Raw materials for life

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What experiments specifically? As far as I know, many different experiments in abiotic organic chemistry that attempt to mimic early Earth environments of different kinds, yield compounds that bacteria can use as nutrients. Since bacteria evolve, then yes. But of course that depends on the specific experiment and the environment it simulates, and therefore the products produced.

Some experiments have shown that iron can reduce CO2 to common metabolites found in the Kreb’s cycle. All life on Earth can eat that.

You seem to be asking a much deeper question than what this thread(and the paper in the 2nd post) is trying to address. Here we are discussing(and the purpose for which I am citing that paper) whether genes with new functions can evolve when there is already evolution going on. This whole thread (though not necessarily the scenario conceived as the context in that paper) is based on the premise that life already exists and is evolving.

But I get the sense you want to know how evolution itself began. How did there come to be something that was evolving, such as RNA molecules, or living cells? - and since the researchers in the paper cited in the 2nd post did not begin with experiments in abiotic geochemistry, they’re not addressing the question you want answered. The paper is obviously based on the assumption that RNA was somehow produced and was replicating, and given this premise, could selection facilitate this evolving RNA finding new functions even from a polymer of minimal sequence complexity? The answer turns out to be yes.

But nobody knows how evolution, or life, began. Nor how(or if) the scenario assumed in the 2nd paper relates to life’s origin(nor am I referencing it to argue that). Some posit evolution(not necessarily life) began with the emergence of the first biological polymers such as RNA, and that these evolved into living cells, others argue evolution could have begun even before this:

Whether you think any particular step in such a hypothetical scenario constitutes life is a matter of personal preference, there is no universally agreed upon definition of life. So nobody knows. They’re actively trying to find out. But if you want to discuss origin of life research I suggest you create a new thread because it’s off topic here.

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Okay, I will assume the existence of RNA. I actually agree with your second post that the experiments done by the author of the second paper are relevant to the points made by the author of the paper that wrote the paper that you used to begin this thread, I just see really advanced engineering. It is that second paper that I am asking questions about:

In the experiment in the paper above the researchers used an RNAeasy mini kit to separate the RNA from the chemical mixture that made it, I don’t think the equivalent is available in a pre enzyme biology to enable this protocell without RNA polymerase to isolate a strand of RNA so I would like to know how they imagine that would have actually happened. Then they used sepharose, an polysaccharide formulated using seaweed extracts, (there was no seaweed in RNA world) to create a negative selection step which is fine today, but how is any of the above supposed to happen in nature without chemists or modern cells making compounds like the seaweed extract that they used?

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Thanks. I appreciate that.

Definitely. They are using advanced biochemical technology to perform these experiments. They are not recreating any kind of plausible RNA world in these experiments, as that is both totally outside the scope of the question they are trying to address, and second, how such an RNA world even began (and therefore what experiment could produce it) is still largely an unknown.

I don’t think the authors are saying any of those things happened, or were required to happen, for selection towards a function to occur. I think these steps are performed for analytical and practical reasons, as @Jordan has explained.

More generally speaking with respect to separating RNA from putative side-products produced in the chemical reactions that yield RNA, I think it is often postulated that RNA could have separated either thermophoretically from different products (not entirely disanalogous to electrophoresis), or by surviving by selectively adhering to mineral surfaces while some other products wash or evaporate away under conditions of intermittent flow and wet-dry cycles.

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Very interesting paper I read it very carefully, so I have three simple questions. Some of the compounds needed to make enzymes, DNA and RNA can be found in trace amounts in comets, and in chemical reactions that attempt to simulate various models of the primordial earth. Is it possible to use the products of such experiments to allow evolution to create enzymes? Did the researchers need to purchase laboratory chemicals, and then used their advanced knowledge of chemical engineering to purify them beyond what the laboratory had already done? Here is what the researchers said they did:

DNA and RNA oligonucleotides (listed in Supplementary Table 1) were from Integrated DNA Technologies and if necessary were purified, by denaturing PAGE (8M urea, TBE). The 2 poly-T (T2, T4) and 3 poly-A (T5, T7, T8) starting sequences consist of 69 nt, containing an either 39 nt poly-A or poly-T sequence flanked by different 15 nucleotide (nt) primer binding sites on both ends (Supplementary Table 1). The sequences were designed with non-overlapping primer binding sites to avoid cross contamination from different evolution-selection experiments.

If such an experiment cannot be done without first using chemical engineering techniques to manufacture and purify the necessary compounds, used in the experiment, how can actually experimentally demonstrate that unguided organic chemistry is even capable of causing the evolution of the pure ingredients needed to synthesize enzymes in nature, at a bare minimum?

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@Geremy, I had a quick look at the methods section and it looks like pretty standard. It’s not that the chemistry can’t happen without purification, etc. it’s that in order to properly study the chemistry you need to make sure you have very pure ingredients in order to limit contamination or adding uncontrolled variables. So if I were, for example, studying the reaction between salicylic acid and acetic anhydride to make aspirin, if my bottle of acetic anhydride was actually half acetic anhydride and half propionic anhydride, it would be hard to make strong conclusions about the reaction because it’s actually multiple reactions happening.

Using purified reagents or reagents synthetically derived do not mean pure or “manufactured” reagents are needed for the reaction to occur in nature. It just means that the pre-biotic environment would have a lot more going on because there are more possible reactions. Simplifying the conditions of an experiment down to the specific reaction of interest is just the only way we can limit the variables.

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Thank you Jordan, I’m sure that this standard practice but therein lies the problem if one is speculating about a simpler primordial biology existing before enzymes. My wife is a pharmacist, so back when I was in Respiratory school I used her knowledge to help me beef up on pharmocology. Thanks to that experience, I know that RNA polymerase is a target at least two classes of antibiotic drugs namely the rifamycins and the lipiarmycins. If we are to assume that some sort of protocell used RNA as a template as suggested by the paper, the question of how it managed to transcribe it’s RNA without enzymes seems to be valid, because, not even viruses can do that today. Perhaps you are aware of some plausible mechanism that could of been used by early cells?

As far as the existence of RNA on a primordial earth outside of cells, some have pointed out that the borate precipitates that are use to in many models of the early earth, didn’t exist in sufficient quantities on the early earth to make the stable synthesis of RNA possible. An example of such an article is linked below, using researchgate:

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Primordial environments may have been much simpler in terms of biology (by definition) but they would have been very chemically rich. It would have been much more complex than than most modern chemical experiments.

Presumably a ribozyme under that scenario.

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That article doesn’t say it didn’t exist in sufficient quantities, but rather that the factors that affect this question are still largely unknown, and hotly debated. If certain things were the case, then it is likely it would have existed in those quantities - and if these things weren’t the case - then it didn’t. It’s a typical article giving an overview of a scientific argument by presenting both sides pro and con, without coming down hard on a particular conclusion.

But the relevance of all of this thing about borate and it’s stabilizing effect on ribose is based on another assumption, which is also an unknown, which is that the RNA-world somehow began by a chemical process that had ribose as an intermediate that would need to be stabilized against competing products(produced in something like the formose reaction), so it could later be joined to the different nitrogenous bases through a glycosidic bond, which is also heavily disputed.

Many others have argued there are other ways to make RNA than this.

So if you’re going to say there couldn’t have been an RNA world, you need to show a lot of evidence that settles a lot of big unknowns about the early Earth and it’s environments, and about abiotic organic chemistry. Merely pointing to one or both sides in a lot of different debates for a selection of quotations arguing that opposing views are unlikely given assumption X does not constitute meaningful discussion.

At any given moment in science there is some advancing frontier of research, where certain topics are hotly contested, and in those moments you can find statements by people on different sides arguing that the views of their opposition are somehow all unlikely, implausible, or impossible. Yet such debates usually eventually settle, and one side comes out being right and the other side wrong. You can go pick quotes from the period when the mechanism of oxidative phosphorylation was unknown and a subject of hot contest, to “prove” that (taking the arguments from both camps) life must be impossible, because apparently there’s no way any mechanism of oxidative phosphorylation could possibly occur and suffice to power life. But one side won that debate eventually, and the other side lost, and we now know ATP is generated by chemiosmosis.

You can find lots of papers arguing that “the other guy’s scenario for the RNA world is wrong and here’s why”, it’s just that it’s all based on innumerable assumptions that have yet to be settled(some argue there was no dry land at all, not even volcanoes of any appreciable size, which would basically rule out all versions that involve evaporation and wet-dry cycles, leaving only submarine hydrothermal vents among presently conceived settings for life’s emergence), and are likely to remain unknowns for quite a while, because there’s scant little evidence for what the earliest periods in Earth’s history was really like.

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What experiments specifically? As far as I know, many different experiments in abiotic organic chemistry that attempt to mimic early Earth environments of different kinds, yield compounds that bacteria can use as nutrients. Since bacteria evolve, then yes. But of course that depends on the specific experiment and the environment it simulates, and therefore the products produced.

Some experiments have shown that iron can reduce CO2 to common metabolites found in the Kreb’s cycle. All life on Earth can eat that.

You seem to be asking a much deeper question than what is thread(and the paper in the 2nd post) is trying to address. Here we are discussing whether genes with new functions can evolve when there is already evolution going on. This whole thread(though not necessarily the scenario addressed in the OP paper) is based on the premise that life already exists and is evolving.

But I get the sense you want to know how evolution itself began. How did there come to be something that was evolving, such as RNA molecules, or living cells? - and since the researchers in the paper cited in the 2nd post did not begin with experiments in abiotic geochemistry, they’re not addressing the question you want answered. The paper is obviously based on the assumption that RNA was somehow produced and was replicating, and given this premise, could selection facilitate this evolving RNA finding new functions even from a polymer of minimal sequence complexity? The answer turns out to be yes.

But nobody knows how evolution, or life, began. Nor how(or if) the scenario assumed in the 2nd paper relates to life’s origin. Some posit evolution(not necessarily life) began with the emergence of the first biological polymers such as RNA, and that these evolved into living cells, others argue evolution could have begun even before this:

Whether you think any particular step in such a hypothetical scenario constitutes life is a matter of personal preference, there is no universally agreed upon definition of life. So nobody knows. They’re actively trying to find out. But if you want to discuss origin of life research I suggest you create a new thread because it’s off topic here.

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Thanks for your answers Jordan, when I read about ribozymes I always wondered what the error rate would be, but for years I couldn’t find any reasonable estimates. My thinking is that Darwinian evolution requires some sort of error correction mechanism, because the natural error rates of RNA and DNA are too high to be useful without it. However, I had no idea of what the error rate of the best ribozymes engineered to date were until I read the paper linked below last year which estimated error rates of 8- 17% per generation.

I don’t think that sort of error rate is low enough to yield any sort of evolutionary advantage to any RNA protocell since it is hard to fixate any mutation with such rates, but I aim hoping that someone models exactly how many generations such organism could sustain such a high error rate before they became unable to reproduce, mostly out of curiosity.

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This is completely off the mark. Error rates of ribozymes with no proofreading mechanisms are on the order of ~10-4.

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Every experiment in chemistry (including prebiotic), immunology, oncology biochemistry, virology etcetera cannot be done without reagents purified and concentrated in some form or tools like spectrometers, test tubes and pipettes. Tumorigenesis is an unguided process but no one knew how it happened until experiments using artificial environments like petri-dishes, test tubes, incubators and purified/concentrated chemicals like mutagens were done. Viral infection in nature is unguided but we did not know how it happened without experiments involving reagents derived using chemical engineering principles and devices.

Life originated once and if it happened through the interplay of yet to be identified physical and chemical principles on a prebiotic earth, then its only via experimentation that we might uncover what those principles are. Experimentation is necessary to provide a controlled environment that mimics the possible environments on an early earth because the conditions of today are sharply different from what obtained 4 billion years ago (like the absence of abundant atmospheric oxygen, for example). Of course, the more artificial the experiment is, the less likely its finding would be applicable to real life and vice versa.

In summary, if we couldn’t demonstrate how unguided processes like tumorigenesis, immune development, viral infection, protein-ligand binding etcetera which occur repeatedly without experimentation using purified chemicals and quite sophisticated devices, then its seems absurd that the same won’t apply to origin of life research, especially since life originated once.

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Isn’t the paper that you are using as evidence that ribozymes have low error rates out of date? Cells that use ribozymes and RNA only are not in evidence in nature, and at the time that the paper that you mentioned was written the author stated:

Nobody has yet seen or constructed a functional riboorganism, but we know how mutations affect the functionality of certain ribozymes.

This statement includes both a fact and an opinion, it is a fact riboorganisms do not exist in nature, but were imagined by OOL theorist as a hypothetical organism that if it were able to exist could be seen as an evolutionary ancestor of modern cells. Speculation is great but it never should trump actual empirical evidence, which is what the 2020 paper that I mentioned was referencing. He referred to a real life ribozyme that was after 14 rounds of guide evolution and the help of advanced chemical engineering able to make a copy of it’s own ancestor, something that a ribozyme would have to do autonomously in a hypothetical RNA only, cell if RNA world actually existed. The paper that the author of the paper mentioned can be found in the link below:

https://www.pnas.org/content/117/6/2906

And it was this empirical evidence derived result that led the author to write:

Does this help us to understand how an RNA world could have arisen? On the contrary, it points to another problem. The best RNA polymerase the researchers obtained this way had a roughly 8% chance of inserting any nucleotide wrongly, and any such error increased the chance that the full chain encoded by the molecule would not be replicated. What’s more, making the original class I ligase was even more error-prone and inefficient – there was a 17% chance of an error on each nucleotide addition, plus a small chance of a spurious extra nucleotide being added at each position.

So if they is experimental evidence that a RNA molecule that can be guided to self replication has a lower error rate great. But it surely isn’t in a paper written 15 years before the experiments that the author was discussing.

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@moderators is there a forum bug here of some sort or is @Geremy posting multiple times? I’ve flagged the post as off topic as I think it should be moved to the other thread here:

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This is weird, because I don’t think @Geremy is in the habit of triple posting. :slight_smile:

I’ll clean up …

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Extras deleted. It’s possible I accidentally created duplicates this morning (my connection has been intermittent), but not the duplicated this afternoon.

If your posts are not showing up right away, try holding the control key and clicking the refresh button, which should force a full page reload.

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Hi @Geremy, if I might jump in here, I wonder what your evidence is for this claim.

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Why would it be?

No, but evidence shows there was some sort of RNA world - not necessarily one made purely of RNA - but where RNA played much more prominent roles in information storage and catalysis than it does today. How that RNA world arose, how pure it was (were there small peptides and other cofactors involved?) and how it evolved into the DNA+RNA+Protein world of today is largely an unknown.

No that’s not a fact. None are known, that doesn’t mean they don’t exist somewhere of course.

And their tested molecules appear unable to support extended evolution because of accumulating errors. So much the worse for the system they tested.

Sorry but it’s an assumption that for there to have been some sort of RNA world, that this would require a self-replicating ribozyme to operate. Alternatively you could have a mutually catalytic (autocatalytic) cycle of RNA molecules that catalyze each other’s synthesis, either by ligation of smaller RNA fragments instead of requiring any particular molecule to replicate itself, or by polymerization using a specific template, rather than having to rely on a sort of generalist ribozyme that can synthesize a lot of different molecules including itself using many different templates. Instead of a system where molecule A creates both itself and B, C, D… - you can have a system where A creates B creates C creates D creates A - an autocatalytic cycle.

I think you’ve conflated two different ideas. One concerns the replication fidelity of a sort of generalist polymerase ribozyme that can replicate both itself and other functional RNA molecules, which very well might(or might not) be extremely difficult for RNA (though what can be selectively derived from the class I ligase with the particular selection protocol employed, it is rather absurd to extrapolate that to some sort of fundamental limitations to RNA-catalyzed replication fidelity), the other concerns the replication fidelity of other known ribozymes (which aren’t necessarily self-replicators).

The RNA world hypothesis takes many forms, only one of which involves the sort of generalist self-replicating ribozyme sought and explored by Joyce and colleagues. Nothing can really be ruled out at this stage from such a simple experiment as the one you referenced. Neither the possibility of self-replicating RNA polymerase ribozymes with higher fidelity, nor the concept of the RNA world more broadly even in the absence of highly accurate self-replicating ribozymes.

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You are correct absence of evidence is not evidence of absence. I should say that there are no known riboorganisms in nature.

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Having now read the paper in full it seems I have to retract this implicit acceptance of Geremy’s stament, which is nowhere stated by the authors and doesn’t follow from their work at all.

The authors state that they have only indirectly and weakly been selecting for replication fidelity of their ribozyme in their previous work, by requiring it to synthesize a piece of the hammerhead ribozyme in turn, which has rather low sequence constraints, and make no claims about it not being possible to improve the replication fidelity of their polymerase ribozyme.

It is entirely possible that with a modified selection scheme the replication fidelity of their system can be significantly improved.

In fact, this article on the biorxiv indicates that they are aiming to do exactly that in the future:

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