I have read that Miller used a
mixture that had mostly methane, ammonia, and water
vapor. But then I’ve read that today most scientists
think the early atmosphere had carbon dioxide,
nitrogen, and water vapor because the hydrogen would
have escaped into space. So I’ve heard that if you
replace the Miller/Urey atmosphere with the modern
model you don’t end up with amino acids, but organic
compounds such as formaldehyde and cyanide. So my
question is: I the Miller/Urey experiment truly
accurate? Can formaldehyde and cyanide really give
rise to life?

I really cant answer that. But I can tell you that I am performing the experiment in a matter of weeks with the gasses presently on Titan :)

Got the glassware, power supply, and all the rest.... even someone to analyze my product.

Muhahhaha
Later

Proof of what a lot of optimism and determination will accomplish to all of those who said I couldnt do it!!!!!! :P

I think methane, ammonia, and water vapor might have existed in the early atmosphere, because cyanide and formaldehyde seems like an unlikely bet to give rise to life; they are poisonous. Hydrogen may have escaped early on, but perhaps before all of it could escape, the gases methane and ammonia may already have existed from reactions in the early earth's hot climate.

I think methane, ammonia, and water vapor might have existed in the early atmosphere, because cyanide and formaldehyde seems like an unlikely bet to give rise to life; they are poisonous.

Poisonous to us, but not necessarily to everything.

I think methane, ammonia, and water vapor might have existed in the early atmosphere, because cyanide and formaldehyde seems like an unlikely bet to give rise to life; they are poisonous

But do you have proof of this, or is it just because the other altenative doesn't seem likely.

It does not matter, perbiotic organics was raining down on earth from space, no need for life requiring organics to have arisen here.

http://www.google.com/search?hl=en&ie=UTF-8&q=amino+acids+from+space

Well, still the question remains, where did the perbiotic organics come from?

I have read that Miller used a
mixture that had mostly methane, ammonia, and water
vapor. But then I’ve read that today most scientists
think the early atmosphere had carbon dioxide,
nitrogen, and water vapor because the hydrogen would
have escaped into space. So I’ve heard that if you
replace the Miller/Urey atmosphere with the modern
model you don’t end up with amino acids, but organic
compounds such as formaldehyde and cyanide. So my
question is: I the Miller/Urey experiment truly
accurate? Can formaldehyde and cyanide really give
rise to life?
I don't believe it's exactly known how prebiotic molecules formed on/came to Earth, though you are correct that the Miller and Urey experiment does not accurately model what we believe to be the nature of Earth's early atmosphere. It is still very important, though, since it demonstrates how easily those molecules can be formed from almost wholely inorganic constituents. That's an interesting, though not extremely practical, area of research.

I don't have proof, because ammonia is all but nearly nonexistent in the order of abundances of gases in our atmosphere. Formaldehyde and cyanide compounds seem absent as well. Quite puzzling.

I have read that Miller used a
mixture that had mostly methane, ammonia, and water
vapor. But then I’ve read that today most scientists
think the early atmosphere had carbon dioxide,
nitrogen, and water vapor because the hydrogen would
have escaped into space. So I’ve heard that if you
replace the Miller/Urey atmosphere with the modern
model you don’t end up with amino acids, but organic
compounds such as formaldehyde and cyanide. So my
question is: I the Miller/Urey experiment truly
accurate? Can formaldehyde and cyanide really give
rise to life?Luckily for us Miller continued on with his experiments.


"But one problem the theory has had to confront was a possible shortage in the primeval oceans of two key pieces in the structure of an RNA molecule, known as cytosine and uracil. Dr. Miller and Dr. Robertson believe they have solved the difficulty.

In companion pieces in the journals Science and Nature, the two scientists report that both substances might have been produced by the lifeless young oceans in ample quantities by a process involving the evaporation of sea water in tropical lagoons, the freezing of sea water in polar regions and the mixing of their products in the open ocean.

The freezing part of the process could have increased sea water concentrations of hydrogen cyanide, Dr. Miller believes. Cyanide is a deadly poison to animals, but it was an essential precursor to many of the molecules from which primitive life arose.

The evaporative part of the process, Dr. Miller said, could have concentrated the traces of urea that accumulate in sea water as a result of reactions in the atmosphere caused by lightning flashes. In experiments, Dr. Miller and Dr. Robertson showed that when the concentration of the simple chemical urea in sea water is high enough, it reacts with another quite common component of sea water that also owes its formation partly to lightning bolts. Under these conditions, the scientists found, the reaction between urea and the second chemical, known as cyanoacetaldehyde, yields fairly large amounts of cytosine, which is one of the nucleotide bases (or "letters") the DNA and RNA molecules use to spell out the genetic "words" controlling protein production and the growth and reproduction of organisms. "

http://www.swcp.com/~diamond/rnabase.html

~Raithere

I was just wondering if there is a list of some or all of the proteins that this experiment yeilded. I have been dabbling in the research area on this and am a little curious. I first heard about this experiment from one of my chemistry professors and wasn't fully informed.

I was just wondering if there is a list of some or all of the proteins that this experiment yeilded.

There were no proteins formed. What was formed was a "sludge" of various organic molecules (ie. carbon chains and rings) that included, in small quantities, some simple sugars and simple amino acids. Mind you, that's still a very significant result that pre-biotic materials can give rise to organic molecules (even if it turns out that the experimental conditions did not accurately represent Earth's environment at that time).<P>

There are many theories as to what the early earth's atmosphere was like, and to my knowledge there is no difinitive proof one way or another. The most important thing you have to realize about this experiement is that It proved that organic compounds could have formed spontaneously, WITHOUT the need of some higher being. the experiment was essential in help prove that evolution from nothing to us is possible.

Btw, I still havent been able to find anyone or a lab to help me finish the experiment. Ill be taking my glassware with me to college though and hopefully a bio or chem prof there will be interested in doing the experiment :)

Later
T

There were no proteins formed. What was formed was a "sludge" of various organic molecules (ie. carbon chains and rings) that included, in small quantities, some simple sugars and simple amino acids. Mind you, that's still a very significant result that pre-biotic materials can give rise to organic molecules (even if it turns out that the experimental conditions did not accurately represent Earth's environment at that time).<P>
I've read that at least one protein was formed:

Then the German biochemist Klaus Dose and his associates succeeded in showing that one of the products of Fox's experiments was flavin, a naturally-occurring protein.
http://www.daviddarling.info/encyclopedia/T/thermalprotein.html

Does anyone knows the differences between proteinoids/thermal proteins and proteins? I wonder if it's strictly defined by a minimal number of aminoacids, or maybe structure.... could it be that the only meaningful difference is that proteins are synthesised by living organisms weather proteinoids are not? And if some day someone finds a proteinoid ocurring in an organism, then it would be "promoted" to a protein? As if the definition of proteinoids was a large group of molecules (in a certain pattern), and proteins was an inner group, not essentially different, just like "cars" and "red cars"?

I've read that at least one protein was formed...

Thanks for that Danniel; I didn’t know that. :) :eek:

OK, after minimal research it appears that “thermal proteins” are thermal polymers (often referred to as ‘polyamino acids’) of three to eight amino acids that can form synthetically (in the sense that they aren’t made by living cells) at high temperatures. It appears that they can only form when glutamic acid is present in excess and that their chemistry is slightly different to “conventional” polypeptides formed by living cells. But I’m no biochemist so I cannot comment further.

It seems that the polyamino acid theory is one theory as to how the first proteins arose on Earth. Just how well supported this theory is, I do not know. But it cannot be at the forefront of mainstream abiogenesis theories as up until now I have never heard of it! (Not that I’m any sort of expert in this area, but I do have a long standing interest.)<P>

Well, still the question remains, where did the perbiotic organics come from?Ah, the $64,000 question! RNA will assemble out of free nucleotides if a protein enzyme is present. Howsomever, that protein is large, many kilodaltons, and so won't assemble by itself (and last long enough before degrading). It needs an existing substantial RNA strand to code for this enzyme. This means you need the protein to get the protein. It's like needing a key to unlock a safe when the key's inside it.

So basically, something happened back then that can no longer occur in today's world.

I'm not willing to go quite that far. I am willing to say that we do not yet understand how it all started.

But this proscess isn't going on any more- more life forms arn't randomly developing on our planet.

So basically, something happened back then that can no longer occur in today's world.

Correct.

There is still much debate is to the composition of the atmosphere when life first arose. There is also much debate is to <I>where</I> life first arose - water on the planet's surface vs hydrothermal vents on the bottom of the ocean vs subterrainean pockets of water deep inside the Earth's crust. But one thing is certain - the Earth was a vastly different place 4 billion years ago (when life first arose) than it is today. With the oxidizing atmosphere of today and the plethora of already-established life, I think the chances of any new life arising <I>de novo</I> are negligable, if not non-existant.<P>

The building blocks of proteins were formed: amino acids. Miller and Urey nor anyone else can duplicate all the possible other perimeters of their experiments that might have led to protein development an thus of life. How can we simulate all those variables inside a lab when we don't even know what they all were in an outside natural environment. To many possible variables, but it is still possible to do so.

I am not a creationist but the more I know about genetics the less plausible it seems that a living organism was created on Earth by random combination of materials. That first organism needed to be able to exist in the absence of any other organism, reproduce, and evolve.

What do we think is the simplest current organism that can do that?

How much could this current organism be simplified and still meet the minimum criteria? That is, how much of the organism is devoted to anything but simply existing and reproducing? Aren't we talking about at least 5 million base pairs of DNA plus all the machinery necessary to interpret the DNA and execute the necessary functions.

It seems more plausible that life came here from elsewhere in space.

Actually, it is thought that a molecule of a tens of thousands of parts could reproce itself in a nutrient rich environment free of competition. Life probably didn't start as a complete cell, just a self replicating protien similar to today's prions. Things like a cell membrane and organels almost certainly were later adaptations.

There was room for untold millions of different combinations to work themselves out every second in as many pools across our new and arcane world. There was time for this to repeat a trillion times in the eons that heralded in life. What would having it come from space matter? The molecule would have still had to have started somewhere, be it here or elsewhere. It matters not which.

The origin of life on earth occurred over 4 billion years ago when the earth's atmospere had no oxygen. They were anaerobic single-cellular prokarytes without a nucleus. Anaerobic means without oxygen and "prokarytes" all lack a nucleus. If you do a search on the web, use a search engine like www.goole.com and type in "origin of life" and you might be able to come up with an earlier form of life. Don't know. A lot depends on how you define life, then it gets philosophical.

on the subject: Life's origins were easier than was thought (http://www.biologynews.net/archives/2005/09/16/lifes_origins_were_easier_than_was_thought.html).

No, they didn't claim to have figured it all. The thing is that they now think that the minimal number of needed genes is smaller than previously thought.

I don't remember at this point if it was mentioned in this topic, but it's interesting to read about the "Spiegelman's monster" and Eigens experiments with RNA too.



Does someone proposes that life may have originated multiple times, but at the same time, being considerably identical, chemically?

Imagine a situation that a certain environment is formed, and this environment is more or less something that continuously form "semi-lifeforms" or "almost replicators"... then, eventually would arise one successful replicator... but that wouldn't be necessarily the only one

And since all the successful replicators were fabricated by the same process and source materials, they could be very similar, anyway. To the point of an initial "population" or whatever, be in fact "polyphyletic", if the term really applies, but at the same time something like a population, exchanging genetic information in a rudimentary way...

it seems reasonably to me, but maybe that's the standard thought and I just don't know...

Correction: The origin of life on earth is 3.8 billion years ago and started with archaebacteria.

The Miller/Urey experiments produced amino acids - the building blocks of the neccisary proteins - but not enough to account for the origin of life. There were more amino acids found on the two meteorites that crashed on earth in 1996.

The mostly popular consensus is that life originated multiple times in multiple places - at least if you believe in extraterrestrials? I would think that because so many similar simultaneous events occur throughout history that multiple forms of life originated on earth at about the same time, but some existed and others went extinct, yet still others "converged." There are species in phylogenic clades that have converged, thus at least semi-polyphyletic.

Thanks for mentioning "Spiegelman's monster" and Eigen's experiments: RNA reduplications. Haven't read about but will.

Correction: The origin of life on earth is 3.8 billion years ago and started with archaebacteria.
That's definitively wrong.
A long time ago archaea were indeed believed to be ancient bacteria, however, now it is quite clear that they most likely split from a common ancestor, which might have possessed the characteristics of a Gram-positive eubacterium.

In the traditional tree of life archaebacteria and eubacteria are thought to have a common ancestor with the eubacterias considered to contain the oldest divergence, but now that is being questioned. Archaebacteria include the extremophiles (thermophile bacteria that live in very hot places) and methanogens (methane producing bacteria found in swamps and marshes). The subject is still under debate, with considerablt disagreement among taxonimists about the details of bacterial classifications, especially since the eubacterium contain such a wide variety of different types. But many scientists believe that the origin of life started in extremely hot environments where the archae- extremophile/thermophile bacteria thrive.

We currently have another sciforum that is discussing the same thing called "The Origin of Life," and they ought to be combined, but I will try to put forth a more clearer explanation here so as not to be redundant.

This is the traditional tree of life:

Eubacteria
- Archaebacteria
- - Eukaryotes
? viruses

"The rooting of the Tree of Life, and the relationships of the major lineages, are controversial. The monophyly of Archaea is uncertain, and recent evidence for ancient lateral transfers of genes indicates that a highly complex model is needed to adequately represent the phylogenetic relationships among the major lineages of life." There are currently too competing views:

The "archaea tree":

Archaea
- Eubacteria
- Euryarchaia
--- Crenarchaeota-Eocytes
--- Eukaryotes

The "eocyte tree":

Eubacteria
- Euryarchaeota
- Crenarchaeota-Eocytes
- Eukaryotes

see: "Life n Earth," by The Tree of Life Web Poject, http://tolweb.org/tree?group=Life%20on%20Earth

A partial list of Eubacteria can be found at http://tolweb.org/tree?group=Eubacteria but even though there is more support for the eocyte tree, (see http://genomics.ucla.edu/eocyte/eotree.html) what happens to the archaebacteria (extremophile bacteria: thermopolies and metanogens)? They get divided half in the Euryarchaeota branch and half in the Crenarchaeota with Eubacteria being the origin. How can this be?I

"The archaea are so different from the [eu]bacteria that they must have had a long, independent evolutionary history since close to the dawn of life. In fact, there is considerable evidence that you are more closely related to the archaea than they are to the [eu]bacteria."

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/E/Eubacteria.html

"Gram-positive Eubacteria is a group of bacteria, the great majority of whose members display unique staining patterns when exposed to certain gram stains (hence making them gram-positive). Actually, not all of these bacteria are gram-positive; some are placed in the group because they are molecularly similar to the gram-positive bacteria."

http://www.sidwell.edu/us/science/vlb5/Labs/Classification_Lab/Bacteria/Eubacteria/

While several aspects are still disputed (for instance, whether archaea are monophyletic) none (including the links you provided) indicated that archaea are a precursor of bacteria or the first organisms as you pointed out in your earlier post (in fact your links are dealing with a complete other issue, e.g. if you look closely you will find in all trees a common ancestor of bacteria and archaea).
This was a notion (which was indeed based on the extremophile lifestile and was actually the namegiver to the archaea) dropped quite a while ago.


It was indeed also assumed for a while that archaea are in fact closer to eukaryotes than to eubacteria. But this has been challenged by the extensiveness of horizontal gene transfer.
One paper for instance suggested the origin of eukaryotic cells as a symbiotic interaction between Pyococcus and gamma-proteos. But of course, this is also disputed
(BTW is it possible that your links and quotes have a somewhat "random feeling in it"? ;)

Traditionally archae were assumed to be the precursors, and originally they were thought to be bacteria themselves, but they are unicullar microorganisms also found in extreme hot environments (thermophiles). Then the debate shifted to where they came from and how and where the amino acids came from that created them. Now the shift seems to be going to eocytes as the precursor to the origin of life and the tree of life. Eocytes are also thermophile bacteria.

"The phylogenetic origin of eukaryotes has been unclear because eukaryotic nuclear genes have diverged substantially from prokaryotic ones. The genes coding for elongation factor EF-1alpha were compared among various organisms. The EF-1alpha sequences of eukaryotes contained an 11-amino acid segment that was also found in eocytes (extremely thermophilic, sulfur-metabolizing bacteria) but that was absent in all other bacteria. The related (paralogous) genes encoding elongation factor EF-2 and initiation factor IF-2 also lacked the 11-amino acid insert. These data imply that the eocytes are the closest surviving relatives (sister taxon) of the eukaryotes."

Abstract from "Evidence That Eukaryotes and Eocyte Prokaryotes Are Immediate Relatives," by Rivera, M. C.; Lake, J.., Science, V257, I. 5066, pp.74-76, 1992
http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=1992Sci...257...74R&amp;db_key=GEN&amp;d ata_type=HTML&amp;format=

"Most data argue for a monophyletic Archaeacomposed of two kingdoms, crenarchaeotes and euryarchae-otes, with eukaryotes and eubacteria each arising separately. However, Lake et al. have argued for apolyphyletic Archaea, with a paraphyletic Euryarchaeota giv-ing rise to eubacteria (the photocyte hypothesis) and a mono-phyletic Crenarchaeota arising with eukaryotes (the eocyte hypothesis).... Root of the Universal Tree: The strong similarity in theamino termini of EF-Tu and EF-G, both in terms of structure and of sequence, supports a relationship of homology—i.e., they appear to be the products of an ancient geneduplication. In fact, secondary structure comparisons strongly suggest that this homology also includes the second domain of both proteins."

from "The root of the universal tree and the origin of eukaryotes basedon elongation factor phylogeny," by Sandr, L.B. et. al., Proc. Natl. Acad. Sci. USA Vol. 93, pp. 7749–7754, July 1996
http://66.102.7.104/search?q=cache:6BDCNju7r8wJ:www.sou.edu/biology/Courses/Bi332/BaldaufDoolittle1998.pdf+A+monophyletic+polyphylet ic+archaeal+domain+versus+the+%27eocyte+tree%27&hl=en

"Perhaps the most satisfying support for the eocyte theory has come from sequence analyses of EF-1 genes to reconstruct the tree of life. This is paraticularly true in the last several years, as more sophisticated tree reconstruction algorithms have been developed, and as new methods have been devised to correct for the variation of evolutionary rates at different nucleotide positions within a sequence. During the 1990's, many analyses of EF-1 , as well as EF-G and 16/18S rRNAs, have supported the eocyte tree, in contrast to the situation in the late 1980's. A representation of the results obtained can be seen by clicking here. In support of the eocyte theory, virtually every recent analysis of EF-1 sequence has supported the eocyte theory and rejected the archael theory."

from "Recent Analyses Show the Eocyte Tree to be Correct"
http://genomics.ucla.edu/eocyte/eotree.html

"The phylogenetic position of Methanopyrus kandleri has been difficult to determine because reconstructions of phylogenetic trees based on rRNA sequences have been ambiguous. The most probable trees determined by most algorithms place the genus Methanopyrus at the base of a group that includes the halobacteria and the methanogens and their relatives, although occasionally some algorithms place this genus near the eocytes (the hyperthermophilic, sulfur-metabolizing prokaryotes), suggesting that it may belong to this lineage."

Abstract from "The phylogeny of Methanopyrus kandleri, " by MC Rivera and JA Lake, International Journal of Systematic Bacteriology, by Vol 46, 348-351, 1996.
http://ijs.sgmjournals.org/cgi/content/abstract/46/1/348

"To date, some analyses have supported monophyly of the Archaea, and some have placed the eocyte Archaea as sister taxa to Eukaryotes. This lack of resolution results partly from the fact that the inference depends on distantly related sequences that are difficult to align.... The 5S rRNA left the location of the eocyte Archaea unresolved on the tree. However,based on EF-Tu/EF-1α, we find strong evidence against monophyly in that the eocytes areplaced as sister taxa to the Eukaryotes. Furthermore, we find strong supportthat the remaining Archaea are also paraphyletic. Our strong support for this topologystems from our methodology’s use of evidence from common indels shared by eocytes and Eukaryotes."

from "Joint Bayesian Estimation of Alignment and Phylogeny," by Benjamin D. Redelings and Marc A. Suchard.
http://66.102.7.104/search?q=cache:jTaGri8gYEAJ:recomb04.sdsc.edu/posters/bredelinATucla.edu_295.pdf+eocyte&hl=en

"Several competing theories have been proposed to ex-plain the origin of eukaryotic nuclear genes. Accordingto one of these, the eocyte theory, the nu-clear genes for translation are most closely related to those of eocyte prokaryotes (hyperthermophilic prokar-yotes living at near-boiling temperatures that typicallyobtain energy by reducing sulfur using H2). In contrast,the archael theory posits that eukaryotes are most closely related to a common ancestor of the halobacteria, methanogens, andeocytes (crenarchaeota) and are therefore equally related to all three.... from three eukaryotes, two eocytes, two halobacteria, and two eubacteria (taxa described in Methods), we grouped sites evolving at similar rates....When all replacement sites were analyzed (i.e., allsites with substitution rates 0.58), the bootstrap support for the archael tree was 54% and that for the eocyte tree was 46%....However, when trees were calculated with the more rapidly evolving sites removed, support for the eocyte tree increased, while that for the archael tree diminished.

from "Optimally Recovering Rate Variation Information from Genomes andSequences: Pattern Filtering," by James A. Lake.
http://66.102.7.104/search?q=cache:UrE-mtVFWJEJ:www.evogenomics.org/Publications/lake1998.pdf+eocyte&hl=en

"We present a testable model for the origin of the nucleus, the membrane-bounded organelle that defines eukaryotes. A chimeric cell evolved via symbiogenesis by syntrophic merger between an archaebacterium and a eubacterium. The archaebacterium, a thermoacidophil resembling extant Thermoplasma, generated hydrogen sulfide to protect the eubacterium, a heterotrophic swimmer comparable to Spirochaeta or Hollandina that oxidized sulfide to sulfur."

from "The chimeric eukaryote: Origin of the nucleus from the karyomastigont in amitochondriate protists" by Lynn Margulis, Michael F. Dolan, and Ricardo Guerrero., colloqium, Proc. Natl. Acad. Sci. USA. 2000 June 20; 97 (13): 6954–6959
http://bioinformatica.uab.es/biocomputacio/treballs02-03/S_Serrano/articulo%20nucleo.htm

"THE CHIMERA: ARCHAEBACTERIUM\EUBACTERIUM MERGER
Study of conserved protein sequences [a far larger data set than that used by Woese et al. (1990)] led Gupta (1998a) to conclude “all eukaryotic cells, including amitochondriate and aplastidic cells received major genetic contributions to the nuclear genome from both an archaebacterium (very probably of the eocyte, i.e., thermoacidophil group and a Gram-negative bacterium . . . [t]he ancestral eukaryotic cell never directly descended from archaebacteria but instead was a chimera formed by fusion and integration of the genomes of an archaebacerium and a Gram-negative bacterium” (p. 1487). The eubacterium ancestor has yet to be identified."

from "Variation and Evolution in Plants and Microorganisms: Toward a New Synthesis 50 Years after Stebbins," (2000) National Academy of Sciences (NAS).
http://books.nap.edu/books/0309070996/html/24.html

"We have thus revisited all composite protein trees thathave been used to root the universal tree of life up to now(elongation factors, ATPases, tRNA synthetases, car-bamoyl phosphate synthetases, signal recognition particle proteins) with updated data sets. In general, the two prokaryotic domains were not monophyletic with several aberrant groupings at different levels of the tree."

"The universal ancestor is not a discrete entity. It is, rather, a diverse community of cells that survives and evolves as a biological unit. This communal ancestor has a physical history but not a genealogical one. Over time, this ancestor refined into a smaller number of increasingly complex cell types with the ancestors of the three primary groupings of organisms arising as a result.

No consistent organismal phylogeny has emerged from the many individual protein phylogenies so far produced.

Phylogenetic incongruities can be seen everywhere in the universal tree, from its root to the major branchings within and among the various taxa to the makeup of the primary groupings themselves. Yet there is no consistent alternative to the rRNA phylogeny, and that phylogeny is supported by a number of fundamental genes. The aminoacyl-tRNA synthetases (aaRSs) epitomize this confused situation. For example, it is common to see archaeal versions of some of the aaRSs scattered throughout the Bacteria. The aaRSs can in principle be used to root the universal tree (because some of them obviously reflect common ancestral gene duplications). Yet different (related) aaRSs root that tree differently: the ileRS tree roots (using the valRSs) canonically; i.e., the Archaea and eukaryotes are sister groups. The valRS tree, however, roots on the archaeal branch, which makes sister groups of the Bacteria and eukaryotes. Exceptions to the topology of the rRNA tree such as these are sufficiently frequent and statistically solid that they can be neither overlooked nor trivially dismissed on methodological grounds. Collectively, these conflicting gene histories are so convoluted that lateral gene transfer is their only reasonable explanation.

The further back in evolutionary time we look, the more the notion of an "organismal lineage"indeed, the very definition of "organism" itselfcomes into question. It is time to release this notion of organismal lineages altogether and see where that leaves us. Let molecular phylogenetic trees represent exactly what they in the first instance do represent, histories of individual genes or gene groupings. When do individual gene histories define an organismal history, an organismal lineage? Did organismal lineages even exist at the time of the universal ancestor? If not, then what exactly was this ancestor, and what was the nature of the evolutionary process that formed it?

Primitive Cells: Progenotes.....At this stage, only small proteins could evolve along with any larger, imprecisely translated ones that the primitive cell was able to produce and use. Entities in which translation had not yet developed to the point that proteins of the modern type could arise have been termed "progenotes," and the era during which these were the most advanced forms of life, the "progenote era."

There are different ways of looking at such a community of progenotes. On the one hand, it could have been the loose-knit evolutionary (genetic) community just discussed. On the other, it could have been more like a modern bacterial consortium, with cells cross-feeding one another not only genetically but also metabolically. Cell-cell contacts would have facilitated both processes. In both views of the community, the latter in particular, it is not individual cell lines but the community of progenotes as a whole that survives and evolves. It was such a community of progenotes, not any specific organism, any single lineage, that was our universal ancestora genetically rich, distributed, communal ancestor."

from "The universal ancestor," by Carl Woese, "Evolution," Vol. 95, Issue 12, 6854-6859, June 9, 1998.

So where do we go from here?

Sorry mate, but apparently you don't quite understand what you are talking about.
Traditionally archae were assumed to be the precursors, and originally they were thought to be bacteria themselves,

Yes archaea were believed to be bacterial precursors. A looong time ago so actually this is not a of interest here.

but they are unicullar microorganisms also found in extreme hot environments (thermophiles).

Well, here it is obvious that you know the words but maybe you are confused about the implications/meanings? Archaea are unicellular organisms, but so are bacteria and protists. Furthermore a number of (eu-)bacteria are also thermophiles. So basically in this sentence there is still no distinction between bacteria and archaea.


Then the debate shifted to where they came from and how and where the amino acids came from that created them.

Now this is pure nonesense. First they were not created by amino acids (do you know what that is btw?) and it was clear that archaea and bacteria share a common ancestor. The real question was always whether archaea are monophyletic (that is, all archaea are derived from a single ancestor.

Now the shift seems to be going to eocytes as the precursor to the origin of life and the tree of life. Eocytes are also thermophile bacteria.

OK and the eocyte theory is something completely different again. It deals with the phylogeny of eukaryotes. Not that of bacteria nor does it deal with the origin of life. BTW do you know what the tree of life is? Not, as you suggest the depiction of the origin of life but the modelling of the phylogenetic relationship of extant organisms. The eocyte theory states that that archaea are not a true monophyletic group but that one group, the Crenarchaeota (eocytes), are closer to the eukaryotes.

While you do give nice links and quotes, it would be helpful, if you would at least try to understand them. In fact, so far you (and me too, as I unfortunately joined in) were merely discussing phylogeny of extant prokaryotes. None of this has any impact on the Miller/Urey experiment or the origin of life. I suppose if you really want to discuss phylogeny you should start a new thread to avoid further off topics.

Eocytes are types of thermophile unicellular prokaryote bacteria considered by some to be the first because of reasons stated above.

If we are talking about the Miller/Urey experiments, then we are talking about the creations of amino acids in a test tube - the precursors to the proteins necessary for RNA transcription and translation to produce DNA.

If we are talking about the tree of life and its origins, we are talking about finding the Last Universal Cellular Ancestor (LUCA) ancestrial to the three main domains: Bacteria, Archaea, and Eukarya. Archaea are now known through genome sequencing not to be bacteria, but to be more closely related to eukarya than they are to bacteria - although some people still refer to the archaebacteria kingdom - so the LUCA would have to either be an ancestrial bacteria or something that came before it. Either way, it was a unicellular prokaryote surrounded by a membrane, lacking a nucleus, but had to possess tRNAs for the transcription and translation and the amino acids necessary for the proteins. These are the "simple" facts.

The question is then, where do we go from here?

Eocytes are types of thermophile unicellular prokaryote bacteria considered by some to be the first because of reasons stated above.

Still wrong. Or let's say misleading. According to one theory one of the first organisms might have shared some features of eocytes, but the eocytes themselves are not one of the first organisms.

One must be careful not to confuse characteristics of an assumed LUCA with taxons that share this feature...
And while we are at it, the latest universal common ancestor is something totally different from the first living thing (which is actually the topic of this thread...).
See for instance in one of the links you provided the eocyte tree http://genomics.ucla.edu/eocyte/eovsarch.gif
Notice how deeply branched the eocytes are with the eukarya in this representation?
Eocytes are a single major group of archaea. According to the eocyte tree however (and this is quite disputed btw) they do not in fact share a common ancestor with the archae but with eukaryotes.
Archaeas on the other hand are actually not considered to be an ancient cell form. As they share certain features with eukaryotes it was even proposed that they may have split from the bacteria at a later time point (that is, the archaea are younger than the bacteria). This is btw. also evident from some of the trees in your links.
One theory for instance argues that there was first a split of bacteria into the Gram-negative and Gram-positive bacteria and then the archaea split from within the Gram-positive.

What is interesting is that in your third paragraph you somewhat contradict your first. In the first you state that an early organism is an eocyte, in the third you are talking about a a common ancestor, which has to be a bacterium....

What are your sources? Can you recommend an up-to-date text that describes the LUCA and the descending phylogenic relationships better, and the first living organism and the consequent ascending phylogeny. The object is to find a place where they meet.

I think the place to look is in sulfur-reducing hyperthermophilic bacteria: unicellular prokaryotes, with a membrane, lacking a nuclues, and containing the amino acids necesserary for the proteins and tRNA for transcription and translation of DNA.

The Eocyte Tree:
-Bacteria
--Halobacterium Volcanii---Methanococcocus, ----Thermocococcus
--Karyotes (---Archae, ---Eukaryotes)

see: http://genomics.ucla.edu/eocyte/eovsarch.gif

Again: ""Several competing theories have been proposed to ex-plain the origin of eukaryotic nuclear genes. According to one of these, the eocyte theory, the nuclear genes for translation are most closely related to those of eocyte prokaryotes (hyperthermophilic prokar-yotes living at near-boiling temperatures that typicallyobtain energy by reducing sulfur using H2). In contrast,the archael theory posits that eukaryotes are most closely related to a common ancestor of the halobacteria, methanogens, andeocytes (crenarchaeota) and are therefore equally related to all three.... from three eukaryotes, two eocytes, two halobacteria, and two eubacteria (taxa described in Methods), we grouped sites evolving at similar rates....When all replacement sites were analyzed (i.e., allsites with substitution rates 0.58), the bootstrap support for the archael tree was 54% and that for the eocyte tree was 46%....However, when trees were calculated with the more rapidly evolving sites removed, support for the eocyte tree increased, while that for the archael tree diminished.

from "Optimally Recovering Rate Variation Information from Genomes andSequences: Pattern Filtering," by James A. Lake.
http://66.102.7.104/search?q=cache:...df+eocyte&hl=en

""Perhaps the most satisfying support for the eocyte theory has come from sequence analyses of EF-1 genes to reconstruct the tree of life....In support of the eocyte theory, virtually every recent analysis of EF-1 sequence has supported the eocyte theory and rejected the archael theory."

from "Recent Analyses Show the Eocyte Tree to be Correct"
http://genomics.ucla.edu/eocyte/eotree.html

"The most probable trees determined by most algorithms place the genus Methanopyrus at the base of a group that includes the halobacteria and the methanogens and their relatives, although occasionally some algorithms place this genus near the eocytes (the hyperthermophilic, sulfur-metabolizing prokaryotes), suggesting that it may belong to this lineage."

Abstract from "The phylogeny of Methanopyrus kandleri, " by MC Rivera and JA Lake, International Journal of Systematic Bacteriology, by Vol 46, 348-351, 1996.
http://ijs.sgmjournals.org/cgi/cont...stract/46/1/348

I am not saying that eocytes are the LUCA and I did not say that they were one of the first organisms, but I have found no other tree of life anywhere that tries to root it with anything farther back than that of the eocytes. If the eocytes are not the closest organism to thermophile bacteria than please update my information by giving me the sources that define it differenty.

Let's get on the right track - the same track! - so that we can both progress and learn from there. You keep saying "wrong," "wrong again," and do nothing but criticize without offering up anything better. I keep telling you, so now where do we go from here? And you have yet to answer that question. I think the goal is to try and conect or root the LUCA with the first living thing. If that is possible?

*sigh* actually everything you need is in mosf of your links. You just happen to misinterpret them. i don't have the time to go to everything point by point again, but here are some pointers.

First: Eocyte vs. archae tree:

everal competing theories have been proposed to ex-plain the origin of eukaryotic nuclear genes.
See? Here you write yourself that the eocyte theory is trying to explain the formation of eukaryotic cells. But you keep saying that they were thusly the ancestral organisms which is clearly wrong. You do know what eukaryotic cells are, don't you?
You have to understand that all your quotes regarding eocytes and archae are dealing with the phylogenic relationship between bacteria and archae, as well as archae (or rather the eocyte group) with eukaroytes. Nothing more. These theories are as such not dealing with the origin of life as the thread was about (as I repeat now for the third time). As such all your further links only argue for a closer relationship with eocytes to eukarya and that's it. And even this and several other older theories are disputed, if you look at other papers: e.g. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15965028&query_hl=39
as horizontal gene transfer have been largely ignored in the older studies.
So basically our discussion has no impact on the topic of this thread.
Reiterating the same stuff again and again (and even putting in links which are not in context with your arguements) won't change that.

I am not saying that eocytes are the LUCA and I did not say that they were one of the first organisms,

So and what is that?

The origin of life on earth is 3.8 billion years ago and started with archaebacteria
Now the shift seems to be going to eocytes as the precursor to the origin of life and the tree of life. Eocytes are also thermophile bacteria.

Now, to me this appears to be a rather fruitless discussion. The fact that you keep misinterpreting the quotes you give, give me the impression that you don't know the basics regarding phylogeny for instance.
So basically the information or links you give are not wrong. But you seemingly either didn't read them yourself or don't understand them. Sorry, but if you want an introduction to phylogenic relationships I'd recommend a textbook first.

"James Lake and co-workers have lately proposed a radical re-structuring of the "universal" phylogenetic tree, to split Archaea into Halobacteria, Methanogens and Eocytes. This would mean there are three major groupings of prokaryotes (Eubacteria + Halobacteria, Methanogens and Eocytes), which could all constitute kingdoms on their own, given each is as unrelated to the others as any are to Eukarya."

picture of the tree is at http://www.mcb.uct.ac.za/tutorial/unitree.gif

"The Eocyte Tree Makes Sense

A number of fundamental molecular properties have been thought to have an idiosyncratic distribution on the tree of life, principally because they did not fit the archael tree. Yet these same molecular properties fit the eocyte theory perfectly. This is particularly true for the organization of ribosomal rRNA operons.

Because small subunit ribosomal RNA sequences are the standard for defining the phylogenetic positions of organisms, a large data base of ribosomal RNAs exists and one knows far more about the organization of ribosomal operons than about any other operons. Eubacteria, halobacteria, methanogens, and eocytes contain three rRNAs, 16S, 23S, and 5S, which are homologous to the eukaryotic 18S, 5.8S+28S, and 5S. (For simplicity we will refer to both the eukaryotic and prokaryotic homologues using the prokaryotic labels.) The number of ribosomal rRNA transcriptional units varies between one and four in the halobacteria and the methanogens. Ribosomal operons are arranged in the same general pattern in eubacteria, halobacteria, and methanogens, namely 16S-tRNA-23S-5S. Occasionally an additional tRNA gene will be found between the 16S and 23S genes or following the 5S gene (reviewed in Brown, Daniels, & Reeve, 1989). Thermoplasma, which routinely clusters in phylogenetic trees with the methanogens, is an exception to this general rule and unlike any other prokaryote. Thermoplasma contains unlinked 16S, 23S and 5S genes (Tu & Zillig, 1982). The pattern in eocytes and eukaryotes is different from the eubacteria, halobacteria, and methanogens. In the eocytes, the 16S-23S genes are linked without a tRNA spacer and there is a variable linkage of 5S rRNA encoding genes to the 16S-23S unit. The non-operon-associated 5S rRNA gene of D. mobilis forms its own transcriptional unit (Kjems & Garrett, 1988), but those of many other eocytes contain a 16S-23S-5S transcriptional unit. The eukaryotic pattern is similar with a 16S-23S (equivalent) transcription unit lacking tRNA spacers and with the 5S either separately transcribed or linked (Gerbi, 1985). An exception to this rule is found among the Cryptomonads where the rRNA genes are unlinked (Gray, 1992).


Although it can not be easily explained by the archaebacterial theory, this pattern of rRNA operon organization fits the eocyte tree well. [Click to see the tree.] Only a single change of operon type is required to accommodate this distribution on the eocyte tree. Namely, the 16S-tRNA-23S-5S pattern found in eubacteria, halobacteria, and methanogens is substituted by the derived 16S-23S type at the position on the tree shown by the box. Depending upon the operon organization in Methanopyrus (presently unknown), the site of the box will be either before or after Methanopyrus branches. In either case, only a single change will be required. The archael tree, does not explain this distribution, unless one postulates multiple independent creations of operon types. Since ribosomal operon organization is generally regared as being a slowly evolving character, this again lends considerable support to the eocyte theory.

The Universal Tree of Life

Because of the long branch attraction artifacts, we searched for molecular sequences which contained structural features, such as inserted segments. Since the insertion of segments happens much less frequently than individual nucleotide changes, they are much less sensitive to long branch artifacts, and can, therefore, be more easily interpreted.

The molecule we chose to study was protein synthesis elongation factor EF-Tu (EF-1 in eukaryotes), (Rivera & Lake, 1992). EF-Tu is an ubiquitous protein that transports aminoacyl-tRNAs to the ribosome and participates in their selection by the ribosome. Within the GDP-binding domain of EF-Tu, the amino acid sequence, KNMITG 94 , which is strictly conserved in EF-1 and EF-Tu sequences, terminates an -helix and is followed by a -strand that is terminated by GPMP 113 at the GDP binding site. The sequence QTREH 118 then starts a 3 10 helix. The amino acid motifs of the eukaryotic EF-1 are similar, except that the four-amino acid sequence GPMP 113 in prokaryotes is replaced by the 11-amino acid sequence GEFEAGISKDG, and its variants, in eukaryotes, as shown below.

Taxon Organism Left
Sequence 11 a. a.
Segment 4 a. a.
Segment Right
Sequence

Eukaryotes Human KNMITG TSQADCAVLIVAAGV GEFEAGISKNG QTREH

" Tomato KNMITG TSQADCAVLIIDSTT GGFEAGISKDG QTREH

" Yeast KNMITG TSQADCAILIIAGGV GEFEAGISKDG QTREH

Eocytes P.occu. KNMITG ASQADAAILVVSARK GEFEAGMSAEG QTREH

" D.muco. KNMITG ASQADAAILVVSARK GEFEAGMSAEG QTREH

" A.infe. KNMITG ASQADAAIIAVSAKK GEFEAGMSEEG QTREH

" Su.sol. KNMITG ASQADAAILVVSAKK GEYEAGMSAEG QTREH

Methanogens T.celer KNMITG ASQADAAVLVVAVTD ---GVMP QTKEH

& Relatives Mc.van. KNMITG ASQADAAVLVVNVDD AKSGIQP QTREH

Halobacteria H.maris KNMITG ASQADNAVLVVAADD ---GVQP QTQEH

Eubacteria Tt.mar. KNMITG AAQMDGAILVVAATD ---GPMP QTREH

" S.plat. KNMITG AAQMDGAILVVSAAD ---GPMP QTREH

" Mitoch. KNMITG AAQMDGAIIVVAATD ---GQMP QTREH

Since the eukaryotic 11 amino acid insert is so well conserved among eukaryotic sequences we thought that eocyte sequences might also contain the 11 amino acid insert. Using the polymerase chain reaction and DNA primers designed for use with the KNMITG and QTREH sites, we amplified, cloned, and sequenced the insert region. The eocyte amino acid sequences, translated from DNA, shared the eukaryotic motif (11 amino acids) rather than that found in methanogens, halobacteria, and eubacteria (4 amino acids). The longer 11-amino acid segment, present in eocytes and eukaryotes, shares little similarity with the shorter, four-amino acid segment found in other prokaryotes.

Based on these results, we could directly test the eocyte and archael theories for the origin of the nucleus. [Click on the trees to the left to get a higher resolution image.] The fundamental difference between these two theories is that in the eocyte tree (at the top of the figure) the eukaryotic nucleus shares a most recent common ancestor solely with the eocytes, whereas in the archaebacterial theory eocytes are no closer to eukaryotes than are methanogens or halobacteria, since they are all included within archae.

We have mapped the changes onto the trees representative of both theories. Starting from the four amino insert at the root of the tree, each solid box indicates a change from the four-amino acid segment to the 11-amino acid form. The eocyte tree is favored because it requires only a single change, whereas the archaebacterial tree requires two independent but identical changes. (The archael tree could also be explained by one appearance of the 11-amino acid form and one reappearance of the 4-amino acid form, but even so, two changes would be required.)

Several lines of reasoning buttress the interpretation that eocytes are the closest relatives of the eukaryotes. First, the 11-amino acid segments present in eocytes and eukaryotes are very likely homologous. Eight of eleven amino acids (seven in Sulfolobus and Acidianus) are identical to the consensus eukaryotic sequence. Amino acid shuffling of the segments produced random alignments that score 6-7 standard deviations lower than those found for the eukaryotic-eocyte alignment, thereby implying homology (Waterman & Eggert, 1987). Second, the alignments are well defined. No gaps are needed to align the eukaryotic and eocytic EF-1 sequences, and no gaps are needed to align the eubacteria, methanogen, and halobacterial sequences. Third, the sequences encoding EF-1 are not likely to have been laterally transferred between organisms, since EF-1 is present in all cells and, during protein synthesis, interacts with cellular components encoded by genes dispersed throughout the bacterial genome, including aminoacyl-tRNAs, ribosomal proteins, elongation factor EF-Ts, and 16S and 18S ribosomal RNAs. These results lend strong support to the proposal that the eukaryotes and eocytes are sister taxa within the tree of life.

Recent Analyses Show the Eocyte Tree to be Correct

Perhaps the most satisfying support for the eocyte theory has come from sequence analyses of EF-1 genes to reconstruct the tree of life. This is paraticularly true in the last several years, as more sophisticated tree reconstruction algorithms have been developed, and as new methods have been devised to correct for the variation of evolutionary rates at different nucleotide positions within a sequence. During the 1990's, many analyses of EF-1 , as well as EF-G and 16/18S rRNAs, have supported the eocyte tree, in contrast to the situation in the late 1980's. A representation of the results obtained can be seen by clicking here. In support of the eocyte theory, virtually every recent analysis of EF-1 sequence has supported the eocyte theory and rejected the archael theory.

Conclusions

Of all the genes functioning in translation that have been sequenced to date, the EF-Tu molecule seems to offer the most reliable indication of early divergences. Genome analyses show it is the slowest evolving sequence of its class and should, therefore, be the most reliable for phylogenetic purposes. It is also unlikely to be laterally transferred between organisms because it is present in all cells and, during protein synthesis, interacts with cellular components that are dispersed throughout the bacterial genome. Furthermore, direct phylogenetic analyses of this molecule by almost all authors support the eocyte tree. Significant support for the eocyte tree also comes from the observations that eukaryotic ribosomal operons are organized like those of Sulfolobus, Desulfurococcus, and Thermoproteus and not organized like the tRNA containing rRNA operons of halobacteria, methanogens, and eubacteria."

9-13-2000 http://genomics.ucla.edu/eocyte

I have no better up-to-date information on the rooting of the tree of life and the LUCA than this. Do you have more up-to-date information? Sharing?

I am taking a course in phylogeny and vertebrate evolution right now. We are using Kardong's "Vertebrates: Comparative, Anatomy, Function, Evolution," and a substantial amount of supplementary cladistic phylogeny articles and handouts. Why do you think I am posting this? Not to prove a point. Not to argue. Not to be criticized. But to get a firmer grasp of the concepts and foundations and to see if there is anything more recent and up-to-date and more explanatory. From everything I've been reading, the consensus goes with the eocyte tree as being the best phylogenic explanatory cladistic diagram compared to the seemingly outdated archae tree: the two most recent competing views.

Okay, then lets regress back to the buildup of amino acids into proteins and the RNA for transcription and translation for the origin of life. This is the contemporary extension of the Miller/Urey experiments. So what can you say about developments in this area: the origin of life? And where do we go from here?

Current experiments, related to Miller/Urey, were carried out by Dr. Albert Eschenmoser. Are you familiar with his experiments?

RNA is supposed to be the predecessor to DNA. So Eschenmoser asked "what is the ancestor of RNA?" He suggests that it may be a nucleic acid called (L)-a-threofuranosyl oligonucleotides, also known as TNA.

"Dr. Albert Eschenmoser chemically synthesized TNA and found that complementary TNA strands can form stable double helices. The TNA strands can also pair up with complementary strands of RNA and DNA. This ability is thought to be one of the requirements of any system that would be considered a possible ancestor of RNA.

Eschenmoser is creating nucleic acids that are structurally similar to RNA. They study the properties of the alternatives, such as TNA, and compare them with corresponding properties of RNA."

http://nai.arc.nasa.gov/news_stories/news_detail.cfm?ID=189

Carl R. Woese way back in the 60's also thought that RNA came first.

Yups, it is in general consensus that RNA predates DNA. However, a few argue that due to its instability RNA is not a likely candiate.

Well, I didn't want to go off-topic, but if you really are interested in newer phylogenetic analyses (the book you provided deals more with comparative anatomy, from what I've seen, and does not deal with prokaryotes in depth at all) check this for instance. if you are in an uni you should be able to get the full text easily.:

Proc Natl Acad Sci U S A. 2005 May 3;102 Suppl 1:6608-13. Epub 2005 Apr 25. Related Articles, Links
Click here to read
Decoding the genomic tree of life.

Simonson AB, Servin JA, Skophammer RG, Herbold CW, Rivera MC, Lake JA.

Molecular Biology Institute, Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, 90095, USA.

Genomes hold within them the record of the evolution of life on Earth. But genome fusions and horizontal gene transfer (HGT) seem to have obscured sufficiently the gene sequence record such that it is difficult to reconstruct the phylogenetic tree of life. HGT among prokaryotes is not random, however. Some genes (informational genes) are more difficult to transfer than others (operational genes). Furthermore, environmental, metabolic, and genetic differences among organisms restrict HGT, so that prokaryotes preferentially share genes with other prokaryotes having properties in common, including genome size, genome G+C composition, carbon utilization, oxygen utilization/sensitivity, and temperature optima, further complicating attempts to reconstruct the tree of life. A new method of phylogenetic reconstruction based on gene presence and absence, called conditioned reconstruction, has improved our prospects for reconstructing prokaryotic evolution. It is also able to detect past genome fusions, such as the fusion that appears to have created the first eukaryote. This genome fusion between a deep branching eubacterium, possibly an ancestor of the cyanobacterium and a proteobacterium, with an archaeal eocyte (crenarchaea), appears to be the result of an early symbiosis. Given new tools and new genes from relevant organisms, it should soon be possible to test current and future fusion theories for the origin of eukaryotes and to discover the general outlines of the prokaryotic tree of life.


Newer findings are in favour of a "ring of life" due to the high amount of horizontal gene transfer.

Dr. James Lake, who I keep referring to about the Eocyte Tree, says that this tree is a ring of life: the genomes of the ring of life are from two yeasts, a proteobacterium, a hallobacterium, an eocyte, and a bacilli. He says that "an endosymbiosis between two prokaryotes is probably the mechanism responsible for the genome fusion." He also says something earlier in the paper that "the yeast lineage is the fusion product of prokaryotes."

This is a very recent theory and everything written on it always only refers back to him and no one else, except him and his coworkers. I know what lateral gene transfer is but I do not yet have a firm grasp on HGT, genome fusion, or what bootstrap analyses is. Either way they always refer back to an ancient proteobacteria.