Re: Show me the polymers!

On 20/12/2024 4:57 am, LDagget wrote:

On Thu, 19 Dec 2024 16:11:22 +0000, erik simpson wrote:
 

On 12/18/24 9:17 PM, MarkE wrote:

Would you like fame and fortune? This is not a scam. All you need to do
is perform an updated variation on the Miller-Urey experiment:
>
Simply set up simulated warm little ponds with an unlimited supply of
activated concentrated canonical enantiomerically pure nucleotides,
along with your choice of wet/dry cycles, temperature variability,
mechanical agitation, mineral substrates, pH changes, UV, electricity,
other chemicals, ions etc, physical pockets and sub-ponds, geothermal
activity, etc etc, and observe the development of RNA strands. As many
ponds as you like, for as long as you like. You can do it in the lab or
in actual ponds in Iceland. Of course, no cheating by sprinkling with
pre-existing rybozymes etc.
>
Wait...why has no-one done this? What better way to progress OoL
research? "Look, our little warm ponds have produced a population of
RNAs from 3 to 13 units long...we are on the road to life!" The
incentive is certainly there - peer accolades and grant funding would
flow in.
>
I can tell you why no-one is doing this and reporting the results.
Because it will not and does produce growing RNA polymers. It will yield
tar.
>
No? Then show me the polymers!
>
Indeed, Damer and Deamer have issued precisely this challenge, and it's
been crickets:
>
“[OoL research has] been mainly focused on individual solution chemistry
experiments where they want to show polymerization over here, or they
want to show metabolism over here, and Dave and I believe that it's time
for the field to go from incremental progress to substantial progress.
So, these are the four points we've come up with to make substantial
progress in the origin of life, and the first one is to employ something
called system chemistry, having sufficient complexity so instead of one
experiment say about proteins, now you have an experiment about the
encapsulation of proteins for example, and informational molecules built
from nucleotides in an environment that would say be like an analog of
the early Earth, build a complex experiment. Something we're calling
sufficient complexity, and all of these experiments have to move the
reactions away from equilibrium. And what do we mean by that? Well, in
in your high school chemistry experiments, something starts foaming
something changes color and then the experiment winds down and stops.
Well, life didn't get started that way. Life got started by a continuous
run-up of complexity and building upon in a sense nature as a ratchet.
So we have to figure out how to build experiments that move will move
away from equilibrium...”
>
“You can't sit in a laboratory just using glassware. You have to go to
the field. You have to go to hot springs, you have to go to [...]
Iceland and come check and sit down and see what the natural environment
is like, rather than being in the ethereal world of pure reactants and
things like that...”
>
Source: A new model for the origin of life: A new model for the origin
of life: Coupled phases and combinatorial selection in fluctuating
hydrothermal pools. https://youtu.be/nk_R55O24t4?feature=shared
>
Also: https://www.liebertpub.com/doi/full/10.1089/ast.2019.2045
>

I'm sure you could this if you could keep the microbes we've already
from eating the experiment.  It's almost impossible as we've see from
efforts to keep comet dust clean.  Even if you could keep it clean it
would take a long time, probably millions of years to get a living cell,
or even a reproducing RNA strand.  It'd be very interesting just to go
as far as you could and see how long it takes.

 I grad school I did a rotation in a lab that did a great deal of
mammalian cell culture. I'd previously done some work on bacteria
and yeast cultures but this was my first experience with mammalian
cells. Everyone I met seemed to lecture me on sterile technique.
 Ultimately, I cultivated 480 Petri dishes of cells just to throw away
the actual cells and harvest the extra-cellular matrix they had laid
down on the plate because my ultimate job was to characterize a minor
protein that was part of that extra-cellular matrix. But I digress.
 I proudly report that none of my plates showed signs of contamination:
no molds or bacteria or other signs that I had allowed my cells to
become infected. All those hours of carefully working within a sterile
laminar flow hood, feeding the cultures a plate at a time, alcohol wipe
down of anything coming into the hood, sash held low, arms extended
awkwardly, meticulous care about anything touched, somehow I didn't
mess up. Others with more experience had some disasters during the
time I was there and they wanted to blame the new guy (me) but that
really didn't make sense because if I was working dirty it should have
affected my cultures.
 But the point of that is both the bragging on my part but also that
experts at sterile technique, using sophisticated lab equipment, still
struggle to avoid contamination. So yes, a long term experiment to
await a miracle polymerization event is a huge challenge in keeping
thing sterile. It's not the sort of thing that an honest supervisor
would ask a young researcher to spend time on.
 Of course beyond that, no competent supervisor would suggest such a
foolish experiment either. The conceptual model of abiogenesis behind
the experiment MarkE suggests is a dead end. His mental model for
abiogenesis is indeed a pathway that is ridiculously improbable.
 So give him credit in that he has imagined a way that abiogenesis
could have NOT occurred. Of course there are many more such wrong
models so it's not clear what he thinks he's achieved by doing so.
It mostly seems to be the end product of having not really understood
the point and purpose of things like the Miller-Urey experiment.
 

Interesting point regarding contamination. Sounds like that could be a significant problem, which your lab experience does highlight.
Actually, the experimental approach proposed by Damer and Deamer needs some thought as to what results would constitute support or otherwise.
For example, pumping in activated nucleotides will easily lead to polymer formation to some degree if I understand correctly. Will give this further consideration.
In any case, what do you think of D&D's challenge, and their argument for warm little ponds of hydrothermal vents?