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A Question on Abiogenesis

volatile

Scholar and a Gentleman
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Aug 19, 2006
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Dear JREF,

I know there are plenty of you more well versed in evolutionary theory than I am, and so I wondered if you could help with a question that just popped into my head. I was listening to a radio interview with a guy who's a specialist in mammalian extinction, and is particularly concerned in raising the conservation profile of number of endangered species with unique evolutionary traits such as the elephant shrew or the yangtze dolphin.

Anyway, he was talking about how species survive and mentioned that "all species alive on the planet today are the result of a lineage of survival that goes back to the moment at which life first began". From this, I undersand that the model is of a single moment of abiogenesis - there was a one-off event which created a single proto-lifeform, a single "cell", which then evolved into everything else.

What I was wondering, though, if evolution could have begun more than once. Could the "soup" of inorganic chemicals which gave rise to organic life have happened more than once, or in more than once place?
 
What I was wondering, though, if evolution could have begun more than once. Could the "soup" of inorganic chemicals which gave rise to organic life have happened more than once, or in more than once place?

It could have, especially depending upon what you decide "happened." Perhaps there were many competing forms of life, but one particular strain won. Perhaps there were many competing forms that ended up merging (a la Lynn Margolis). But there are enough similarities among various life forms that it all looks pretty much the same from a chemical point of view -- enough to make multiple independent abiogenesis events unlikely.

For example, why is all life -- down to viruses -- DNA/RNA based? Why does it all use a three-triplet codon, not two or four? Why does it all use the same set of 20 amino acids out of the thousands or millions of amino acids possible? Why does it use the same base pairs in DNA/RNA? Why is the chirality the same across all life forms? And, perhaps most devastatingly, why does all life follow the same "genetic code" (correspondence between DNA/RNA base codons and amino acids)?

The easiest explanation is a single abiogenesis event. Anything else gets complicated and therefore unlikely.
 
Unless there is something about the physical and chemical environment back then that forced all abiogenesis events to produce the same results. That is a more complex explanation, however.

It's also possible that there were multiple lifeforms, but competition knocked off all but one.

~~ Paul
 
The easiest explanation is a single abiogenesis event. Anything else gets complicated and therefore unlikely.

Unless one invokes coevolution between our early (and distinct) abiogenetic ancestors. If these facts are not independent, but are instead the results of a selective process, they cease to be unlikely.

As always, one of the best resources on this (or any) evo-devo is The TalkOrigins Archive
 
As Drkitten says, the fact that every form of life we have found uses the same code makes it extremely unlikely that more than one event started life. Recently there have been discoveries of a few things that use a couple of different amino acids and/or base codons, but these are extremely rare and can easily be explained by simple mutation, and the fact that all the other parts of their genetics are identical to everything else supports this.

There are in fact hypotheses that would involve multiple abiogenesis events. Dawkins describes one on one of his books (possibly The Blind Watchmaker) where self-replicating clays could form a scaffolding that eventually helped modern life form. Whatever the case, it is also important to remember that we will never know how life started. It is possible that life formed millions of times, and indeed still could be, but since there is one type of life that became successful all the other have been wiped out, along with any record of them. Bear in mind that there is no record of life, apart from possibly trace elements in rocks, for hundreds of millions of years after we think life started. Anything could have happened in this time, and we will never know about it.
 
I heartily dispute that anything involving natural selection is complicated. NS is possibly the simplest theory in science: -

Living things make other living things.
These new living things are very much like the things that made them.
Some living things die easier than other living things.

Everything else is just 'details'.
;)
 
Dear JREF,

I know there are plenty of you more well versed in evolutionary theory than I am, and so I wondered if you could help with a question that just popped into my head. I was listening to a radio interview with a guy who's a specialist in mammalian extinction, and is particularly concerned in raising the conservation profile of number of endangered species with unique evolutionary traits such as the elephant shrew or the yangtze dolphin.

Anyway, he was talking about how species survive and mentioned that "all species alive on the planet today are the result of a lineage of survival that goes back to the moment at which life first began". From this, I undersand that the model is of a single moment of abiogenesis - there was a one-off event which created a single proto-lifeform, a single "cell", which then evolved into everything else.

What I was wondering, though, if evolution could have begun more than once. Could the "soup" of inorganic chemicals which gave rise to organic life have happened more than once, or in more than once place?

It is true that one can build a tree of life for advanced organisms (multicellular organisms) and place them onto an evolutionary hierarchy. This is consistent with the notion that all these things arise from the same root stock. However, it is much less clear that one can build a similar tree for the prokaryotes - bacteria, blue green algae and archea, for example. In fact, I understand that it is rather difficult to arrange those organisms onto a single tree with a single root.

For this, and for other reasons, I think it is better to try to understand abiogenesis as the outcome of a prebiotic evolutionary process rather than as the product of a single creative event.
My own analysis of this problem can be found on the files available under the prebtiotic evolution link of my web site
http://www.sexandphilosophy.co.uk
 
However, it is much less clear that one can build a similar tree for the prokaryotes - bacteria, blue green algae and archea, for example. In fact, I understand that it is rather difficult to arrange those organisms onto a single tree with a single root.

Several published trees do just this.

Starting from LUCA, the (hypothetical) ancestor of eubacteria and archaea, with archaea later branching to produce the eukaryotes (Stetter and Huet?).
 
For this, and for other reasons, I think it is better to try to understand abiogenesis as the outcome of a prebiotic evolutionary process rather than as the product of a single creative event.
My own analysis of this problem can be found on the files available under the prebtiotic evolution link of my web site
http://www.sexandphilosophy.co.uk

But this is not any different, all you are doing is moving the opoint at which you declare something to be life. Evolution cannot occur without self-replication, and it is the point where self-replication occurs and evolution is possible that most people would call abiogenesis. All you seem to be saying is that that point wasn't the start of life and the self-replicating thingies evolved a bit into a few different forms, at which point you declare them alive. You are not saying anything new or different, and appear to be arguing either simply for the sake of it or from a severe lack of understanding.
 
Anyway, he was talking about how species survive and mentioned that "all species alive on the planet today are the result of a lineage of survival that goes back to the moment at which life first began".
His statement actually goes a bit beyond the evidence we have now, but a dramatic statement can be made: All complicated life, virtually everything large enough to see, can be traced back to a common ancestor that lived about 1.3 billion years ago. To be specific, the complicated life is the branch call the Eukaryotes. And someone already pointed out that there are branches of more primitive organisms which haven't been completely organized yet so we can't make complete assertions about their ancestry. And some of them exchange genes in ways that are going to make analyzing their ancestry a bit more difficult. And the earliest two or three billion years of life really haven't left enough evidence for us to know if they are related to the life of today.
 
But this is not any different, all you are doing is moving the opoint at which you declare something to be life. Evolution cannot occur without self-replication, and it is the point where self-replication occurs and evolution is possible that most people would call abiogenesis. All you seem to be saying is that that point wasn't the start of life and the self-replicating thingies evolved a bit into a few different forms, at which point you declare them alive. You are not saying anything new or different, and appear to be arguing either simply for the sake of it or from a severe lack of understanding.
Prokarytes are alive.
 
Several published trees do just this.

Starting from LUCA, the (hypothetical) ancestor of eubacteria and archaea, with archaea later branching to produce the eukaryotes (Stetter and Huet?).
I attended a meeting about these things early last year and, my understanding from that meeting was as I have stated, namely that, at present it is hard to construct a tree with a clear root for the prokaryotes. Howeevr, I have no wish to make any great point out of it - by all means correct that misunderstanding.
 
While abiogenesis certainly seems one of the most rational and reasonable explanations, it doesn't necessarily have to be so simple as one 'living' cell one day popping into existence, or that 'life' was created only once.

I would tend to picture a wide variety of proto-cells developing first...not quite what we may consider fully alive, but capable of at least some limited degree of replication. These days, we see plenty of examples of RNA literally swapping genes from one life form to another (a process that plays a role in the adaptation of bird flu from a purely avian disease to one that can also affect humans, for example). I would therefore have little difficulty in seeing this wide variety of different potential models of life swapping information and material with each other. It wouldn't even be necessary that one single life form developed RNA (or some simpler precursor); if we accept a hypothesis of numerous such proto-cells coming into existence, it is also reasonable to assume that such structures could have been developed more than once.

And, in the normal process of evolution, these many different proto-lifeforms would compete with each other, swapping information as they went along, until finally one form developed that got everything right...and ended up being the precursor of life as we know it on this planet. Now, that specific cell -- the one that 'got everything right' -- may well have existed only once. I just don't see it being as simple as "one day there was no life, the next day there was"; I tend to see instead an early pool of incredible diversity, trying out every possible combination and permutation, until finally the one that worked best rose out of the mix, and went on to dominate our planet.
 
As Drkitten says, the fact that every form of life we have found uses the same code makes it extremely unlikely that more than one event started life. Recently there have been discoveries of a few things that use a couple of different amino acids and/or base codons, but these are extremely rare and can easily be explained by simple mutation, and the fact that all the other parts of their genetics are identical to everything else supports this.
That supports the arising of a succesful trait that became predominate. The nature of natural slection can allow for the dismissal of non-optimal forms.
There are in fact hypotheses that would involve multiple abiogenesis events. Dawkins describes one on one of his books (possibly The Blind Watchmaker) where self-replicating clays could form a scaffolding that eventually helped modern life form. Whatever the case, it is also important to remember that we will never know how life started. It is possible that life formed millions of times, and indeed still could be, but since there is one type of life that became successful all the other have been wiped out, along with any record of them. Bear in mind that there is no record of life, apart from possibly trace elements in rocks, for hundreds of millions of years after we think life started. Anything could have happened in this time, and we will never know about it.

Very true and just as in many cases there is the grey line area, how do we say one point is abiogenesis and another is life?

It is likely that there could have been many areas that had pockets of self catalyzing aggregates of chemicals, some would be subject to dispersion and be diluted to the point where they were no longer effective. The biggest question is how they might have become enclosed in a lipid layer. But if the self catalyzing aggregate involes lipid prodoction that becomes more likely.

Most people would not look at a self catalyzing set of chemicals and say 'this is life'. Yet it is possible that is where life started.
 
I attended a meeting about these things early last year and, my understanding from that meeting was as I have stated, namely that, at present it is hard to construct a tree with a clear root for the prokaryotes. Howeevr, I have no wish to make any great point out of it - by all means correct that misunderstanding.

We're probably at cross-purposes. I would probably describe it as too easy to construct such a tree, as there is only a meagre amount of data to be accounted for by any hypothesis.

Hence there are a number of hypothetical trees in the literature that feature a LUCA*, though it is by no means proven that one is required.

AFAIK, a prebiotic abiogenesis is perfectly reasonable hypothesis, be it the latest variant of Cairns-Smith's clays as mentioned by Cuddles, or - I imagine - your own argument (which I admit I haven't got round to reading yet).

* Last universal common ancestor.
 
We're probably at cross-purposes. I would probably describe it as too easy to construct such a tree, as there is only a meagre amount of data to be accounted for by any hypothesis.
<snip>

AFAIK, a prebiotic abiogenesis is perfectly reasonable hypothesis, be it the latest variant of Cairns-Smith's clays as mentioned by Cuddles, or - I imagine - your own argument (which I admit I haven't got round to reading yet).
Yes, on the point of this thread, I think we are in accord. There is, I think, quite a lot of comparative sequence data but there will be no timeline data to speak of.
I will refrain from commenting about clays.
 
There are a number of different threads here that are worth following up on. The most obvious is the question of the original formation of nucleic acids. There is equivocated evidence in favor of the view that this took place more than once; mitochondrial DNA uses a slightly different genetic code than eukaryotes use, and there is a theory called the endosymbiotic theory that is substantiated by genetic analysis showing that their ancestor was a proteobacterium, probably an alpha-proteobacterium; it may have been related to rickettsia, but this last is somewhat controversial. However, it is worth noting that even with such variations (and the mitochondrial variation is only the first among many), the code is so similar across all of Earth's species that it is unlikely to have developed in separate events.

In addition, as I have pointed out elsewhere (and I was not the first to note it), there are many possible genetic codes. How likely an alternate genetic code is to be more (or less!) prone to point defects could be a characteristic subject to natural selection; as could speed of expression, or ease of replication, or other factors that we currently know nothing of. The fact that there are any alternates at all at least hints that this and potentially (likely?) many other factors may have militated toward the code most life forms on Earth use now.

It is also important to keep in mind that the fact that we (that is, living things on Earth) use the same genetic code implies in turn that almost all primary proteins, that is, proteins created directly from amino acids by expression of the genes through transcription into mRNA and protein synthesis from that mRNA by tRNA and ribosomes, are made from the same twenty amino acids. Now, these proteins, depending on their structure, can theoretically create secondary proteins, utilizing other amino acids than the twenty; but by and large, to the best of my knowledge, this process is not used. If someone has an example, I'd love to hear about it.

Now, one of the things to keep in mind about RNA is that it functions in at least three different ways in the eukaryotic cell. First, there is mRNA, made by RNA polymerase from the DNA (and note that the RNA so created is not a duplicate of that DNA strand, but its complement- in other words, a copy of the other side (assuming that the DNA is double-stranded in that spot)). Second, there is rRNA, making up the ribosomes, the "protein factories" of the cell. Third, there is tRNA, which attracts a particular amino acid, and is in turn attracted by a particular codon (i.e., trio of bases) when it is inside the ribosome; tRNA, therefore carries the amino acids to the "factory" where each amino acid is added to the end of the growing protein molecule being "manufactured" by the ribosomes.

But it turns out if you look into it, that unlike DNA, in nature there are many alternate bases used in RNA; quite literally hundreds, in fact. It is by far the more complexly used molecule of the two nucleic acids. RNA also doesn't generally exist as single strands; the attraction for other nucleotides, and the weakness of the single strand, apparently militate against this. The strands are far more than the simple double-helix, however; they encompass the ability for RNA to form complex shapes, shapes which are capable of acting as enzymes (so-called "ribozymes") by doubling or further foldings of the strands onto one another.

So this is not some rare, docile worker molecule, with only one possible purpose; instead, it is a dynamic, active, highly common molecule that has functions woven all through cellular metabolism and reproduction. Molecular biologists are slowly coming to understand how many different roles it can take on. And this is the reason for the proposal of "RNA world." This molecule might, by itself, be capable of forming an autocatalytic network, without any proteins. Such a network would "eat" nucleotides and create new copies of its member RNA strands; this is the minimal functioning of life. I grant that this is currently only a hypothesis, but the evidence it explains is widely spread, and it is extremely plausible. The strongest two pieces of evidence are:
1. While the Urey-Miller experiments did not produce nucleotides, only amino acids, later (and probably more accurate) laboratory simulations of conditions on the early Earth (notably that of Joan Oro) did produce nucleotides.
2. Nucleotides also have been found inside meteorites. This indicates that they may have been formed in the solar nebula, or that they can form from the heat of passage through the Earth's atmosphere at the Earth's orbital speed. In either case, it is clear that they would have been present very early in Earth's history.

Finally, even if it was not RNA itself, but a precursor, such as PNA, or GNA, the above facts still work; and once you have viruses using RNA, and a virus switches to DNA to protect its genes from attack during the cell-invasion-virus-replication process, then you have cells that have DNA in them. And you can't use DNA directly to make protein, it's too delicate; but you CAN use it to make RNA, and of course the virus would have to provide a mechanism for that, encoded in RNA, if it were to survive (since the cell, of course, would have no DNA before then).

So much for "problems" with the plausibility of the RNA world hypothesis.

I'll also point out that autocatalysis among amino acids and the resulting proteins need not be affected by the presence or absence of this "RNA world;" the two need not be combined until a great deal of time had passed.

And finally, it appears that lipid spheres form spontaneously upon exposure to water. That would be why they are so important in the formation of cell membranes. Such lipid spheres are present in carbonaceous chondrites, which are meteorites with a great deal of carbon in them; they are also present in Oro's experiments.

So what do we have?
1. An abundant source of novel amino acids.
2. A source, perhaps not quite so abundant, but perhaps more so, of nucleic acids. (Oro's first major discovery was proving that adenine could be synthesized from ammonium cyanide, a common chemical found in stellar nebulae, and presumably also on the early Earth and in early comets).
3. An abundant source of lipids.
These are the most important ingredients for life. Pardon me for paraphrasing several generations of biologists, but what this looks to me like is a very nice "life soup;" put it on simmer and stir regularly for a few hundred million years.
 
It is likely that there could have been many areas that had pockets of self catalyzing aggregates of chemicals, some would be subject to dispersion and be diluted to the point where they were no longer effective. The biggest question is how they might have become enclosed in a lipid layer. But if the self catalyzing aggregate involes lipid prodoction that becomes more likely.
It seems to me that a lipid-producing aggregate needs a pocket to accumulate in before it can make its own membrane pocket and head off to unexploited pastures. Such pockets must have been very small, which implies a highly fractal environment, which in turn implies a very small chance of the highly-successful independent lipid-membrane-enclosed model of life only happening once. It's equivalent to the argument that life on Earth implies life elsewhere in a galaxy this big, which I also subscribe to. How they interacted is arguably outside the subject of abiogenesis.

To me, the big unknown is the fractal environment that produced membrane-based life. I favour Black Smokers. Highly fractal environment and high entropy gradient.
 

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