Abiogenesis Update

[bokonon]

We don't know how many metabolic path , or way to pass genetic code there is. We only know two.

I guess we all believe some things without good evidence. I believe there is probably more than one way to encode and replicate genetic material, even though, as you say, we only know of two (which I would say is really one).

If I'm wrong, and DNA/RNA is actually a REQUIREMENT for life, rather than just one way out of many, that would mean abiogenesis is less likely rather than more likely.

So even if my assumption is wrong, my conclusion is more likely to be right.

 

[Skeptic Ginger]

I guess we all believe some things without good evidence. I believe there is probably more than one way to encode and replicate genetic material, even though, as you say, we only know of two (which I would say is really one).

If I'm wrong, and DNA/RNA is actually a REQUIREMENT for life, rather than just one way out of many, that would mean abiogenesis is less likely rather than more likely.

So even if my assumption is wrong, my conclusion is more likely to be right.

Position shifting (my emphasis above) duly noted.

The issue was not how common is abiogenesis. We've all been saying one cannot judge how common or uncommon abiogenesis is until we collect more evidence.

The issue is you claimed that the default position is one should assume abiogenesis is entirely unique in all the Universe until we find evidence it isn't. That position is rather absurd given we've not found anything else to be unique in all the Universe except maybe the Big Bang.

Now I see you've changed your position trying to tell us we don't know abiogenesis occurred more than once and you are now using language consistent with everyone else, "less likely/more likely".

 

[Taffer]

Unbelievable.

It isn't just DNA, it's the code: UAA -> Stop, CUx -> leucine, etc.

I don't think you'll find any reputable scientists who would support your claim that this precise system might have evolved independently "over and over".

Let me stop you there. You are obviously not a geneticist, so I feel I should explain something which seem to be unaware of.

The genetic code, i.e. the codon "values", are not universal. For example, there are variations from the 'universal code' in the human mitochondrial genome, and other mitochondrial and plastid genomes. Further, several bacterial species have been found to use alternative codes. For example, bacteria often use GUG as a start codon, whereas GUG codes for Valine in the 'universal code'. So it is not accurate to say that all living creatures use the same code set, and thus your argument that the use of the same code set is evidence for a single evolutionary event is false.

Furthermore, there is evidence that the code is not a happy random chance, and that the physical properties of amino acids plays a role in the codons which code for it. This suggests that the code set we see is evolutionarily beneficial over a random set, and thus very possibly could be a case of Convergent Evolution^WP.

Wikipedia has a good summary of the main theories of genetic code evolution, none of which exclude convergent evolution of separate evolutionary lines.

 

[bokonon]

I'm convinced abiogenesis was inevitable given the composition and conditions on our planet at the time it occurred, and, think it is inevitable that said conditions are not unique to our planet.

Position shifting (my emphasis above) duly noted.

I see [...] you are now using language consistent with everyone else, "less likely/more likely".

I've been using "likely/unlikely" all along:

Okay, and I think the evidence at this point suggests "not very likely". As far as we know today, there is only one planet in the universe upon which life arose, and on that planet it only arose once.

Which leads me to conclude that life is not only not "inevitable", but is quite likely unlikely.

You can add this to your growing collection of straw men.

Let me stop you there. You are obviously not a geneticist, so I feel I should explain something which seem to be unaware of.

The genetic code, i.e. the codon "values", are not universal. For example, there are variations from the 'universal code' in the human mitochondrial genome, and other mitochondrial and plastid genomes. Further, several bacterial species have been found to use alternative codes. For example, bacteria often use GUG as a start codon, whereas GUG codes for Valine in the 'universal code'. So it is not accurate to say that all living creatures use the same code set, and thus your argument that the use of the same code set is evidence for a single evolutionary event is false.

Furthermore, there is evidence that the code is not a happy random chance, and that the physical properties of amino acids plays a role in the codons which code for it. This suggests that the code set we see is evolutionarily beneficial over a random set, and thus very possibly could be a case of Convergent Evolution^WP.

Wikipedia has a good summary of the main theories of genetic code evolution, none of which exclude convergent evolution of separate evolutionary lines.

Thanks for the information, and the links.

Based on a quick skim of the links you provided, I'm not sure they make a strong case for independent origin and convergent evolution. English and French have common roots, but "maman" "mama" "mommy" and "mom" are different ways of expressing the same thing.

In your opinion, is it likely that DNA was developed multiple times in multiple single-celled origins of life on Earth?

 

[noreligion]

In your opinion, is it likely that DNA was developed multiple times in multiple single-celled origins of life on Earth?

You don't think too often do you? Is it too hard for you? Considering that DNA is a successful mechanism if life arose more than once, and we have no reason to think it didn't although only one line left descendants, of course it would have used DNA. The same chemistry, physics, biology and countless other scientific laws would have still been in effect and as DNA was used once as a successful mechanism, because it was an INEVITABILITY it would have been used again and again. Please try to think things through before making yourself look sillier than you already do.

 

[bokonon]

Wikipedia has a good summary of the main theories of genetic code evolution, none of which exclude convergent evolution of separate evolutionary lines.

Doesn't exclude convergent evolution, but having done a bit more than skim, it seems unlikely.

Notwithstanding these differences, all known codes have strong similarities to each other, and the coding mechanism is the same for all organisms: three-base codons, tRNA, ribosomes, reading the code in the same direction and translating the code three letters at a time into sequences of amino acids.

A practical consequence of redundancy is that some errors in the genetic code only cause a silent mutation or an error that would not affect the protein because the hydrophilicity or hydrophobicity is maintained by equivalent substitution of amino acids; for example, a codon of NUN (where N = any nucleotide) tends to code for hydrophobic amino acids. NCN yields amino acid residues that are small in size and moderate in hydropathy; NAN encodes average size hydrophilic residues.[16][17] These tendencies may result from the shared ancestry of the aminoacyl tRNA synthetases related to these codons.

It seems to me more likely that the minor differences represent divergences from a common ancestor, rather than that the substantial similarities came about by convergence.

 

[Taffer]

I've been using "likely/unlikely" all along:

You can add this to your growing collection of straw men.


Thanks for the information, and the links.

Based on a quick skim of the links you provided, I'm not sure they make a strong case for independent origin and convergent evolution. English and French have common roots, but "maman" "mama" "mommy" and "mom" are different ways of expressing the same thing.

In your opinion, is it likely that DNA was developed multiple times in multiple single-celled origins of life on Earth?

I'm not arguing that DNA developed multiple times, no. I'm arguing that it's possible it has, and there is no good evidence to falsify such a hypothesis.

Personally, I consider it probable that it arose separately, but from similar sets of initial conditions such that the resultant pseduo-metabolic pathways were very similar. Think of several separate pools with very similar chemical makeups. It is entirely possible that DNA arose separately in each pool, but due to the initial ratios of chemicals this led to the same chemical reactions producing essentially the same thing.

 

[Taffer]

Doesn't exclude convergent evolution, but having done a bit more than skim, it seems unlikely.

It seems to me more likely that the minor differences represent divergences from a common ancestor, rather than that the substantial similarities came about by convergence.

Again, it doesn't exclude convergent evolution. We may not think it likely, but the current evidence does not exclude it. If we cannot exclude it here on earth, why presume to exclude it on every other planet in the universe?

Another thing to remember is the physical properties of amino-acids. Given the same chemical ratios in the initial 'soup', it is probably that similar amino-acids arose. If those amino-acids have an optimal configuration in terms of codons, then it is conceivable that these codons could evolve separately several times.

Yet another thing to remember is that it is entirely possible that many other forms of life arose from separate abiogenesis events, and that the current form of life is the only extant example of those events.

 

[bokonon]

Again, it doesn't exclude convergent evolution. We may not think it likely, but the current evidence does not exclude it. If we cannot exclude it here on earth, why presume to exclude it on every other planet in the universe?

It doesn't exclude time-traveling sponges from the 18th dimension, but such an origin is unlikely to be the actual one. Has any scientist studying abiogenesis published a paper proposing that DNA may have been the product of multiple independent metabolic bootstrap events, which "converged" on such a common code? If so, I'd be interested in reading their rationale. If not, perhaps there's a good reason no one has.

Another thing to remember is the physical properties of amino-acids. Given the same chemical ratios in the initial 'soup', it is probably that similar amino-acids arose. If those amino-acids have an optimal configuration in terms of codons, then it is conceivable that these codons could evolve separately several times.

As I've mentioned elsewhere, the physical properties of amino acids include chirality -- there are left-handed versions and right-handed versions of every amino acid in existence, and there is no chemical reason which precludes a complete metabolism using either version. Yet, all the life we're aware of today utilizes the left-handed version to construct the enzymes which drive its metabolic engines. If life on Earth actually began more than once, why is there no right-handed amino acid chemistry among the multitude of creatures we observe today?

Yet another thing to remember is that it is entirely possible that many other forms of life arose from separate abiogenesis events, and that the current form of life is the only extant example of those events.

This seems much more plausible than independent invention of DNA and the machines which use it, but consider: We know of an immense variety of single-celled organisms. Simply among bacteria, there are rods and spheres and flagellates, photosynthesizers and chemical extremophiles, and there are scores of one-celled plants and animals more complex and varied than bacteria. Yet, among all that biodiversity, we're not aware of one which doesn't use the same DNA machines shared by mushrooms and mangoes and man.

Yes, life on earth has gone through several "mass extinction" bottlenecks, and we don't have tools for evaluating how hadean life played its genetic games. It's possible that different kinds of life arose that we haven't discovered yet, or which didn't leave behind the kind of evidence we could point to and conclude it used some method other than DNA and left-handed amino acids to survive and reproduce.

But when you hear hoofbeats, it's probably not unicorns. Until there is evidence for which "multiple origins" is the simplest explanation, there is no compelling reason to assume that such a thing occurred.

 

[Taffer]

It doesn't exclude time-traveling sponges from the 18th dimension, but such an origin is unlikely to be the actual one. Has any scientist studying abiogenesis published a paper proposing that DNA may have been the product of multiple independent metabolic bootstrap events, which "converged" on such a common code? If so, I'd be interested in reading their rationale. If not, perhaps there's a good reason no one has.


As I've mentioned elsewhere, the physical properties of amino acids include chirality -- there are left-handed versions and right-handed versions of every amino acid in existence, and there is no chemical reason which precludes a complete metabolism using either version. Yet, all the life we're aware of today utilizes the left-handed version to construct the enzymes which drive its metabolic engines. If life on Earth actually began more than once, why is there no right-handed amino acid chemistry among the multitude of creatures we observe today?

This seems much more plausible than independent invention of DNA and the machines which use it, but consider: We know of an immense variety of single-celled organisms. Simply among bacteria, there are rods and spheres and flagellates, photosynthesizers and chemical extremophiles, and there are scores of one-celled plants and animals more complex and varied than bacteria. Yet, among all that biodiversity, we're not aware of one which doesn't use the same DNA machines shared by mushrooms and mangoes and man.

Yes, life on earth has gone through several "mass extinction" bottlenecks, and we don't have tools for evaluating how hadean life played its genetic games. It's possible that different kinds of life arose that we haven't discovered yet, or which didn't leave behind the kind of evidence we could point to and conclude it used some method other than DNA and left-handed amino acids to survive and reproduce.

But when you hear hoofbeats, it's probably not unicorns. Until there is evidence for which "multiple origins" is the simplest explanation, there is no compelling reason to assume that such a thing occurred.

That is all very well and good, but you were using a common origin of life here on earth as a sort of reason for disregarding the possibility, or rather the probability, that life exists elsewhere in the universe. You are seeing the unicorn of unique life here on earth.

ETA: Please realize I am not arguing that life arose multiple times. I am well aware of the consensus, and have no inclination or reason to buck the trend. I am simply arguing that your cited reason, that is DNA codons, is not a good argument for life not arising elsewhere in the universe. That is all.

 

[bokonon]

I am not arguing that life arose multiple times. I am well aware of the consensus, and have no inclination or reason to buck the trend. I am simply arguing that your cited reason, that is DNA codons, is not a good argument for life not arising elsewhere in the universe. That is all.

Fair enough. I agree that my cited reason was not as strong as I'd originally supposed, and I learned something new (several somethings, actually) by following your links. Thank you.

 

[John Hewitt]

As I've mentioned elsewhere, the physical properties of amino acids include chirality -- there are left-handed versions and right-handed versions of every amino acid in existence, and there is no chemical reason which precludes a complete metabolism using either version. Yet, all the life we're aware of today utilizes the left-handed version to construct the enzymes which drive its metabolic engines. If life on Earth actually began more than once, why is there no right-handed amino acid chemistry among the multitude of creatures we observe today?

Just a couple of slight points of fact
1. Glycine does not exhibit chirality.
2. The bacterial cell wall contains D-amino acids, parrticularly D-alanine, and there are numerous bacterial membrane peptides and antibiotics which also contain D-amino acids. Note, however, that all these peptides are made non-ribosomally.

You may wish to take a look at my own work on the origin of chiral specificity, which can be found on "Evolution and Origin."

 

[bokonon]

Just a couple of slight points of fact
1. Glycine does not exhibit chirality.

I did not know that. Looks like I'll have to change the qualifier I use when employing this argument in the future. Thank you.

2. The bacterial cell wall contains D-amino acids, parrticularly D-alanine, and there are numerous bacterial membrane peptides and antibiotics which also contain D-amino acids. Note, however, that all these peptides are made non-ribosomally.

I just learned that this week, as the result of some fact checking I did for the parallel discussion of this topic over in R&P. That's why I am now saying things like "to construct the enzymes which drive its metabolic engines," but I'll try to refine both my understanding and my phrasing.

 

[Generally Rational]

The way I've often thought of it is if vessicles form and trap a bit of water and other molecules inside, they're already "selecting" for molecules that are more abundant. Some molecules will be more abundant based on non-organic chemical processes. (This might explain why amino acids are fairly ubiquitous.)

In the Alkaline Hydrothermal vent theory by Mike Russell and Bill Martin, the Last Universal Common Ancestor to bacteria and archaea doesn't even have to have cell walls or even a cell membrane to start. The microscopic cavities made of gel that those vents would form in the iron filled carbonic acid oceans of the Hadean era would serve as the first vessicles and would have iron-sulfur catalytic interiors to boot.

Of course, once you get a self-replicating molecule, that process would swamp selection based on those other processes.

I think the line between life and non-life will become blurrier and blurrier. It's all really just chemical/mechanical processes. There's nothing magical about life.

As somebody said, life is a method of turning disequilibrium into equilibrium.