
A chemical clue to how life started on Earth - dnetesn
https://phys.org/news/2019-08-chemical-clue-life-earth.html
======
gus_massa
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](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.

------
raz32dust
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.

~~~
kashyapc
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](https://news.ycombinator.com/item?id=18714115)

[2] [http://nick-lane.net/books/life-ascending-the-ten-great-
inve...](http://nick-lane.net/books/life-ascending-the-ten-great-inventions-
of-evolution/)

~~~
jcims
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.

~~~
sfkdjf9j3j
Billions of years, but that's probably not far enough for you. _The Vital
Question_ is about the origin of eukaryotic cells.

~~~
jcims
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](https://www.youtube.com/watch?v=O6f3ZbKaL7A)

~~~
raz32dust
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/](https://www.ncbi.nlm.nih.gov/books/NBK6360/)

------
_Microft
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...](https://www.pagepress.org/journals/index.php/eb/article/viewFile/eb.2013.br1/3833)

[1] [https://www.amazon.de/What-Life-Chemistry-Becomes-
Landmark/d...](https://www.amazon.de/What-Life-Chemistry-Becomes-
Landmark/dp/0198784791/) [2]
[http://www.bgu.ac.il/~pross/](http://www.bgu.ac.il/~pross/)

------
quotha
All Good Things...
[https://en.wikipedia.org/wiki/All_Good_Things..._(Star_Trek:...](https://en.wikipedia.org/wiki/All_Good_Things..._\(Star_Trek:_The_Next_Generation\))

~~~
freedomben
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/Explorers_\(Star_Trek:_Deep_Space_Nine\))

------
sampleinajar
[https://en.wikipedia.org/wiki/Miller%E2%80%93Urey_experiment](https://en.wikipedia.org/wiki/Miller%E2%80%93Urey_experiment)

~~~
gus_massa
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.

------
apo
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](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.

------
taejavu
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](https://youtu.be/zU7Lww-sBPg?t=15)

~~~
freedomben
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...](https://reasonsforjesus.com/respected-science-professor-dr-james-
tour-converts-to-christianity-after-seeing-jesus/)

------
VeninVidiaVicii
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.

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

