Pharyngula::Journalists getting it right

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Monday, September 26, 2005

Journalists getting it right

PZ Myers • 65 Comments (last page)

Rick Weiss and David Brown of the Washington Post, take a bow. You've written the best article on evolutionary theory I've seen in a newspaper yet.

But decoding chimpanzees' DNA allowed scientists to do more than just refine their estimates of how similar humans and chimps are. It let them put the very theory of evolution to some tough new tests.
If Darwin was right, for example, then scientists should be able to perform a neat trick. Using a mathematical formula that emerges from evolutionary theory, they should be able to predict the number of harmful mutations in chimpanzee DNA by knowing the number of mutations in a different species' DNA and the two animals' population sizes.
"That's a very specific prediction," said Eric Lander, a geneticist at the Broad Institute of MIT and Harvard in Cambridge, Mass., and a leader in the chimp project.
Sure enough, when Lander and his colleagues tallied the harmful mutations in the chimp genome, the number fit perfectly into the range that evolutionary theory had predicted.

It explains well how biology has a rich supply of tests and predictions, that evolution has passed them all for years, and that support for the theory is strengthening, not weakening. The Intelligent Design creationists are left looking like sad sacks who are missing all the excitement.

My only nitpicks (yeah, sorry, it's in my nature—even a good article stirs up the urge to criticize) are minor things, like the mention of Darwin above—not to knock the guy, but you can discuss evolution without mentioning Darwin. They do get the usual competing quote from a lackey of the Discovery Institute, a vague prediction that '"junk" DNA in animals' genomes… will someday be found to have a function', a claim that is currently clearly false and which lacks any evidence in support. The article could have done a little more to point out how poor that idea is.

Otherwise, though, the article is solid, substantive stuff. I want more like this.

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Comments:

#41636: Adam Ierymenko — 09/26 at 07:14 AM
In regard to junk DNA:

I do in fact think that *some* "junk" DNA will be found to have a function. Indeed, some already has.

However, that function is probably not what the Discovery Institute would want. The function of at least some of this functional "junk" DNA such as long tandem repeats and transposons is... drum roll... eeeevilution!

Look up "evolution of evolvability" in an academic search engine or even scholar.google.com and enter the fascinating world where evolution evolves new ways to evolve.

Transposons, for example, are genetic permutation generators and could have been conserved in the genome due to their evolvability effects.

#41639: Redshift — 09/26 at 07:34 AM
I agree it was great. I liked the fact that they managed to follow the obligatory "present both sides" of modern journalism, but emphasized the relative importance by giving the ID guy two paragraphs. And they really let him hang himself -- the contrast between a vague "prediction" about "junk DNA" and the kind of evidence discussed in the rest of the article is stark. I just hope it's equally clear to most readers how unscientific his "it's up to the Darwinists to disprove ID" is.

#41641: Alon Levy — 09/26 at 07:39 AM
My only nitpicks (yeah, sorry, it's in my nature—even a good article stirs up the urge to criticize) are minor things, like the mention of Darwin above—not to knock the guy, but you can discuss evolution without mentioning Darwin.

Actually, in this case I think quoting Darwin is right on. He was the first to conclude from evolutionary evidence that chimps are humans' closest cousins, so describing a test that confirms that is exactly a vindication of Darwin. In similar vein, I think it's good to talk about Einstein when writing about evidence for relativity. The article only mentions Darwin in an irrelevant context once, where it paraphrases a creationist.

#41642: Mrs Tilton — 09/26 at 07:48 AM
May I just say that, if junk DNA turns out to be useless, that would of course be grounds for sorrow, not joy.

I for one will continue to hope that we discover ways of putting our huge stores of junk DNA to work. For example, to allow us to make enormous tentacles grow out of the sides of our heads at will.

#41643: — 09/26 at 07:52 AM
From my letter to the WaPo:

...I did want to point out an erroneous assertion attributed to John West of the Discovery Institute: "In any case, West said, it is up to Darwinists to prove ID wrong." This misstatement of the burden of proof in scientific discovery betrays either ignorance or dishonesty on West's part; it is akin to a prosecutor insisting that a defendant prove himself innocent of a crime. The burden is on the proponents of Intelligent Design to elaborate some kind of theoretical construct and present affirmative, objective, and reproducible evidence in support of it. The example of so-called junk DNA shows how laughably far they are from this goal, and from any kind of scientific credibility.

#41644: — 09/26 at 07:54 AM
You cannot go wrong if you start with Darwin. Not only was he one of the giants on whose shoulders we stand, he remains a grand metaphor in our fight to free the mind of science from the clouds of religion, a difficult feat that many scientists are still unable to achieve today.

He did astounding science; his personal life and conduct remain an outstanding role model; like Lincoln, he belongs to the ages. No matter how much we embellish his theory, he was and is the seed at the center of evolution.

#41646: David Winter — 09/26 at 08:00 AM
It’s seems particularly odd to invoke Darwin in that paragraph since it’s about the weakness of purifying selection in small effective population sizes and molecular evolution. That’s hardly straight from The Origin of Species and although it's a test of evolutionary theory it says noting about our shared ancestory with chimps

#41647: David Winter — 09/26 at 08:00 AM
It’s seems particularly odd to invoke Darwin in that paragraph since it’s about the weakness of purifying selection in small effective population sizes and molecular evolution. That’s hardly straight from The Origin of Species and although it's a test of evolutionary theory it says nothing about our shared ancestory with chimps

#41651: — 09/26 at 08:32 AM
There's an interesting article in the October 2005 issue of Scientific American on trypanosome genomes. The genomes are done now for the parasites which cause Chagas' disease, Leishmaniasis and African sleeping sickness. Aside from the potential for medical advancement, one of the three genomes (I forget which) apparently underwent a whole-genome duplication in recent evolutionary history.

I am also pleased to see quite a few articles and editorials like this one in the Toledo Blade being straightforward in reporting that IDC is creationism, and IDC is religion.

...
Similar conflicts have been flaring around the country, as fundamentalist believers wage a new battle against Charles Darwin.
...
The debate is about perhaps the longest and most serious conflict in modern times between science and religion. The Dover case comes almost exactly 85 years after the famous Scopes Monkey Trial in Tennessee first tested the legality of teaching evolution.

Make no mistake. Intelligent design is old-time creationism given a new name. Living things, it maintains, are far too complex to have arisen through natural selection and other tools of evolution. That demands the biblical version of the origin of the universe and life.
...

#41652: — 09/26 at 08:39 AM
"Rick Weiss and David Brown of the Washington Post, take a bow. You've written the best article on evolutionary theory I've seen in a newspaper yet."

And all by the amazing expedient of getting science writers to write about science. Who'd have thunk it?

#41653: John Timmer — 09/26 at 08:43 AM
Whole genome duplications aren't all that uncommon, apparently. Xenopus, the frog used in lots of developmental biology work, is pseudo-tetraploid (which is why nobody's done genetics on it). Zebrafish, which people are doing genetics on (including, i think PZ, who will probably correct me here), is part of a lineage with an older genome duplication which has been substantially reduced over time. Lots of genes which exist in several copies in other vertebrates have even more copies in fish (ie - hedgehog: 1 copy in flies, 3 copies in mammals, 4 in fish). This has generally led to greater specialization in the expression/function of each copy in the fish.

#41654: — 09/26 at 08:48 AM
I thought it was somewhat scary when clicking on the "see what bloggers are saying" link from the WashPost page that the Technorati search included one ad for the American Red Cross (fine) and four for anti-evolution websites (not fine). A case where money is being spent to mislead searchers.... Too bad we can't take up a collection and get some ads in favor of evolution in.

#41656: bill — 09/26 at 09:32 AM
In the article is this statement made by John West of the Discovery Institute regarding "intelligent design":

In any case, West said, it is up to Darwinists to prove ID wrong.

Would anyone care to comment on this astounding statement? Does the DI not understand what science is? D'oh!

#41659: Jason Malloy — 09/26 at 09:37 AM
I read it earlier this morning, and I had the exact same feeling that a MSM news journalist was finally "getting it".

#41660: PZ Myers — 09/26 at 09:38 AM
You're such a cynic. As we all know, elves exist, and if anyone wants to claim otherwise they are the ones obligated to provide evidence.

PZ Myers
Division of Science and Math
University of Minnesota, Morris

#41661: — 09/26 at 09:45 AM
Quoth David Winter: "It’s seems particularly odd to invoke Darwin in that paragraph since it’s about the weakness of purifying selection in small effective population sizes and molecular evolution."

That was my thought, as well. It almost makes it sound like Darwin developed Mendelian genetics, invented the modern synthesis and population genetics, and discovered DNA ...

#41663: franky — 09/26 at 10:17 AM
Eric Lander is such a cool guy. He teaches like Bio 101 at MIT and even though I hated biology, it was always great to hear him lecture about the Human Genome project and stuff like that. Cool article.

#41664: — 09/26 at 10:17 AM
Our definition of junk DNA has been getting more refined. First, it was everything that didn't specify amino acid sequences. Now, we've got control codes (start/stop, expression). We've discovered that depending on how a sequence is read, what was intron in one reading, becomes exon in another, allowing the same stretch of DNA to encode more than one protein. (Epigenetics)

So, a larger portion of the genome is functional than we used to think. Then there is the idea that genomes need lots of non-informative bits because it lowers the chance that a mutation will affect anything that actually does something. (A cosmic ray is far more likely to hit a nonfunctional piece of the genome than one that actually does something.)

#41665: PZ Myers — 09/26 at 10:22 AM
No, that last argument is wrong. Mutation rates are on a per nucleotide basis, so increasing the number of nucleotides does not reduced the effective error rate.

One way to think of it is that increasing junk increases the size of the ineffectual part of the target, but does not reduce the size of the part of the target that is critical for function.

PZ Myers
Division of Science and Math
University of Minnesota, Morris

#41666: PZ Myers — 09/26 at 10:25 AM
Also, the first part is wrong, too. You are talking about alternative splicing; it's not equivalent to epigenetics, and it's also not sufficient to explain the function of junk DNA. It would not have been counted as junk before, for one thing.

There are important regulatory regions in DNA. They are not junk. They are also not very big relative to the mass of junk.

PZ Myers
Division of Science and Math
University of Minnesota, Morris

#41667: — 09/26 at 10:31 AM
The most important things about this article are that it's a *news* story, not an editorial; that it appeared high on the Post's online front page with a big headline; and that it doesn't even pretend that ID might have some validity. This is a breakthrough in reporting on the ID "debate" that we can only hope will replicate elsewhere. Compare it with the NYT's wimpy article today on the Dover school board suit.

#41669: — 09/26 at 10:56 AM
I agree with fyreflye. This is a good piece of journalism that is treating the issue the right way, and it is run as such by the newspaper. That's remarkable in today's US political climate.

#41670: mark — 09/26 at 11:09 AM
Perhaps the numerous statements presented by organizations of real scientists (and recognized individual scientists) are beginning to have effect.

Regarding ID "theory" predictions and junk DNA--IDiots can claim design even if no apparent functions are determined. After all, who can read the inscrutable mind of G--err, the Anonymous Intelligent Designer? After all, our explanatory filters show us that automobiles are designed, and back in the early 1960s quite a few had large tail fins--for what function? (Well, maybe there was a form of sexual selection at work.)

#41671: — 09/26 at 11:23 AM
I am but a poor, scientifically interested laymen, so my vocabulary is imprecise. I thought that epigenetics referred to the functional DNA that didn't directly code amino acid sequences.

What I meant by the second part is that if every single nucleotide was functional (absolutely NO junk DNA), then any change of any nucleotide would be likely to have an effect on the function/development of the organism (protein structure or gene expression). By having a large amount of non-functional DNA in a genome, then the chances of, say, a cosmic ray hittin a functioning part are reduced. I read that this was one of the explanations of why so much of the genome would be junk, when it was first discovered that a lot of the genome didn't appear to do anything.

Regarding the first part, I was taught that when the 3-nucleotide = 1 amino acid coding was discovered, that anything that didn't code for a protein was considered junk. Am I wrong about this? Aren't genes defined as the parts of the genome that code for proteins, and didn't scientists at one time, decades ago, consider anything that didn't code for proteins to be junk?

#41672: spencer — 09/26 at 11:24 AM
From the story:

"Chance and necessity don't seem to be good candidates for explaining the appearance of higher-order complexity, so the best explanation is an intelligent cause," West said.

Mr West might have a point, if not for the fact that one of those potential explanations actually does have a ton of scientific evidence backing it up - and unfortunately for him, it's not the one he finds more intuitive, which is still evidence-free, oddly enough.

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Monday, September 26, 2005

Journalists getting it right

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