On BioScience and Life and Such

Hitting three peeves with one stone

In Uncategorized on October 11, 2008 at 10:36 am


post to news.thinkgene.com

Everyone’s talking about their pet peeves, I thought maybe I should too. Here are three of them

1. Labeling DNA with unknown function as “junk”

2. Scientists in ivory towers and on top of their high horses.

3. Holding back on scientific arguments in fear that someone will use them in an unscientific way.

The two last ones are really about how scientists communicate with the rest of the world, and I’ll get back to that

The post that lets me comment on these issues all at the same time is: Scientists Cynical use of “Junk DNA” at Michael Eisens blog (I know the post is rather old, but it is new to me). Coincidentally his post allows me to sum up my recent “junk” posts and the “creationist terror” post.

Quotes for each peeve

Unfortunately, for initially practical reasons, a disproportionate amount (surely in excess of 90%) of research has focused on protein-coding genes, fostering the faulty impression – amongst scientists as well as science writers – that the ~3% of the human genome that is protein-coding contains > 90% of the function.

This is good…..if it means what I mean: that labeling DNA of unknown function as “junk” by default is wrong. Which it most certainly is. For more on this topic, see my 6 post discussion with Larry Moran (1,2,3,4,5,6).

But, then Eisen starts criticizing the press release for the fact that they used this “junk” term:

They work on non-coding DNA precisely because they know it is NOT junk. So why, when it’s time to make a pitch to the local press officer, do they fall back on this old bromide? It obviously appeals to writers – who love it when they can pitch a story as overturning orthodoxy. It seems minor, but pegging it this way leads to some really attrocious misrepresentations of current biological knowledge.

This is bad, because of two reasons. Firstly, the term is not wrong, it’s used on a piece of DNA with an previously unknown function. A lot of this DNA is currently labeled “junk” by the “junk-people“. The only wrongdoing here is that they didn’t specify that regulatory elements have been known for some time, – that’s hardly a grave error. On the contrary, phrasing it like this in the press release underscores and highlights that much of what we previously labeled as “junk” in fact isn’t. That is really, really good, in fact it’s an excellent way of enlightening the public that non-coding DNA isn’t necessarily “junk”. Secondly, when scientists communicate with the rest of the world it is important to use terms that will not serve to alienate. Only to a certain extent of course, because oversimplification can easily distort the true message. But, this press release is not an example of oversimplification. The critique of these news-pieces constitutes nitpicking, and strengthens the view of scientist as locked inside ivory towers or sitting on top of their high horses. There are plenty of examples of press releases that is misrepresenting science, are inaccurate or just plain wrong. The over-hyping of imminent cures for cancer, diabetes and Alzheimer are good examples of bad science news reporting, and this happens almost daily all over the world. Another example is getting statistics all wrong in reporting on genetic tests (there are however, initiatives to try and fix this situation. You are hereby encouraged to go see HelixGene, I also strongly recommend you to join if you can help, or report bad news coverage of science if you find any).

Towards the end of the post I find my third pet peeve:

A second, and less obvious, problem is that this view has played into the hands of the intelligent design crowd.

and

And every time a new study comes out reporting that “junk DNA” is not junk, the ID’ers jump on it as validation of the predictions of ID. It’s hooey of course, but we needn’t give them the opportunity.

Which shows us Eisen is a victim of creationist-terror (see my previous post on this topic), and it makes me sad that we as scientists do not have the guts to stand up against this terror. We must feel free to express whichever valid scientific argument we find relevant in a given topic or field. That some of us don’t makes me really, really unhappy….

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  1. I don’t have any statistics handy, but computer code is mostly “junk” too: low density data, not instructions. Most computer code is a few lines of algorithm and everything else is either data, addresses, or “this is that” glue code.

  2. The term “junk DNA” is not simply a catchall for pieces of DNA with no KNOWN function, it was specifically coined, and is nearly exclusively used, to refer to DNA with NO function period. These press releases aren’t purporting to have discovered a function for a particular piece of DNA, they are claiming to have overturned the broad hypothesis that 95% of the human genome has no function – a hypothesis that we have long known to be false.

    And I certainly don’t think scientists should be afraid of creationists in any way. Indeed, I think the best defense against creationism is loudly and unashamedly trumpeting everything we know about evolution. Whay I was pointing out is precisely the opposite – that there is a danger in continuing bring up ideas that we know to be untrue – even as straw men – because it makes evolutionary biology look flighty and inconsistent.

  3. Andrew: Code is different in that you usually know it’s function, and hence can discriminate between what is “junk” or not, – that’s not always the case with DNA.

    Michael: I like your definition of “junk”-DNA – “DNA with NO function period.”. When is that statement true, that’s my question. At what point do you know that a given piece of DNA has no function. My argument is that I have seen few examples where the “junk” conclusion was reached by that criterium. The label is very often put on “DNA with no KNOWN function”. Therefore, reporting that something is not “junk” anymore when a function has been ascribed to it, is not “untrue”. I also do not think one should shy away from admitting that science sometimes can be “flighty and inconsistent”, isn’t that the nature of science sometimes and also the reason we keep refining our hypothesis and theories ?

  4. Yes, it was only a metaphor for comparison.

    Also, 23andMe has good reporting, and I’m not aware of better compilation reports like these. I do think that their penetrance estimate is too confident, particularly considering the incoherent estimates in all the literature, and that they should disclose exactly how they generated that number.

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