New study sheds light on how amino acids “evolved”(salon.com)
salon.com
New study sheds light on how amino acids “evolved”
https://www.salon.com/2023/03/01/first-life-on-earth-amino-acid-study/
16 comments
Man I been always so fascinated by the Miller-Urey experiment. Ever since I learned about it on YouTube over a decade ago, I went on a PBS binge on evolution and science shows even though I have no formal education only high school. Anyways I found this article fascinating.
It discusses the mystery of how life emerged on Earth, and how scientists have some theories about how complex cellular life was generated around 3.7 billion years ago. Scientists believe that amino acids existed in great abundance in the Earth's early years and contributed to the creation of the first cell. Experiments, such as my favorite lol “Miller-Urey Experiment”, simulate the conditions of Earth's early atmosphere and have produced organic compounds such as amino acids. Proteins are the building blocks of all living organisms, and understanding how they formed is crucial to understanding how life started. Although hundreds of different amino acids may have been present on the early Earth, all living things rely on only about 20 of these compounds. It’s Science man…:)
It discusses the mystery of how life emerged on Earth, and how scientists have some theories about how complex cellular life was generated around 3.7 billion years ago. Scientists believe that amino acids existed in great abundance in the Earth's early years and contributed to the creation of the first cell. Experiments, such as my favorite lol “Miller-Urey Experiment”, simulate the conditions of Earth's early atmosphere and have produced organic compounds such as amino acids. Proteins are the building blocks of all living organisms, and understanding how they formed is crucial to understanding how life started. Although hundreds of different amino acids may have been present on the early Earth, all living things rely on only about 20 of these compounds. It’s Science man…:)
Can you share some of your favourite pbs videos?
Thank you for asking! For anyone who is interested in science for the first time , here are some I found so fun:)
https://youtu.be/c_jyHp3bmEw
https://youtu.be/_uAJY1mqtw4
https://youtu.be/mnYSMhR3jCI
https://youtu.be/c_jyHp3bmEw
https://youtu.be/_uAJY1mqtw4
https://youtu.be/mnYSMhR3jCI
Ah the ages old debate about which was the beginning of it all: DNA, RNA, or protein.
My favorite superhero fight, or the very first "my origin of life can beat your origin of life" discussion. How fun.
My favorite superhero fight, or the very first "my origin of life can beat your origin of life" discussion. How fun.
So how did they replicate, and what was the selection process?
They stitched 25 random amino acids together and then assess the resulting polymer for solubility and foldability. Solubility requirement is self explanatory, can't have life that is insoluble in water. Foldability is basically how likely for these polymers to entangle and collapse on itself. This is critical because protein folding depends on this process to generate highly compact and dense atomic machineries.
They find out stuff that are too soluble can't fold well because they prefer water over other amino acid. And that seems to exert a selection pressure, ending up with a specific set of amino acids that life depends on.
They find out stuff that are too soluble can't fold well because they prefer water over other amino acid. And that seems to exert a selection pressure, ending up with a specific set of amino acids that life depends on.
>Solubility requirement is self explanatory, can't have life that is insoluble in water. Foldability... is critical because protein folding depends on this process to generate highly compact and dense atomic machineries.
That's a teleological fallacy. Evolution doesn't have a destination, therefore you can't assume the evolution criteria from the end result only. Imagine looking at all of life, adding a 'resulting in human life' criteria and therefore completely failing to understand the evolution of avians.
If the authors want to argue amino acids 'evolved', they need criteria that make sense for amino acids in early Earth environment and not assume the result.
That's a teleological fallacy. Evolution doesn't have a destination, therefore you can't assume the evolution criteria from the end result only. Imagine looking at all of life, adding a 'resulting in human life' criteria and therefore completely failing to understand the evolution of avians.
If the authors want to argue amino acids 'evolved', they need criteria that make sense for amino acids in early Earth environment and not assume the result.
Not sure what part are you arguing although I get the general gist. Still, to make sure I don't misinterpret you, can you expand a bit on which part of those requirements are teleological fallacy?
The context is for life on earth. All life on earth depends on proteins that are (mostly) soluble in water and almost all protein requires folding to be functional. It is a valid hypothesis to say solubility and foldability are necessary criteria. Then they tested it and found based on these criteria, the current set of amino acids is favored over other sets. Look like good science to me.
The context is for life on earth. All life on earth depends on proteins that are (mostly) soluble in water and almost all protein requires folding to be functional. It is a valid hypothesis to say solubility and foldability are necessary criteria. Then they tested it and found based on these criteria, the current set of amino acids is favored over other sets. Look like good science to me.
>It is a valid hypothesis to say solubility and foldability are necessary criteria.
Necessary criteria for life, yes. Is it neccesary for evolution? The article's argument is that amino acids 'evolved'. Evolution needs a selection mechanism, and the article does not explain why evolution would favour solubility and foldability, so the article* doesn't come close to proving evolution happened much less explaining its details. Perhaps some other unexplained chemical process favoured these acids, or it was an accident.
It's like looking at current status of biosphere, and concluding that life optimizes for insectoids because insects have the largest biomass. It's just an argument that assumes the result.
* Perhaps the article is bad reporting and the reported study had an actual argument for this.
Necessary criteria for life, yes. Is it neccesary for evolution? The article's argument is that amino acids 'evolved'. Evolution needs a selection mechanism, and the article does not explain why evolution would favour solubility and foldability, so the article* doesn't come close to proving evolution happened much less explaining its details. Perhaps some other unexplained chemical process favoured these acids, or it was an accident.
It's like looking at current status of biosphere, and concluding that life optimizes for insectoids because insects have the largest biomass. It's just an argument that assumes the result.
* Perhaps the article is bad reporting and the reported study had an actual argument for this.
I see, the actual scientific paper is always a much better source for this stuff than a popsci article.
The term "evolution" was used very loosely in the salon article. By your standard it would be more appropriate to call the process "selection". The amino acids never changes or evolved to become anything different, just that some were chosen to become the building blocks of life while others were ignored. The reasons for this selection were likely the two criteria mentioned above and that was backed up by the main study.
You will notice I never used "evolution" to describe the process in my posts. I skipped the salon article entirely and only used the link they provided to read the real study so I didn't notice what they said in the salon page. Anyway, it is just some semantic stuff.
The term "evolution" was used very loosely in the salon article. By your standard it would be more appropriate to call the process "selection". The amino acids never changes or evolved to become anything different, just that some were chosen to become the building blocks of life while others were ignored. The reasons for this selection were likely the two criteria mentioned above and that was backed up by the main study.
You will notice I never used "evolution" to describe the process in my posts. I skipped the salon article entirely and only used the link they provided to read the real study so I didn't notice what they said in the salon page. Anyway, it is just some semantic stuff.
Right, so I read the study instead of the article. Good idea. It's simply that the popsci article claims something that isn't the original study. The article does argue for evolution before life[0], and the study doesn't claim that at all. Either Salon simply misunderstood the study, or spiced it up so that aggregators like HN would pick it up.
[0] "So by testing which libraries had the best solubility and structure, the researchers could conclude that proteins were evolving and driving natural selection before even forming living things."
[0] "So by testing which libraries had the best solubility and structure, the researchers could conclude that proteins were evolving and driving natural selection before even forming living things."
I wonder how this selection process varied as proteins started mixing, or even bonding, with lipids and sugars. Probably not that much, though those processes may have allowed the gradual inclusion of the other amino acids.
Forgive the plug, but I just wrote up a post[1] on simulating Hypercycles, which are a model showing how self-replication behaviors can emerge through the interactions of simple molecules. Not to say that they are the mechanism, but are an interesting model for exploring emergent behaviors and the conditions under which self-replicating systems can arise.
[1] https://blog.devgenius.io/origins-of-life-building-a-hypercy...
[1] https://blog.devgenius.io/origins-of-life-building-a-hypercy...
Selection is what the article describes (solubility and structure). They don't claim that they reproduced; they're just talking about amino acids that come about by non-reproductive chemical processes.
Popsci pictures of biomolecules are truly the most terrible horrorshow. Couldn't you use some nice molecular surface? They look interesting and actually describe reality...
From the article:
> Now, a new study in the Journal of the American Chemical Society suggests that evolution began long before life emerged and that proteins swirling around in the primordial soup selected for preferable traits. In other words, there was a sort of Darwinian selection effect taking place (even prior to the emergence of life) among the un-living proteins and amino acids in the primordial soup.
I don't agree the research paper says that.
> * Stephen Fried, a Johns Hopkins chemist who co-led the research with scientists at Charles University in the Czech Republic, said in a statement. "We're describing the events that shaped why that ancestor got the amino acids that it did."*
That is what I understand. The research paper is about amino acid selection in the early living things.
> So by testing which libraries had the best solubility and structure, the researchers could conclude that proteins were evolving and driving natural selection before even forming living things. Over time, the proteins that were the best shape for biochemical processes were incorporated into the fundamental cycles of life.
I don't agree the research paper says the first sentence.
The second sentence is very very unlikely, because there is no known way at the cell level to look at a useful protein and reverse engineer it and get the DNA or RNA code to produce it.
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I'm a fan of the RNA word hypothesis. https://en.wikipedia.org/wiki/RNA_world It's still not proven, so take the rest of my comment like an opinion.
The idea is that RNA can store info and be copied so it can replace DNA, and it can be a catalyst so it replace proteins. So you can start with the tools to build one type of molecule instead of three.
One of the problem is the transition from RNA to DNA, but they are quite similar and we still see transference of info in both direction, so it's not unimaginable.
The transition form RNA to proteins is harder. The translation in the cell is not straightforward and there are many proteins and pieces of RNA to make it possible. Another problem is that if the initial cell has good RNA catalyst https://en.wikipedia.org/wiki/Ribozyme , how to get an equivalent protein catalyst https://en.wikipedia.org/wiki/Enzyme
One of the current unproven ideas is that the transition can be done in steps:
1) 100% RNA catalyst
2) RNA catalyst with a short chain of amino acids to help
3) A catalyst with a part that is RNA and another part that is a long chain of amino acids or a short protein
4) An enzyme that need s a coenzyme that is a short RNA chain.
5) 100% enzyme.
And there are many intermediate steps. The transition can be done step by step removing one RNA base and adding one amino acid (not necessary to replace one by one simultaneously) I think we have seen 1), 4) and 5). Ribosomes can be interpreted as a huge 3). I'm not sure we have seen a 2), but it's would be not surprising.
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Back to the article, if at the beginning of the transition from RNA to proteins the initial cells used a safe list of only 10 amino acids in the brute force search, it may have been slightly easier.