Comments on: Trouble in the Fourth Domain?

By: MarshelindaI

MarshelindaI — Mon, 25 Jul 2011 13:19:03 +0000

I agree with you Sergio on the fact that the fourth domain is nothing more than a artifact.”Just because two species have stretches of DNA that look alike doesn’t necessarily mean that they inherited that DNA from a recent ancestor”…this means that somethings are happening that we might get tricked by and not realize it because they look alike. I honestly think it’s smart for the scientists to be forced to rebuild the tree of life. Maybe then the comparisons will be more clearer and the results will be easier to see. The scientists are doing everything they can to see where every virus that comes from and how.

By: Ray Kepner

Ray Kepner — Tue, 19 Jul 2011 17:48:41 +0000

I’ve always thought of Cafeteria as a flagellate, not an “amoeba”

By: Sergio Munoz

Sergio Munoz — Sat, 16 Jul 2011 01:49:21 +0000

I tend to think that what they got in their fourth domain tree is no more than a artifact caused by long branch attraction, their homoplasy due to the high rate of evolution of laterally acquired genes in the giant virus. I’ve never been too akin to these premature strong claims.

By: Jonathan Eisen

Jonathan Eisen — Fri, 15 Jul 2011 14:20:28 +0000

I note I am still reserving judgement on the origin of these viruses. They are very strange relative to “normal” viruses (if there is a such thing) in that they are (1) very large (2) have very large genomes (3) encode some pretty standard “housekeeping” genes and (4) even apparently have their own viruses.

I note, in our phylogenetic analysis related to finding unusual sequences in environmental samples, we were/are a bit worried about phylogenetic artifacts. We did use some of the methods Embley used in their paper and found that the sequences we found to be novel still appeared to be phylogenetically novel. However, issues like homoplasy are hard to rule out when one has very long branches in a tree – and this is one of the reasons we took a toned down approach to our claims.

By: Christopher Taylor

Christopher Taylor — Fri, 15 Jul 2011 14:13:50 +0000

Seeing as Cafeteria roenbergensis is a unicellular protist, I presume that you're referring to a virus from this species. And David, Cafeteria got its name from its ability to feed on a wide range of foods. [CZ: Thanks, Chris. I've fixed the post.]

By: David Dobbs

David Dobbs — Thu, 14 Jul 2011 19:49:39 +0000

Nicely done, Carl, and it’s wonderful you’re doing a follow-up semi-refutation — or more like a tap on the brakes. It seems like a pullback from “Tantalizing possibility” to something closer to “Interesting if true.” This is one of the lovely things about having a blog: You’d have a hard time selling this to anyplace that got as wide a readership. Now you can just do it.

Your post did disappoint me in one way, however: Having read that the first giant virus was found only in the water in air conditioners (WTF?), I was really hoping the new one, Cafeteria roenbergensis, would be found exclusively in that slightly scary water trapped between cafeteria trays after washing. I was betting on it when I saw the name. Alas, no.

Science has a way of generating expectations … and then disappointing them.

Oh — did I mention the writing? I particularly admire the passage on homoplasy, the most slippery part of this thing: clear as a bell and phrased in terms of human endeavor.

By: Marco Ferrari

Marco Ferrari — Thu, 14 Jul 2011 19:00:26 +0000

Lucky me. I was about to suggest an article on the Fourth domain for my magazine (it is a good story, isn’t it?), but you stop me on my tracks. Thanks

Marco F

By: Wilson

Wilson — Thu, 14 Jul 2011 18:18:56 +0000

Two things:

1. The first instance of the word ‘homoplasy’ has a typo. (If it weren’t the first, I wouldn’t bring it up.)

2. How is “homoplasy” pronounced, please?

[CZ: Thanks--fixed the typo. Prononciation is hoe-moe-play-zee. You can listen here.]