What is the origin of life on Earth?

[invert_nexus]

Invert: pessimist

Bullshit. The glass isn't half-empty. It's (oops. Forgot to insert witty comment here. Can't think of one so.... Fuck it. The glass is half-empty.)

We shall solve the origin of life as a consequence of three factors:
1) We shall figure out how to create life, or more precisely engineer the conditions in which it can arise. Your refutation of figuring out by backward analysis may or may not be valid, but it is certainly irrelevant.
2) We shall find other life 'forms out there'. By 'comparing and contrasting' the different life types we encounter, a clearer picture of my 'plausible pathway' will emerge.
3) We shall witness life originating in situ, 'out there'.

How do these solve the origin of life? Yes. They would show how life could form. But not necessarily how life did form.

1.) Why would you call it irrelevant? Why would this irrelevancy be connected to the ability to create and/or engineer life within the laboratory? How could this ever equate to an exact derivation of the precise axioms that led to our particular form of life? Only one method springs to mind. If there were some form of limiting factor that leads back to only a singular method of generation of life. However, even if all research led to this conclusion, how could you ever be sure that there's not some derivation that is just eluding us for the present? This is, of course, the age old problem of induction. How do we justify our knowledge?

I will grant that steps can be taken which make certain theories more plausible than others, and to some extent this argument is... nitpicky. But, at the same time it is vital to our very understanding of the universe and the processes within it and should not be dismissed out of hand as 'irrelevant'.

2. Again. What will this have to do with the origins of our life? I can think of a way. If they somehow turn out to operate on similar if not identical mechanisms. DNA for instance.

3. Yes. But, this doesn't relate to life orginating 'back then'.

In short, the problem of how might life originate is decidable. It's decidable by many means. The problem lies in trying to quantitativly derive our own origins. There will always be another possible derivation.

The paths can be limited through improvements in archeology (not the proper term... What would be the term of digging up ancient life forms?). By finding fossils of ancient life forms closer to the beginnings of life (with their life mechanics intact enough for us to understand their workings) would allow us to delineate this 'plausible' scenario to a much narrower degree. Statistics can also limit the field. But, no matter how far the field is narrowed, there will always be an exceedingly large amount of possible paths of derivation. And none can ever be truly justified.

 

[CharonZ]

One thing that is always on my mind regarding this question is always "what the heck is actually life?"
The "hard" definitions given tend to be derived from observations of organisms which were intuitively identified as living beings. As such these definitions tend to be something of a circular arguement. One of the most open definitions is that life is defined as open thermodynamic systems in competition with each other.

In fact there are (of course) several theories how early life could have been. A general consensus (with few dissents) assume that the RNA-genomes predated the DNA-genomes (that is RNA-world predated DNA-world). One theory assumes that in the RNA-world free RNA-molecules prevailed. These molecules could then be described as “living-molecules” according to the definition given above.
An interesting paper I just found while looking for something else deals with the transition from the RNA to the DNA world. It argues for early RNA-organisms being outcompeted by later DNA-organisms.
A very interesting if controversial (but then what in this field isn’t) read:

The two ages of the RNA world, and the transition to the DNA world: a story of viruses and cells

Abstract

Most evolutionists agree to consider that our present RNA/DNA/protein world has originated from a simpler world in which RNA played both the role of catalyst and genetic material. Recent findings from structural studies and comparative genomics now allow to get a clearer picture of this transition. These data suggest that evolution occurred in several steps, first from an RNA to an RNA/protein world (defining two ages of the RNA world) and finally to the present world based on DNA. The DNA world itself probably originated in two steps, first the U-DNA world, following the invention of ribonucleotide reductase, and later on the T-DNA world, with the independent invention of at least two thymidylate synthases. Recently, several authors have suggested that evolution from the RNA world up to the Last Universal Cellular Ancestor (LUCA) could have occurred before the invention of cells. On the contrary, I argue here that evolution of the RNA world taken place in a framework of competing cells and viruses (preys, predators and symbionts). I focus on the RNA-to-DNA transition and expand my previous hypothesis that viruses played a critical role in the emergence of DNA. The hypothesis that DNA and associated mechanisms (replication, repair, recombination) first evolved and diversified in a world of DNA viruses infecting RNA cells readily explains the existence of viral-encoded DNA transaction proteins without cellular homologues. It also potentially explains puzzling observations from comparative genomic, such as the existence of two non-homologous DNA replication machineries in the cellular world. I suggest here a specific scenario for the transfer of DNA from viruses to cells and briefly explore the intriguing possibility that several independent transfers of this kind produced the two cell types (prokaryote/eukaryote) and the three cellular domains presently known (Archaea, Bacteria and Eukarya).

Source: Patrick Forterre; Biochimie
Volume 87, Issues 9-10 , September-October 2005, Pages 793-803

 

[valich]

The general consensus assumes a RNA-world (RNA ribosome), but other's are looking at self-replicating metabolic pathways (self-replicating organic polymers) that came before it and may or may not include a necessitated RNA-world. The problem with assuming a strictly RNA-world as the origin of life seems to be that you then have to assume that the different RNA sequences and their catalysts - possibly ribozyme? -were created spontaneously on Earth, else without catalysts they could not be self-replicating - which could be true. So some are searching for self-replicating metabolic reactions that include catalysts. The source of the problem seems to be to find the origins of replication in general. Other researchers are focussing on the creation and origin of the lipid bilayer membranes that were able to encapsulate these self-replicating metabolic reactions. I think that bringing these two processes together might solve the problem:

pre-RNA > RNA > DNA + encapsulation = origin of life

see "Prebiotic Chemistry and the Origin of the RNA World," by Orgel, Leslie E. in Critical Reviews in Biochemistry and Molecular Biology, 39, pp.99-121, 2004
www.crbmb.com/cgi/content/abstract/39/2/99

also:

"There are other potential prebiotic pathways being explored for the synthesis of ribose from small phosphorylated aldehydes in the presence of hydroxide minerals under neutral conditions (Krishnamurthy et al., 1999), but equivalent pathways to 2-deoxyribose have not been studied....ribosugar- and deoxysugar acids in the 4.6 x 10+9 year old Murchison meteorite suggest that they may have been present on primitive Earth, derrived from the accretion of extraterrestrial sources (Cooper et al., 2001) or from endogenous processes involving formaldehyde and its derivitatives. It has been argued (Robertson and Miller, 1995; Robertson et al., 1996) that drying lagoon conditions could have acted as a prebiotic reactor....earlier metabolisms, and the existence of an earlier self-replicating molecule precludes the necessity of an (all) RNA world."

from: "The roads to and from the RNA world," by Dworkin, Jason P., et al., Journal of Theoretical Biology 222, pp. 127-134, 2003.

 

[Mr Anonymous]

If the problem i.e. the origin of life, actually lies elsewhere, then it is wholly proper to shift it there....

Which would remain the operative problem. IF.

We simply don't know for anything like a fact that either life or life forming process exists outside of the confines of this world, but we do know for absolute that here it does.

Certainly, on the surface, the idea appear ti suggest tantalising results - but its based on a what if, not a quantitative certainty or necessity that we know of.

Y'say the rapid appearance of life here on Earth presents a problem - longevity in organisms even very basic is a relatively speaking new phenomena life wise. Most of the history of life on Earth has consisted of virus and bacteria - by far still the most successful life strategy the process as a whole has ever undertaken and most likely a direct consequence of the organisms which precursed that very basic, autonomous, function form.

Generations within such organisms pass within weeks, days in some cases. It would be unlikely whatever precursed these kinds of life would be any less expedient in their reproduction and mutation.

Only on the level of cellular and multi-cellular life do we find a gradual elongation of individual life span.

Life itself to a hell of a long time to get to that point.

If we exclude the possibility of life forming autonomously here what we say in effect is that sure, out there, life or life forming process can take place when ever it likes - we may not know or understand the conditions of that process, but what the hey...

But here, on the one world in the entire Universe we do know for absolute fact life exists, couldn't have happened. Not without help from out there.

Its exactly like the old Humans As Alien Experiment argument - on the one hand we appear to explain how man is so very different from all other life native to our world and why there exist so many similarities to these Aliens the notion posits that made us - but on the other hand we're saying the evolution by natural process of a species like our own (albeit older and more technologically advanced) is fine as long as it takes place elsewhere out there on some other world we don't know exists and will never see.

The same occurring here couldn't possibly happen, not without ET's help.

Its a reductionist argument which undermines itself by its own reasoning, Pan Spermia essentially is no different.

 

[Ophiolite]

Sorry Mr Anonymous I disagree with you on virtually every point above. I think we shall simply be arguing in circles. There is absolutely no comparison between pan spermia and 'humans as aliens'.
Despite your platitudes about generation times for early life forms we simply, as you noted, do not know. That means we need to consider all possibilities, especially when we find more and more increasingly complex organic molecules in space. The more we look, the more we find.
And I am unaware of any refutation of Hoyle's observation of the close match of the spectrum of interstellar dust and microbial spores.

 

[Mr Anonymous]

Despite your platitudes about generation times for early life forms we simply, as you noted, do not know.

Well... not wanting to be all contentious and everything but doing it anyway... We do know about short generational development of bacteria and viruses Ophiolite. We're rather suffering the consequences of that with the increasing number of Penicillin resistant bacteria that are cropping up in our Hospitals, equally we've known full damn well about shifting antigen viruses pretty much forever - the common cold being just one example which has plagued us since time immemorial.

Hardly platitudes, just standard knowing things.

Now, in pre-cellular times were looking at Earth as Planet of The Bugs, and this is eons in advance to what preceded it.

Now, if you could possible illuminate us with an acceptable mechanism by which bacteria and viral life forms gradually evolve in to shorter generation life spans rather than being the long lived things the must originally have started as in your contention - please, do, by all means share.

I like to learn and I can't help but feel we'd all profit greatly from your insight here. It sounds fascinating.

Please, expand.

 

[valich]

But here, on the one world in the entire Universe we do know for absolute fact life exists, couldn't have happened. Not without help from out there.

Come on Mr Anonymous. Your reply is exactly why I stated when I started this thread "Please do not offer any extraterrestrial explanations." Then in one reply I said, "because I know where that will lead: UFOs, aliens, etc." Now we all know that amino acids have been found on meteorites, the same as on earth, but unless you can provide proof of "Not without help from out there," then please do not turn this thread into a discussion about extraterrestrial alien life, okay?

 

[Ophiolite]

We do know about short generational development of bacteria and viruses Ophiolite.

Two points:
1) I am talking about the biolgical and pre-biotic developments and the rate at which they occured. If you have some data on that, I'd certainly welcome a chance to examine it.
2) Despite the undoubted complexity of prokaryotes, which for an origin of life on Earth would be required to emerge in a couple of hundred million years, it was a billion years before we got eukaryotes. It was then another billion ros years before we got complex metazoans. The differences between mutli-celled, differentiated organisms, or between prokaryotes and eukaryotes, are much less than the difference between life and non-life. It is therefore logical, unless we can identify a mechanism that would promote this transition, that the life to non-life change needed more time than was available on the Earth.
Now we may come up with such a mechanism. We should certainly be looking. But we should also be looking at the perfectly plausible alternative explanation of pan spermia

.

Now, if you could possible illuminate us with an acceptable mechanism by which bacteria and viral life forms gradually evolve in to shorter generation life spans rather than being the long lived things the must originally have started as in your contention - please, do, by all means share.

Not relelvant for the reasons noted above.

I like to learn and I can't help but feel we'd all profit greatly from your insight here. It sounds fascinating.

Yes, I thought platitudes would generate a burst of your trademark irony, that for most of us is indistinguishable from sarcasm. Are you going to fall for this probe as well?

By the way I am not decrying irony and sarcasm. I use them a great deal. But we both know that most of the time, apart from bringing a smile to the faces of supporters, and raised blood pressure to the detractors, that they contribute very little to the argument. I generally enjoy your posts and find myself agreeing with you a lot more frequently than disageeing. It's just that this time you are wrong.

 

[spuriousmonkey]

The differences between mutli-celled, differentiated organisms, or between prokaryotes and eukaryotes, are much less than the difference between life and non-life.

I would like to see the data on that then.

 

[Ophiolite]

Spurious I am prepared to bow to your greater authority on the matter. But the impression I have gained from reading of textbooks on biology has very much suggested to me that the differences I have identified are the case. I would genuinely welcome your input here since I think this is an important issue and I'm wallowing in the dark a bit. I'd especially like it if you could say why you think the Prokaryote - eukaryote differences are large i.e. larger than the life/non-life difference.

To expand a little further on why I hold the view I do: the change from a non-sustaining, non-replicating, auto-catalytic system is a change of quality. The change from a prokaryote to a eukaryote is more of a quantitative change.
The prokaryote already has its cell membrane. Is it that much of a challenge to add a further membrane for the nucleus? Is it too difficult for a symbiotic relationship too arise between two diverse bacteria, that lead, eventually to one giving up its DNA, as in the case of chloroplasts, or not, as in the case of mitochondria?
I ask these questions as questions, not as rhetorical devices.

 

[Hercules Rockefeller]

…I am prepared to bow to your greater authority on the matter.

I don’t think there is any such thing as an “authority” in this area as it’s mostly all pure speculation. We just don’t know the likelihood of life developing given the right planetary conditions as we have only one example of it happening. Finding life on Mars or Europa or Titan will really ‘throw the cat among the pigeons’.

But I see where you are coming from and I tend to agree. From what we know of cell biology and evolution, the progression from prokaryotic to eukaryotic cells, and from unicellular to multicellular organisms, seems almost inevitable. The progression from inanimate to animate matter seems much less assured. But as we learn more it may turn out that abiogenesis is equally assured given the right conditions. We just don’t know.

By the way…

Is it too difficult for a symbiotic relationship too arise between two diverse bacteria, that lead, eventually to one giving up its DNA, as in the case of chloroplasts, or not, as in the case of mitochondria?

Chloroplasts have not “given up their DNA”; they have their own genome just like mitochondria.<P>

 

[valich]

the change from a non-sustaining, non-replicating, auto-catalytic system is a change of quality. The change from a prokaryote to a eukaryote is more of a quantitative change.
The prokaryote already has its cell membrane. Is it that much of a challenge to add a further membrane for the nucleus? Is it too difficult for a symbiotic relationship too arise between two diverse bacteria, that lead, eventually to one giving up its DNA, as in the case of chloroplasts, or not, as in the case of mitochondria?

Current theory holds that the tree of life is actually a ring of life consisting of multiple unicellular organsims: protobacterium, cyanobacterium, hallobacterium, yeasts, eoctyes, and bacillus. It has been proposed that eukaryotes are the result of "genome fusion" between prokaryotes.

I think it not much of a challenge to imagine encapsulating a nucleus, or a replicating metabolic system, in a membrane. So I think what we have to do is look for the origin of metabolic replicating systems as the origin of life.

The symbiotic relationship between two diverse bacteria that you are referring to is called endosymbiosis: where two living systems are able to live together within one cell. In the case of chloroplasts in one unicellular organism, they were engulfed via way of endocytosis.

 

[cyber_indian]

How about "Archaea" it's a different type of single cell organisam than Bacteria. And are also called "Extremophiles".

Those are quotes:
- Archaeans dine on a variety of substances for energy, including hydrogen gas, carbon dioxide and sulfur. One type of salt-loving archaean uses sunlight to make energy, but not the way plants do it. This archaean has a light-harvesting pigment in the membrane surrounding its cell. This pigment, called bacteriorhodopsin , reacts with light and enables the cell to make ATP, an energy molecule.

- A recent article in Astrobiology Magazine (May 19, 2004) by Leslie Mullen reports that halobacteria may be the oldest life form on earth. Comparisons of small ribosomal RNA sequences indicate that halophilic bacteria are closely related to the methanogens. Both types of bacteria are now classified in the kingdom Euryarchaeota within the Archaea domain. Halophiles need oxygen while methanogens are anaerobic; however, halophiles can produce energy without oxygen in two ways: from the degradation of arginine, and by using the photosynthetic molecule bacteriorhodopsin). It has been suggested that these two methods of anerobic energy production are the last remnants from the halophile's anaerobic ancestry when the earth's atmosphere lacked free oxygen gas more than 2 billion years ago. Another survival adaptation of extreme halophiles is their exceptional resistance to solar radiation.

- Thermococcus gammatolerans - archaeon is nearly as radioresistant as Deinococcus radiodurans, which is capable of withstanding an instantaneous dose of up to 5,000 Gy with no loss of viability, and an instantaneous dose of up to 15,000 Gy with 37% viability. While a dose of 10 Gy is sufficient to kill a human, and a dose of 60 Gy is sufficient to kill all cells in a culture of E. coli.

- Endoliths can survive by feeding on traces of iron, potassium, or sulfur. As water and nutrients are rather sparse, endoliths have a very slow procreation cycle. Early data suggests that some only engage in cell division once every hundred years. As most endoliths are autotroph, they can generate organic compounds essential for their survival on their own from inorganic matter.

- Halobacteria can repair badly damaged DNA. "We have completely fragmented their DNA. ...And they can reassemble their entire chromosome and put it back into working order within several hours," says Adrienne Kish, a member of the research group studying Halobacteria at the University of Maryland. These Archaea can also survive extreme dryness, a hard vacuum, and of course, high salt concentrations. We are not the only ones to notice that Halobacteria could use these capabilities to survive in space.

- The most recent view is that the first cells on earth might have been extreme thermophiles.

- Archaeal photosynthesis - the earliest photosynthetic organisms lived in an anaerobic atmosphere.

 

[Ophiolite]

By the way…
Chloroplasts have not “given up their DNA”; they have their own genome just like mitochondria.<P>

Thank you for the correction. Since the phrase 'mitochondrial DNA' seems to appear in every second paragraph on primate evolution one tends to overlook that it is not unique.

vallich]Current theory holds that the tree of life is actually a ring of life consisting of multiple unicellular organsims: protobacterium, cyanobacterium, hallobacterium, yeasts, eoctyes, and bacillus.

Please explain what you mean by 'a ring of life'.

 

[cyber_indian]

Chloroplasts have not “given up their DNA”; they have their own genome just like mitochondria.<P>

- Human mitochondrial DNA consists of 5-10 rings of DNA and appears to carry 16,569 base pairs with 37 genes (13 proteins, 22tRNAs and two rRNA) which are concerned with the production of proteins involved in respiration. However they all need sub-units created by nuclear DNA in order to work.

 

[valich]

- Human mitochondrial DNA consists of 5-10 rings of DNA and appears to carry 16,569 base pairs with 37 genes (13 proteins, 22tRNAs and two rRNA) which are concerned with the production of proteins involved in respiration. However they all need sub-units created by nuclear DNA in order to work.

Your previous posting is very insightful and does an excellent job of concisely outlining the possible biotic (yet not pre-biotic) origins of life. Great job!

Hercules is not wrong in his posting, but you are elaborating on it. The chloroplasts were engulfed by endocytosis and contained DNA. What are rings of DNA: constructs around the helix?

Current theory is that they do not need sub-units of DNA in order to work, they need the RNA to translate and transcript the info.

 

[cyber_indian]

Dose are not my words - it's all quotes.

Current theory is that they do not need sub-units of DNA in order to work, they need the RNA to translate and transcript the info.

How about the different translations tables ?

<option> 1 Standard
<option> 2 Vertebrate Mitochondrial
<option> 3 Yeast Mitochondrial
<option> 4 Mold, Protozoan, and Coelenterate Mitochondria and the Mycoplasma Code
<option> 5 Invertebrate Mitochondrial
<option> 6 Ciliate, Dasycladacean and Hexamita Nuclear
<option> 9 Echinoderm Mitochondrial
<option> 10 Euplotid Nuclear
<option> 11 Bacterial Code
<option> 12 Alternative Yeast Nuclear
<option> 13 Ascidian Mitochondrial
<option> 14 Flatworm Mitochondrial
<option> 15 Blepharisma Nuclear
<option> 16 Chlorophycean Mitochondrial
<option> 21 Trematode Mitochondrial
<option> 22 Scenedesmus obliquus mitochondrial

http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c

 

[Mr Anonymous]

Come on Mr Anonymous. Your reply is exactly why I stated when I started this thread "Please do not offer any extraterrestrial explanations." Then in one reply I said, "because I know where that will lead: UFOs, aliens, etc." Now we all know that amino acids have been found on meteorites, the same as on earth, but unless you can provide proof of "Not without help from out there," then please do not turn this thread into a discussion about extraterrestrial alien life, okay?

Valich.... For the love of Puppies will you please put your reading specs on before wading in like this? I'm not actually in anyway, shape or form intimating anything like an extraterrestrial explanation - I'm the one pointing out the fundamental flaws in the argument for that sort of nonsense, not advocating it in any way - that's what you've actually quoted. Me not advocating extraterrestrial explanations.

Dear God it's in black and white man....

It's just that this time you are wrong.

.... Personally, I'm perfectly happy to conceed to an eminently more interesting argument than my dull wits are probably capable of today....

My hat off to you.

Besides, Valich just pissed me off royally and here's me holding up his corner... Can I pick 'em or what?

I dunno. Truth be told I don't entirely discount the possibility of Pan Spermia being a possibility - truth of it is my objections largely are just gut. It's all just a tad too slick, somehow too convienient.... y'know?

No reason at all really why complex hydrocarbons can't be formed out there and collected up by passing bodies and so forth - but then you've got here and how the Earth was back then and if you could find a greater antithesis from the conditions such deposited materials would be finding themselves introduced to you'd have to be looking at the surface of a star.

Not quite that extreme I know but really not all that far off.

Processes tempered in that actual fire of that far back giving rise to ever more increasing complexity on the otherhand... It just strikes me that only something forged here would have any possibility of enduring, unless the planet underwent a global cooling off point considerably earlier than anyone currently imagines...

 

[Hercules Rockefeller]

Human mitochondrial DNA consists of 5-10 rings of DNA...

To be more precise, the mitochondrial genome is usually a single circular chromosome (indicative of its bacterial origin). The circular DNA molecule is usually present in multiple copies per organelle (which is probably what you were getting at). The size of the mitochondrial genome and the copy number per organelle varies from organism to organism. The size of the mitochondrial genome is not linear with organism complexity. For example, yeast has a much bigger mitochondrial genome than humans.

Current theory is that they do not need sub-units of DNA in order to work, they need the RNA to translate and transcript the info.

To be more precise, most mitochondrial genomes do not encode the proteins required for DNA replication, transcription, or translation. Instead, the genes that encode proteins required for the replication and expression of mitochondrial DNA are contained in the nucleus.<P>

 

[cyber_indian]

I guess you realize that Bacteria, Humans and etc. have different set of tRNA called also translation tables.