Thursday, June 17, 2010

Boo Science!

So the other flip of the coin. The New York Times recently published an article complaining about the lack of progress. See my last post for some "Yay science!"

Be prepared. I'm about to jump on my soap box.

My responses to parts of the article...

"But the primary goal of the $3 billion Human Genome Project — to ferret out the genetic roots of common diseases like cancer and Alzheimer’s and then generate treatments — remains largely elusive. Indeed, after 10 years of effort, geneticists are almost back to square one in knowing where to look for the roots of common disease."

Ummm...back to square 1 huh? We can map genes to the 'reference genome'. Let's just start with Francis Collins since I discussed him in my last entry and his story is fresh on my brain. He found a single nucleotide difference in 1 gene that causes Progeria. The human genome has thousands of Single Nucleotide Polymorphisms and other changes in our DNA. If our DNA was the same, we wouldn't all have so many differences. THAT shouldn't come as a surprise to anyone. But no, linking a single base pair change to a disease...that's not progress at all. Oh, and btw, they discovered what that single base pair chain causes and a potential treatment to alleviate the problem. It's in a Phase II trial. Yep, back to square 1.

"In announcing on June 26, 2000, that the first draft of the human genome had been achieved, Mr. Clinton said it would 'revolutionize the diagnosis, prevention and treatment of most, if not all, human diseases.' "

Yes, because turning in your first draft for your final paper will always yield the best results...We didn't have a draft of the genome that we felt confident in until 2003. The 'reference genome' is made of sequences from several different people so it can be a better reference because we are all different.

"It was far too expensive at that time to think of sequencing patients’ whole genomes. So the National Institutes of Health embraced the idea for a clever shortcut, that of looking just at sites on the genome where many people have a variant DNA unit. But that shortcut appears to have been less than successful." [the 'clever' shortcut involves looking at common variants in different human populations] "But with most diseases, the common variants have turned out to explain just a fraction of the genetic risk."

Clearly, because it didn't answer the riddle, we have failed as scientists. Oh, and btw, the reason we did that was because of how ridiculously expensive it was to sequence a genome. Currently, we're down to $30,000/complete genome sequence. It's estimated to be down to $1,000/genome in the next 2 years. Filtering through the info contained in billions of base pairs will be easier when we can take out the noise that is common differences between you and me.

"But most of the sites linked with diseases are not in genes — the stretches of DNA that tell the cell to make proteins — and have no known biological function, leading some geneticists to suspect that the associations are spurious."

Ummm...who is your source calling this spurious? Between genes are thousands of binding sites for things like transcription factors that regulate the expression of proteins coded by genes. Some are certainly spurious but we don't know all the interactions between proteins and DNA. I doubt they are all spurious just because we haven't figured it out yet...

"The only way to find rare genetic variations is to sequence a person’s whole genome, or at least all of its gene-coding regions. That approach is now becoming feasible because the cost of sequencing has plummeted, from about $500 million for the first human genome completed in 2003 to costs of $5,000 to $10,000 that are expected next year. "

Several points I already mentioned but they didn't seem to care about earlier...

"But while 10 years of the genome may have produced little for medicine, the story for basic science has been quite different. Research on the genome has transformed biology, producing a steady string of surprises. First was the discovery that the number of human genes is astonishingly small compared with those of lower animals like the laboratory roundworm and fruit fly." ... "Little, if any, of this research could have been done without having the human genome sequence available. Every gene and control element can now be mapped to its correct site on the genome, enabling all the working parts of the system to be related to one another."

So, they are telling us that having the 'reference sequence' has been really helpful. Ok, so we haven't solved cancer yet. Just because we haven't done what some president predicted in the time he allotted, doesn't mean we failed. Eventually this writer kind of ish came around. But they sure as hell tried to make it as much like a failure by their wording.

Ugh. I'm off my soapbox. For now.

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