Talk:Archaea/Archive 3

Expanding upon the stub Woese's Dogma
As the title suggests, i’m trying to expand upon a stub article that is titled “Woese’s Dogma”. I want this article to focus on the controversy behind challenging the prior established dogma and reference the evolutionary means by which his discovery is supported, as well as refuted. I’ve read through the Archaea article and I came across the term -The Woeseian Revolution- in quotation marks. I would like to change the stub article name to this phrase and in doing so, give credit to whomever might have coined the term (also referencing this article). Seeing as to how there are a lot of intelligent minds on this thread that are for more knowledgeable on the subject than I, any feedback or suggestions you all are willing to provide will be greatly appreciated. Thank you!

Link to article: https://en.wikipedia.org/wiki/Woese%27s_dogma Mejia.25.osu (talk) 02:36, 1 October 2014 (UTC)

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&lt;col&gt; (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. 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? 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, 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 40-60oC, 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)


 * 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 - 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)

Prokaryotic Doris215 (talk) 15:18, 16 November 2013 (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)

Spelling: archaebacteria vs. archeabacteria, both is used here. — Preceding unsigned comment added by 131.173.10.47 (talk) 11:24, 31 October 2014 (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)