Sea Urchins and a Lesson in Taxonomy, Systematics, and Facts

In case you didn't hear, a sea urchin genome has been sequenced, analyzed, and the results published (Science has a page dedicated to it here). I say a sea urchin genome because there are many species of sea urchins. This paper reports the sequence of one species, Strongylocentrotus purpuratus, a model organism in developmental biology.

Despite the fact they are quite common-place, genome sequencing projects still draw some attention in the popular science press (see the honeybee as an example). And, as usual, the articles written about this scientific study are fraught with errors and misstatements. Take, for example, this article from LiveScience which was fact-checked by Chris Miller.

Chris reports that the original article claimed that this sea urchin was the first chordate to have its genome sequence. This is wrong on two counts. First, the sea urchin is an echinoderm, not a chordate. And, second, even if the sea urchin were a chordate, it would not be the first one to have its genome sequenced. That honor goes to some insignificant species known as Homo sapiens (that's the human genome if you're not fast on your feet). There have also been many more chordate genomes sequenced since human: mouse, rat, and dog to name a few.

Chris actually got LiveScience to correct their error, but they're still not quite right. Here is how the new version of the article reads:

They [sea urchins] belong to the phylum Echinodermata, which includes starfish and sea cucumbers, whereas humans belong to the phylum Chordata, or all animals with backbones. Both the echinoderms and chordates belong to a larger group called the deuterostomes.

Here's a little lesson in deuterostome taxonomy for everyone out there. These are animals in which the first embryonic opening become the anus, and the second opening becomes the mouth (the name literally means mouth second). This is in contrast the majority of animals, which form their mouth first (see here for a review of the animal phylogeny). The deuterostomes are made up of chordates (which contain the vertebrates), echinoderms (sea stars, sea urchins, etc), and a couple other lineages (for some recent findings in deuterostome systematics, see this post from Pharyngula).

The article is correct that both echinoderms and chordates are deuterostomes, but they incorrectly define chordates. You see, chordates all have dorsal nerve chords. It's the vertebrates -- a group found within the chordates -- that have backbones. The backbones contain the dorsal nerve chord.

But that's not the only flaw in the coverage of this story. This next mistake, however, is not due to a reporter misunderstanding the biology, but from a lead author of the paper saying something that just doesn't make any sense:

"The sea urchin is surprisingly similar to humans," said co-director of the sea urchin sequencing project George Weinstock, of Baylor College of Medicine. "Sea urchins don't look any more like humans than fruit flies, but about 70 percent of sea urchin genes have a human counterpart whereas only about 40 percent of fruit fly genes do."

Weinstock's quote was then paraphrased in this article:

The genetic ties were far closer than scientists expected and make the sea urchin a closer genetic cousin of man than the worm or fruit fly, the study in the November 10 issue of Science found.

If you had been following what I wrote above, it should come as no surprise to you that the human genome is more similar to the sea urchin genome than it is to Drosophila or Caenorhabditis genomes. After all, sea urchins and humans are deuterostomes, whereas flies and worms are protostomes (mouth first developers). I could have told you that sea urchins would be more similar to humans genetically than flies and worms are before any of those genome projects had been completed. And I would have even put a decent sum of money on it.

What have we learned? The popular science press doesn't understand animal systematics and taxonomy, and they aren't sure what sea urchins are. But the problem is compounded by the fact that certain researchers are providing the media with misleading information.

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The sad part for me here is not that the press mixed up some of the details. It is that one of the lead authors (and many of the press releases) fed them such BS. Yes, I know press releases (including some of my own) frequently have misleading things in them. But the quotes by Weinstock are pretty lame. It's too bad too - of all the major leaders of genome centers I like him more than many. Maybe that because we have similar backgrounds - DNA repair and microbiology. But even so - he clearly is out in left field in terms of evolution, taxonomy, common sense, etc.

Weinstock was the right person to talk to about the sequencing process, but probably not the best person to explain the importance of sea urchins.

People who work on the sequencing side of things are really interested in improving and speeding up the sequencing pipelines. Their involvement after the publishing of the genomes is often extremely limited. That's not surprising, though, considering that the genome center is currently sequencing everything from cows to aphids to bacterial species.


By Christian G. Taoc (not verified) on 02 Oct 2008 #permalink