evolgen

New York Times Cracks

Let’s go through the basics again. Cracking the genetic code refers to figuring out how DNA encodes the information to make proteins — that was done decades ago. Sequencing a genome does not mean that you have decoded the genome; presumably, decoding a genome would mean you’ve figured out the function of every part of a sequenced genome, but there really isn’t a proper definition. In genetics, mapping refers to determining the location of genetic elements, which is different than sequencing. And deciphering has no real meaning.

With that said, check out the newest New York Times article on the sequencing of James Watson’s genome. Here’s the first sentence:

JAMES D. WATSON, who helped crack the DNA code half a century ago, last week became the first person handed the full text of his own DNA on a small computer disk.

Jim Watson did not “crack the DNA code”. Watson helped figure out the structure of DNA and double strand pairing of DNA strands. But it only gets better worse:

Soon enough, scientists say, we will all be able to decipher our own genomes — the six billion letters of genetic code containing the complete inventory of the traits we inherited from our parents — for as little as $1,000.

Decipher our own genomes? What the fuck does that mean? Six billion letters of genetic code? The genetic code consists of triplets of nucleotides called codons, which you can view in this handy dandy codon table. Considering that most of the human genome does not encode protein coding sequences, far less than six billion nucleotides are even involved in the genetic code. And that bit about our genome “containing the complete inventory of the traits we inherited from our parents” — I ain’t touching that with a poorly mixed metaphor.

In the first two paragraphs, we’ve already hit a trifecta: attributing some accomplishment to James Watson that he did not do, mixing up sequencing and decoding, and deciphering the spirit of Nicholas Wade. But that was only the first race of the day. In the showcase, we have Decode, a favorite at 3:2 odds to irk any respectable geneticists. The decode horse comes out of the gates fast and takes a huge lead coming around the first bend:

As thousands of people decode their DNA over the next few years, they are likely to find themselves facing a genetic mirror whose reflection changes on an almost daily basis.

Oh, no, she didn’t? Oh, yes, she did! Everyone is going to be decoding their genomes in the next few years. I know I want to decode my genome. Our craptacular author, Amy Harmon, is just throwing around words willy nilly, with no regard for what they really mean. She’s probably been reading the articles by Wade and other journalists with a poor command of terminology. Now, with her chance to shine, she doesn’t want to write a boring article in which she uses the word “sequence” (and its variants) over and over again. So she samples from the works of others — the mistakes they’ve made become her mistakes. The dastardly diction disease is spreading through the science journalism community like my inability to craft clever metaphors.

And if you haven’t had enough (and if you’re not sick of me scratching my pet peeve), here’s Harmon inventing a new false synonym for DNA sequencing:

There are other reasons to unravel your genome. Embracers of nature over nurture may sift through their 20,000 genes to find an explanation for personality traits thought to have a partial genetic basis — like early rising, risk-taking, shyness and addiction.

Yes, my friends, soon you too will be able “unravel your genome” for the low cost of $1,000. I’m guessing they’ll be using helicase to do the unraveling. So, let’s add another word to the list of those that make a science writer look ignorant. Stephen, add “unravel” to the big board.

i-651474221babca09e3353a59fea4ddab-OnNotice_decode.jpg

Thanks Stephen.

Comments

  1. #1 Amit
    June 3, 2007

    RPM,

    You should chair a session at the next ASHG meeting on Decoding Nicholas Wade’s Genome.

  2. #2 Alan Kellogg
    June 3, 2007

    And you trust their reporting on other subjects.

  3. #3 p-ter
    June 4, 2007

    does it make me less of a geneticist if I say the “decode” thing doesn’t bother me at all? the word doesn’t have a precise scientific meaning, and even now people probably aren’t just getting only their raw sequence reads — there’s some functional information known (disease susceptibility alleles and the like), which are likely included.

    especially for a person that doesn’t understand a lot of genetics, having someone sequence your genome and tell you that you have an increased probability of disease x and protection against disease y sound kind of like a popular use of the word “decode”.

    “unravel”, as well, has a pretty well-known popular meaning outside of the DNA helicase one, which could be appropriate here.

  4. #4 Tim
    June 13, 2007

    Hey
    They decoded, deciphered, discovered Watson’s genome the other day, and Venter claimed to have figured his out earlier. does anyone actually know where to find it? and dont just say GenBank, becasue I’ve been searching there for so long and cannot find either of their genomes.

  5. #5 RPM
    June 13, 2007

    I think the trace files are available in the NCBI trace database, but I don’t think Watson’s assembled genome has been deposited in Genbank.

  6. #6 Tim
    June 14, 2007

    Hey, what do you mean trace files? I’m just a student trying to learn more about this, so my background isn’t stellar.

    do you have a direct link to the site with his DNA?

    Also, what about J. Craig Venter? Apparently, the news has been telling us that Mr. Venter has already posted his genome in GenBank as well.

    I guess you can’t believe everything you read, huh?

  7. #7 RPM
    June 16, 2007

    A trace file is a raw sequencing read. I don’t know if the assembled genome has been deposited in any public databases.