Darwin Unhinged: The Bugs in Evolution

New theory addresses how life on Earth arose from the primordial muck
Life on Earth originated in an intimate partnership between the nucleic acids (genetic instructions for all organisms) and small proteins called peptides, according to two new papers from biochemists and biologists at the University of North Carolina at Chapel Hill and the University of Auckland. Their "peptide-RNA" hypothesis contradicts the widely-held "RNA-world" hypothesis, which states that life originated from nucleic acids and only later evolved to include proteins.

The new papers - one in Molecular Biology and Evolution, the other in Biosystems - show how recent experimental studies of two enzyme superfamilies surmount the tough theoretical questions about how complex life emerged on Earth more than four billion years ago.
"Until now, it has been thought to be impossible to conduct experiments to penetrate the origins of genetics," said co-author Charles Carter, PhD, professor of biochemistry and biophysics at the UNC School of Medicine. "But we have now shown that experimental results mesh beautifully with the 'peptide-RNA' theory, and so these experiments provide quite compelling answers to what happened at the beginning of life on Earth."


Read more at: https://phys.org/news/2017-11-theory-lif...l.html#jCp

I'm also having trouble understanding the argument for origin of life from the point of view of probability.

This is from  Evolution FAQ:

In fact, if we assume the volume of the oceans were 1024 liters, and the amino acid concentration was 10-6M (which is actually very dilute), then almost 1031 self-replicating peptides would form in under a year, let alone millions of years. So, even given the difficult chances of 1 in 1040, the first stages of abiogenesis could have started very quickly indeed.

And this from Talk Origins:

Similarly, of the 1 x 10130 possible 100 unit proteins, 3.8 x 1061 represent cytochrome C alone! There's lots of functional enyzmes in the peptide/nucleotide search space, so it would seem likely that a functioning ensemble of enzymes could be brewed up in an early Earth's prebiotic soup.

So, even with more realistic (if somewhat mind beggaring) figures, random assemblage of amino acids into "life-supporting" systems (whether you go for protein enzyme based hypercycles , RNA world systems, or RNA ribozyme-protein enzyme coevolution) would seem to be entirely feasible, even with pessimistic figures for the original monomer concentrations [23] and synthesis times.

Yet, unless I'm mistaken, life has originated only once in 4.5 billion years of planetary history. If it is so likely as to be "entirely feasible", why then has it not happened multiple times? Crick calls it a "frozen accident" indicating its uniqueness and unlikeliness. So my mind got to wondering whether, if some blast of radiation from the sun obliterated all life from this planet yet allowed the earth to return quickly to its life-friendly status, are we assuming that another frozen accident would occur quickly? And, if so, would that be another one-off?

The point I'm trying to make is that the arguments seem to be self contradicting.

Right - so we get right down to it - everything is done by random processes unguided even by natural selection

Hang on. The peptides are generated at random, but some are useful and some are not. So the chemical processes that produce the useful ones remain and the other processes disappear. So over time, various processes stick around. 

Sorry, I didn't mean to suggest that the processes are completely uniformly random. That is confusing. There would be various chemical processes, some producing useful products and some not. There would have to be some way to "hang onto" the useful ones and ignore the useless ones. That rudimentary system is subject to natural selection.

The question is, how does the system hang onto the useful products? Check out the next post for one possibility.

... but a 3-base code can't possibly evolve from a 2-base code because the code is needed to specify all sorts of little details little details like ribosomes!

Who says there were modern ribosomes when the 3-base code evolved? Perhaps there was a proto-ribosome that stepped along the RNA by 3 bases but paid attention to only 2 of them. Again, see the next post.

~~ Paul

New theory addresses how life on Earth arose from the primordial muck
Life on Earth originated in an intimate partnership between the nucleic acids (genetic instructions for all organisms) and small proteins called peptides, according to two new papers from biochemists and biologists at the University of North Carolina at Chapel Hill and the University of Auckland. Their "peptide-RNA" hypothesis contradicts the widely-held "RNA-world" hypothesis, which states that life originated from nucleic acids and only later evolved to include proteins.

The new papers - one in Molecular Biology and Evolution, the other in Biosystems - show how recent experimental studies of two enzyme superfamilies surmount the tough theoretical questions about how complex life emerged on Earth more than four billion years ago.
"Until now, it has been thought to be impossible to conduct experiments to penetrate the origins of genetics," said co-author Charles Carter, PhD, professor of biochemistry and biophysics at the UNC School of Medicine. "But we have now shown that experimental results mesh beautifully with the 'peptide-RNA' theory, and so these experiments provide quite compelling answers to what happened at the beginning of life on Earth."

Ooh, those will be fascinating papers. They propose a protein-RNA world.

https://academic.oup.com/mbe/advance-art...65/4430325

http://www.sciencedirect.com/science/art...4717302332

~~ Paul

Yet, unless I'm mistaken, life has originated only once in 4.5 billion years of planetary history. If it is so likely as to be "entirely feasible", why then has it not happened multiple times? Crick calls it a "frozen accident" indicating its uniqueness and unlikeliness. So my mind got to wondering whether, if some blast of radiation from the sun obliterated all life from this planet yet allowed the earth to return quickly to its life-friendly status, are we assuming that another frozen accident would occur quickly? And, if so, would that be another one-off?

First, of course, we don't know how many times life started on the primordial Earth. I can think of two reasons why it wouldn't start up again today: (1) the conditions aren't right; (2) there is too much competition from current life.

If we reset the Earth to its primordial conditions, I see no reason life wouldn't start again. It might come out the same or it might not. I believe the two papers Steve linked will suggest that it would come out more or less the same.

~~ Paul

Here is one of the Wills and Carter papers:

https://www.biorxiv.org/content/biorxiv/...7.full.pdf

And here is the other:

https://www.biorxiv.org/content/biorxiv/...9.full.pdf

~~ Paul

First, of course, we don't know how many times life started on the primordial Earth. I can think of two reasons why it wouldn't start up again today: (1) the conditions aren't right; (2) there is too much competition from current life.

If we reset the Earth to its primordial conditions, I see no reason life wouldn't start again. It might come out the same or it might not. I believe the two papers Steve linked will suggest that it would come out more or less the same.

~~ Paul

I think that Crick and others are saying that life originated once and once only. Hence the "frozen accident".  Here's what Crick said:

The Frozen Accident Theory


This theory states that the code is universal because at the present time any change wovld be leihal, or at least very strongly selected against.
 
This is because in all organisms (with the possible exception of certain virases) the code determines (by reading the mRNA) the amino acid sequences of so many highly evolved protein molecules that any change to these would be highly disadvantageous unless accompanied by many simultaneous mutations to correct the “mistakes” produced by altering the code.

This accounts for the fact that the code does not change.
 
To account for it being the same in all organisms one must assume that all life evolved from a single organism (more strictly, from a single closely interbreeding population).
 
In its extreme form, the theory implies that the allocation of codons to amino acids at this point was entirely a matter of “chance”.

Should we dismiss Crick as some kind of religious nut too? Let's consider what you are saying:

1. Conditions are pretty good for life to survive and prosper but not for life to get started. Doesn't that strike you as counter intuitive?

2. Even if life could start under today's conditions, it would be snuffed out by life itself. So presumably the steps leading from lifeless chemicals to cellular life forms would be recognised by other life forms and the prebiotic forms eaten? No prospective life form could possibly escape this fate? 

3. The earth would have to return to primordial conditions even though we are not sure what they were. For example, one popular theory is that life could have started in the deep ocean around hydrothermal vents. But hang on - we still have such vents. Exactly what is to prevent abiogenesis happening around them right now?

I think that Crick and others are saying that life originated once and once only. Hence the "frozen accident". Should we dismiss Crick as some kind of religious nut too?

What does the frozen accident hypothesis have to do with being a religious nut? He might simply be wrong. If Wills and Carter are right, it's no accident.

Let's consider what you are saying:

    1. Conditions are pretty good for life to survive and prosper but not for life to get started. Doesn't that strike you as counter intuitive?

No. Perhaps the Earth had to be warmer. Perhaps a fortuitous piece of space material landed on the Earth. Perhaps there is too much competition. Anyway, I'm not claiming that it couldn't start again if we disappeared all extant life.

2. Even if life could start under today's conditions, it would be snuffed out by life itself. So presumably the steps leading from lifeless chemicals to cellular life forms would be recognised by other life forms and the prebiotic forms eaten? No prospective life form could possibly escape this fate?

There could be competition for resources that might rule out the new kids on the block.

3. The earth would have to return to primordial conditions even though we are not sure what they were. For example, one popular theory is that life could have started in the deep ocean around hydrothermal vents. But hang on - we still have such vents. Exactly what is to prevent abiogenesis happening around them right now?

Competition from other organisms living around the vents?

This is a complex issue. I certainly make no claim to have a definitive answer.

~~ Paul

What does the frozen accident hypothesis have to do with being a religious nut? He might simply be wrong. If Wills and Carter are right, it's no accident.

No. Perhaps the Earth had to be warmer. Perhaps a fortuitous piece of space material landed on the Earth. Perhaps there is too much competition. Anyway, I'm not claiming that it couldn't start again if we disappeared all extant life.

There could be competition for resources that might rule out the new kids on the block.

Competition from other organisms living around the vents?

This is a complex issue. I certainly make no claim to have a definitive answer.

~~ Paul

Religious nut seems to be the go-to accusation around here but, no, of course there is no reason to suppose that Crick, right or wrong, had religious motives. I wish that some of the Darwin doubters were given similar latitude.

The rest of you post is not very convincing as, I think, you concede.

Hang on. The peptides are generated at random, but some are useful and some are not. So the chemical processes that produce the useful ones remain and the other processes disappear. So over time, various processes stick around. 

Sorry, I didn't mean to suggest that the processes are completely uniformly random. That is confusing. There would be various chemical processes, some producing useful products and some not. There would have to be some way to "hang onto" the useful ones and ignore the useless ones. That rudimentary system is subject to natural selection.

The question is, how does the system hang onto the useful products? Check out the next post for one possibility.

Who says there were modern ribosomes when the 3-base code evolved? Perhaps there was a proto-ribosome that stepped along the RNA by 3 bases but paid attention to only 2 of them. Again, see the next post.

~~ Paul

If the odd 'useful' molecule is generated, there isn't any way to select it (unless perhaps there is an intelligent observer   ) this is the real core of the problem.

I'll take a look at the second paper you cited, but I obviously can't comment on it immediately:

https://www.biorxiv.org/content/biorxiv/...9.full.pdf
[url=https://www.biorxiv.org/content/biorxiv/early/2017/05/17/139139.full.pdf][/url]
If you have digested this paper, or the other one that derives rate equations, you could do everyone a favour by summarising the steps that are being proposed to get to the genetic code, or anything else that is revealed in them.

Your idea of a 2-base reader that conveniently always skips the third base is ingenious, but I must say that would be an extraordinarily lucky accident (an act of God perhaps) for such a system to arise. Note also that if the third base was irrelevant, suddenly giving it meaning would still do enormous damage to an existing genome. 

One problem I have with this, is that there is an unfortunate tendency to assume that any intelligence is omniscient - basically because people think of God. That doesn't need to be true, and if the intelligence is finite there are more interesting possibilities.  A finite intelligence may need to experiment to produce some desired result.

Maybe a finite intelligence really did assemble a 2-base reader that skipped the third base (just in case it became useful).

Think of native people in a jungle. They acquire knowledge about the many plants that surround them. They say that some of that knowledge is acquired from dreams and visions (maybe rather as Ramanujan acquired some of his mathematical ideas). The trouble is in these discussions, that one side sees an acceptance of ID as being total defeat, so they use none of their ingenuity in exploring exactly what finite intelligence might be doing. J. Scott Turner makes a good case that purposeful action (intelligence?) operates all the way through biology. You can see that even in single cell macrophages chasing down their prey. I think it is an intelligence of that sort that might have been operating even mack in the pre-biotic era. Of course, such an intelligence would not have to be supported by life, but by an existence in another realm - the same realm that people seem to re-enter when they have an NDE (my thought, not JST's).

David