Talk:Carl Woese

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''Such famous figures as Salvador Luria and Ernst Mayr found the idea that prokaryotes were not all of one kind absurd, and did not restrict their mockery to the scientific level.

This is a badly stereotyped view of Woese's critics. Actually, one of Mayr's criticisms of the three-domain system was that prokaryotes may be of more than two kinds, i.e. that the Eubacteria and criticism of him was restricted to the scientific level.

which leaves a lot to be said, but I think does more justice.

Contents 1 Pronunciation 2 Date inconsistency 3 Not so obvious 4 Misconception = 5 Not so obvious 6 Response to anonymous critic 7 Legend for the image "Phylogenetic Tree of Life"

[edit] Pronunciation

Can somebody please include how the name Woese is pronounced correctly?

I say Woe-Zee, you say what? (He sends his power tools to my shop for repair, but how to pronounce, I can't really say.)

M dorothy 05:19, 20 January 2006 (UTC)

I took a course from Carl Woese in 1993. The second "e" in his last name is silent.

[edit] Date inconsistency

Can someone please check the date that Woese identified Archaea? This article says 1976, but Archaea says 1977

Thank, GabrielF 00:40, 31 January 2006 (UTC)

The relevant paper was published in November 1977 - changing the article to reflect this. Dooky 19:25, 19 February 2006 (UTC)

[edit] Not so obvious

The article looks like written 20 years ago. Now, at least in the case of Eukaryotes it is known that the phylogenetic tree presented by Woese is false. The critics of Woese were right. See Eukaryotes (in English or French Wikipedia) for more current phylogenetic classification, and learn about "long branch attraction" artefacts (in Wikipedia, too).

The idea of three domains and the name Archaea was proposed not in 1977, but in 1990, and not by Woese alone (Woese, Kandler and Wheelis,Proc. Natl. Acad. Sci. USA, 87, 4576-4579, June 1990, available in the internet, I don't know how to link it). In 1977 it was recognized that some prokaryotes form a separate branch on rRNA trees, but they were called archaebacteria.

There is no obvious reason why to believe that Archaea (or Archaebacteria) are more ancient than other prokaryotes. Some good biologists (like Cavalier-Smith) show strong evidence they are the latest branch of the bacterial tree, not the earliest.

I change the text just a little.

[edit] Misconception =

I deleted the insertion -- it is simply misleading to suggest that current debates about the classification of eukaryotes in any way bring into question the objective existence of the Archaea as a distinct group. It is also certainly incorrect to suggest that the "critics of Woese were right" if the critics in question are the original group of critics such as Luria, who questioned the uniqueness of the Archaea. Certainly, the 1990 rRNA tree wasn't the final word on phylogeny, and some groups (such as the "crown eukaryotes") may prove to be artifacts, but that is more properly addressed in articles on the classification of eukaryotes.

In addition, you seem to be confused by terminology. Certainly the words "Archaea" and "domain" are from 1990, but the *concepts* behind the words was already there in 1977. The early rRNA catalogs did show three groups.

--- Jonathan Badger, The Institute for Genomics Research

[edit] Not so obvious

Yes, "defining the Archaea (a new domain or kingdom of life) in 1977" is (at least) misleading. The correct date of defining Archaea as a domain of life is 1990.

I did not say the existence of "Archaea" as a distinct group is being questioned, but their status as a "fundamental domain" is.

This is not quite true that the problems with rRNA trees are limited to eukaryotes. Contrary to the tree, Aquifex seems to be related to proteobacteria and Thermotoga seems to be a gram-positive (e.g. Gupta et. al.). The basalmost position of both seems to be an artefact. If this is true, the tree is false (as it is false in the case of Eukaryotes, why not to say this openly?). And it is doubtful that the position of the two basalmost prokaryotic branches is false and the third (the Archaea) is artefact-free; also the root of the tree was based on speculation. Some people say this, and this is a scientific level of criticism.

And in many other places the text is biased.

One example is "Lateral transfer during this period was responsible for the fast, early evolution of complex biological structures". The sentence is written in such a way that a reader may think this is a biological fact that Woese explained. But "fast, early evolution" is not a fact, but a speculation within the same theory (and unnecessary in other theories).

"This classification subdivides the Eukaryotes into four domains...". Unfair. None of Woese's critics classify Eukaryotes into four DOMAINS. They classify them into four (or 2, or 3, 5...) KINGDOMS. And what is wrong with "four kingdoms" of Eukaryotes?

"old system (...) still remains popular among some scientist." Unfair. The newly proposed classification recommended by the Society of Protistologists (Adl et. al, 2005, see protists) completely ignores the "system" of Woese and his "universal phylogenetic tree". They even suggest using the term "Bacteria" as a valid and recommended synonym of prokaryotes. They are not just "some scientists" - they are the mainstream of science.

"Prior to Woese, Archaea were thought to be extreme organisms...". There were no Archaea prior to Woese. And the first known prokaryotes included by him in Archaea were not extreme organisms, but methanogens from the rumen. This is not an extreme environment.

Let show at least minimal criticisms about Woese's results in Wikipedia.

[edit] Response to anonymous critic

The distinction "discovered" vs "defined" is not what you seem to make it out to be. Originally, the article said "discovered", but somebody changed it to "defined" -- I suppose for philosophical reasons arising from the idea, held by some systematists, that higher level taxa cannot be "discovered" but only "defined". But in any rate "archaeabacteria" circa 1977 is exactly the same group as "archaea" circa 1990. It is simply playing silly linguistic games to suggest otherwise.

Secondly, while there certainly exist criticisms to this day of the three domains, they are hardly in the "mainstream of science" -- all major references of prokaryotic systematics such as Bergey's Manual and Barlow's "The Prokaryotes" firmly support the three domains, and Woese received the Crafoord Prize in Bioscience (the Nobel Prize of evolutionary biology, awarded by the King of Sweden on the advice of a board of scientists) for the discovery quite recently in 2003. This doesn't mean that he has to be correct, of course -- but it is pretty clear that at this point in time the mainstream opinion includes the three domains. If and when Bergey's Manual abandons the concept, and people like Gupta win the Crafoord, then it would be reasonable to argue that the mainstream opinion has changed. And arguing that a society of protistologists dislikes the concept of Archaea is pretty irrelevant because prokaryotic systematics is no more their field than is the systematics of fishes.

If anything, the article as written already bows too far in the favor of critics, IMHO.

However, personally, I would agree with your criticism about the line "Prior to Woese, Archaea were thought to be extreme organisms..." -- however, that wasn't a section you changed.

By the way -- why don't you sign your discussions?

-- Jonathan Badger, The Institute for Genomics Research

xxxxxxxxxxxx xxxxxxxxxx

I was just an accidental visitor who looked for a year when Woese was born and I was surprised by the one-sided (and ironical) way the opinions of His critics were presented.

An example. Woese seems to distinguish domains and kingdoms clearly, isn't it? What about "four Eukaryotic domains" of his critics? Many people use four kingdoms, but who uses four domains? Or, if taxonomy of Eukaryotes is irrelevant to his system, why bother to criticize them here?

Unfortunately, Woese do not limit his tree to Prokaryotes, but includes various eukaryotic lineages as well. The phylogenetic tree is well known, the famous author calls it "universal" or "ultimate", and people publish it in biology textbooks as the last word of taxonomy of life. Let say them somehow that the tree does not necessarily strictly reflects phylogenesis, at least in the case of Eukaryotes (protistologists seem competent there). Otherwise the spread of new ideas will be hindered.

And well, I think it is a pity one should not mention other critical opinions for another many years. You know Bergey's taxonomic outline cannot change radically every 5 or 10 years, and for Crafoord prizes one has to wait even longer.

And I simply did not know how to sign my remarks. Sorry: Witold, 84.10.114.174 10:09, 4 April 2006 (UTC), Poland, a publisher.

[edit] Legend for the image "Phylogenetic Tree of Life"

I have a problem with the legend for the image "Phylogenetic Tree of Life" in that the image itself shows a rooted tree (which is how Woese et al. drew it in PNAS (vol 87 p 4576) but as far as I know (which admittedly is not that much on this topic) modern taxonomist don't root a tree unless there is something to root it with. Should the legend be expanded to say that this is based on Woese's diagram of the tree of life, or say that a root in the tree of life in this diagram is speculative (as previously commented above)? PS sorry about the poor grammar. English is my second language - Bad English being my first. PRH969 00:17, 24 March 2007 (UTC)

Well, I don't know that it's necessary as the image caption itself says almost nothing, and clicking on it takes you to the image page. Go ahead and say, "speculatively rooted Tree of Life" by Carl Woese, if you like. It sounds awkward and raises questions that aren't at issue in an article about Woese rather than his research. The image is almost always used with the caption, "speculatively rooted tree of life." This tree isn't about modern taxonomy, but about evolutionary taxonomy, so what modern taxonomists do can be different without there being any conflict. The article on phylogenetic trees on Wikipedia has at least the basic information on this. KP Botany 01:54, 24 March 2007 (UTC)

Oops. My mistake. I clicked on the image but don't remember reading the discription properly. My concern was that someone with no knowledge of the topic would see the tree and think of it as the definitive tree of life. I was going to change the legend to "...tree of life based on Woese et al. rRNA analysis." and then include a link to reference #1 PRH969 03:06, 24 March 2007 (UTC)

To edit an image, you have to edit the section in which the image is located. First copy some of the text under the image so you can find it--it can be messy finding the image if it is in the main section, and you have to click on "Edit this page." Then click on the "edit this page" tab at the top, or click on the "edit" tab in the section on interest. Use a browser function to search for the text. In this case, I would copy part of the text under the image. When you find the image's html in the edit box, edit it as you would anything else. In this case, I clicked "edit this page," went to the edit box, searched for the string "Phylogenetic tree based on Woese et al" and found this:

[[image:Phylogenetic_tree.svg|left|thumb|250px|Phylogenetic tree based on Woese et al. rRNA analysis <ref name="Woese_1990">{{cite journal | author = Woese C, Kandler O, Wheelis M | title = Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. | url=http://www.pnas.org/cgi/reprint/87/12/4576 | journal = Proc Natl Acad Sci U S A | volume = 87 | issue = 12 | pages = 4576-9 | year = 1990 | id = PMID 2112744}}</ref>]].

What I want to edit is the part of this text after the 250px, which is the caption. I'll let you try it. KP Botany 20:57, 24 March 2007 (UTC)

Yep, that was my edit. I changed it from - [[image:Phylogenetic_tree.svg|left|thumb|250px|Phylogenetic tree based on rRNA genes]] to the above text. You were right, "speculatively rooted Tree of Life" sounds weird, and like you said, its explained fully in the description. Hopefully the change implies that this was how Woese drew it at the time and not necessarily how the tree is viewed today. PRH969 03:53, 25 March 2007 (UTC)

Yeah, I think it's fine like that, especially with the specific link to a source, as the underlying concepts are way beyond the scope of an article on Woese. KP Botany 04:03, 25 March 2007 (UTC)