see the chicken? What shapes do you see?

Login for a greater good

When you want to post a comment to a blog or send an email from a relatively new email account, you have to type in a series of distorted letters and numbers (a CAPTCHA) to prove you're a person and not a computer looking to add comment spam to a blog.

What if – instead of wasting your time and energy on typing ‘SGO9DXG’ you could label an image that will help someone who is visually impaired go shopping?

That’s exactly what computer scientists from UC San Diego led by computer science professor Serge Belongie are working on. They are presenting this work at a computer vision conference in October in Rio (
ICCV 2007).
The image describes one of the many useful tasks that could be done by people who are proving that they are live humans and not computers trying to put spam comments on a blog. These kinds of labeling tasks are time consuming but important for Belongie's Grozi project -- which is an effort to create a grocery shopping assistant for the visually impaired (2006 press release).

You can download the PDF of the paper here.

Here is the press release.

Parlez-vour francais? Read the story in on the French tech site: L'Atelier

This work is related the work from Luis von Ahn that has been described by the BBC, TechCrunch and others.