A chemical clue to how life started on Earth | Hacker News Reader

A chemical clue to how life started on Earth

phys.org

89 pointsdnetesn19 comments

From the article:

> The new study suggests that life's dependence on these 20 amino acids is no accident. The researchers show that the kinds of amino acids used in proteins are more likely to link up together because they react together more efficiently and have few inefficient side reactions.

Note that this part is overoptimistic. Much more optimistic that the text in the research article.

In the research paper they analyzed a few amino acids like Lysine. Lysine is an amino acid that has the usual amino group and the usual acid group in one side, and it has an additional amino group in the other side. In the study they compared Lysine with Lysine-like amino acids that are shorter and the additional amino group are closer to the usual amino group and the usual acid group. For example https://en.wikipedia.org/wiki/Ornithine

They found that the usual amino acids like Lysine are better to form spontaneously protein-like chains than the shorter versions when they are in a solution that gets dried. I'm not sure if this is enough to explain why Lysine is used in proteins but it's an interesting result anyway.

In the more optimistic case, the research article "explain" why the 3 usual amino acids that they used are better than the 3 shorter variants that they used. It doesn't "explain" why the other 17 amino acids where selected.

In particular they used amino acids with an additional amino group, so the polymerization can get "confused" and instead of using the usual amino group use the other group, so instead of a nice chain, you get some other structure. There are 7 of the other usual amino acids that don't have an additional amino group, so the polymerization process can't get confused.

For anyone interested in this topic, I highly recommend the book, "The Vital Question" by Nick Lane. The book dives deep into the fundamental requirements for life, and why just the simple presence of amino acids does not lead to life. He develops a reasonable timeline for how inorganic chemicals can lead to living cells, in what conditions and even theorizes some "universal" principles of how life would look like on other planets, if it exists.

Yes to Nick Lane and "The Vital Question".

However, as excellent as Laine is at explaining, after the first 100 pages or so, the book gets quite technical (necessarily so). Unless your biochemistry is reasonably good, it is suggested (by biochemists themselves[1]) to first read his other book, 'Life Ascending'[2], which lays out the ground work for the deep dive into "hydrothermal vents", a key topic in 'The Vital Question'.

[1] As shared here on HN before:

When I was reading the book on a plane, a seasoned biologist happened to be sitting next to me. When I said that it's the first book of Nick Lane that I picked up, he said: "I'd rather suggest you to pick up Laine's other book, Life Ascending, and then get back to The Vital Question."

[1] https://news.ycombinator.com/item?id=18714115

[2] http://nick-lane.net/books/life-ascending-the-ten-great-inve...

How far along do these books make it in the evolutionary process? I've been reading up on the mechanisms behind how cancer works (and how we try to fight it) recently, and it has unveiled a level of complexity and specificity that I had no idea existed. It almost doesn't compute how these systems have evolved through pure chance in the time-frames that we are talking about.

Billions of years, but that's probably not far enough for you. The Vital Question is about the origin of eukaryotic cells.

Actually that would help for me. One of the early walls in the evolutionary curve would appear to be DNA replication. The level of complexity in the associated protein/enzyme machinery is one of those 'weird things' to me that I don't really understand. Will take a look, thank you.

Edit: Some context, a 'realistic' animation of the DNA replication process: https://www.youtube.com/watch?v=O6f3ZbKaL7A

The Vital question doesn't delve into the DNA replication part of it as far as I remember. It focuses more on the initial conditions needed for the living cell machinery to bootstrap, and the physical constraints that are necessary or need to be overcome to achieve life, and kind of glosses over the genetics part. I myself wondered about this after reading the book, and the best resource I could find was this: https://www.ncbi.nlm.nih.gov/books/NBK6360/

It goes into a lot of detail about how complex life arose through the "deadly rise" of 'eukaryotes'. (All complex life forms, "including plants, animals, fungi, algae and protists such as the amoeba, are made of eukaryotic cells.)

So the timeframe is indeed "billions of years", as noted below.

There's a very interesting book called "What is Life - How Chemistry becomes Biology" [1] by Addy Pross (homepage: [2]) in which he claims, among other things, that there is no clear boundary between chemistry and biology.

Here's a review if you don't want to go hunting for information on it [PDF]: https://www.pagepress.org/journals/index.php/eb/article/view...

[1] https://www.amazon.de/What-Life-Chemistry-Becomes-Landmark/d... [2] http://www.bgu.ac.il/~pross/

All Good Things... https://en.wikipedia.org/wiki/All_Good_Things..._(Star_Trek:...

Haha, this is exactly what I thought of when I read this article :-D

Same with the recent story of the Light Sail 2 spacecraft, I couldn't think of anything else except https://en.wikipedia.org/wiki/Explorers_(Star_Trek:_Deep_Spa...

https://en.wikipedia.org/wiki/Miller%E2%80%93Urey_experiment

The article here is somewhat like the second part of the Miller experiment that you linked. (Don't take the "second part" too literally.)

In the Miller experiment (and the dozens/hundreds variants) the main idea is how to obtain organic molecules mixing some common inorganic molecules and using a energy source like a spark or something. In the Miller experiment you can build some "soup" of the amino acids and other stuff.

The experiment in the article is about how to use the evaporation of the "soup" to make the amino acid to form small chains that are like small proteins. So it's somewhat like the part two of the Miller experiment. In this particular experiment they analyzed which amino acids are more prone to form small chains/proteins.

In a nutshell:

> The new study suggests that life's dependence on these 20 [naturally-occurring] amino acids is no accident. The researchers show that the kinds of amino acids used in proteins are more likely to link up together because they react together more efficiently and have few inefficient side reactions.

This is an odd leap.

Protein synthesis is an extremely complex process involving not just enzymes (amino acid chains), but other stuff like DNA, RNA, lipids, energy transduction, and sugars. Highly organized compartments are key - without them nothing remotely resembling life occurs.

The lack of any convincing pathway from random amino acid chains to life is a big limitation here.

For example, it's entirely possible that peptides occurred relatively late in the chemical evolution of self-replicating systems. Only after sufficient machinery had been built up could anything as complex as a well-defined peptide chain be produced.

Along these lines, a different study looking at how chemical microenvironment could have developed abiotically might be of interest: https://news.ycombinator.com/item?id=20505689

On the other hand, if it turned out that certain chemically active amino acid chains tended to form more readily than others in a re-evaporator environment, that could offer an explanation: enzymes (amino acid chain catalysts) form naturally without any other intervention by virtue of the relative reactivity of the growing chain with the next amino acid. Maybe there's even some self-catalysis and/or other selection mechanism at some point. AFAICT, the paper doesn't deal with this possibility, though.

Here's a talk by one of the world’s top synthetic organic chemists offering a blunt assessment of the current state of origin of life research: https://youtu.be/zU7Lww-sBPg?t=15

From the first comment:

> "amino acids don't hook together by themselves" https://www.youtube.com/watch?v=zU7Lww-sBPg&t=26m58s

This is a very weird remark considering that the article posted here is about how amino acids hook together by themselves, and which amino acids hook in the correct way and which hook in the incorrect way.

---

It's a long talk (1h). Which are the main points? I only skimmed, so I hope I have a not very unfair selection:

* We don't know the details about how life begun.

I agree. I think we all agree.

* Most press articles (and many research article) are overhyped.

I agree. Can I get a bot to post that in every scientific post in HN?

* The recipes to build organic molecules are complex, with many steps that are not posible to find in the wild (somewhat like https://www.youtube.com/watch?v=zU7Lww-sBPg&t=12m47s , and many slides with technical details after that)

I agree. The problem is that the recipe for the natural formation of some compounds is something like

"Get a big pool like the Mediterranean, kill all the bacterias so they don't eat the mix of chemical compounds, wait a million years. And then you will get only an efficiency of 0.0000001."

And probably nobody is sure that it is the correct recipe, perhaps it need some metal as catalyzer, perhaps light, perhaps darkness, perhaps lack of oxygen, ...

So the recipes he show in the slides are about how to get the same compounds in a lab, preferably in some flask that you can put over a table, waiting only a few hour, with something like a 10% or 1% of efficiency. So you must use weird conditions.

In particular in the slide in 12:47 it's weird to put Miller in the last bullet point when the first two bullet points don't apply to the Miller experiment at all. The slide is not wrong, just very misleading.

If you're somebody that likes to know people's backgrounds/biases, James Tour (the speaker here) is a Christian [1].

[1]: https://reasonsforjesus.com/respected-science-professor-dr-j...

I suppose it depends on your definition of life. The RNA World Hypothesis supposes that RNA functioned as both storage and catalytic molecules prior to the advent of DNA and proteins.

TL;DR: Not all amino-acids are created equal.

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