Talk:Archaea

Date for the accepted three domain system

is given as 1990 by: http://en.wikipedia.org/wiki/Three-domain_system but here, it says 1977. I guess the references check out, but why is one quoted as 13 years later? Is this the date that the system was finally accepted? Betaben (talk) 05:49, 11 March 2008 (UTC)

I think hte difference is that it was 1977 when the difference was first noted, but only 1990 when they were formally divided into domains. Previously they were divergent "archaebacteria". Tim Vickers (talk) 13:53, 11 March 2008 (UTC)

Was it really 1990? Back in middle school (2001-2004) we learned the old paradigm with Kingdom as the very highest rank. It would surprise me that the Domains weren't finalized in 2004 or so, as that is definitely when my old schools switched over. We did learn the current Domain-topped system when I was in high school (2004-2008). Of course, I am now a college Bio. Major and could probably wow my middle and high school bio. teachers even more now than I did when they had me in class (and I wowed them then, to be sure)! My speaking highly of myself aside, was it really as long ago as 1990? The Mysterious El Willstro (talk) 09:59, 21 April 2010 (UTC)

Misinterpretation?

One possibility is that last common ancestor of the bacteria and archaea may have been a non-methanogenic thermophile, which raises the possibility that lower temperatures are extreme environments in archaeal terms, and organisms that can survive in cooler environments appeared later in the evolution of these organisms. [19]

It is not said in reference [19]:

This phylogeny supports a hyperthermophilic and non-methanogenic ancestor to present-day archaeal lineages, and a profound divergence between two major phyla, the Crenarchaeota and the Euryarchaeota, that may not have an equivalent in the other two domains of life.

91.117.50.91 (talk) 07:14, 30 April 2008 (UTC)

The reference now cited for this conclusion (Link) states:

"Curiously, if the last common archaeal ancestor was a hyperthermophile, low temperature environments can be considered as extreme to Archaea." Tim Vickers (talk) 04:13, 24 June 2008 (UTC)

Archaea liveing somewhere besides Earth

can archaea live somewhere other then earth yes or no? Why? —Preceding unsigned comment added by 74.173.222.143 (talk) 19:34, 16 May 2008 (UTC)

They probably could, but there is no data on life on other plants, so we can't include it in the article. Tim Vickers (talk) 19:36, 16 May 2008 (UTC)

If someone else had enough research to back it up (not you, because it would be original research), then you could add a section about theories of life on other planets. I think it's a pretty common idea, but I would have to check my references before I would post anything. I seem to remember once hearing about such life forms on Mars...but I honestly don't remember. Just make sure you cite your sources and make it clear that this is all theoretical. Bob the Wikipedian (talk) 21:19, 17 May 2008 (UTC)

What about ALH84001? Of course it has never been established that the "fossils" in the meteor are from life forms, neverless archaea life forms but it is the primary option given the morphology and their simplicity with what could be also bacterial fossils. --ometzit<col> (talk) 03:36, 24 June 2008 (UTC)

that's still unconfirmed though, and if it was then I guess you can add it and get the sources, if there are any reliable ones. Lonerguy_87 18:23, 24 June 2008 (UTC)

There's also the Phoenix incident that made the news recently. Of course, these would be considered invasive extramartian species, not native to Mars. Bob the Wikipedian ^{(talk • contribs)} 13:38, 24 June 2008 (UTC)

But all that is beside the point. Those are examples that would nbe noted on articles about Panspermia or the possible extraterrestrial origin of life of on an article about life beyond Earth. There is nothing to tie any of that specifically to Archaea, so mentioning it here would create a new association not published in the literature, and that constitutes OR. Such information should only be included here if a reputable source can be cited making a possible connection to the Archaea. --EncycloPetey (talk) 15:15, 24 June 2008 (UTC)

All the ALH84001 sources discuss magnetic bacteria specifically, but I added some discussion of this in the general context of extremophiles. Tim Vickers (talk) 23:50, 24 June 2008 (UTC)

Typo

In the 2nd paragraph under Origin and early evolution, the sentence should probably read, "One possibility is that *the* last common ancestor of the bacteria and archaea may have been a ..." Pcrooker (talk) 04:17, 28 May 2008 (UTC)

Fixed. For future reference, you can go ahead and make those changes yourself, if you like. It's a wiki wiki world! – ClockworkSoul 04:41, 28 May 2008 (UTC)

ARMAN

This group of Archaea is listed in the taxobox, but according to their article, they are classified within the Euryarchaeota. Can someone who has access to the relevant references determine whether the link belongs in the Taxobox here, or whether it is better included on the Euryarcheota taxobox? --EncycloPetey (talk) 20:11, 26 June 2008 (UTC)

The article says "Comparative analysis of these genes with sequences in the public databases consistently indicated that ARMAN-1 and -2 are representatives of a deeply branching lineage within Euryarchaeota with no cultivated representatives." Looking at the phylogenetic tree in the paper, this is a highly divergent group, but it hasn't (yet) been designated as a different phylum. Tim Vickers (talk) 20:32, 26 June 2008 (UTC)

Thanks; I've added a "See also" link from Euryarchaeota. --EncycloPetey (talk) 20:56, 26 June 2008 (UTC)

Cyclopentane rings

Howland (p.78-79) makes mention of 5-carbon rings which may appear in archaeal membranes. He says the number present (1 to 5) is dependant upon the environmental temperature, with higher temperatures correlated with more rings per isoprene chain. It is believed that the rings reduce fluidity of the membrane, making them more stable at high temperature. Unfortunately, he does not name his source for any of this information, but it would seem to be another way in which archaeal membranes differ from all other organisms.

Crenarchaeol

Brock and Madigan (7th ed, p816-817) have this information as well, and note that the formation of rings also reduces the width of the cell membrane. --EncycloPetey (talk)

Christ, that is just bizarre, I've found some archaeal lipids that contain a alkyl ring (tetraether lipids) with both cyclopentane and cyclohexane rings within the lipid! This one is called crenarchaeol. I'll draw a structure. Tim Vickers (talk) 23:25, 26 June 2008 (UTC)

Does that mean we're going to get a new Crenarchaeol article? :) --EncycloPetey (talk) 01:02, 27 June 2008 (UTC)

Ecological importance

I haven't been able to find an explicit statement that's citable, but since methanogens live in the guts of cattle, and since they are responsible for the methane content of flatulence, and since methane from cattle is often cited as a major contributor to greenhouse gases and global warming, it seems there may be an important global climate impact worth mentioning in this article. --EncycloPetey (talk) 00:29, 27 June 2008 (UTC)

OK, I've found a little and started a new section for it, since it doesn't quite fit into any existing section. --EncycloPetey (talk) 01:02, 27 June 2008 (UTC)

I'll add some stuff on the nitrogen cycle to this, it's a bit human-centric to see this as pollution though, I've recast this as a section on their importance in global cycles. Tim Vickers (talk) 01:46, 27 June 2008 (UTC)

I see what you mean, but think the new sxn title isn't quite descriptive of the content. I've relabelled it "Role in chemical cycling", although if the section becomes broader in scope it might be better titled "Interactions with the physical environment" in order to parallel the previous sxn header of "Interactions with other organisms". --EncycloPetey (talk) 01:58, 27 June 2008 (UTC)

Tim, did you notice this reference, given as a comment above?

Nature vol 442/17 August 2006, Letters, Archea predominate among ammonia-oxidizing prokaryotes in soil. Leininger et al

It looks like it would be an ideal source to bolster the paragraph about nitrogen cycling. I'd add the information myself, but do not have ready access to quality journals or their articles, unless I happen to have a copy in my personal library. --EncycloPetey (talk) 19:45, 27 June 2008 (UTC)

Good point and well spotted. Added. Tim Vickers (talk) 19:54, 27 June 2008 (UTC)

Classification summary

Should we add a summary table to the Classification section, such as the one on the German wikipedia: de:Archaeen#Systematik? The acid-mine drainage image could be moved down to the Role in chemical cycling section, if we chose to include the table. --EncycloPetey (talk) 17:47, 28 June 2008 (UTC)

I don't think that adds all that much useful information. Could be good content at that article on Prokaryotic classification that User:Wikiality123 is writing though. Tim Vickers (talk) 17:53, 28 June 2008 (UTC)

OK. I was of two minds about including it myself; it provides a quick navigation to the major subgroups, but that's of little benefit to a general audience. I'm currently checking all the links to foreign-language WPs and sister projects for accuracy and scanning content for potential additions. --EncycloPetey (talk) 18:01, 28 June 2008 (UTC)

The Japanese article (ja:古細菌) has a number of nice images and diagrams, but they seem to either be in Japanese, or else are loaded only on thier local project. :( --EncycloPetey (talk) 18:20, 28 June 2008 (UTC)

EEEE! The Ukrainian WP has a killer image of Haloarcula quadrata [1], but it's stamped with a copyright tag. Anyone read Ukrainian here, who can determine whether it's possible to upload to the English WP as well? --EncycloPetey (talk) 18:27, 28 June 2008 (UTC)

Thermophiles

Don't they live at rather low temperatures, like 40-60^oC, and not in boiling water? Narayanese (talk) 19:02, 29 June 2008 (UTC)

I added boiling water as an example, not an exclusive definition. Tim Vickers (talk) 19:11, 29 June 2008 (UTC)

I object to that revert. "Warm places" is wrong. The human gut is warm, but organisms that live there are not thermophiles. Tim Vickers (talk) 19:17, 29 June 2008 (UTC)

(edit conflict) Oops, I reverted without looking here first. Anyway, hot springs don't have boiling water, and I still don't think it's an example that can be used. But feel free to change warm to a better expression. Narayanese (talk) 19:18, 29 June 2008 (UTC)

No problem, I'll add something more specific, which should solve the problem. Tim Vickers (talk) 19:21, 29 June 2008 (UTC)

Is that better? Tim Vickers (talk) 19:25, 29 June 2008 (UTC)

Yes. I'll see if I can find a source for this particular range (not that there is any strict definition of thermophily), since the thermophile page has a fact tag. Narayanese (talk) 21:15, 29 June 2008 (UTC)

From Brock & Madigan (7th ed., p335): "Organisms whose growth temperature optimum is above 45⁰C are called thermophiles and those whose optimum is above 80⁰C are called hyperthermophiles. --EncycloPetey (talk) 21:58, 29 June 2008 (UTC)

Mistake concerning Nanoarchaeum

It seems that Nanoarchaeum equitans does not have the smallest genome of all microbes. Recently, a bacterium called candidatus Carsonella ruddii has been sequenced and appears to have aven fewer base pairs. Could you please correct it in the text? --212.20.74.230 (talk) 17:37, 27 July 2008 (UTC)

Thank you, changed to "smallest archaean genome", although it is arguable whether that "bacteria" has now become and organelle and might no longer be an independent organism. Tim Vickers (talk) 17:49, 27 July 2008 (UTC)

Thanks. Additionally, I am not sure whether archea have RNA polymerase II, I think it is unique to eukaryota, as the article says. Archaeal polymerase is only an ancestor to all of the three eukaryotic polymerases. --212.20.74.230 (talk) 10:00, 28 July 2008 (UTC)

Damn, yes you're quite right. Thanks again! Tim Vickers (talk) 15:02, 28 July 2008 (UTC)

You're welcome. I'm currently translating the article into Czech, so this is how I found the mistakes ;)) --Vojtech.dostal (talk) 15:54, 28 July 2008 (UTC)

Furthermore, what do archaea have in common with anammox? this article is cited, but I can't find anything concerning archaea in it. Can you explain it? --Vojtech.dostal (talk) 16:10, 11 August 2008 (UTC)

That was simply wrong, they do ammonia oxidation in aerobic and suboxic environments, but anaerobic oxidation (anammox) is (so far) only found in bacteria. I've corrected the text and put in two better references. Tim Vickers (talk) 17:40, 11 August 2008 (UTC)

Maybe somebody should add a few words about the composition of the archaeal cell wall. (as it is there). --Vojtech.dostal (talk) 09:01, 12 August 2008 (UTC)

There was a bit about S-layers, which are the most common cell wall structure, but I've also added a sentence on pseudopeptidoglycan. Tim Vickers (talk) 15:04, 12 August 2008 (UTC)

Sentence "However, the archaea that do this, such as Sulfolobus, can cause environmental damage." and "This group of archaea produces sulfuric acid as a waste product" needs references. The Brock et Gustafson article lacks this kind of information. --Vojtech.dostal (talk) 06:26, 24 August 2008 (UTC)

PMID 18072246 looks useful, but I can't access this from home. However, what exactly is missing - information on if Sulfobolus oxidise sulphur, or information on the types of environmental damage this causes? Tim Vickers (talk) 15:07, 24 August 2008 (UTC)

Maybe both of them.--Vojtech.dostal (talk) 07:29, 25 August 2008 (UTC)

New ref added. Tim Vickers (talk) 18:42, 2 September 2008 (UTC)

Scale of Image:Bacteriorhodopsin.png

Does anyone know where to find what the proportions of a bacteriorhodopsin molecule are? There is a model of its molecule and I would like to add an approximate scale to the czech version. Thank you, --Vojtech.dostal (talk) 09:49, 20 August 2008 (UTC)

The protein is 56 angstroms from top to bottom and 36 angstroms wide. Tim Vickers (talk) 16:03, 20 August 2008 (UTC)

Thanks --Vojtech.dostal (talk) 16:27, 20 August 2008 (UTC)

Tim, I and my friend from the Czech Wikipedia are discussing whether Haloarchaea photosynthetise or not. This article says they do not, but why there are so many links on google? Thanks for your kind assistance, --Vojtech.dostal (talk) 16:25, 2 September 2008 (UTC)

Depends on what you mean by "photosynthesis". The exact definition of photosynthesis is the use of light to drive carbon fixation, it is also possible to use light to drive ATP synthesis, but this isn't technically photosynthesis. Archaea do not use light to fix CO2, but do use it to make ATP. Archaea are therefore photoheterotrophs, or photolithotrophs, but are not photoautotrophs. There is a good review on this - PMID 16997562 Tim Vickers (talk) 16:34, 2 September 2008 (UTC)

OK, this is what I thought--Vojtech.dostal (talk) 18:25, 2 September 2008 (UTC)

Pronounciation guide

Archaea is correctly pronounced using three syllables: Ar-che-ae (Ar-kee-a), and the audio file correctly does this. I interpret the written pronounciation guide on the first page, following the heading of Archaea, as indicating it as two syllables. If I am right, this should be changed, especially since I have heard some people using just two syllables.Drhx (talk) 15:53, 4 November 2008 (UTC)

The pronunciation transcription does not indicate the number of syllables; it merely indicates the location of the stress. By Wikipedia convention, the syllable breaks are not marked, since their location often varies geographically even for common English words. --EncycloPetey (talk) 18:20, 4 November 2008 (UTC)

Origin/Evolution

Re: "Probable fossils of these cells have been dated to almost 3.5 billion years ago,[21] "

I am not a scientist or learned in this field, but I believe there is resason to suspect that the above statement is mistaken. The footnote cites a 2006 paper by Schopf that mentions "Archaean" in the title and text, but it obviously refers to the geological time division of that name, not the life form that that is the subject of this article. As I understand it, Archaea and bacteria are impossible to distinguish merely from gross morphology. I think Schopf would be the first to acknowledge that we have no way to assign such a specific classification to the creatures that produced the 3.5 billion year old fossils.

--James Chapman —Preceding unsigned comment added by 24.205.45.201 (talk) 22:53, 26 November 2008 (UTC)

Perhaps you should read the paper, instead of speculating based on its title alone. We do have a way to recognize fossil Archaea chemically, and Schopf points this out in his paper. Please re-read the sections of the Archaea article on "Origin and Evolution" and the subsection on "Cell membranes", as well as the cited Schopf article. --EncycloPetey (talk) 23:31, 26 November 2008 (UTC)

James does have a good point, as the following sentence tried to say, these microfossils can't be identified as Archaea. I've rewritten that first sentence and added a more up-to-date source on biomarkers. Tim Vickers (talk) 23:36, 26 November 2008 (UTC)

I've been continuing to look as well. There is a chapter entitled "Biomarkers in the Proterozoic record" by Guy Orrison (pp 259-269) in the Nobel Symposium Volume No. 84. The volume was published as a book in 1994 under the title Early Life on Earth. However, this article doesn't seem to address archaeal compounds. The best additional evidence I can find (in the material at hand) is on p510 in the same volume, in the article by George L. Gabor Mikos & K. S. W. Campbell entitled "From protein domains to extinct phyla: Reverse-engineering approaches to the evolution of biological complexities" (pp. 501-516). The section in question says, in part: "the acyclic isoprenoids derive from lipids of archaebacteria". The authors state that such acyclic isoprenoids have been found in abundance in the Barney Creek Formation of the McArthur Basin in northern Australia, with a date of 1.69 Ga. Based on the additional presence of chemical fossils unique to bacteria, they conclude that both major lineages of prokaryotes were in existence by this date. --EncycloPetey (talk) 23:51, 26 November 2008 (UTC)

Term for one who studies the Archaea

A scientist who studies the Bacteria is termed a Bacteriologist and their field is Bacteriology. What is the correct rendering of the term for one who studies the Archaea? Does an Archaeologist studied Archaeology? 137.205.26.238 (talk) 21:28, 5 December 2008 (UTC)

No, but I think I'll steal your comment as a joke for my next lab meeting.... Archaea are bacteria, so those studying them are still bacteriologists. Technically, I suppose at the domain level most bacteriologists should be called eubacteriologists and archaea researchers archaeabacteriologists - but that gets hard to say, let alone write. -- MarcoTolo (talk) 21:36, 5 December 2008 (UTC)

Archaea are not Bacteria - they are a distinct domain, as are Eukarya. The term "Eubacteria" hasn't been used for years! 137.205.26.238 (talk) 02:48, 20 December 2008 (UTC)

The term "microbiologist" is also possible for those researchers who object to using "bacteriologist". --EncycloPetey (talk) 01:09, 6 December 2008 (UTC)

I would like to clarify that archaea are not bacteria. They have been found to be so different that they have been placed in a different domain. Drhx (talk) 21:20, 17 December 2008 (UTC)

Archaea is a taxonomic term

Archaea is a defined taxonomic term, as such, all incidences of the word "Archaea" in this article need to be capitalised and italicised - i.e. Archaea. The same goes for Bacteria and Eukarya. 137.205.26.238 (talk) 02:50, 20 December 2008 (UTC)

This is difficult, since as well as being used to refer to the domain, archaea and bacteria are also used less strictly to refer to individuals within this domain, for example it is common to say things such as "The archaea were observed under oil-immersion microscopy." Here the word is not referring to all "Archaea", but instead a sub-set of "archaea". If you glance through the titles of the papers cited in the article you can see this variation as well, although there is little consistency on this point. In this article I therefore used Archaea when I was talking about taxonomy and the domain in general, and archaea when I was talking about examples of organisms or features within the domain. Tim Vickers (talk) 18:03, 20 December 2008 (UTC)

Number of Phyla

The introduction to this article currently states : "Archaea are further divided into four phyla".

Five phyla are listed in the box to the right. Looking at the individual articles, one states :"Thaumarchaeota are a newly-proposed phylum of the Archaea".

The current classification section states : "estimates of the total number of phyla in the archaea range from 18 to 23, of which only 8 phyla have representatives".

This field is obviously in flux, and I am not a SME.

I suggest that someone rewrite the introductory statement, so that there is at least a hint that the number of phyla is not precisely four. —Preceding unsigned comment added by 75.52.224.9 (talk) 22:04, 11 March 2009 (UTC)

Good point, thank you. I've added a note to this effect to the lead. Tim Vickers (talk) 00:58, 12 March 2009 (UTC)

Morphology

I was just wondering why there was no mention in this seciton about Thermoplasma or Ferroplasma which do not have cell walls and instead resemble more of an ameboid shape
http://microbewiki.kenyon.edu/index.php/Image:Thermoplasma_2.jpg
Additionally the second paragraph of the introduction has this odd statement "Generally, archaea and bacteria are quite similar in size and shape," when the morphology section directly contradicts this statement.--Jonthecheet (talk) 19:47, 16 March 2009 (UTC)

True, those species are discussed in the section on "cell wall and flagella", but they should also be added earlier. Tim Vickers (talk) 15:55, 14 April 2009 (UTC)

Bacterial Flagellum evolved from Type III secretory protein??

The article makes this claim when contrasting bacerial and archaean flagella. I've only read the abstract of the reference provided, but it looks like it only discusses the archaean flagellum, not the evolution of the bacterial flagellum. I always thought that it was believed that the Type III secretory protein evolved from the flagellum, not the other way round, because its only use is in pathogenicity and so it must have evolved after the organisms they parasitise whereas the bacterial flagellum is found in a wide range of bacteria from earlier on. I've only found 1 rather old reference to support this: Nguyen L., Paulsen I. T., Tchieu J., Hueck C. J., Saier M. H. Jr. 2000. Phylogenetic analyses of the constituents of Type III protein secretion systems. J. Mol. Microbiol. Biotechnl. 2(2):125-44 (freely available here: [2]) Can anyone here confirm if this is the current consensus? If so, perhaps the article should be changed. —Preceding unsigned comment added by 79.64.178.86 (talk) 14:05, 14 April 2009 (UTC)

Yes, it looks like it is accepted that the bacterial flagella and the type III secretion system share a common ancestor, but the function of that ancestor (flagella or secretion system) is controversial. I've reworded the article a bit and added two references. Tim Vickers (talk) 15:53, 14 April 2009 (UTC)

Archaea don't do Anammox

I removed the words in energy metabolism that is mistakenly citing articles about Archae being involved in Anammox.

REMOVED: in anammox metabolism

Riennn (talk) 14:01, 9 June 2009 (UTC)

See Talk:Archaea#Mistake_concerning_Nanoarchaeum above, I thought this had been corrected already. Tim Vickers (talk) 16:15, 9 June 2009 (UTC)

Thanks, I missed that, but it had not been fixed indeed. Archaea somehow contribute indirectly to anammox by feeding it with NO2, in the same way bacterial ammonia oxidizers do. I think it is out of scope here, if we start speaking about the fate of the product of ammonia oxidation by Archaea, this article would have to include a paragraph about importance of Archaea in removal of nitrogen from aquatic ecosystems. I will try to include all this in the denitrification article, which needs serious additions. Riennn (talk) 06:19, 10 June 2009 (UTC)

That sounds good. Would it also be possible for you to check this article over again to see if there are any other errors? Although I am a microbiologist, I'm not an expert on Archaea and might have got a few other things wrong. Tim Vickers (talk) 16:36, 10 June 2009 (UTC)

I certainly can do this although I am not an expert either... I don't think anyone can pretend being an expert on archaea I've been thinking about a person to ask to read it through...

Riennn (talk) 05:16, 11 June 2009 (UTC)

Image of plankton in the oceans

I do not see any plankton in the image. Is the plankton blue or yellow? —Preceding unsigned comment added by 83.24.23.199 (talk) 07:10, 5 July 2009 (UTC)

They are the parts in light green. Tim Vickers (talk) 17:10, 5 July 2009 (UTC)

Edits /27

>If you believe there is such an error, please present it on the Talk:Archaea page

1:'"Although archaea have, in the past, been classed with bacteria as prokaryotes, this classification has been described as outdated, since it fails to distinguish between the three very distinct domains of life"

>three very distinct domains of life< are "new product" of new classification, not the reason to update the classification. In other words, until new classification was introduced, the stated fault ("since it fails") was nonexistent.

Common example : John Sulfolobus & Ann Escherichia: Although John married Ann, this marriage was outdated, since they fails to distinguish they are divorced.

Anyway this sentence was redundant. It duplicate better written information in : In the past they were viewed as an unusual group of bacteria and named archaebacteria but since the Archaea have an independent evolutionary history and show many differences in their biochemistry from other forms of life, they are now classified as a separate domain in the three-domain system .

It is not redundant, as the prokaryote/eukaryote "dichotomy" is still commonly-seen. Tim Vickers (talk) 14:52, 28 August 2009 (UTC)

2 "Archaea are further divided into four recognized phyla."

• Infobox list five.
• Only two phyla are unquestionably accepted.

Xook1kai Choa6aur (talk) 05:08, 28 August 2009 (UTC)

I was following a 2005 review (PMID 15630422) for this taxonomy, so this does not include the proposed (but not accepted) phylum of Thaumarchaeota from 2008. What source disputes the classification of Korarchaeota and Nanoarchaeota as phyla? Tim Vickers (talk) 14:52, 28 August 2009 (UTC)

Possible error in terminology

"These two groups were originally named the Archaebacteria and Eubacteria and treated as kingdoms or subkingdoms, which Woese and Fox termed Urkingdoms". My problem here is with the word *subkingdom*. In my amateur layman understanding, the groups Archaebacteria and Eubacteria must have been regarded either as kingdoms or as something higher, bigger than kingdoms, which would then be something like superkingdoms or megakingdoms - which is why, as I understand, we now work with domains. In any case, Urkingdom or Urkönigreich can never mean sub-kingdom, as Ur refers to something either older or greater than the word it precedes. Duchiffre

It wasn't Woese and Fox who treated them as subkingdoms. That issue was the result of other authors sometimes placing the groups at the level of subkingdom within the kingdom Monera. Woese and Fox used the term "Urkingdom" instead, which later came to be called "Domain", to emphasize that they were something more than the traditional kingdom. So there is not an error in terminology, as such, merely an unclear wording of the article text. --EncycloPetey (talk) 04:20, 25 September 2009 (UTC)

Ambiguous sentence

"Archaea are genetically distinct from bacteria and eukaryotes, with up to 15% of the proteins encoded by any one archaeal genome being unique to the Archaea,"

does this mean to say that up to 15% of the genome is unique, or up to 15% of the proteins created by the genome are unique (e.g. it creates "pseudoglobin" whereas no known eukaryte genome produces this protein) (and thus, presumably, much more than 15% of the genome is unique)? As worded, it seems to refer to the latter, but it also seems from the context that it is supposed to refer to the former. Whichever it is, I think it needs to be made clearer. Kevin Baas^talk 20:14, 3 December 2009 (UTC)

It did refer to proteins, so the literal meaning was the one I intended. I've reworded the context a bit to make a smoother transition. Tim Vickers (talk) 20:25, 3 December 2009 (UTC)

Yeah, that's much clearer. Thanks. FWIW, I was curious as to whether one could make an argument for multiple origin (life starting in multiple places independently) based on variations in genomes at the base of the phylogenetic tree. So I wanted to know how much of the genome was different. I still don't know, but since that sentence does refer to the proteins, it could be quite a bit. Kevin Baas^talk 15:40, 4 December 2009 (UTC)

Out of curiosity I just looked up "pseudoglobin", turns out it's a real protein (pseudoglobulin). Oh geez, you can't shake a stick w/out hitting one! Kevin Baas^talk 15:43, 4 December 2009 (UTC)

One current idea is that life emerged out of a set of "replicators" that engaged in extensive horizontal gene transfer, making the "root" of the tree of life more of a basketwork than a single point. See this review for more details. Tim Vickers (talk) 17:47, 4 December 2009 (UTC)

Thanks. That was my argument that spurred my curiosity: that at such an early stage of evolution gene transfer would be ubiquitos so by definition of "species" you would have only one species. But then i recalled that "speciation" can mean that even though they CAN genetically reproduce they are separated geographically enough such that they DON'T. i'm a little fuzzy on the subtleties of that definition but in any case it brings up an interesting question: where they separated geographically enough such that they didn't; did there actually end up being a few baskets or just one; was the weaving above or below the percolation threshold? One way to approximate the answer would be to compare the amount of genome variation in the earliest known (non-ubiquitiously reproducing) organisms. Hence my curiosity. The paper you referred me to does a good job of reminding me that it's not that simple.

Either case I was curious if the basis of my argument was valid; if my ubiqiuotos gene transfer in primordial organisms idea was scientifically credible. i didn't think I would find an answer to that very easily, but there it is! Thanks! Kevin Baas^talk 20:24, 14 December 2009 (UTC)

[3] - I love being right! (still curious if it was ubiquitois. I think it'd be pretty cool if it wasn't (if there are two "origin(s) of life")!)Kevin Baas^talk 16:46, 1 February 2010 (UTC)

Tranlation and transcription

The navigation box for gene expression (akin to an book index for the topic) (link: Template:MolBioGeneExp) was edit some time back to include archeal translation and transcription, two pages that do not exist. As several months have passed, it is clear that the edit was for form as the other two domains had respectiove pages. Could an archean microbiologist add these pages if possible or redirect them correctly (I would assume to eukaryotic transcription and to prokaryotic translation). Thanks --Squidonius (talk) 13:21, 15 December 2009 (UTC)

Odd Chemical Claim

"Ether bonds are chemically more resistant then ester bonds, which might contribute to the ability of some archaea to survive at extremes of temperature and in very acidic or alkaline environments."

This doesn't make sense: why would a less chemically resistant bond increase survivability? Surely it should be "Ester bonds are chemically more resistant then ether bonds..." Hasname (talk) 17:56, 19 May 2010 (UTC)

"Which" here is referring to the increased chemical resistance. I'll reword this to be clearer - ""Ether bonds are chemically more resistant then ester bonds, this increased stability might contribute to.." Tim Vickers (talk) 19:34, 19 May 2010 (UTC)

I was having a really dense moment, confusing esters and ethers :s. Sorry to waste your time.

Hasname (talk) —Preceding undated comment added 20:33, 19 May 2010 (UTC).

Edit request from Mikejones2255, 11 June 2010

{{editsemiprotected}}

spelling error: under "Structure, composition development, operation", the first bullet point under membranes, it reads"... In ester lipids this is an ester bond, whereas in ether lipids this is an ether bond. Ether bonds are chemically more resistant then ester bonds...." The "then" in the last sentence needs to be "than."

Mikejones2255 (talk) 11:50, 11 June 2010 (UTC)

I've made the change, thanks for spotting that. Mikenorton (talk) 12:07, 11 June 2010 (UTC)

Copy-edits

Copy-edits complete. Reduced word count by ~20%. Enjoy. Lfstevens (talk) 02:22, 12 June 2010 (UTC)

Copy-edits

Copy-edits complete. Reduced word count by ~20%. Enjoy. Lfstevens (talk) 02:43, 12 June 2010 (UTC)

Challenging the antiquity of Archaeans

Tim, I have just finished reading two articles by Thomas Cavalier-Smith in which he puts forward a very convincing case for the relatively recent emergence of Archaea (only 850 mya!!). In his Neomuran hypothesis he proposes that archaeabacteria and eukaryotes are sisters, rather than archaeabacteria being ancestral to eukaryotes. In addition to making a number of convincing arguments based upon molecular and cellular data, he also points out that there is no definitive paleontological evidence for archaean or eukaryotic fossils prior to 850 mya. He also notes that steranes which have been used as biomarkers to indicate the presence of eukaryotes 2.7 bya is unreliable due to the presence of these molecules in Arabobacteria and several other Eubacterial species. His analysis of how quantum evolution distorts the supposed "molecular clock" and the cladistic and phylogenetic conclusions drawn from such techniques is quite compelling.

I have long admired the work of Woese, Margulis, Schopf and others working on the origin and evolution of early life but these articles have forced me to radically reconsider my former understanding on these issues. In many ways Cavalier-Smith has struck at the heart of many burning questions and contradictions in the view put forward by the mainstream of the biological community. At minimum, I would think that these ideas deserve space in this article on Archaea. I would greatly appreciate your feedback on these issues before making any additions to this article.

Selected Articles:

This issue of Philosophical Transactions is dedicated to the topic... http://rstb.royalsocietypublishing.org/content/361/1470.toc

Thomas Cavalier-Smith - http://ijs.sgmjournals.org/cgi/reprint/52/1/7 - The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification - International Journal of Systematic and Evolutionary Mircobiology (2002) 52, 297-354

Thomas Cavalier-Smith - http://ijs.sgmjournals.org/cgi/reprint/52/2/297 - The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa - International Journal of Systematic and Evolutionary Mircobiology (2002) 52, 297-354

Jtwsaddress42 (talk) 19:32, 4 July 2010 (UTC)

Medo

In the section 'Current classification' a sentence starts "Most of the culturable medo". The word 'medo' is not in the Oxford or Cambridge online dictionaries. What does it mean or is it a typo? It seems surprising that an article of the day should use a word so obscure it is not in standard dictionaries. Dudley Miles (talk) 19:59, 10 January 2011 (UTC)

It was added by an anonymous user without comment. I've removed it. mgiganteus1 (talk) 20:39, 10 January 2011 (UTC)

Spore versus endospore

Okay, it's kind of a nit. But the use of "spore" in the lead section clearly refers to endospores, yet it links an article that heavily emphasizes reproductive spores and barely mentions endospores at all. I prefer the more specific term. Yaush (talk) 22:58, 10 January 2011 (UTC)

The more specific term applies to a single order of bacteria. The point of the sentence in the article is that archaeans do not produce any kind of spore, neither bacterial-type spores nor eukaryotic-type spores. Linking to endospore would thus be far too specific for the article's content. --EncycloPetey (talk) 23:31, 10 January 2011 (UTC)

First sentence

"The Archaea are a group of single-celled microorganisms with no cell nucleus nor any other membrane-bound organelles."

The first sentence is a poor definition. It reads (to a layman) like any arbitrary group of microorganisms is called an "Archaea." It should be defined as a category of microorganisms, not a group.129.10.173.73 (talk) 23:05, 10 January 2011 (UTC)

Only the taxon label Archaea is a category. This article is about the organisms that belong to that category, not about the category itself. The category Archaea has a place on Wikispecies, but we don't generally write articles about such categories in an encyclopedia. --EncycloPetey (talk) 23:29, 10 January 2011 (UTC)

That does not make sense. The article on Eukaryotes or Cordata is about the category as well as all the similarities shared between subcategories of the category and the individual species, as well as their differences and differences from other categories. Similarly for Archaea. -Pgan002 (talk) 06:40, 28 February 2011 (UTC)

No, the articles you meantioned are about the collected group of organisms, the similarities and differences between those groups of organisms. The category is an artificially constructed name and arbitrary circumscription, with a history of who coined the name, where the name was published, and when. A cat can walk into a room, yes? But if you define "cat" as a "category" with certain characteristics, then that clearly doesn't make sense, because a category does not walk into a room. See the difference? --EncycloPetey (talk) 05:47, 5 January 2012 (UTC)

Split Article

I recommend this article be split, because it is about 90KB, and it should be split in 2 or 3 sections. Aerosprite the Legendary (talk) 02:51, 2 February 2011 (UTC)

Copy-edit of sentence under "Relation to Eukaryotes"

Under section "Relation to Eukaryotes", this sentence can be improved

"The leading hypothesis is that the ancestor of the eukaryotes diverged early from the Archaea, and that eukaryotes arose through fusion of an archaean and eubacterium, which became the nucleus and cytoplasm; this explains various genetic similarities but runs into difficulties explaining cell structure"

Is it correct to say the following:

"The leading hypothesis is that the ancestor of eukaryotes diverged early from Archaea, and that eukaryotes arose through fusion of an archaean and a bacterium, which became respectively the nucleus and cytoplasm of the Eukaryote cell. ... "

-Pgan002 (talk) 07:11, 28 February 2011 (UTC)

Domain names function in English as weak proper nouns, just as kingdom names do. Such weak proper nouns prefer use of the definite article. --EncycloPetey (talk) 05:41, 5 January 2012 (UTC)

New Domain - sentence does not compute

The following sentence - referring to PCR - is ambiguous and in some readings, tautologous.

This allows the detection and identification of organisms that cannot be cultured in the laboratory, which generally remains difficult.

What exactly "remains difficult" ? Allowing? Detecting? Culturing? And if it is now allowed, why still difficult?

And why is any remaining difficulty relevant to the existence of the New Domain?

Please consider rewording, or maybe just drop the last clause.

[But thanks for a really interesting article] Shannock9 (talk) 14:20, 2 April 2011 (UTC)

Candidatus formatting

The newly added section on Phylogeny includes several Candidatus forms. They are currently formatted as:

'Candidatus Micrarchaeum acidiphilum'

However, per the Candidatus article, it looks like they should be formatted as:

"Candidatus Micrarchaeum acidiphilum"

I'm not an expert, so I will just note this here and not change anything. -- Donald Albury 00:57, 5 January 2012 (UTC)

"Prokaryotes are obsolete" - POV?

This article includes the assertion that:

"In the past [Archaea] had been classed with bacteria as prokaryotes (or Kingdom Monera) and named archaebacteria, but this classification is regarded as outdated."

This assertion is supported by a reference to an article in Nature [May 2006] by Dr. Norman Pace. Several microbiologists have expressed disagreement with Dr. Pace's ideas (e.g. William Whitman; Michael Dolan). I have seen no sign that the wider microbiological community is abandoning the term "prokaryote". This assertion may therefore raise a POV issue.

In Nov 2010, I (quite gently) addressed this by softening the assertion to read "...this classification is regarded by some as outdated."

This edit was reverted (deliberately or accidentally) by user Pot in April 2011, as part of a larger and well-executed "tidy up" edit. Pot does not appear to be a subject matter expert (no offence intended - neither am I!), so it is my intention to re-apply my original edit unless someone objects here, providing citable evidence that the term "prokaryote" is now regarded as obsolete or outdated by a majority of the relevant professional community. FredV (talk) 16:39, 5 January 2012 (UTC)

Is it perhaps proper to say that "prokaryote" as a clade or synonym for Monera is outdated, but is still valid as a grade. Now, is there a reliable source that says something like that? -- Donald Albury 22:07, 5 January 2012 (UTC)

The statement in question pertains to classification of a formal group called prokaryotes, not to usage of the informal morphological description of prokaryote. It is the classification that is outdated, and the sentence clearly says that. You haven't demonstrated that this is not the case, and you seem to have misconstrued the meaning of the original sentence. It is the same as the issue of the term "algae", which is no longer used as part of any formal classification, but is still used in morphological and ecological contexts. It's not the term that's obsolete, but merely the classification. --EncycloPetey (talk) 02:47, 6 January 2012 (UTC)

I take your point. I had read "classed" as more or less synonymous with "grouped", rather than "formally classified". Since I may not be the only person to make this assumption, I will edit the passage to make this clearer. On the wider issue of rigorous cladistic classification at the domain level, I believe that evidence of a high degree of horizontal gene transfer during the early divergence of the domains, together with uncertainty regarding the precise nature and timing of the evolution of the eukaryotic cell, may render "classical" cladistic classification difficult - or even impossible. This would lend more weight to the retention of "useful" grade-like groupings such as "prokaryotes" (I do not agree with Dr Pace's argument that "prokaryotes" can not be reasonably well defined - but that is a much more complicated argument, and is probably off-topic on this page). FredV (talk) 12:12, 6 January 2012 (UTC)