Monday, July 2, 2007

Mark this day in 2007, the day that gene networks were discovered

There are at least two major ways that science articles in newspapers can fail.

The first is the "No, duh." coverage. That is, the article is presenting things that scientists have known for years if not decades, but presenting it like it's a major new discovery that will require major rethinking of how that area is studied. The second is the "the goblins will get you!" coverage, that is that if it weren't for the genius working at PETA, we wouldn't know that we're all going to die, when in fact the data say nothing of the sort.

Denise Caruso managed to hit a double this weekend in the New York Times entitled (stupidly): A Challenge to Gene Theory, a Tougher Look at Biotech. Let's start with her grandiose opening statement:

The $73.5 billion global biotech business may soon have to grapple with a discovery that calls into question the scientific principles on which it was founded.
Gee whiz! That sounds exciting! If only it were true...
Last month, a consortium of scientists published findings that challenge the traditional view of how genes function... (snip) ...To their surprise, researchers found that the human genome might not be a “tidy collection of independent genes” after all... (snip) ...Instead, genes appear to operate in a complex network, and interact and overlap with one another and with other components in ways not yet fully understood.
*gasp!* Really? They operate in networks? Sort of like this paper by Jacob and Monod suggested in 1961? The statement that "genes appear to operate in a complex network" is like saying that "the liver operates in a complex environment". Of course the liver works with other organ systems. This is not news. We've known about networks for a really long time, and with each year we're understanding more and more of these networks, and finding more and more spokes to them. In the last ten years, the study of networks has even become a discipline of its own, called systems biology. This is not new.
Biologists have recorded these network effects for many years in other organisms. But in the world of science, discoveries often do not become part of mainstream thought until they are linked to humans.
Or at least, in the world of newspapers. This has been mainstream for years.

Unfortunately, Francis Collins (director of the National Human Genome Research Institute) gave a misleading quote on their website, which is quoted in the New York Times article:
Because of the hard work and keen insights of the ENCODE consortium, the scientific community will need to rethink some long-held views about what genes are and what they do, as well as how the genome's functional elements have evolved.
While Ms. Caruso seems to think this means that he's discovered that gene networks exist, it seems more likely that he means that they have discovered particular networks that will make it easier to understand particular diseases. I admit, he's not being clear, and she bases the first half of her article off of this quote. (And I find it hard to believe that Francis Collins is stupid enough to think this study marks the discovery of gene networks).

So where does she take this credulous party off to next? Why not fearmongering?! (I've covered her scaremongering here in the past). Enter fearmonger Jack Heinemann, (director of the Center for Integrated Research in Biosafety):
“Because gene patents and the genetic engineering process itself are both defined in terms of genes acting independently,” he said, “regulators may be unaware of the potential impacts arising from these network effects.”
They're also unaware of the possible interactions between cheese and tomato sauce, and yet we don't test these in combination (and cheese is a living food product, after all!). This is yet another case of someone demanding that testing be done of every possible interaction between different genes and the food that they are placed in. Why? Knowing that your food has a complex network of genes that may be changed by the introduction of a foreign gene doesn't change the fact that the constituents of that food don't change.

Here's an analogy. If you remove someone's kidneys, you will find that they now require dialysis because they can no longer process out the urea from their blood. Without dialysis, they will eventually poison themselves and have multiple organ failure. However, you can say for sure that they will not grow wings and breathe fire, just because you messed up their organ homeostasis.

In the same way, adding foreign genes to plants, you can only get what you put in. You may increase the amount of protein, or decrease the amount of carbohydrate, or make the plant grow slower, but you won't get a corn plant with wings that is poisonous to humans merely by inserting the BT-gene. You can only get what you put in.

From Denise Caruso:
Now that the consortium’s findings (that there are gene networks) have cast the validity of (the gene) theory into question, it may be time for the biotech industry to re-examine the more subtle effects of its products, and to share what it knows about them with regulators and other scientists.
Oy. This just makes me cringe. Please, Ms. Caruso. Please. The stupid. It burns...


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