Thursday, July 10, 2008

J Craig Venter-Brilliantly Inspired, and Changing the World

The J. Craig Venter Institute

J. Craig Venter Interview in Wired
Picture this: You are standing at the edge of a lagoon on a South Pacific island. The nearest village is 20 miles away, reachable only by boat. The water is as clear as air. Overhead, white fairy terns hover and peep among the coconut trees. Perhaps 100 yards away, you see a man strolling in the shallows. He is bald, bearded, and buck naked. He stoops every once in a while to pick up a shell or examine something in the sand...

Wikipedia Biography

Venter is an ex-surfer and a Vietnam war veteran. According to Time, it was not always evident that he would become a transformative figure, particularly when he was a boy; according to his biography, A Life Decoded, he was said to be never a terribly engaged student, having Cs and Ds in his eighth grade report cards.
He enlisted in the United States Navy and served a tour of duty during the Vietnam War. While in Vietnam, he attempted to commit suicide by swimming out to sea, but changed his mind more than a mile out.

Venter began his academic career at a community college, College of San Mateo in California.


He received his bachelor's degree in biochemistry in 1972, and his Ph.D. in physiology and pharmacology in 1975 — both from the University of California, San Diego. In San Diego, he married former Ph.D. candidate, Barbara Rae. After working as a professor at the State University of New York at Buffalo, he joined the National Institutes of Health in 1984. In Buffalo, he divorced Dr. Rae-Venter and married his student, Claire M. Fraser,[ and remained married to Ms. Fraser until 2005.
While at NIH, Venter learned of a technique for rapidly identifying all of the mRNAs present in a cell, and began to use it to identify human brain genes. The short cDNA sequence fragments discovered by this method are called expressed sequence tags, or ESTs, a name coined by Anthony Kerlavage at The Institute for Genomic Research. In a controversial court case, Venter tried to patent these gene fragments and lost the case.

Human Genome Project

He was the former president and founder of Celera Genomics, which became famous for running a parallel version of the Human Genome Project of its own for commercial purposes, using shotgun sequencing technology in 1999. The method was blasted by the international genetics community who derided it as unfeasible. The aim of the Celera project was to create a database of genomic data that users could subscribe to for a fee. This proved very unpopular in the genetics community and spurred several groups to redouble their efforts to produce the full sequence and release it as open access. At the same time, the HGP consortium applied political pressure to appropriate the shotgun technology and the collected data from Venter's company. There were also concerns that Venter might shatter what was supposed to be an "international" face on a landmark event in history. DNA from 5 individuals was used by Celera to generate the sequence of the human genome; one of the 5 individuals used in this project was Venter. In the end, Celera Genomics submitted to the pressure and shared its data and the credit for sequencing of the human genome with the international consortium of the Human Genome Project, which was composed of many groups from around the world. After his inability to collect royalties for the Human Genome, Venter was fired by Celera in early 2002.

Venter resisted efforts by the company board to change the strategic direction of the company.
Despite their differing motivations, Venter and rival scientist Francis Collins of the National Institute of Health jointly made the announcement of the mapping of the human genome in 2000, along with US President Bill Clinton. Venter and Collins thus shared an award for "Biography of the Year" from A&E Network.

Current work

Venter founded The Institute for Genomic Research (TIGR) in 1992. He is currently the president of the J. Craig Venter Institute, created and funded by TIGR's board (which Venter chairs). In June of 2005, he co-founded Synthetic Genomics, a firm dedicated to using modified microorganisms to produce ethanol and hydrogen as alternative fuels. He used his sloop, Sorcerer II, in the Global Ocean Sampling Expedition to help assess genetic diversity in marine microbial communities.

On September 4, 2007, a team led by Sam Levy published the first complete (six-billion-letter) genome of an individual human — Venter's own DNA sequence. Some of the sequences in Venter's genome are associated with wet earwax, increased risk of antisocial behavior, Alzheimer's and cardiovascular diseases. This publication was especially interesting since it contained a diploid instead of a haploid genome and shows promise for personalized medicine via genotyping.
The Human Reference (HuRef) Genome Browser is a Web application ( for the navigation and analysis of the Venter's recently published genome.

The HuRef database consists of approximately 32 million DNA reads sequenced using Sanger methods, assembled into 4,528 scaffolds and 4.1 million DNA variations identified by genome analysis. These variants include Single Nucleotide Polymorphisms (SNPs), block substitutions, short and large indels, structural variants like insertion, deletions, inversions and copy number changes.

The browser enables scientists to navigate the HuRef genome assembly and sequence variations, and to compare it with the NCBI human build 36 assembly in the context of the NCBI and Ensembl annotations. The browser provides a comparative view between NCBI and HuRef consensus sequences, the sequence multi-alignment of the HuRef assembly, Ensembl and dbSNP annotations, HuRef variants, and the underlying variant evidence and functional analysis. The interface also represents the haplotype blocks from which diploid genome sequence can be inferred and the relation of variants to gene annotations. The display of variants and gene annotations are linked to external public resources including dbSNP, Ensembl , Online Mendelian Inheritance in Man (OMIM) and Gene Ontology (GO).

Users can search the HuRef genome using HUGO gene names, Ensembl and dbSNP identifiers, HuRef contig or scaffold locations, or NCBI chromosome locations. Users can then easily and quickly browse any genomic region via the simple and intuitive pan and zoom controls; furthermore relevant data in specific loci can be exported for further analysis.
[edit]Mycoplasma laboratorium

Venter is seeking to patent the first life-form created by humanity, possibly to be named Mycoplasma laboratorium. There is speculation that this line of research could lead to producing bacteria that have been engineered to perform specific reactions, e.g. produce fuels, make medicines, combat global warming, etc.

In a recent interview with New Scientist when asked "Assuming you can make synthetic bacteria, what will you do with them?", Venter replied

Over the next 20 years, synthetic genomics is going to become the standard for making anything. The chemical industry will depend on it. Hopefully, a large part of the energy industry will depend on it. We really need to find an alternative to taking carbon out of the ground, burning it, and putting it into the atmosphere. That is the single biggest contribution I could make.
Furthermore it suggests that one of the main purposes for creating synthetic bacteria would be to reduce the dependence on fossil fuels.

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