I Write, Nicholas Wade Listens

Or maybe his copy editor reads this blog. Either way, there are changes afoot at the NY Times.

Three days ago I ragged on NY Times science reporter Nicholas Wade for using the word 'decode' when describing genome sequencing. In his latest article he has improved. Last time he wrote about cheap whole genome sequencing; this time he has written about sequencing of a Neanderthal nuclear genome. Now, Wade hasn't entirely kicked the decoding habit:

The project is a collaboration between Dr. Svante Paabo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, and 454 Life Sciences, a Connecticut company that has developed a new method of sequencing, or decoding, DNA.

454 is getting some sweet free advertising from one of the world's largest newspapers. Wade's also performing better. He's started to refer to genome sequencing as what it is: sequencing, not decoding. But he still feels the need to qualify it by referring to it as decoding. He even slips back into his decoding ways later in the article:

The first goal of the project will be to sequence three billion units of Neanderthal DNA, corresponding to the full length of the Neanderthal genome. This will require decoding 20 times as much DNA, because so much of the DNA in the Neanderthal bones belongs to bacteria.

Genomes must usually be decoded several times over to get a complete and accurate sequence, but the first three billion bases of Neanderthal should "hit all the essential differences," Dr. Egholm said.

The rest of the article is pretty good, and Nicholas Wade is a good science writer. If we could only get him to stop butchering the terminology.

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As I wrote in May, there have been some signs that scientists were gearing up to reconstruct the Neanderthal genome. Now it's official, as Nicholas Wade reports in the NY Times. [link fixed] I'm particularly intrigued that the paleoanthropologists doing this work are teaming up with a hot little…

I don't think this is a big deal, and definitely don't think wade is wrong here, as most of the HGP people use the term "decode" interchangeably with "sequence". in a very real sense the information is physically encrypted and not directly readable by our computers till we "decode" it.

one of 100's of cites from the web.


Human Genome Research: Decoding DNA

The U.S. Department of Energy (DOE) has historically been active in supporting human genome research. On September 10, 2003, Secretary of Energy Spencer Abraham presented the Secretary's Gold Award to Aristides Patrinos and Francis Collins for their leadership of the government's Human Genome Project. At DOE's Office of Science, Dr. Patrinos is the Associate Director for Biological and Environmental Research. He has been a researcher at the department's Oak Ridge National Laboratory and Brookhaven National Laboratory.

DOE and Secretary of Energy Spencer Abraham announced the celebration of the fiftieth anniversary of the description of the DNA double helix during April 2003. James D. Watson, Francis Crick, and Maurice Wilkins were awarded the 1962 Nobel Prize in Physiology or Medicine for their research in this area.

On June 26, 2000, President Clinton, leaders of the Human Genome Project (HGP) and representatives of the biotechnology company Celera announced the completion of a "working draft" reference DNA sequence of the human genome. The achievement provides scientists worldwide with a road map to an estimated 90% of genes on every chromosome.

Human Genome

Previously, on April 13, 2000, U.S. Secretary of Energy Bill Richardson announced that researchers at DOE's Joint Genome Institute in Walnut Creek, California, had decoded in draft form the genetic information on human chromosomes 5, 16, and 19. The chromosomes contain an estimated 10-15,000 genes, including those whose defects may lead to genetically linked diseases such as certain forms of kidney disease, prostate and colorectal cancer, leukemia, hypertension, diabetes, and atherosclerosis.

The human genome is the full complement of genetic material in a human cell; it contains instructions for making all the protein molecules for all the different kinds of cells of the human body - neurons in the brain, red blood cells, bone tissue, liver cells, etc. In decoding DNA, researchers determine the "sequence" or exact order of the individual chemical building blocks, or bases, that make up the DNA. The three chromosomes sequenced by Department of Energy researchers contain more than 300 million base pairs, or an estimated 11 percent of the total human genome.