I don’t think you quite understand the papers i linked. As far as Shapiro, I don’t know what he would think. Reach out to Mike Russell (prominent metab-first researcher) and ask him.
And did Shapiro actually say that? I’m pretty sure he meant DNA and RNA arising first was fantasical
If he said DNA and RNA arising naturally was impossible then yes he would change his mind. But if he meant that DNA and RNA arising first is impossible then probably not.
I will tell you why the papers you linked do not constitute any great advance in convincing people that large molecules like DNA and RNA could have arisen first strictly from natural processes.
Looking at the paper from 2013 on proteomes.
https://www.tandfonline.com/doi/pdf/10.4161/rna.25977?needAccess=true
So, the first question we ask is: What did the researchers do?
" Using experimentally and computationally derived measures of solubility of amino acids in aqueous
solutions of pyrimidine analogs together with knowledge-based interaction preferences
of amino acids for different nucleobases…"
Fair enough.
Second question: What did they find?
“…we have revealed a statistically significant matching between the composition of mRNA coding sequences and the base-binding preferences of their cognate protein sequences.”
Fine. So, there is a matching between mRNA and the proteins generated. I don’t find that to be startling. This rather sounds like something we should have expected.
Next questions: What did the researchers conclude? Are their conclusions reasonable?
Actually, the authors don’t have any breakthrough conclusions regarding origin of life. They certainly don’t provide any evidence related to origin of life. Rather, based on findings that shouldn’t be considered surprising, they conclude their findings are support for the “stereochemical hypothesis of genetic code’s origin.” This particular theory is one of several that has been around for years and was mentioned in the 2005 article below.
See https://www.sciencedirect.com/science/article/pii/S0303264704002175
Shapiro was certainly aware of this theory when he wrote in 2007. This is not a breakthrough. It doesn’t prove anything. It certainly doesn’t make RNA World any more plausible.
To demonstrate that large molecules like DNA and RNA could arise first is plausible, you would need to demonstrate a natural environment that can provide a suitable setting for advanced organic synthesis including just-in-time delivery of new chemicals and proper purifications after each step in the chemical development. There have not been any advances of this type since 2007.
You’re right. My wording was sloppy. I will try to be more careful.
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The common ground should be that I’m trying to uphold the standards of science in origin of life research. I wish that you would join me in that effort.
A simple search on Google scholar shows this is being done. When I get home I’ll open up my collection of OOL journals and collections of essays and see what else I can find.
Really, all I see you doing is criticizing the work of origin of life researchers who work long and hard to produce scientific results that are peer reviewed and published in scientific journals. These researchers are working hard to learn more about the origin of life on this planet. They really don’t need you to uphold the standards of science in origin of life research. When did you get that job? And from whom?
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this will be my last time addressing you. But it looks like these scientists had courage and did real science in OOL. Things you said don’t exist. Peace.
I would be most gratified if you can point me to journal articles that have actually attempted to falsify any approach: RNA World, metabolism first or any other.
You didn’t even click the link of the article @Ronald_Cram. You know there is a counter on it right?
We understand that you are committed to this polemic argument. It seems you have it worked out in your head. It is not clear why you even need us here to make your point. It is not like you are engaging with those with whom you disagree. Maybe just hire an actor to play the part you’ve cast us in? That might be less frustrating for you. You could script out how you’d like him to respond, and even maybe win at the end!
Is this the paper that attempts to falsify metabolism first? I haven’t had a chance to read it yet. It is new to me.
After a quick check, I see that it has been cited 118 times by other papers. It will be interesting to see if others accept this paper as a full falsification.
https://scholar.google.com/scholar?cites=8481024137297708868&as_sdt=2005&sciodt=0,5&hl=en
If so, then we only have to attempt to falsify RNA World, DNA First and Cell Membrane First. Unless you know of papers that attempt to do that already?
I don’t know what you mean. I just sat down to the computer. I haven’t had time to read the paper yet. I’ve only just clicked on it and started some initial reading.
First, I want to thank you for linking to this paper. It is new to me. I would like to talk to you about it if you are open to talking.
Here’s a quote from the end of the abstract:
“We conclude that this fundamental limitation of ensemble replicators cautions against metabolism first theories of the origin of life, although ancient metabolic systems could have provided a stable habitat within which polymer replicators later evolved.”
I have to admit. I’m not sure what the authors are saying here. It seems like they are saying that their research indicates the metabolism first model is less plausible than previously thought, but they are leaving the possibility open. Is that how you interpret the sentence?
In the conclusion the authors write, “We now feel compelled to abandon compositional inheritance as a jumping board toward real units of evolution.”
I interpret this to mean these authors are assuming metabolism first is no longer worthy of consideration or further research. Is that how you interpret it?
As I mentioned, I haven’t fully digested the article yet. I did note that it has been cited 118 times so far. In many of those citations, the papers are apparently still pursuing a role for metabolism first, even if the claim is not that the metabolism is living. Now it appears to be the claim that a stable, active metabolizing solution is necessary for the developing of RNA or DNA. See https://boa.unimib.it/retrieve/handle/10281/36531/52857/PhysRevE_2011.pdf
Regarding the paper you linked, I have a question. Typically, research papers will end with a call for more research on the topic at hand. And they will do so by pointing out the specific area where more information is needed. I’m wondering why the authors of this paper didn’t do that? Was it because they felt they had already sufficiently falsified metabolism first? Or, is there some other reason? Is seems to me they are still leaving the possibility open.
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Honestly, I interpret it as a lot of uncertainty about an important event about which we have very little evidence. In cases like this, there will always be lots of opinions. The arguments are not definitive.
Yes, because we have not settled these questions. It is not clear if we will in our lifetimes. Some people will think any given direction is a waisted of time, others will disagree and dive in. We don’t come to consensus till we find a strong solution. Even then consensus can take time. OOL looks very much like a field making progress but not knowing yet what is going to be the must fruitful direction, or even if the problem they’ve chosen is tractable.
Great question.
It is not a standard to call for new research. That is not how we teach our students. Especially in high level papers, one is supposed to be reserved and explain what would be need to done to solidify findings. One reason they may leave this out is because it is not clear how to settle these debates. So yes, they are leaving the possibility open. Really everything is on the table.
OOL sits on the boundary of chemistry and biology. In biology, the story is always complex. It is always multiple things collaborating together. Biology is full of paradoxes. Biologists know this, so even when they attack an idea, they are usually cautious not to say the idea is not part of the story. For something as complex as the OOL, if it is by abiogenesis, it is very likely to be a complex collaboration between several factors, not a clean separation of one, then two, then three.
What we do know now is that we do not have the answer. There is a shadow we are seeing, dimly through a cloudy glad. We are not sure precisely what it is yet. We are not sure if we ever will. There has been real excitement in OOL work lately, because they have made some progress lately, and are getting a fresh infusion of ideas. In the end, I’m not sure we know what will or won’t pan out. In speculative research programs build on such a grand and difficult question, we cannot predict where it will go. We are not sure if it is right in grasp, or totally beyond our grasp, or something else.
For these indeterminacies, you are not going to see any thoughtful scientist rule out any option. It very may well be all of them collaborating. We want to explore as much as possible, and get as much accessible knowledge on the table as possible. We don’t know how many puzzle pieces there are though. We don’t know what the final picture looks like. So it is hard to gauge how much longer it will take, or if we will even get their in our lifetime or not.
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I have read this entire thread with great interest, not least because Bob Shapiro and I were friends at NYU, and we co-taught a class together. He was a wonderful man, a fine teacher and a brilliant thinker. His ideas and work on abiogenic synthesis of cytosine and his idea on chemical, non enzymatic synthesis of nucleic acid polymers have since been addressed, but not in my opinion been over turned.
I am also intensely interested in the process by which chemistry became biological, which started with my conversations (arguments actually) with Bob over many lunches. I was an adamant replicator-first proponent, and he of course was adamantly in the opposing camp. At the time (early 90s) neither of us were theists, so the theistic alternative never came up.
I now think that Ronald Cram has a point: the two sides of this debate (replicator vs metabolism) have actually been quite successful in falsifying their opponents views. This is the actual crisis in abiogenesis research. For example Eugene Koonin, a leading replicator guy has come to accept that it is impossible to conceive of a way that the translation system could evolve in a non RNA only world, so he is now committed to finding proof for an RNA only world, (possibly involving viruses) or an alternative pre RNA world.
The PNAS paper linked by TJ demonstrates very nicely my old argument about the impossibility of metabolism first. The communicator of the paper is Gerald Joyce, a leading replicator firster. But the problem is the issue of how is it possible to have a nucleic acid only life form, since ribozymes are not very good catalysts, and RNA cannot replicate itself (TJ, please dont bother linking Joyce’s papers about RNA self replication. Those are unfortunate, I prefer not say dishonest, uses of the term “self replication”. What Joyce shows is the ability of ribozymes to perform ligation of preexisting large RNA primers, something that could not happen in a prebiotic world.)
Jack Szostack, a Nobelist, and in my mind the best OOL researcher, almost solved the problem with a recent paper on RNA replication using oligopeptides, but it turned out that was an error and he had to retract the paper (I have posted about this on my blog). The bad news is that in repeating the experiment, Szostack’s group found that indeed, RNA replication without protein enzymes is probably impossible.
So in a way, @Ronald_Cram’s request for falsification of abiogenesis is underway, by OOL researchers, each of whom are happily falsifying their opponents ideas (Szostack being the exception, and the most honest of all the workers in the field in my view.)
This is not to say that headlines like “New study shows how life could have originated” are about to stop. I predict at least another decade of funding and active research until the entire field just sputters to a halt. This actually happens quite frequently in science; I should know, I have been part of at least one such field.
Of course none of this says anything about God as the designer and creator of life. Even assuming that is true (which I do assume) it would still be really nice to know how!.
What I havent touched on here, is the main issue with origin of life, which I like to say is the origin of evolution. But I have gone on long enough, and I will be presenting my ideas on that in about a week at the ASA meeting so I might be able to present some of that here.
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That is the opposite of his point @sygarte, right? He has been arguing that they are not even attempting to falsify each other’s views.
Which again @Ronald_Cram has been complaining that OOL researchers are unwilling to falsify different models.
Except he doesn’t consider this valid. What he misses is that this is just what scientific processes looks like before we know an answer. If no answer is possible, this will just go on indefinitely. There is no way to know when we have reached the end of science here.
Could not agree more.
This isn’t exactly right. I know that certain researchers, like Shapiro, have written about the weaknesses of alternative approaches. But I still believe that no one has really attempted to falsify alternative approaches. Shapiro talked down the RNA World, but didn’t design any experiments to falsify it. TJ linked a paper that is the closest I’ve seen to an attempt to falsify. I don’t think the authors really claimed they achieved falsification, just that it was no longer worth their research time. Normally, you would expect the researchers to say “We need more research on this topic to fully falsify this approach” but the authors didn’t do that.
Yes, it would be nice to know how but if it was a miracle then the how may be unsearchable. For example, with the Big Bang we can model the universe mathematically going back to Planck time but then the math breaks down. But that’s exactly what we should expect to happen if a miracle occurred. How can math model a miracle? I’m not saying that we should assume a miracle every time math breaks down, but the break down of math is consistent with a supernatural event. There’s no harm in pointing that out.
Thank you for saying so. It feels strange for me to try to uphold the standards of science and to get so little support. Certainly I’m aware of researchers talking down alternative approaches but am not aware of papers written with the express intention of falsifying alternative approaches. TJ has linked a paper that is the closest I’ve seen to that. If you have other papers you could link, I would be most appreciative. It’s been some years since I’ve studied this topic and I know I will need to re-study it again.
Interesting comment.
Interesting. Why do you say Szostack is the exception?
I would be interested to read or see your presentation!
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